U.S. patent application number 14/300362 was filed with the patent office on 2014-09-25 for dominant gene suppression transgenes and methods of using same.
The applicant listed for this patent is PIONEER HI BRED INTERNATIONAL INC.. Invention is credited to Andrew Mark Cigan, Erica Unger-Wallace.
Application Number | 20140289895 14/300362 |
Document ID | / |
Family ID | 39760793 |
Filed Date | 2014-09-25 |
United States Patent
Application |
20140289895 |
Kind Code |
A1 |
Cigan; Andrew Mark ; et
al. |
September 25, 2014 |
Dominant Gene Suppression Transgenes and Methods of Using Same
Abstract
Pairs of plants are provided in which complementing constructs
result in suppression of a parental phenotype in the progeny.
Methods to generate and maintain such plants, and methods of use of
said plants, are provided, including use of parental plants to
produce sterile plants for hybrid seed production. Also provided
are methods for testing allelic variants.
Inventors: |
Cigan; Andrew Mark;
(Johnston, IA) ; Unger-Wallace; Erica; (Ames,
IA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
PIONEER HI BRED INTERNATIONAL INC. |
Johnston |
IA |
US |
|
|
Family ID: |
39760793 |
Appl. No.: |
14/300362 |
Filed: |
June 10, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12907433 |
Oct 19, 2010 |
8785722 |
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14300362 |
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11685956 |
Mar 14, 2007 |
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12907433 |
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11014071 |
Dec 16, 2004 |
7696405 |
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11685956 |
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60530478 |
Dec 16, 2003 |
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60591975 |
Jul 29, 2004 |
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Current U.S.
Class: |
800/270 ;
435/419; 435/6.1; 800/260; 800/298; 800/303 |
Current CPC
Class: |
C12N 15/8216 20130101;
C12N 15/8289 20130101; C12N 15/8241 20130101; G01N 33/5097
20130101; C12N 15/829 20130101 |
Class at
Publication: |
800/270 ;
435/419; 435/6.1; 800/298; 800/303; 800/260 |
International
Class: |
C12N 15/82 20060101
C12N015/82; G01N 33/50 20060101 G01N033/50 |
Claims
1. A breeding pair of plants comprising four polynucleotides,
wherein (a) the first plant of said pair comprises (i) a first
polynucleotide which encodes a gene product and is operably linked
to a promoter A, and (ii) a second polynucleotide which encodes a
pIR polynucleotide targeting a promoter sequence B, wherein
promoter B is not present in said first plant; and (b) The second
plant of said pair comprises (iii) a third polynucleotide which
encodes a gene product and is operably linked to said promoter B,
and (ii) a fourth polynucleotide which encodes a pIR polynucleotide
targeting said promoter A, wherein promoter A is not present in
said second plant.
2. The breeding pair of plants of claim 1, wherein one or more of
said four polynucleotides is exogenous.
3. The breeding pair of plants of claim 1, wherein said gene
products affect the same phenotypic trait.
4. The breeding pair of plants of claim 3, wherein said trait is
male fertility.
5. The breeding pair of plants of claim 3, wherein said trait is
female fertility.
6. The breeding pair of plants of claim 1, wherein (a) said first
polynucleotide is selected from the group consisting of
polynucleotides encoding maize MS45, maize BS7, maize 5126, and the
corresponding orthologs from Arabidopsis and rice; (b) said second
promoter is selected from the group consisting of rice MS45, rice
BS7, rice 5126, Arabidopsis BS7, Arabidopsis 5126, and Arabidopsis
MS45 promoters; (c) said third polynucleotide is selected from the
group consisting of polynucleotides encoding maize MS45, maize BS7,
maize 5126, and the corresponding orthologs from Arabidopsis and
rice; (d) said first promoter is selected from the group consisting
of rice MS45, rice BS7, rice 5126, Arabidopsis BS7, Arabidopsis
5126, and Arabidopsis MS45 promoters.
7. A method of generating plants lacking a particular phenotype
from parents exhibiting said phenotype, comprising crossing the
breeding pair of plants of claim 3.
8. A cell of a plant of claim 1.
9. Seed or progeny of a plant of claim 1.
10. A method of evaluating the function of an exogenous allelic
variant of an endogenous gene in a plant, wherein the endogenous
gene is operably linked to its endogenous promoter in the plant,
comprising: (a) silencing said endogenous gene using a promoter
inverted repeat construct targeting said endogenous promoter; (b)
expressing said exogenous allelic variant operably linked to a
non-target promoter; and (c) evaluating the phenotype of the plant
or its progeny.
11. The method of claim 10, comprising the further steps of (a)
crossing the plant or progeny of claim 10 with a second plant,
wherein said second plant comprises a promoter inverted repeat
targeting the promoter operably linked to said exogenous allelic
variant in the plant of claim 10; and (b) evaluating the phenotype
of the progeny of said cross.
12. The method of claim 10, wherein the exogenous allelic variant
is derived from a second species.
Description
CROSS-REFERENCE
[0001] This application is a continuation of U.S. patent
application Ser. No. 12/907,433 filed Oct. 19, 2010 which claims
the benefit of U.S. patent application Ser. No. 11/685,956 filed
Mar. 14, 2007, which claims the benefit of U.S. patent application
Ser. No. 11/014,071, filed Dec. 16, 2004, now U.S. Pat. No.
7,696,405, which claims priority to U.S. Provisional Patent
Application Ser. No. 60/530,478, filed Dec. 16, 2003 and U.S.
Provisional Patent Application Ser. No. 60/591,975, filed Jul. 29,
2004, all of which are hereby incorporated by reference.
BACKGROUND OF THE INVENTION
[0002] 1. Field of the Invention
[0003] The invention relates generally to compositions and methods
for dominant gene suppression. Certain embodiments provide methods
for preventing transmission of transgenes in gametes. Certain
embodiments comprise pairs of plants in which the phenotype of the
parents is suppressed in the progeny. Certain embodiments provide
constructs and methods useful for generating fertile parental
plants that, when crossed, generate sterile progeny plants and
methods of making, maintaining and using such transgenes and
plants, as well as products of such plants. Certain embodiments
provide a system for evaluating expression of allelic variants of a
gene. Certain embodiments provide a system for simultaneously
disrupting expression of an endogenous gene and complementing its
expression. Certain embodiments employ orthologous promoters and
constructs comprising inverted repeats thereof.
[0004] 2. Background Information
[0005] Plant breeding provides a means to combine desirable traits
in a single plant variety or hybrid, including for example, disease
resistance, insect resistance, drought tolerance, improved yield
and better agronomic quality. Field crops generally are bred by
pollination, including by self-pollination (selfing; selfed), in
which pollen from one flower is transferred to the same or another
flower of the same plant or to a genetically identical plant, and
cross-pollination (crossing; crossed), in which pollen from one
plant is transferred to a flower of a genetically different
plant.
[0006] Plants that are selfed and selected for type over many
generations become homozygous at almost all gene loci and produce a
uniform population of true breeding progeny. A cross between two
different homozygous lines produces a uniform population of hybrid
plants that can be heterozygous at many gene loci. A cross of two
plants, each of which is heterozygous at a number of gene loci,
generates hybrid plants, which differ genetically and are not
uniform.
[0007] Many crop plants, including, for example, maize (corn), can
be bred using self-pollination or cross-pollination techniques.
Maize has separate male and female flowers on the same plant,
located on the tassel and the ear, respectively. Natural
pollination occurs in maize when wind blows pollen from the tassels
to the silks that protrude from the tops of the ears. Many crop
plants, including maize, are grown as hybrids, which generally
exhibit greater vigor than the parental plants from which they are
derived. As such, it is desirable to prevent random pollination
when generating hybrid plants.
[0008] Hybrid plants (F1) are generated by crossing two different
inbred male (P1) and female (P2) parental plants. Hybrid plants are
valued because they can display improved yield and vigor as
compared to the parental plants from which the hybrids are derived.
In addition, hybrid (F1) plants generally have more desirable
properties than progeny (F2) plants derived from the hybrid plants.
As such, hybrid plants are commercially important, and include many
agricultural crops, including, for example, wheat, corn, rice,
tomatoes and melons. Hybridization of maize has received particular
focus since the 1930s. The production of hybrid maize involves the
development of homozygous inbred male and female lines, the
crossing of these lines and the evaluation of the crosses for
improved agronomic performance. Pedigree breeding and recurrent
selection are two of the breeding methods used to develop inbred
lines from populations. Breeding programs combine desirable traits
from two or more inbred lines or various broad-based sources, into
breeding pools from which new inbred lines are developed by selfing
and selecting for desired phenotypes. These new inbreds are crossed
with other inbred lines and the resultant new hybrids are evaluated
to determine which have improved performance or other desirable
traits, thus increasing commercial value. The first generation
hybrid progeny, designated F.sub.1, is more vigorous than its
inbred parents. This hybrid vigor, or heterosis, can be manifested
in many ways, including increased vegetative growth and increased
seed yield.
[0009] Production of hybrid seed requires maintenance of the
parental seed stocks because self-crossing of hybrid plants
produces progeny (F2) that, like P1 and P2, generally exhibit less
desirable characteristics than the F1 hybrid plant. Because the
parental plants generally have less commercial value than the
hybrids (F1), efforts have been made to prevent parental plants in
a field from self-crossing ("selfing"), since such crosses would
reduce the yield of hybrid seed. Accordingly, methods have been
developed to selfing of a parental plant.
[0010] One method for controlling pollination is to use a parental
population of plants that are male sterile, thus providing the
female parent. Several methods have been used for controlling male
fertility, including, for example, manual or mechanical
emasculation (detasseling), cytoplasmic male sterility, genetic
male sterility and the use of gametocides. For example, parental
selfing in a field can be prevented by removing the anthers or
detasseling plants of the female parental (P2) population, thus
removing the source of P2 pollen from the field. P2 female plants
then can be pollinated with P1 pollen by hand or using mechanical
means. Hybrid maize seed generally is produced by a male sterility
system incorporating manual or mechanical detasseling. Alternate
strips of two maize inbreds are planted in a field, and the
pollen-bearing tassels are removed from one of the inbreds (P2
female). Provided that the field is sufficiently isolated from
sources of foreign maize pollen, the ears of the detasseled inbred
are fertilized only by pollen from the other inbred (P1 male);
resulting seed is hybrid and forms hybrid plants. Unfortunately,
this method is time- and labor-intensive. In addition,
environmental variation in plant development can result in plants
producing tassels after manual detasseling of the female parent is
completed. Therefore detasseling might not ensure complete male
sterility of a female inbred plant. In this case, the resultant
fertile female plants will successfully shed pollen and some female
plants will be self-pollinated. This will result in seed of the
female inbred being harvested along with the desired hybrid seed.
Female inbred seed is not as productive as F.sub.1 seed. In
addition, the presence of female inbred seed can represent a
germplasm security risk for the company producing the hybrid. The
female inbred can also be mechanically detasseled. Mechanical
detasseling is approximately as reliable as hand detasseling, but
is faster and less costly. However, most detasseling machines
produce more damage to the plants than hand detasseling, which
reduces F.sub.1 seed yields. Thus neither form of detasseling is
presently entirely satisfactory and a need continues to exist for
alternative hybrid production methods that reduce production costs,
increase production safety and eliminate self-pollination of the
female parent during the production of hybrid seed.
[0011] Another method of preventing parental plant selfing is to
utilize parental plants that are male sterile or female sterile.
Male fertility genes have been identified in a number of plants and
include dominant and recessive male fertility genes. Plants that
are homozygous for a recessive male fertility gene do not produce
viable pollen and are useful as female parental plants. However, a
result of the female plants being homozygous recessive for a male
fertility gene is that they are not capable of selfing and,
therefore, a means must be provided for obtaining pollen in order
to maintain the parental P2 plant line. Generally, a maintainer
cell line, which is heterozygous for the male fertility gene, is
generated by crossing a homozygous dominant male fertile plant with
the homozygous recessive female sterile plant. The heterozygous
maintainer plants then are crossed with the homozygous recessive
male sterile plants to produce a population in which 50% of the
progeny are male sterile. The male sterile plants are then selected
for use in generating hybrids. As such, the method requires
additional breeding and selection steps to obtain the male sterile
plants, thus adding to the time and cost required to produce the
hybrid plants.
[0012] To overcome the requirement of having to select male sterile
from male fertile plants generated by crossing a maintainer plant
line with a female (male sterile) plant line, methods have been
developed to obtain male sterile plants by expressing a cytotoxic
molecule in cells of the male reproductive organs of a plant. For
example, a nucleic acid encoding the cytotoxic molecule can be
linked to a tapetum-specific promoter and introduced into plant
cells, such that, upon expression, the toxic molecule kills anther
cells, rendering the plant male sterile. As above, however, such
female parental plants cannot be selfed and, therefore, require the
preparation and use of a maintainer plant line, which, when crossed
with the male sterile female parent restores fertility, for
example, by providing a dominant male fertility gene, or by
providing a means to inactivate or otherwise inhibit the activity
of the cytotoxic gene product (see, U.S. Pat. No. 5,977,433).
[0013] Additional methods of conferring genetic male sterility have
been described including, for example, generating plants with
multiple mutant genes at separate locations within the genome that
confer male sterility (see, U.S. Pat. Nos. 4,654,465 and 4,727,219)
or with chromosomal translocations (see, U.S. Pat. Nos. 3,861,709
and 3,710,511). Another method of conferring genetic male sterility
includes identifying a gene that is required for male fertility;
silencing the endogenous gene, generating a transgene comprising an
inducible promoter operably linked to the coding sequence of the
male fertility gene and inserting the transgene back into the
plant, thus generating a plant that is male sterile in the absence
of the inducing agent and can be restored to male fertile by
exposing the plant to the inducing agent (see, U.S. Pat. No.
5,432,068).
[0014] While the previously described methods of obtaining and
maintaining hybrid plant lines have been useful for plant breeding
and agricultural purposes, they require numerous steps and/or
additional lines for maintaining male sterile or female sterile
plant populations in order to obtain the hybrid plants. Such
requirements contribute to increased costs for growing the hybrid
plants and, consequently, increased costs to consumers. Thus, a
need exists for convenient and effective methods of producing
hybrid plants, and particularly for generating parental lines that
can be crossed to obtain hybrid plants.
[0015] A reliable system of genetic male sterility would provide a
number of advantages over other systems. The laborious detasseling
process can be avoided in some genotypes by using cytoplasmic
male-sterile (CMS) inbreds. In the absence of a fertility restorer
gene, plants of a CMS inbred are male sterile as a result of
cytoplasmic (non-nuclear) genome factors. Thus, this CMS
characteristic is inherited exclusively through the female parent
in maize plants, since only the female provides cytoplasm to the
fertilized seed. CMS plants are fertilized with pollen from another
inbred that is not male-sterile. Pollen from the second inbred may
or may not contribute genes that make the hybrid plants
male-fertile. Usually seed from detasseled normal maize and
CMS-produced seed of the same hybrid must be blended to insure that
adequate pollen loads are available for fertilization when the
hybrid plants are grown and to insure cytoplasmic diversity.
[0016] Another type of genetic sterility is disclosed in U.S. Pat.
Nos. 4,654,465 and 4,727,219 to Brar, et al. However, this form of
genetic male sterility requires maintenance of multiple mutant
genes at separate locations within the genome and requires a
complex marker system to track the genes, making this system
inconvenient. Patterson described a genetic system of chromosomal
translocations, which can be effective, but is also very complex.
(See, U.S. Pat. Nos. 3,861,709 and 3,710,511).
[0017] Many other attempts have been made to address the drawbacks
of existing sterility systems. For example, Fabijanski, et al.,
developed several methods of causing male sterility in plants (see,
EPO Application Number 89/3010153.8 Publication Number 329,308 and
PCT
[0018] Application Number PCT/CA90/00037 published as WO
1990/08828). One method includes delivering into the plant a gene
encoding a cytotoxic substance that is expressed using a male
tissue specific promoter. Another involves an antisense system in
which a gene critical to fertility is identified and an antisense
construct to the gene inserted in the plant. Mariani, et al., also
shows several cytotoxic antisense systems. See, EP 89/401,194.
Still other systems use "repressor" genes that inhibit the
expression of other genes critical to male fertility. See, WO
1990/08829.
[0019] A still further improvement of this system is one described
at U.S. Pat. No. 5,478,369 in which a method of imparting
controllable male sterility is achieved by silencing a gene native
to the plant that is critical for male fertility and further
introducing a functional copy of the male fertility gene under the
control of an inducible promoter which controls expression of the
gene. The plant is thus constitutively sterile, becoming fertile
only when the promoter is induced, allowing for expression of the
male fertility gene.
[0020] In a number of circumstances, a particular plant trait is
expressed by maintenance of a homozygous recessive condition.
Difficulties arise in maintaining the homozygous condition when a
transgenic restoration gene must be used for maintenance. For
example, the MS45 gene in maize (U.S. Pat. No. 5,478,369) has been
shown to be critical to male fertility. Plants heterozygous or
hemizygous for the dominant MS45 allele are fully fertile due to
the sporophytic nature of the MS45 fertility trait. A natural
mutation in the MS45 gene, designated ms45, imparts a male
sterility phenotype to plants when this mutant allele is in the
homozygous state. This sterility can be reversed (i.e., fertility
restored) when the non-mutant form of the gene is introduced into
the plant, either through normal crossing or transgenic
complementation methods. However, restoration of fertility by
crossing removes the desired homozygous recessive condition and
both methods restore full male fertility and prevent maintenance of
pure male sterile maternal lines. The same concerns arise when
controlling female fertility of the plant, where a homozygous
recessive female must be maintained by crossing with a plant
containing a restoration gene. Therefore there is considerable
value not only in controlling the expression of restoration genes
in a genetic recessive line, but also in controlling the
transmission of the restoring genes to progeny during the hybrid
production process.
BRIEF DESCRIPTION OF THE FIGURES
[0021] FIG. 1 gives identifying information as to the MS45, MS26,
5126 and BS7 genes and/or promoters of Zea mays, Oryza sativa and
Arabidopsis thaliana.
[0022] FIG. 2 represents maintenance of the homozygous recessive
mutation in male-sterile plants for hybrid production.
[0023] FIG. 3 shows that the rice MS45 pIR is effective in
suppressing the corresponding promoter from rice but not from
maize.
[0024] FIG. 4 is a schematic of a generic
complementation/suppression vector.
[0025] FIG. 5 is a schematic of one example of an MS45
complementation/suppression vector.
[0026] FIG. 6 is a schematic showing vector design for maintenance
of recessive lethal genes.
SUMMARY OF THE INVENTION
[0027] The present invention is based on the determination that the
genotype of an organism (e.g., a plant or mammal) can be modified
to contain dominant suppressor alleles or transgene constructs that
reduce, but not ablate, the activity of a gene, wherein the
phenotype of the organism is not substantially affected. For
example, plants can contain dominant suppressor alleles and/or
transgene constructs that suppress the activity of a plant male
fertility gene, without rendering the plant male sterile or can
contain dominant suppressor alleles and/or transgene constructs
that suppress the activity of a gene required for viability,
without killing the plant. Further, pairs of such plants having
selected genotypes comprising the dominant suppressor alleles or
transgene constructs can be crossed to produce progeny that exhibit
the phenotypic change (e.g., male sterility). Progeny of plants
comprising suppressed male fertility genes, for example, can be
useful as females in hybrid plant production.
[0028] Accordingly, in one embodiment, the present invention
relates to a breeding pair of plants, wherein the plants comprising
the breeding pair are fertile (i.e., male fertile and female
fertile), and wherein sterile progeny (e.g., male sterile progeny)
are produced by crossing the breeding pair of plants. A breeding
pair of plants of the invention can include, for example, a first
plant having an inactivated first endogenous fertility gene,
wherein the first plant is fertile and a second plant having an
inactivated second endogenous fertility gene, wherein the second
plant is fertile. Such a breeding pair is further characterized in
that, if the first endogenous fertility gene is a male fertility
gene, then the second endogenous fertility gene also is a male
fertility gene and, similarly, if the first endogenous fertility
gene is a female fertility gene, then the second endogenous
fertility gene also is a female fertility gene.
[0029] In a breeding pair of plants of the invention, the first
endogenous fertility gene and the second endogenous fertility gene
can encode gene products that are present in a single pathway
involved in determining fertility of a plant or the first
endogenous fertility gene and the second endogenous fertility gene
can encode gene products that are in separate but convergent
pathways. In either case, the presence of a single inactivated
fertility gene in a plant does not substantially affect fertility
of the plant, or plants derived therefrom, except that when a first
and second plant as defined herein are crossed, the inactivation of
both a first and a second fertility gene in progeny plants results
in the progeny plants being sterile (i.e., male sterile or female
sterile).
[0030] The inactivated fertility gene can be inactivated due, for
example, to a mutation (e.g., deletion, substitution or insertion
of one or more nucleotides in the coding or non-coding sequence
that reduces or inhibits expression of the fertility gene),
including, for example, knock out of the gene (e.g., by a
homologous recombination event), preferably in both alleles of the
fertility gene. The inactivated fertility gene also can be
inactivated due, for example, to expression of a gene product such
as a transgene product (e.g., an RNA or an encoded polypeptide) in
cells of the plant in which the gene normally is expressed, or in
progenitor cells, wherein the gene product reduces or inhibits
expression of the endogenous fertility gene. Further, in a breeding
pair of plants of the invention, the first endogenous fertility
gene of the first plant and the second endogenous fertility gene of
the second plant can be inactivated in the same or different ways.
For example, the first endogenous fertility gene can be inactivated
due to a mutation and the second endogenous fertility gene can be
inactivated due to expression of a transgene product (e.g., a
hairpin RNA comprising a nucleotide sequence of the promoter of the
second fertility gene). The notation hpRNA as used herein refers to
a promoter hairpin RNA molecule and may be used interchangeably
with the notation "pIR" for promoter inverted repeat. In various
embodiments, the breeding pair can include a first plant, in which
the first endogenous fertility gene is inactivated by a mutation
and a second plant having a second endogenous fertility gene
inactivated in a manner other than a mutation; or can include a
first plant in which the first endogenous fertility gene is
inactivated by a mutation and a second plant in which the second
endogenous fertility gene is inactivated by a mutation or can
include a first plant having a first endogenous fertility gene
inactivated in a manner other than a mutation and a second plant in
which the second endogenous fertility gene is inactivated in a
manner other than by a mutation. In aspects of this embodiment, the
first or second endogenous fertility gene of the first or second
plant is inactivated by knockout of the first or second fertility
gene, respectively or the first or second endogenous fertility gene
of the first or second plant is inactivated by mutation of the
promoter of the first or second fertility gene, respectively. In
further aspects, the first and second endogenous fertility genes of
the first and second plants are inactivated by knockout of the
first and second fertility genes, respectively or the first and
second endogenous fertility genes of the first and second plants
are inactivated by mutation of the promoter of the first and second
fertility genes, respectively.
[0031] In other embodiments, in a breeding pair of plants of the
invention, the first endogenous fertility gene is inactivated due
to expression in the first plant of a first exogenous nucleic acid
molecule comprising a promoter operably linked to a nucleotide
sequence encoding a first hairpin (hp) ribonucleic acid (RNA)
molecule (hpRNA), wherein the first hpRNA comprises a nucleotide
sequence of the first endogenous fertility gene promoter, and
wherein, upon expression, the first hpRNA suppresses expression of
the first endogenous fertility gene; or the second endogenous
fertility gene is inactivated due to expression in the second plant
of a second exogenous nucleic acid molecule comprising a promoter
operably linked to a nucleotide sequence encoding a second hpRNA,
wherein the second hpRNA comprises a nucleotide sequence of the
second endogenous fertility gene promoter, and wherein, upon
expression, the second hpRNA suppresses expression of the second
endogenous fertility gene or both the first endogenous fertility
gene and second endogenous fertility gene are inactivated due to
expression in the first plant and second plant of a first hpRNA and
a second hpRNA, respectively, having the above-described
characteristics. In aspects of this embodiment, the first exogenous
nucleic acid molecule, when present, is stably integrated in the
genome of cells of the first plant; or the second exogenous nucleic
acid molecule, when present is stably integrated in the genome of
cells of the second plant; or both the first exogenous nucleic acid
molecule, when present, and the second exogenous nucleic acid
molecule, when present, are stably integrated in the genome of
cells of the first plant and second plant, respectively.
[0032] Where a first and/or second endogenous fertility gene is
inactivated due to expression in a first and/or second plant,
respectively, of an exogenous nucleic acid molecule comprising a
promoter operably linked to a nucleotide sequence encoding an
hpRNA, the promoter can be any promoter that is active in plant
cells, for example, a constitutively active promoter, (e.g., an
ubiquitin promoter), a tissue specific promoter, particularly a
reproductive tissue promoter (e.g., an anther specific promoter
such as a tapetum specific promoter), an inducible promoter or a
developmental or stage specific promoter. The fertility gene that
is inactivated can be a male fertility gene or a female fertility
gene, provided that, if a male fertility gene is inactivated in a
first plant of a breeding pair (i.e., a first endogenous male
fertility gene), the second plant of the breeding pair has an
inactivated male fertility gene that is different from the first
endogenous male fertility gene and, conversely, if a female
fertility gene is inactivated in a first plant of a breeding pair
(i.e., a first endogenous female fertility gene), the second plant
of the breeding pair has an inactivated female fertility gene that
is different from the first endogenous female fertility gene.
Further, the inactivation of a first or second endogenous fertility
gene, alone, does not render a plant sterile, whereas a cross of a
first plant having the first inactivated fertility gene and a
second plant having the second inactivated fertility gene generates
progeny that are sterile.
[0033] In another embodiment, the present invention relates to a
breeding pair of transgenic plants, which includes a first fertile
transgenic plant having integrated in its genome a first exogenous
nucleic acid molecule comprising a promoter operably linked to a
nucleotide sequence encoding a first hpRNA, wherein the first hpRNA
comprises a nucleotide sequence from a first endogenous fertility
gene promoter, and wherein, upon expression, the first hpRNA
suppresses expression of the first endogenous fertility gene and a
second fertile transgenic plant having integrated in its genome a
second exogenous nucleic acid molecule comprising a promoter
operably linked to a nucleotide sequence encoding a second hpRNA,
wherein the second hpRNA comprises a nucleotide sequence from a
second endogenous fertility gene promoter, wherein the second
endogenous fertility gene is different from the first endogenous
fertility gene, and wherein, upon expression, the second hpRNA
suppresses expression of the second endogenous fertility gene. As
disclosed herein, the first endogenous gene is different from the
second endogenous gene and, further if, in a breeding pair of
plants, the first endogenous fertility gene of the first plant is a
male fertility gene, then the second endogenous fertility gene of
the second plant of the breeding pair also is a male fertility
gene; whereas if the first endogenous fertility gene of the first
plant is a female fertility gene, then the second endogenous
fertility gene of the second plant also is a female fertility
gene.
[0034] In certain embodiments, in an exogenous nucleic acid
molecule contained in a first or second transgenic plant of a
breeding pair of plants of the invention, the nucleotide sequence
encoding the first or second hpRNA, respectively, is such that it
includes the sequence of the promoter of the fertility gene that is
to be inactivated, particularly an inverted repeat of the promoter
sequence such that, upon expression, self-hybridization of the RNA
results in formation of the hpRNA. As such, the nucleotide
sequence, when expressed in a cell, forms a hairpin RNA molecule
(i.e., an hpRNA), which suppresses (i.e., reduces or inhibits)
expression of the endogenous fertility gene from its endogenous
promoter.
[0035] The promoter, which is operably linked to the nucleotide
sequence encoding the hpRNA in an exogenous nucleic acid molecule
contained in a first or second transgenic plant of a breeding pair,
can be any promoter that is active in plant cells, particularly a
promoter that is active (or can be activated) in reproductive
tissues of a plant (e.g., stamens or ovaries). As such, the
promoter can be, for example, a constitutively active promoter, an
inducible promoter, a tissue-specific promoter or a developmental
stage specific promoter. Also, the promoter of the first exogenous
nucleic acid molecule can be the same as or different from the
promoter of the second exogenous nucleic acid molecule.
[0036] In general, a promoter is selected based, for example, on
whether endogenous fertility genes to be inhibited are male
fertility genes or female fertility genes. Thus, where the
endogenous genes to be inhibited are male fertility genes (e.g., a
BS7 gene and an SB200 gene), the promoter can be a stamen specific
and/or pollen specific promoter such as an MS45 gene promoter (U.S.
Pat. No. 6,037,523), a 5126 gene promoter (U.S. Pat. No.
5,837,851), a BS7 gene promoter (WO 2002/063021), an SB200 gene
promoter (WO 2002/26789), a TA29 gene promoter (Nature 347:737
(1990)), a PG47 gene promoter (U.S. Pat. No. 5,412,085; U.S. Pat.
No. 5,545,546; Plant J 3(2):261-271 (1993)), an SGB6 gene promoter
(U.S. Pat. No. 5,470,359) a G9 gene promoter (U.S. Pat. No.
5,837,850; 5,589,610), or the like, such that the hpRNA is
expressed in anther and/or pollen or in tissues that give rise to
anther cells and/or pollen, thereby reducing or inhibiting
expression of the endogenous male fertility genes (i.e.,
inactivating the endogenous male fertility genes). In comparison,
where the endogenous genes to be inhibited are female fertility
genes, the promoter can be an ovary specific promoter, for example.
However, as disclosed herein, any promoter can be used that directs
expression of the hpRNA in the reproductive tissue of interest,
including, for example, a constitutively active promoter such as an
ubiquitin promoter, which generally effects transcription in most
or all plant cells.
[0037] The present invention also provides cells of a first plant
or of a second plant or of both a first plant and a second plant of
a breeding pair of plants of the invention. In addition, seeds of
the first plant and/or second plant are provided, as are cuttings
of the first and/or second plant.
[0038] The present invention further relates to a transgenic
non-human organism that is homozygous recessive for a recessive
genotype, wherein the transgenic organism contains an expressible
first exogenous nucleic acid molecule comprising a first promoter
operably linked to a polynucleotide encoding a restorer gene, the
expression of which restores the phenotype that is otherwise absent
due to the homozygous recessive genotype, and a second exogenous
nucleic acid molecule encoding an hpRNA. The transgenic non-human
organism can be any non-human organism that has a diploid (or
greater) genome, including, for example, mammals, birds, reptiles,
amphibians or plants.
[0039] In one embodiment, the second expressible exogenous nucleic
acid molecule of a transgenic plant of the invention encodes an
hpRNA specific for the first promoter, which drives expression of
the restorer gene. In one aspect of this embodiment, the second
expressible exogenous nucleic acid molecule further comprises a
second promoter operably linked to the nucleotide sequence encoding
the hpRNA. The second promoter generally is different from the
first promoter (of the first expressible exogenous nucleic acid
molecule), and can be, for example, a constitutive promoter, an
inducible promoter, a tissue specific promoter or a developmental
stage specific promoter, such that the hpRNA can be expressed in
the transgenic organism in a constitutive manner, an inducible
manner, a tissue specific manner or at a particular stage of
development. In another embodiment, the second expressible
exogenous nucleic acid molecule of a transgenic plant of the
invention encodes an hpRNA specific for a promoter other than the
first promoter which drives expression of the restorer gene of the
first expressible exogenous nucleic acid molecule.
[0040] A transgenic non-human organism of the invention is
exemplified herein by a transgenic plant that is homozygous
recessive for a recessive sterile genotype (e.g., homozygous
recessive for the ms45 gene, which is a male fertility gene) and
that contains (a) a first expressible transgene comprising a first
promoter operably linked to a nucleotide sequence encoding a
restorer gene, which, upon expression, restores fertility to the
transgenic plant (e.g., transgene comprising an MS45 coding
sequence) and (b) a second expressible transgene encoding an hpRNA,
which, upon expression, suppresses expression by a second promoter,
which is different from the first promoter. In one embodiment, the
first promoter is a constitutive or developmentally regulated
promoter, wherein the fertility restorer gene is expressed in the
transgenic plant and the transgenic plant is fertile. In another
embodiment, the first promoter is an inducible promoter, wherein,
upon contact of the transgenic plant with an appropriate inducing
agent, expression of the fertility restorer gene is induced,
rendering the transgenic plant fertile.
[0041] In another embodiment, the present invention also relates to
a breeding pair of transgenic non-human organisms, including a
first transgenic organism and second transgenic organism each of
which is homozygous recessive for the same recessive genotype. The
breeding pair is further characterized in that the first transgenic
organism contains an expressible first exogenous nucleic acid
molecule comprising a first promoter operably linked to a
nucleotide sequence encoding a restorer gene, the expression of
which restores the phenotype that is otherwise absent due to the
homozygous recessive genotype and a second expressible exogenous
nucleic acid molecule that encodes an hpRNA specific for a second
promoter, which is different from the first promoter. The second
transgenic organism contains an expressible third exogenous nucleic
acid molecule comprising the second promoter operably linked to a
nucleotide sequence encoding a restorer gene, the expression of
which restores the phenotype that is otherwise absent due to the
homozygous recessive genotype and a fourth expressible exogenous
nucleic acid molecule that encodes an hpRNA specific for the first
promoter. The first and second transgenic non-human organism are
further characterized in that, when bred with each other, progeny
are produced in which the second hpRNA inhibits expression of the
restorer gene of the first transgene and the first hpRNA inhibits
expression of the restorer gene of the third transgene, such that
the progeny exhibit the recessive phenotype of the homozygous
recessive genotype.
[0042] A breeding pair of transgenic non-human organisms of the
invention is exemplified by a breeding pair of transgenic plants,
as follows.
[0043] The first plant of the pair is a fertile transgenic plant
having a homozygous recessive sterile genotype, having integrated
in its genome a first exogenous nucleic acid molecule comprising a
nucleotide sequence encoding a fertility restorer gene operably
linked to a heterologous first promoter, wherein expression of the
restorer gene restores fertility to the first transgenic plant and
a second exogenous nucleic acid molecule comprising a first hpRNA,
wherein the first hpRNA comprises a nucleotide sequence of a second
promoter, and wherein, upon expression, the first hpRNA suppresses
expression from the second promoter, which is different from the
first promoter.
[0044] The second transgenic plant of the pair has the same
homozygous recessive sterile genotype as the first transgenic
plant, and has integrated in its genome a third exogenous nucleic
acid molecule, which comprises a nucleotide sequence encoding the
fertility restorer gene operably linked to the second promoter,
which is heterologous to the fertility restorer gene, wherein
expression of the restorer gene restores fertility to the second
transgenic plant and a fourth exogenous nucleic acid molecule
comprising a second hpRNA, wherein the second hpRNA comprises a
nucleotide sequence of the heterologous first promoter, and
wherein, upon expression, the second hpRNA suppresses expression of
the first exogenous nucleic acid molecule comprising the
heterologous first promoter.
[0045] As disclosed herein, in progeny of a cross of the first and
second transgenic plants, the second hpRNA suppresses expression of
the first exogenous nucleic acid molecule, including the fertility
restorer gene contained therein and the first hpRNA suppresses
expression of the third exogenous nucleic acid molecule, including
the fertility restorer gene contained therein. As such, the progeny
are sterile, for example, female sterile. A breeding pair of
transgenic plants of the invention can be homozygous recessive for
male fertility genes (i.e., male sterile, except upon expression of
the fertility restorer gene) or can be homozygous recessive for
female fertility genes (i.e., female sterile, except upon
expression of the fertility restorer gene).
[0046] In one aspect, a breeding pair of transgenic plants of the
invention includes a first transgenic plant, which is homozygous
recessive for ms45, wherein the first exogenous nucleic acid
molecule comprises a nucleotide sequence encoding MS45 operably
linked to a 5126 gene promoter and the second exogenous nucleic
acid molecule comprises a first hpRNA comprising an inverted repeat
of a BS7 gene promoter. Said breeding pair further includes a
second transgenic plant, which is homozygous recessive for ms45,
wherein the third exogenous nucleic acid molecule comprises a
nucleotide sequence encoding MS45 operably linked to the BS7 gene
promoter and the fourth exogenous nucleic acid molecule comprises a
second hpRNA comprising an inverted repeat of the 5126 gene
promoter. Upon crossing such first and second transgenic plants,
male sterile progeny plants are obtained.
[0047] The present invention also relates to methods of producing a
sterile plant. Such a method can be performed by crossing a
breeding pair of plants as disclosed herein. In one embodiment, the
first plant of the breeding pair contains a mutation inactivating a
first endogenous gene of a pathway involved in male fertility, and
the second plant contains a second endogenous gene of the same or a
different but convergent pathway also involved in the male
sterility, wherein the progeny plants are double mutants and have a
male sterile phenotype. In another embodiment, the method is
performed using first and second transgenic plants, each containing
a transgene encoding an hpRNA that inactivates the respective
endogenous fertility gene in the second and first transgenic
plants, wherein progeny plants produced by crossing the parental
plants exhibit the sterile phenotype.
[0048] The present invention also relates to a method of producing
a transgenic non-human organism that exhibits a recessive
phenotype, by breeding parental transgenic organisms that do not
exhibit the recessive phenotype. For example, the invention
provides methods of producing a sterile progeny plant by crossing
first and second transgenic plants, each of which is homozygous
recessive for the same fertility gene, wherein, in the first
transgenic plant, a fertility restorer gene is expressed from a
first promoter and an hpRNA is expressed that suppresses expression
from a second promoter, and in the second transgenic plant, the
fertility restorer gene is expressed from the second promoter, and
a second hpRNA is expressed that suppresses expression of the first
promoter. The sterile progeny plants can be female sterile or male
sterile plants. For example, in a cross of a first transgenic plant
containing a first exogenous nucleic acid molecule comprising a
nucleotide sequence encoding MS45 operably linked to a 5126 gene
promoter, and a second exogenous nucleic acid molecule comprising a
first hpRNA including a nucleotide sequence of a BS7 gene promoter;
and a second transgenic plant containing a third exogenous nucleic
acid molecule comprising a nucleotide sequence encoding MS45
operably linked to the BS7 gene promoter, and a fourth exogenous
nucleic acid molecule comprising a second hpRNA including a
nucleotide sequence of the 5126 gene promoter, male sterile progeny
are produced. Accordingly, the invention provides a plant produced
by a method as disclosed herein, for example, a male sterile
plant.
[0049] The present invention further relates to a method of
producing hybrid plant seed. Such a method can be performed, for
example, by pollinating (e.g., naturally, mechanically or by hand)
a male sterile plant produced as disclosed herein with pollen of a
male fertile plant that contains at least one dominant allele
corresponding to the homozygous recessive sterile genotype of the
male sterile plant, whereby pollinated male sterile plants produce
hybrid seed. As such, the invention also provides hybrid seed
produced by such a method. The present invention relates to a
method of obtaining a hybrid plant by growing such hybrid seed and,
further, provides hybrid plants produced by growing such hybrid
seed.
[0050] The present invention further relates to a method of
identifying a function of a gene expressed in a cell. The gene
expressed in the cell can be any gene containing a promoter,
including an endogenous gene, which contains an endogenous
promoter. A method of identifying a gene function can be performed,
for example, by introducing into a cell in which the gene is
expressed, a first exogenous nucleic acid molecule comprising a
nucleotide sequence encoding a hpRNA operably linked to a first
heterologous promoter, wherein the hpRNA comprises a nucleotide
sequence of an endogenous promoter of the gene whose function is
being examined, and wherein, upon expression, the hpRNA suppresses
expression of the gene; and detecting a change in a phenotype of
the cell upon expression of the hpRNA as compared to a wild type
phenotype in the absence of expression of the hpRNA, whereby the
change in phenotype identifies the function of the gene. In one
aspect, the method further includes introducing into the cell a
second exogenous nucleic acid molecule comprising a nucleotide
sequence encoding a polypeptide encoded by the gene operably linked
to a second heterologous promoter, wherein, upon expression of the
polypeptide encoded by the gene from the second heterologous
promoter, the wild type phenotype is restored.
[0051] A method of the invention can be practiced using single
cells containing the gene of interest, or can be practiced using an
organism containing the cell. The organism can be any organism of
interest in which the gene of interest is expressed. In one
embodiment, the cell is a plant cell, which can be a plant cell in
vitro or can be one or more cells of a plant in situ. In one
embodiment, the organism is a transgenic plant, which contains the
first exogenous nucleic acid molecule stably integrated in its
genome. In an aspect of this embodiment, the transgenic plant
further contains, integrated in its genome, a second exogenous
nucleic acid molecule (comprising a nucleotide sequence encoding a
polypeptide encoded by the gene of interest) operably linked to a
second heterologous promoter, wherein, upon expression of the
second exogenous nucleic acid molecule from the second heterologous
promoter, the wild type phenotype is restored.
[0052] In some embodiments, the present invention addresses the
difficulty in propagating a plant having a homozygous recessive
reproductive trait without losing the homozygous recessive
condition in the resulting progeny. This may be accomplished by
introducing into a plant at least one restoring transgene
construct, operably linking (1) a first nucleotide sequence
comprising a functional copy of a gene that complements the mutant
phenotypic trait produced by the homozygous recessive condition
with (2) a second functional nucleotide sequence which interferes
with the formation, function or dispersal of the male gametes of
the plant and is operably linked to a male-gamete-tissue-preferred
promoter. This construct is maintained in the hemizygous state and
a plant containing such a construct is referred to herein as a
maintainer. When the maintainer plant containing such a linked
construct is used as a pollen donor to fertilize the homozygous
recessive plant, the only viable male gametes provided to the
homozygous recessive plant are those which contain the recessive
allele, and do not contain any component of the transgene
construct. None of the pollen grains which contain the restoring
transgene construct are viable, due to the action of the linked
second gene that prevents the formation of viable pollen.
Therefore, the progeny resulting from such a sexual cross are non
transgenic with respect to this transgene construct.
[0053] While no viable pollen produced by the maintainer contains
the restoring transgene construct, 50% of the ovules (the female
gamete) of the maintainer will contain the restoring transgene
construct. Therefore, the maintainer can be propagated by
self-fertilization, with the restoring transgene construct
segregating such that it will be contained in 50% of the seed of
the ear of a self fertilized maintainer. By linking the restoring
transgene construct with a selectable marker, the 50% of the seed
containing the transgene can be isolated to propagate the
maintainer population, which remains homozygous for the recessive
gene and hemizygous for the restoring transgene construct.
[0054] In a further embodiment, if the female gamete is prohibited
from being formed or functional, it will be desirable to link the
gene capable of complementing this mutant phenotype with an
inducible promoter to aid in maintenance of the maintainer plant.
Such a plant, when exposed to the inducing condition, will have
female fertility restored, and the plant may then be self
fertilized to produce progeny having the both the desired recessive
mutant trait and the restoring transgene construct.
[0055] While the invention is exemplified in plants, a person of
skill in the art would recognize its applicability to other
non-human organisms, including mammals. For example, the invention
encompasses a method of suppressing a phenotype in progeny of a
parental pair of non-human organisms, wherein (a) said phenotype is
expressed in each of said parents; (b) the genome of each parent is
manipulated so as to inactivate a gene affecting the phenotype of
interest; and (c) the gene inactivated in the first parent encodes
a different gene product than the gene inactivated in the second
parent.
DETAILED DESCRIPTION OF THE INVENTION
[0056] Embodiments of the invention reflect the determination that
the genotype of an organism can be modified to contain dominant
suppressor alleles or transgene constructs that suppress (i.e.,
reduce, but not ablate) the activity of a gene, wherein the
phenotype of the organism is not substantially affected.
[0057] In some embodiments, the present invention is exemplified
with respect to plant fertility, and more particularly with respect
to plant male fertility. For example, plants may be genetically
modified to contain a transgene construct encoding hairpin RNA
(hpRNA) molecules that suppress the expression of an endogenous
male fertility gene without rendering the plant male sterile.
[0058] In one example, Gene A and Gene B modulate sequential
(though not necessarily consecutive) steps in a pathway leading to
a product. In a first plant, Gene A is suppressed so as to reduce,
but not ablate, Gene A activity. The pathway is not substantially
inhibited, and thus the phenotype of said first plant is not
affected. In a second plant, Gene B is suppressed so as to reduce,
but not ablate, Gene B activity. The pathway is not substantially
inhibited, and thus the phenotype of said second plant is not
affected. In progeny of a cross of said first and second plants,
the combination of suppression of Gene A and Gene B leads to loss
of the product of the pathway and a change in phenotype.
Suppression of Gene A and/or Gene B could be accomplished by use of
hairpin constructs (hpRNA) as described elsewhere herein.
[0059] In another example, Gene A and Gene B modulate steps of
convergent pathways prior to the point of convergence, and the
converged pathway leads to a product. In a first plant, Gene A is
suppressed so as to reduce, but not ablate, Gene A activity, and
the phenotype of said first plant is not affected. In a second
plant, Gene B is suppressed so as to reduce, but not ablate, Gene B
activity, and the phenotype of said second plant is not affected.
In progeny of a cross of said first and second plants, the
combination of suppression of Gene A and Gene B leads to loss of
the product of the convergent pathways. Suppression of Gene A
and/or Gene B could be accomplished by use of hairpin constructs
(hpRNA) as described elsewhere herein.
[0060] In certain embodiments, Gene A and Gene B modulate steps of
pathways involved in plant fertility. In this way, for example,
crosses of phenotypically fertile plants expressing targeted hpRNA
molecules can generate male sterile plants. For example, parental
plants having a homozygous recessive male sterile genotype can be
transformed such that each expresses a restorer male fertility gene
from different heterologous promoters and hpRNAs that suppress
expression of the restorer gene in the other parental plant. Such
parental plants, which are fertile, can be crossed with each other
to generate male sterile plants. This is exemplified by a pair of
male-fertile plants, A and B. Each has a homozygous recessive male
sterile genotype, ms45 ms45. Plant A is transformed with, in single
or multiple constructs, a 5126 promoter operably linked to a
restorer MS45 gene, and an hpRNA specific for the BS7 promoter.
Plant B is transformed with, in single or multiple constructs, a
BS7 promoter operably linked to a restorer MS45 gene, and an hpRNA
specific for the 5126 promoter. Plant A and Plant B are each
male-fertile due to the presence of the MS45 restorer. In a cross
of Plant A and Plant B, restoration of fertility is reversed due to
the action of the complementing hairpin constructs targeted to the
respective promoters driving the restorer gene, and the progeny of
said cross are male-sterile. Such progeny are useful as females in
hybrid production. Wild-type pollen can restore fertility in the
hybrid due to the recessive nature of the ms45 allele.
[0061] Certain embodiments of the invention comprise a transgenic
non-human organism having a homozygous recessive genotype that
results in absence of a particular phenotype of interest, said
organism further comprising (a) a first exogenous nucleic acid
molecule comprising a restorer gene for the particular phenotype,
operably linked to a first promoter; and (b) a second exogenous
nucleic acid molecule comprising a second promoter operably linked
to a nucleotide sequence encoding a first hairpin ribonucleic acid
molecule (hpRNA), wherein the first hpRNA comprises a nucleotide
sequence of the first promoter or a nucleotide sequence of a third
promoter, wherein said transgenic non-human organism exhibits the
phenotype of interest.
[0062] The agriculture industry produces crops that are used to
feed humans and animals, and that are further used in other
industries to prepare products as diverse as adhesives and
explosives. Maize (corn), for example, is used as human food,
livestock feed (e.g., beef cattle, dairy cattle, hogs and poultry
feed) and a raw material in industry. Food uses of maize include
consumption of maize kernels as well as products of dry-milling and
wet-milling industries (e.g., grits, meal, flour, maize starch,
maize syrups and dextrose). Maize oil is recovered from maize germ,
which is a by-product of the dry-milling and wet-milling
industries. Industrial uses of maize include production of ethanol,
maize starch in the wet-milling industry and maize flour in the
dry-milling industry. The industrial applications of maize starch
and flour are based on their functional properties, including, for
example, viscosity, film formation, adhesive properties and ability
to suspend particles. Maize starch and flour have application in
the paper and textile industries, and also are used in adhesives,
building materials, foundry binders, laundry starches, explosives,
oil-well muds and other mining applications.
[0063] Many crop plants, including rice, wheat, maize, tomatoes and
melons are grown as hybrids, which exhibit greater vigor and
improved qualities as compared to the parental plants. The
development of hybrids in a plant breeding program requires, in
general, the development of homozygous inbred lines, the crossing
of these lines and the evaluation of the crosses. Pedigree breeding
and recurrent selection breeding methods are used to develop inbred
lines from breeding populations. For example, maize plant breeding
programs combine the genetic backgrounds from two or more inbred
lines (or various other germplasm sources) into breeding pools,
from which new inbred lines are developed by self-pollinating
(selfing) and selection of desired phenotypes. The selected inbreds
then are crossed with other inbred lines and the hybrids from these
crosses are evaluated to determine which of those have commercial
potential. As such, plant breeding and hybrid development are
expensive and time-consuming processes.
[0064] Pedigree breeding starts with the crossing of two genotypes,
each of which may have one or more desirable characteristics that
is lacking in the other or which complements the other. If the two
original parents do not provide all the desired characteristics,
other sources can be included in the breeding population. Using
this method, superior plants are selected and selfed in successive
generations until homogeneous plant lines are obtained. Recurrent
selection breeding such as backcrossing can be used to improve an
inbred line and a hybrid can be made using the inbreds.
Backcrossing can be used to transfer a specific desirable trait
from one inbred or source to a second inbred that lacks that trait,
for example, by first crossing a superior inbred (recurrent parent)
to a donor inbred (non-recurrent parent) that carries the
appropriate gene (or genes) for the trait in question, crossing the
progeny of the first cross back to the superior recurrent parent,
and selecting in the resultant progeny for the desired trait to be
transferred from the non-recurrent parent. After five or more
backcross generations with selection for the desired trait, the
progeny are homozygous for loci controlling the characteristic
being transferred, and are like the superior parent for essentially
all other genes. The last backcross generation is selfed to give
pure breeding progeny for the gene being transferred.
[0065] A single cross hybrid (F1) results from the cross of two
inbred lines (P1 and P2), each of which has a genotype that
complements the genotype of the other. In the development of
commercial hybrids in a maize plant breeding program, for example,
only F1 hybrid plants are sought, as they are more vigorous than
their inbred parents. This hybrid vigor (heterosis) can be
manifested in many polygenic traits such as increased vegetative
growth and increased yield. The development of a hybrid in a maize
plant breeding program, for example, involves the selection of
plants from various germplasm pools for initial breeding crosses;
the selfing of the selected plants from the breeding crosses for
several generations to produce a series of inbred lines, which,
although different from each other, breed true and are highly
uniform; and crossing the selected inbred lines with different
inbred lines to produce the hybrid F1 progeny. During the
inbreeding process in maize, the vigor of the lines decreases, but
is restored when two different inbred lines are crossed to produce
the hybrid plants. An important consequence of the homozygosity and
homogeneity of the inbred lines is that the F1 hybrid between a
defined pair of inbred parental plants always is the same. As such,
once the inbreds that provide a superior hybrid are identified, the
hybrid seed can be reproduced indefinitely as long as the inbred
parents are maintained.
[0066] Hybrid seed production requires elimination or inactivation
of pollen produced by the female parent. Incomplete removal or
inactivation of the pollen provides the potential for selfing,
raising the risk that inadvertently self-pollinated seed will
unintentionally be harvested and packaged with hybrid seed. Once
the seed is planted, the selfed plants can be identified and
selected; the selfed plants are genetically equivalent to the
female inbred line used to produce the hybrid. Typically, the
selfed plants are identified and selected based on their decreased
vigor. For example, female selfed plants of maize are identified by
their less vigorous appearance for vegetative and/or reproductive
characteristics, including shorter plant height, small ear size,
ear and kernel shape, cob color, or other characteristics. Selfed
lines also can be identified using molecular marker analyses (see,
e.g., Smith and Wych, (1995) Seed Sci. Technol. 14:1-8). Using such
methods, the homozygosity of the self-pollinated line can be
verified by analyzing allelic composition at various loci in the
genome.
[0067] Because hybrid plants are important and valuable field
crops, plant breeders are continually working to develop
high-yielding hybrids that are agronomically sound based on stable
inbred lines. The availability of such hybrids allows a maximum
amount of crop to be produced with the inputs used, while
minimizing susceptibility to pests and environmental stresses. To
accomplish this goal, the plant breeder must develop superior
inbred parental lines for producing hybrids by identifying and
selecting genetically unique individuals that occur in a
segregating population. The present invention contributes to this
goal, for example by providing plants that, when crossed, generate
male sterile progeny, which can be used as female parental plants
for generating hybrid plants.
[0068] A large number of genes have been identified as being tassel
preferred in their expression pattern using traditional methods and
more recent high-throughput methods. The correlation of function of
these genes with important biochemical or developmental processes
that ultimately lead to fertile pollen is arduous when approaches
are limited to classical forward or reverse genetic mutational
analysis. As disclosed herein, suppression approaches in maize
provide an alternative rapid means to identify genes that are
directly related to pollen development in maize. The
well-characterized maize male fertility gene, MS45, and several
anther-preferred genes of unknown function were used to evaluate
the efficacy of generating male sterility using
post-transcriptional gene silencing (PTGS; see, for example,
Kooter, et al., (1999) Trends Plant Sci. 4:340-346) or
transcriptional gene silencing (TGS; see, for example, Mette, et
al., (2000) EMBO J. 19:5194-5201) approaches.
[0069] To examine PTGS, hairpin-containing RNAi constructs that
have stem structures composed of inverted repeats of the
anther-expressed cDNA sequences, and a loop containing either a
non-homologous coding sequence or a splicable intron from maize,
were introduced into maize.
[0070] To examine TGS as an approach to knock out anther gene
function, a second set of constructs was generated in which the
promoters of the anther-specific gene sequences formed the stem and
a non-homologous sequence formed the loop. The constructs were
expressed using constitutive promoters and anther-preferred
promoters.
[0071] Contrasting fertility phenotypes were observed, depending on
the type of hairpin construct expressed. Plants expressing the PTGS
constructs were male fertile. In contrast, plants expressing the
TGS constructs were male sterile and lacked MS45 mRNA and protein.
Further, the sterility phenotype of the plants containing the hpRNA
specific for the MS45 promoter (i.e., the TGS constructs) was
reversed when MS45 was expressed from heterologous promoters in
these plants. These results demonstrate that TGS provides a tool
for rapidly correlating gene expression with function of unknown
genes such as anther-expressed monocot genes.
[0072] Accordingly, the invention provides breeding pairs of
plants, wherein the plants comprising the breeding pair are fertile
(i.e., male fertile and female fertile), and wherein progeny
produced by crossing the breeding pair of plants are sterile (e.g.,
male sterile). As disclosed herein, a breeding pair of plants of
the invention can include, for example, a first plant having an
inactivated first endogenous fertility gene, wherein the first
plant is fertile; and a second plant having an inactivated second
endogenous fertility gene, wherein the second plant is fertile.
Such a breeding pair is characterized, in part, in that if the
first endogenous fertility gene is a male fertility gene, then the
second endogenous fertility gene also is a male fertility gene;
whereas if the first endogenous fertility gene is a female
fertility gene, then the second endogenous fertility gene also is a
female fertility gene. The methods of the invention may be embodied
to impact male fertility, female fertility, or other traits as
listed elsewhere herein, including photosynthetic efficiency and
plant architecture.
[0073] As used herein, the term "endogenous", when used in
reference to a gene, means a gene that is normally present in the
genome of cells of a specified organism and is present in its
normal state in the cells (i.e., present in the genome in the state
in which it normally is present in nature). The term "exogenous" is
used herein to refer to any material that is introduced into a
cell. The term "exogenous nucleic acid molecule" or "transgene"
refers to any nucleic acid molecule that either is not normally
present in a cell genome or is introduced into a cell. Such
exogenous nucleic acid molecules generally are recombinant nucleic
acid molecules, which are generated using recombinant DNA methods
as disclosed herein or otherwise known in the art. In various
embodiments, a transgenic non-human organism as disclosed herein,
can contain, for example, a first transgene and a second transgene.
Such first and second transgenes can be introduced into a cell, for
example, a progenitor cell of a transgenic organism, either as
individual nucleic acid molecules or as a single unit (e.g.,
contained in different vectors or contained in a single vector,
respectively). In either case, confirmation may be made that a cell
from which the transgenic organism is to be derived contains both
of the transgenes using routine and well-known methods such as
expression of marker genes or nucleic acid hybridization or PCR
analysis. Alternatively, or additionally, confirmation of the
presence of transgenes may occur later, for example, after
regeneration of a plant from a putatively transformed cell.
[0074] An endogenous fertility gene of a plant of a breeding pair
of the invention can be inactivated due, for example, (1) to a
mutation of the endogenous gene such that the function of a product
encoded by the gene is suppressed (e.g., the gene product is not
expressed or is expressed at a level that is insufficient to
mediate its full effect in the plant or plant cell); or (2) to
expression of an exogenous nucleic acid molecule that reduces or
inhibits expression of the gene product encoded by the endogenous
gene. As such, the term "inactivated" is used broadly herein to
refer to any manipulation of an endogenous gene, or a cell
containing the gene, such that the function mediated by a product
encoded by the gene is suppressed. It should further be recognized
that, regardless of whether the inactivated endogenous gene has
reduced activity or is completely inactive, the desired relevant
phenotype is maintained. As such, reference to an inactivated male
fertility gene in a parental plant defined as having a male fertile
phenotype can include, for example, a male fertility gene that is
expressed at a level that is lower than normal, but sufficient to
maintain fertility of the parental plant, or a male fertility gene
that is completely inactive, and wherein fertility of the parental
plant is maintained due to expression of a second gene product.
[0075] Mutation of an endogenous gene that results in suppression
of the gene function can be effected, for example, by deleting or
inserting one or a few nucleotides into the nucleotide sequence of
the gene (e.g., into the promoter, coding sequence or intron), by
substituting one or a few nucleotides in the gene with other
different nucleotides, or by knocking out the gene (e.g., by
homologous recombination using an appropriate targeting vector).
Plants having such mutations in both alleles can be obtained, for
example, using crossing methods as disclosed herein or otherwise
known in the art. Inactivation of an endogenous gene that results
in suppression of the gene function also can be effected by
introduction into cells of the plant of a transgene that suppresses
expression of the endogenous gene or a product expressed from the
endogenous gene (e.g., an encoded polypeptide), or a transgene that
encodes a product (e.g., an RNA) that suppresses expression of the
endogenous gene or a product encoded by the endogenous gene in
cells of the plant in which the gene normally is expressed.
[0076] By way of example, inactivation of endogenous fertility
genes can be effected by expressing hairpin RNA molecules (hpRNA)
in cells of the reproductive organs of a plant (e.g., stamen cells
where the endogenous fertility genes to be inactivated are male
fertility genes). The stamen, which comprises the male reproductive
organ of plants, includes various cell types, including, for
example, the filament, anther, tapetum and pollen. The hpRNAs
useful for purposes of the present invention are designed to
include inverted repeats of a promoter of the endogenous gene to be
inactivated; hpRNAs having the ability to suppress expression of a
gene have been described (see, e.g., Matzke, et al., (2001) Curr.
Opin. Genet. Devel. 11:221-227; Scheid, et al., (2002) Proc. Natl.
Acad. Sci., USA 99:13659-13662; Waterhouse and Helliwell, (2003)
Nature Reviews Genetics 4:29-38; Aufsaftz, et al., (2002) Proc.
Nat'l. Acad. Sci. 99(4):16499-16506; Sijen, et al., (2001) Curr.
Biol. 11:436-440). As disclosed herein, the use of stamen-specific
or stamen-preferred promoters, including anther-specific promoters,
pollen-specific promoters, tapetum-specific promoters, and the
like, allows for expression of hpRNAs in plants (particularly in
male reproductive cells of the plant), wherein the hpRNA suppresses
expression of an endogenous fertility gene, thereby inactivating
expression of the endogenous fertility gene. As such, suppression
using an hpRNA specific for a promoter that directs expression of a
fertility gene provides a means to inactivate an endogenous
fertility gene.
[0077] In one embodiment, a breeding pair of plants of the
invention can include a first plant, which contains a first
exogenous nucleic acid molecule comprising a promoter operably
linked to a nucleotide sequence encoding a first hpRNA, wherein the
first hpRNA comprises a nucleotide sequence comprising an inverted
repeat of the first endogenous fertility gene promoter, and
wherein, upon expression, the first hpRNA suppresses expression of
the first endogenous fertility gene; and a second plant, which
contains a second exogenous nucleic acid molecule comprising a
promoter operably linked to a nucleotide sequence encoding a second
hpRNA, wherein the second hpRNA comprises a nucleotide sequence
comprising an inverted repeat of the second endogenous fertility
gene promoter, and wherein, upon expression, the second hpRNA
suppresses expression of the second endogenous fertility gene.
According to the present invention, the first and/or second
exogenous nucleic acid can, but need not, be stably integrated in
the genome of cells of the first and/or second plant, respectively.
Such first and second plants of the breeding pair are
characterized, in part, in that each is fertile, and is further
characterized in that, when crossed, the progeny of such cross is
sterile (e.g., male sterile).
[0078] The terms "first", "second", "third" and "fourth" are used
herein only to clarify relationships of various cells and molecules
or to distinguish different types of a molecule, and, unless
specifically indicated otherwise, are not intended to indicate any
particular order, importance, or quantitative feature. For example,
and unless specifically indicated otherwise, reference to a "first"
plant containing a "first endogenous gene" is intended to indicate
only that the specified gene is present in the specified plant. By
way of a second example, and unless specifically indicated
otherwise, reference to a "first plant containing a first transgene
and a second transgene" is intended to indicate only that said
plant contains two exogenous nucleic acid molecules that are
different from each other.
[0079] As used herein, the term "nucleic acid molecule" or
"polynucleotide" or "nucleotide sequence" refers broadly to a
sequence of two or more deoxyribonucleotides or ribonucleotides
that are linked together by a phosphodiester bond. As such, the
terms include RNA and DNA, which can be a gene or a portion
thereof, a cDNA, a synthetic polydeoxyribonucleic acid sequence, or
the like, and can be single-stranded or double-stranded, as well as
a DNA/RNA hybrid. Furthermore, the terms are used herein to include
naturally-occurring nucleic acid molecules, which can be isolated
from a cell, as well as synthetic molecules, which can be prepared,
for example, by methods of chemical synthesis or by enzymatic
methods such as by the polymerase chain reaction (PCR). The term
"recombinant" is used herein to refer to a nucleic acid molecule
that is manipulated outside of a cell, including two or more linked
heterologous nucleotide sequences. The term "heterologous" is used
herein to refer to nucleotide sequence that are not normally linked
in nature or, if linked, are linked in a different manner than that
disclosed. For example, reference to a transgene comprising a
coding sequence operably linked to a heterologous promoter means
that the promoter is one that does not normally direct expression
of the nucleotide sequence in a specified cell in nature.
[0080] In general, the nucleotides comprising an exogenous nucleic
acid molecule (transgene) are naturally occurring
deoxyribonucleotides, such as adenine, cytosine, guanine or thymine
linked to 2'-deoxyribose or ribonucleotides such as adenine,
cytosine, guanine or uracil linked to ribose. However, a nucleic
acid molecule or nucleotide sequence also can contain nucleotide
analogs, including non-naturally-occurring synthetic nucleotides or
modified naturally-occurring nucleotides. Such nucleotide analogs
are well known in the art and commercially available, as are
polynucleotides containing such nucleotide analogs (Lin, et al.,
Nucl. Acids Res. 22:5220-5234, 1994; Jellinek, et al., (1995)
Biochemistry 34:11363-11372; Pagratis, et al., (1997) Nature
Biotechnol. 15:68-73). Similarly, the covalent bond linking the
nucleotides of a nucleotide sequence generally is a phosphodiester
bond, but also can be, for example, a thiodiester bond, a
phosphorothioate bond, a peptide-like bond or any other bond known
to those in the art as useful for linking nucleotides to produce
synthetic polynucleotides (see, for example, Tam, et al., (1994)
Nucl. Acids Res. 22:977-986; Ecker and Crooke, (1995) BioTechnology
13:351360). The incorporation of non-naturally occurring nucleotide
analogs or bonds linking the nucleotides or analogs can be
particularly useful where the nucleic acid molecule is to be
exposed to an environment that can contain a nucleolytic activity,
including, for example, a plant tissue culture medium or in a plant
cell, since the modified molecules can be less susceptible to
degradation.
[0081] A nucleotide sequence containing naturally-occurring
nucleotides and phosphodiester bonds can be chemically synthesized
or can be produced using recombinant DNA methods, using an
appropriate polynucleotide as a template. In comparison, a
nucleotide sequence containing nucleotide analogs or covalent bonds
other than phosphodiester bonds generally is chemically
synthesized, although an enzyme such as T7 polymerase can
incorporate certain types of nucleotide analogs into a
polynucleotide and, therefore, can be used to produce such a
polynucleotide recombinantly from an appropriate template
(Jellinek, et al., supra, 1995).
[0082] An exogenous nucleic acid molecule can comprise operably
linked nucleotide sequences such as a promoter operably linked to a
nucleotide sequence encoding an hpRNA, or a promoter linked to a
nucleotide sequence encoding a male fertility gene product. The
term "operably linked" is used herein to refer to two or more
molecules that, when joined together, generate a molecule that
shares features characteristic of each of the individual molecules.
For example, when used in reference to a promoter (or other
regulatory element) and a second nucleotide sequence encoding a
gene product, the term "operably linked" means that the regulatory
element is positioned with respect to the second nucleotide
sequence such that transcription or translation of the isolated
nucleotide sequence is under the influence of the regulatory
element. When used in reference to a fusion protein comprising a
first polypeptide and one or more additional polypeptides, the term
"operably linked" means that each polypeptide component of the
fusion (chimeric) protein exhibits some or all of a function that
is characteristic of the polypeptide component (e.g., a cell
compartment localization domain and a enzymatic activity). In
another example, two operably linked nucleotide sequences, each of
which encodes a polypeptide, can be such that the coding sequences
are in frame and, therefore, upon transcription and translation,
result in production of two polypeptides, which can be two separate
polypeptides or a fusion protein.
[0083] Where an exogenous nucleic acid molecule includes a promoter
operably linked to a nucleotide sequence encoding an RNA or
polypeptide of interest, the exogenous nucleic acid molecule can be
referred to as an expressible exogenous nucleic acid molecule (or
transgene). The term "expressible" is used herein because, while
such a nucleotide sequence can be expressed from the promoter, it
need not necessarily actually be expressed at a particular point in
time. For example, where a promoter of an expressible transgene is
an inducible promoter lacking basal activity, an operably linked
nucleotide sequence encoding an RNA or polypeptide of interest is
expressed only following exposure to an appropriate inducing
agent.
[0084] Transcriptional promoters generally act in a position- and
orientation-dependent manner, and usually are positioned at or
within about five nucleotides to about fifty nucleotides 5'
(upstream) of the start site of transcription of a gene in nature.
In comparison, enhancers can act in a relatively position- or
orientation-independent manner, and can be positioned several
hundred or thousand nucleotides upstream or downstream from a
transcription start site, or in an intron within the coding region
of a gene, yet still be operably linked to the coding region so as
to enhance transcription. The relative positions and orientations
of various regulatory elements in addition to a promoter, including
the positioning of a transcribed regulatory sequence such as an
internal ribosome entry site, or a translated regulatory element
such as a cell compartmentalization domain in an appropriate
reading frame, are well known, and methods for operably linking
such elements are routine in the art (see, for example, Sambrook,
et al., "Molecular Cloning: A laboratory manual" (Cold Spring
Harbor Laboratory Press 1989); Ausubel, et al., "Current Protocols
in Molecular Biology" (John Wiley and Sons, Baltimore Md. 1987, and
supplements through 1995)).
[0085] Promoters useful for expressing a nucleic acid molecule of
interest can be any of a range of naturally-occurring promoters
known to be operative in plants or animals, as desired. Promoters
that direct expression in cells of male or female reproductive
organs of a plant are useful for generating a transgenic plant or
breeding pair of plants of the invention. The promoters useful in
the present invention can include constitutive promoters, which
generally are active in most or all tissues of a plant; inducible
promoters, which generally are inactive or exhibit a low basal
level of expression, and can be induced to a relatively high
activity upon contact of cells with an appropriate inducing agent;
tissue-specific (or tissue-preferred) promoters, which generally
are expressed in only one or a few particular cell types (e.g.,
plant anther cells); and developmental- or stage-specific
promoters, which are active only during a defined period during the
growth or development of a plant. Often promoters can be modified,
if necessary, to vary the expression level. Certain embodiments
comprise promoters exogenous to the species being manipulated. For
example, the Ms45 gene introduced into ms45 ms45 maize germplasm
may be driven by a promoter isolated from another plant species; a
hairpin construct may then be designed to target the exogenous
plant promoter, reducing the possibility of hairpin interaction
with non-target, endogenous maize promoters.
[0086] Exemplary constitutive promoters include the 35S cauliflower
mosaic virus (CaMV) promoter promoter (Odell, et al., (1985) Nature
313:810-812), the maize ubiquitin promoter (Christensen, et al.,
(1989) Plant Mol. Biol. 12:619-632 and Christensen, et al., (1992)
Plant Mol. Biol. 18:675-689); the core promoter of the Rsyn7
promoter and other constitutive promoters disclosed in WO
1999/43838 and U.S. Pat. No. 6,072,050; rice actin (McElroy, et
al., (1990) Plant Cell 2:163-171); pEMU (Last, et al., (1991)
Theor. Appl. Genet. 81:581-588); MAS (Velten, et al., (1984) EMBO
J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026); rice actin
promoter (U.S. Pat. No. 5,641,876; WO 2000/70067), maize histone
promoter (Brignon, et al., (1993) Plant Mol Bio 22(6):1007-1015;
Rasco-Gaunt, et al., (2003) Plant Cell Rep. 21(6):569-576) and the
like. Other constitutive promoters include, for example, those
described in U.S. Pat. Nos. 5,608,144 and 6,177,611, and PCT
Publication Number WO 2003/102198.
[0087] Tissue-specific, tissue-preferred or stage-specific
regulatory elements further include, for example, the
AGL8/FRUITFULL regulatory element, which is activated upon floral
induction (Hempel, et al., (1997) Development 124:3845-3853);
root-specific regulatory elements such as the regulatory elements
from the RCP1 gene and the LRP1 gene (Tsugeki and Fedoroff, (1999)
Proc. Natl. Acad., USA 96:12941-12946, Smith and Fedoroff, (1995)
Plant Cell 7:735-745); flower-specific regulatory elements such as
the regulatory elements from the LEAFY gene and the APETALA1 gene
(Blazquez, et al., (1997) Development 124:3835-3844; Hempel, et
al., supra, 1997); seed-specific regulatory elements such as the
regulatory element from the oleosin gene (Plant, et al., (1994)
Plant Mol. Biol. 25:193-205), and dehiscence zone specific
regulatory element. Additional tissue-specific or stage-specific
regulatory elements include the Zn13 promoter, which is a
pollen-specific promoter (Hamilton, et al., (1992) Plant Mol. Biol.
18:211-218); the UNUSUAL FLORAL ORGANS (UFO) promoter, which is
active in apical shoot meristem; the promoter active in shoot
meristems (Atanassova, et al., (1992) Plant J. 2:291), the cdc2
promoter and cyc07 promoter (see, for example, Ito, et al., (1994)
Plant Mol. Biol. 24:863-878; Martinez, et al., (1992) Proc. Natl.
Acad. Sci., USA 89:7360); the meristematic-preferred meri-5 and H3
promoters (Medford, et al., (1991) Plant Cell 3:359; Terada, et
al., (1993) Plant J. 3:241,); meristematic and phloem-preferred
promoters of Myb-related genes in barley (Wissenbach, et al.,
(1993) Plant J. 4:411); Arabidopsis cyc3aAt and cyc1At (Shaul, et
al., (1996) Proc. Natl. Acad. Sci. 93:4868-4872); C. roseus cyclins
CYS and CYM (Ito, et al., (1997) Plant J. 11:983-992); and
Nicotiana CyclinB1 (Trehin, et al., (1997) Plant Mol. Biol.
35:667-672); the promoter of the APETALA3 gene, which is active in
floral meristems (Jack, et al., (1994) Cell 76:703; Hempel, et al.,
supra, 1997); a promoter of an agamous-like (AGL) family member,
for example, AGL8, which is active in shoot meristem upon the
transition to flowering (Hempel, et al., supra, 1997); floral
abscission zone promoters; L1-specific promoters; the
ripening-enhanced tomato polygalacturonase promoter (Nicholass, et
al., (1995) Plant Mol. Biol. 28:423-435), the E8 promoter (Deikman,
et al., (1992) Plant Physiol. 100:2013-2017), and the
fruit-specific 2A1 promoter, U2 and U5 snRNA promoters from maize,
the Z4 promoter from a gene encoding the Z4 22 kD zein protein, the
Z10 promoter from a gene encoding a 10 kD zein protein, a Z27
promoter from a gene encoding a 27 kD zein protein, the A20
promoter from the gene encoding a 19 kD zein protein, and the like.
Additional tissue-specific promoters can be isolated using well
known methods (see, e.g., U.S. Pat. No. 5,589,379). Shoot-preferred
promoters include shoot meristem-preferred promoters such as
promoters disclosed in Weigel, et al., (1992) Cell 69:843-859
(Accession Number M91208); Accession Number AJ131822; Accession
Number Z71981; Accession Number AF049870 and shoot-preferred
promoters disclosed in McAvoy, et al., (2003) Acta Hort. (ISHS)
625:379-385. Inflorescence-preferred promoters include the promoter
of chalcone synthase (Van der Meer, et al., (1992) Plant J.
2(4):525-535), anther-specific LAT52 (Twell, et al., (1989) Mol.
Gen. Genet. 217:240-245), pollen-specific Bp4 (Albani, et al.,
(1990) Plant Mol. Biol. 15:605, maize pollen-specific gene Zm13
(Hamilton, et al., (1992) Plant Mol. Biol. 18:211-218; Guerrero, et
al., (1993) Mol. Gen. Genet. 224:161-168), microspore-specific
promoters such as the apg gene promoter (Twell, et al., (1993) Sex.
Plant Reprod. 6:217-224) and tapetum-specific promoters such as the
TA29 gene promoter (Mariani, et al., (1990) Nature 347:737; U.S.
Pat. No. 6,372,967), and other stamen-specific promoters such as
the MS45 gene promoter, 5126 gene promoter, BS7 gene promoter, PG47
gene promoter (U.S. Pat. Nos. 5,412,085; 5,545,546; Plant J
3(2):261-271 (1993)), SGB6 gene promoter (U.S. Pat. No. 5,470,359),
G9 gene promoter (U.S. Pat. Nos. 5,8937,850; 5,589,610), SB200 gene
promoter (WO 2002/26789), or the like (see, Example 1).
Tissue-preferred promoters of interest further include a sunflower
pollen-expressed gene SF3 (Baltz, et al., (1992) The Plant Journal
2:713-721), B. napus pollen specific genes (Arnoldo, et al., (1992)
J. Cell. Biochem, Abstract No. Y101204). Tissue-preferred promoters
further include those reported by Yamamoto, et al., (1997) Plant J.
12(2):255-265 (psaDb); Kawamata, et al., (1997) Plant Cell Physiol.
38(7):792-803 (PsPAL1); Hansen, et al., (1997) Mol. Gen. Genet.
254(3):337-343 (ORF13); Russell, et al., (1997) Transgenic Res.
6(2):157-168 (waxy or ZmGBS; 27 kDa zein, ZmZ27; osAGP; osGT1);
Rinehart, et al., (1996) Plant Physiol. 112(3):1331-1341 (FbI2A
from cotton); Van Camp, et al., (1996) Plant Physiol.
112(2):525-535 (Nicotiana SodA1 and SodA2); Canevascini, et al.,
(1996) Plant Physiol. 112(2):513-524 (Nicotiana Itp1); Yamamoto, et
al., (1994) Plant Cell Physiol. 35(5):773-778 (Pinus cab-6
promoter); Lam, (1994) Results Probl. Cell Differ. 20:181-196;
Orozco, et al., (1993) Plant Mol. Biol. 23(6):1129-1138 (spinach
rubisco activase (Rca)); Matsuoka, et al., (1993) Proc Natl. Acad.
Sci. USA 90(20):9586-9590 (PPDK promoter) and Guevara-Garcia, et
al., (1993) Plant J. 4(3):495-505 (Agrobacterium pmas promoter). A
tissue-specific promoter that is active in cells of male or female
reproductive organs can be particularly useful in certain aspects
of the present invention. "Seed-preferred" promoters include both
"seed-specific" promoters (those promoters active during seed
development such as promoters of seed storage proteins) as well as
"seed-germinating" promoters (those promoters active during seed
germination). See, Thompson, et al., (1989) BioEssays 10:108. Such
seed-preferred promoters include, but are not limited to, Cim1
(cytokinin-induced message), cZ19B1 (maize 19 kDa zein), mi1ps
(myo-inositol-1-phosphate synthase); see WO 2000/11177 and U.S.
Pat. No. 6,225,529. Gamma-zein is an endosperm-specific promoter.
Globulin-1 (Glob-1) is a representative embryo-specific promoter.
For dicots, seed-specific promoters include, but are not limited
to, bean .beta.-phaseolin, napin, .beta.-conglycinin, soybean
lectin, cruciferin, and the like. For monocots, seed-specific
promoters include, but are not limited to, maize 15 kDa zein, 22
kDa zein, 27 kDa zein, gamma-zein, waxy, shrunken 1, shrunken 2,
globulin 1, etc. See also, WO 2000/12733 and U.S. Pat. No.
6,528,704, where seed-preferred promoters from end1 and end2 genes
are disclosed. Additional embryo specific promoters are disclosed
in Sato, et al., (1996) Proc. Natl. Acad. Sci. 93:8117-8122 (rice
homeobox, OSH1) and Postma-Haarsma, et al., (1999) Plant Mol. Biol.
39:257-71 (rice KNOX genes). Additional endosperm specific
promoters are disclosed in Albani, et al., (1984) EMBO 3:1405-15;
Albani, et al., (1999) Theor. Appl. Gen. 98:1253-62; Albani, et
al., (1993) Plant J. 4:343-55; Mena, et al., (1998) The Plant
Journal 116:53-62 (barley DOF); Opsahl-Ferstad, et al., (1997)
Plant J 12:235-46 (maize Esr) and Wu, et al., (1998) Plant Cell
Physiology 39:885-889 (rice GluA-3, GluB-1, NRP33, RAG-1).
[0088] An inducible regulatory element is one that is capable of
directly or indirectly activating transcription of one or more DNA
sequences or genes in response to an inducer. The inducer can be a
chemical agent such as a protein, metabolite, growth regulator,
herbicide or phenolic compound or a physiological stress, such as
that imposed directly by heat, cold, salt or toxic elements, or
indirectly through the action of a pathogen or disease agent such
as a virus or other biological or physical agent or environmental
condition. A plant cell containing an inducible regulatory element
may be exposed to an inducer by externally applying the inducer to
the cell or plant such as by spraying, watering, heating or similar
methods. An inducing agent useful for inducing expression from an
inducible promoter is selected based on the particular inducible
regulatory element. In response to exposure to an inducing agent,
transcription from the inducible regulatory element generally is
initiated de novo or is increased above a basal or constitutive
level of expression. Typically the protein factor that binds
specifically to an inducible regulatory element to activate
transcription is present in an inactive form which is then directly
or indirectly converted to the active form by the inducer. Any
inducible promoter can be used in the instant invention (see, Ward,
et al., (1993) Plant Mol. Biol. 22: 361-366).
[0089] Examples of inducible regulatory elements include a
metallothionein regulatory element, a copper-inducible regulatory
element, or a tetracycline-inducible regulatory element, the
transcription from which can be effected in response to divalent
metal ions, copper or tetracycline, respectively (Furst, et al.,
(1988) Cell 55:705-717; Mett, et al., (1993) Proc. Natl. Acad.
Sci., USA 90:4567-4571; Gatz, et al., (1992) Plant J. 2:397-404;
Roder, et al., (1994) Mol. Gen. Genet. 243:32-38). Inducible
regulatory elements also include an ecdysone regulatory element or
a glucocorticoid regulatory element, the transcription from which
can be effected in response to ecdysone or other steroid
(Christopherson, et al., (1992) Proc. Natl. Acad. Sci., USA
89:6314-6318; Schena, et al., (1991) Proc. Natl. Acad. Sci., USA
88:10421-10425; U.S. Pat. No. 6,504,082); a cold responsive
regulatory element or a heat shock regulatory element, the
transcription of which can be effected in response to exposure to
cold or heat, respectively (Takahashi, et al., (1992) Plant
Physiol. 99:383-390); the promoter of the alcohol dehydrogenase
gene (Gerlach, et al., (1982) PNAS USA 79:2981-2985; Walker, et
al., (1987) PNAS 84(19):6624-6628), inducible by anaerobic
conditions; and the light-inducible promoter derived from the pea
rbcS gene or pea psaDb gene (Yamamoto, et al., (1997) Plant J.
12(2):255-265); a light-inducible regulatory element (Feinbaum, et
al., (1991) Mol. Gen. Genet. 226:449; Lam and Chua, (1990) Science
248:471; Matsuoka, et al., (1993) Proc. Natl. Acad. Sci. USA
90(20):9586-9590; Orozco, et al., (1993) Plant Mol. Bio.
23(6):1129-1138), a plant hormone inducible regulatory element
(Yamaguchi-Shinozaki, et al., (1990) Plant Mol. Biol. 15:905;
Kares, et al., (1990) Plant Mol. Biol. 15:225), and the like. An
inducible regulatory element also can be the promoter of the maize
In2-1 or In2-2 gene, which responds to benzenesulfonamide herbicide
safeners (Hershey, et al., (1991) Mol. Gen. Gene. 227:229-237;
Gatz, et al., (1994) Mol. Gen. Genet. 243:32-38), and the Tet
repressor of transposon Tn10 (Gatz, et al., (1991) Mol. Gen. Genet.
227:229-237). Stress inducible promoters include salt/water
stress-inducible promoters such as P5CS (Zang, et al., (1997) Plant
Sciences 129:81-89); cold-inducible promoters, such as, cor15a
(Hajela, et al., (1990) Plant Physiol. 93:1246-1252), cor15b
(Wlihelm, et al., (1993) Plant Mol Biol 23:1073-1077), wsc120
(Ouellet, et al., (1998) FEBS Lett. 423:324-328), ci7 (Kirch, et
al., (1997) Plant Mol Biol. 33:897-909), ci21A (Schneider, et al.,
(1997) Plant Physiol. 113:335-45); drought-inducible promoters,
such as, Trg-31 (Chaudhary, et al., (1996) Plant Mol. Biol.
30:1247-57), rd29 (Kasuga, et al., (1999) Nature Biotechnology
18:287-291); osmotic inducible promoters, such as Rab17 (Vilardell,
et al., (1991) Plant Mol. Biol. 17:985-93) and osmotin (Raghothama,
et al., (1993) Plant Mol Biol 23:1117-28); and heat inducible
promoters, such as heat shock proteins (Barros, et al., (1992)
Plant Mol. 19:665-75; Marrs, et al., (1993) Dev. Genet. 14:27-41),
smHSP (Waters, et al., (1996) J. Experimental Botany 47:325-338),
and the heat-shock inducible element from the parsley ubiquitin
promoter (WO 2003/102198). Other stress-inducible promoters include
rip2 (U.S. Pat. No. 5,332,808 and US Patent Application Publication
Number 2003/0217393) and rd29a (Yamaguchi-Shinozaki, et al., (1993)
Mol. Gen. Genetics 236:331-340). Certain promoters are inducible by
wounding, including the Agrobacterium pmas promoter
(Guevara-Garcia, et al., (1993) Plant J. 4(3):495-505) and the
Agrobacterium ORF13 promoter (Hansen, et al., (1997) Mol. Gen.
Genet. 254(3):337-343).
[0090] Additional regulatory elements active in plant cells and
useful in the methods or compositions of the invention include, for
example, the spinach nitrite reductase gene regulatory element
(Back, et al., Plant Mol. Biol. 17:9, 1991); a gamma zein promoter,
an oleosin ole16 promoter, a globulin I promoter, an actin I
promoter, an actin cl promoter, a sucrose synthetase promoter, an
INOPS promoter, an EXM5 promoter, a globulin2 promoter, a b-32,
ADPG-pyrophosphorylase promoter, an Ltp1 promoter, an Ltp2
promoter, an oleosin ole17 promoter, an oleosin ole18 promoter, an
actin 2 promoter, a pollen-specific protein promoter, a
pollen-specific pectate lyase gene promoter or PG47 gene promoter,
an anther specific RTS2 gene promoter, SGB6 gene promoter or G9
gene promoter, a tapetum specific RAB24 gene promoter, an
anthranilate synthase alpha subunit promoter, an alpha zein
promoter, an anthranilate synthase beta subunit promoter, a
dihydrodipicolinate synthase promoter, a Thi I promoter, an alcohol
dehydrogenase promoter, a cab binding protein promoter, an H3C4
promoter, a RUBISCO SS starch branching enzyme promoter, an actin3
promoter, an actin7 promoter, a regulatory protein GF14-12
promoter, a ribosomal protein L9 promoter, a cellulose biosynthetic
enzyme promoter, an S-adenosyl-L-homocysteine hydrolase promoter, a
superoxide dismutase promoter, a C-kinase receptor promoter, a
phosphoglycerate mutase promoter, a root-specific RCc3 mRNA
promoter, a glucose-6 phosphate isomerase promoter, a
pyrophosphate-fructose 6-phosphate-1-phosphotransferase promoter, a
beta-ketoacyl-ACP synthase promoter, a 33 kDa photosystem 11
promoter, an oxygen evolving protein promoter, a 69 kDa vacuolar
ATPase subunit promoter, a glyceraldehyde-3-phosphate dehydrogenase
promoter, an ABA- and ripening-inducible-like protein promoter, a
phenylalanine ammonia lyase promoter, an adenosine triphosphatase
S-adenosyl-L-homocysteine hydrolase promoter, a chalcone synthase
promoter, a zein promoter, a globulin-1 promoter, an auxin-binding
protein promoter, a UDP glucose flavonoid glycosyl-transferase gene
promoter, an NTI promoter, an actin promoter, and an opaque 2
promoter.
[0091] An exogenous nucleic acid molecule can be introduced into a
cell as a naked DNA molecule, can be incorporated in a matrix such
as a liposome or a particle such as a viral particle, or can be
incorporated into a vector. Incorporation of the polynucleotide
into a vector can facilitate manipulation of the polynucleotide, or
introduction of the polynucleotide into a plant cell. Accordingly,
the vector can be derived from a plasmid or can be a viral vector
such as a T-DNA vector (Horsch, et al., (1985) Science
227:1229-1231). If desired, the vector can include components of a
plant transposable element, for example, a Ds transposon (Bancroft
and Dean, (1993) Genetics 134:1221-1229) or an Spm transposon
(Aarts, et al., (1995) Mol. Gen. Genet. 247:555-564). In addition
to containing the transgene of interest, the vector also can
contain various nucleotide sequences that facilitate, for example,
rescue of the vector from a transformed plant cell; passage of the
vector in a host cell, which can be a plant, animal, bacterial, or
insect host cell; or expression of an encoding nucleotide sequence
in the vector, including all or a portion of a rescued coding
region. As such, a vector can contain any of a number of additional
transcription and translation elements, including constitutive and
inducible promoters, enhancers, and the like (see, for example,
Bitter, et al., (1987) Meth. Enzymol. 153:516-544). For example, a
vector can contain elements useful for passage, growth or
expression in a bacterial system, including a bacterial origin of
replication; a promoter, which can be an inducible promoter; and
the like. A vector also can contain one or more restriction
endonuclease recognition and cleavage sites, including, for
example, a polylinker sequence, to facilitate insertion or removal
of a transgene.
[0092] In addition to, or alternatively to, a nucleotide sequence
relevant to a fertility gene (e.g., an hpRNA comprising an inverted
repeat of a fertility gene promoter, or a coding sequence of a
fertility gene, alone or operably linked to a heterologous
promoter), an exogenous nucleic acid molecule, or a vector
containing such a transgene, can contain one or more other
expressible nucleotide sequences encoding an RNA or a polypeptide
of interest. For example, the additional nucleotide sequence can
encode an antisense nucleic acid molecule; an enzyme such as
.beta.-galactosidase, .beta.-glucuronidase, luciferase, alkaline
phosphatase, glutathione .alpha.-transferase, chloramphenicol
acetyltransferase, guanine xanthine phosphoribosyltransferase and
neomycin phosphotransferase; a viral polypeptide or a peptide
portion thereof or a plant growth factor or hormone.
[0093] In certain embodiments, the expression vector contains a
gene encoding a selection marker which is functionally linked to a
promoter that controls transcription initiation. For a general
description of plant expression vectors and reporter genes, see,
Gruber, et al., "Vectors for Plant Transformation" in Methods of
Plant Molecular Biology and Biotechnology 89-119 (CRC Press, 1993).
In using the term, it is meant to include all types of selection
markers, whether they be scorable or selective. Expression of such
a nucleotide sequence can provide a means for selecting for a cell
containing the construct, for example, by conferring a desirable
phenotype to a plant cell containing the nucleotide sequence. For
example, the additional nucleotide sequence can be, or encode, a
selectable marker, which, when present or expressed in a plant
cell, provides a means to identify the plant cell containing the
marker.
[0094] A selectable marker provides a means for screening a
population of organisms or cells of an organism (e.g., plants or
plant cells) to identify those having the marker and, therefore,
the transgene of interest. A selectable marker generally confers a
selective advantage to the cell, or to an organism (e.g., a plant)
containing the cell, for example, the ability to grow in the
presence of a negative selective agent such as an antibiotic or,
for a plant, an herbicide. A selective advantage also can be due,
for example, to an enhanced or novel capacity to utilize an added
compound as a nutrient, growth factor or energy source. A selective
advantage can be conferred by a single polynucleotide, or its
expression product, or by a combination of polynucleotides whose
expression in a plant cell gives the cell a positive selective
advantage, a negative selective advantage, or both. It should be
recognized that expression of the transgene of interest (e.g.,
encoding a hpRNA) also provides a means to select cells containing
the encoding nucleotide sequence. However, the use of an additional
selectable marker, which, for example, allows a plant cell to
survive under otherwise toxic conditions, provides a means to
enrich for transformed plant cells containing the desired
transgene. Examples of suitable scorable or selection genes known
in the art can be found in, for example, Jefferson, et al., (1991)
in Plant Molecular Biology Manual, ed. Gelvin, et al., (Kluwer
Academic Publishers), pp. 33; DeWet, et al., (1987) Mol. Cell.
Biol. 7:725-737; Goff, et al., (1990) EMBO J. 9:2517-2522; Kain, et
al., (1995) Bio Techniques 19:650-655 and Chiu, et al., (1996)
Curr. Biol. 6:325-330.
[0095] Examples of selectable markers include those that confer
resistance to antimetabolites such as herbicides or antibiotics,
for example, dihydrofolate reductase, which confers resistance to
methotrexate (Reiss, Plant Physiol. (Life Sci. Adv.) 13:143-149,
1994; see also, Herrera Estrella, et al., (1983) Nature
303:209-213; Meijer, et al., (1991) Plant Mol. Biol. 16:807-820);
neomycin phosphotransferase, which confers resistance to the
aminoglycosides neomycin, kanamycin and paromycin
(Herrera-Estrella, (1983) EMBO J. 2:987-995) and hygro, which
confers resistance to hygromycin (Marsh, (1984) Gene 32:481-485;
see also, Waldron, et al., (1985) Plant Mol. Biol. 5:103-108;
Zhijian, et al., (1995) Plant Science 108:219-227); trpB, which
allows cells to utilize indole in place of tryptophan; hisD, which
allows cells to utilize histinol in place of histidine (Hartman,
(1988) Proc. Natl. Acad. Sci., USA 85:8047); mannose-6-phosphate
isomerase which allows cells to utilize mannose (WO 1994/20627);
ornithine decarboxylase, which confers resistance to the ornithine
decarboxylase inhibitor, 2-(difluoromethyl)-DL-ornithine (DFMO;
McConlogue, 1987, In: Current Communications in Molecular Biology,
Cold Spring Harbor Laboratory ed.); and deaminase from Aspergillus
terreus, which confers resistance to Blasticidin S (Tamura, (1995)
Biosci. Biotechnol. Biochem. 59:2336-2338). Additional selectable
markers include, for example, a mutant EPSPV-synthase, which
confers glyphosate resistance (Hinchee, et al., (1998)
BioTechnology 91:915-922), a mutant acetolactate synthase, which
confers imidazolinone or sulfonylurea resistance (Lee, et al.,
(1988) EMBO J. 7:1241-1248), a mutant psbA, which confers
resistance to atrazine (Smeda, et al., (1993) Plant Physiol.
103:911-917), or a mutant protoporphyrinogen oxidase (see, U.S.
Pat. No. 5,767,373) or other markers conferring resistance to an
herbicide such as glufosinate. Examples of suitable selectable
marker genes include, but are not limited to, genes encoding
resistance to chloramphenicol (Herrera Estrella, et al., (1983)
EMBO J. 2:987-992); streptomycin (Jones, et al., (1987) Mol. Gen.
Genet. 210:86-91); spectinomycin (Bretagne-Sagnard, et al., (1996)
Transgenic Res. 5:131-137); bleomycin (Hille, et al., (1990) Plant
Mol. Biol. 7:171-176); sulfonamide (Guerineau, et al., (1990) Plant
Mol. Biol. 15:127-136); bromoxynil (Stalker, et al., (1988) Science
242:419-423); glyphosate (Shaw, et al., (1986) Science
233:478-481); phosphinothricin (DeBlock, et al., EMBO J. (1987)
6:2513-2518), and the like. One option for use of a selective gene
is a glufosinate-resistance encoding DNA and in one embodiment can
be the phosphinothricin acetyl transferase ("PAT"), maize optimized
PAT gene or bar gene under the control of the CaMV 35S or ubiquitin
promoters. The genes confer resistance to bialaphos. See,
Gordon-Kamm, et al., Plant Cell (1990) 2:603; Uchimiya, et al.,
(1993) BioTechnology 11:835; White, et al., (1990) Nucl. Acids Res.
18:1062; Spencer, et al., (1990) Theor. Appl. Genet. 79:625-631 and
Anzai, et al., (1989) Mol. Gen. Gen. 219:492). A version of the PAT
gene is the maize optimized PAT gene, described at U.S. Pat. No.
6,096,947.
[0096] In addition, markers that facilitate identification of a
plant cell containing the polynucleotide encoding the marker
include, for example, luciferase (Giacomin, (1996) Plant Sci.
116:59-72; Scikantha, (1996) J. Bacteriol. 178:121), green
fluorescent protein (Gerdes, (1996) FEBS Lett. 389:44-47; Chalfie,
et al., (1994) Science 263:802) and other fluorescent protein
variants or .beta.-glucuronidase (Jefferson, (1987) Plant Mol.
Biol. Rep. 5:387; Jefferson, et al., (1987) EMBO J. 6:3901-3907;
Jefferson, (1989) Nature 342(6251):837-838); the maize genes
regulating pigment production (Ludwig, et al., (1990) Science
247:449; Grotewold, et al., (1991) PNAS 88:4587-4591; Cocciolone,
et al., (2001) Plant J 27(5):467-478; Grotewold, et al., (1998)
Plant Cell 10:721-740); .beta.-galactosidase (Teeri, et al., (1989)
EMBO J. 8:343-350); luciferase (Ow, et al., (11986) Science
234:856-859); chloramphenicol acetyltransferase (CAT) (Lindsey and
Jones, (1987) Plant Mol. Biol. 10:43-52) and numerous others as
disclosed herein or otherwise known in the art. Such markers also
can be used as reporter molecules. Many variations on promoters,
selectable markers and other components of the construct are
available to one skilled in the art.
[0097] The term "plant" is used broadly herein to include any plant
at any stage of development, or to part of a plant, including a
plant cutting, a plant cell, a plant cell culture, a plant organ, a
plant seed and a plantlet. A plant cell is the structural and
physiological unit of the plant, comprising a protoplast and a cell
wall. A plant cell can be in the form of an isolated single cell or
aggregate of cells such as a friable callus or a cultured cell or
can be part of a higher organized unit, for example, a plant
tissue, plant organ or plant. Thus, a plant cell can be a
protoplast, a gamete producing cell or a cell or collection of
cells that can regenerate into a whole plant. As such, a seed,
which comprises multiple plant cells and is capable of regenerating
into a whole plant, is considered a plant cell for purposes of this
disclosure. A plant tissue or plant organ can be a seed,
protoplast, callus or any other groups of plant cells that is
organized into a structural or functional unit. Particularly useful
parts of a plant include harvestable parts and parts useful for
propagation of progeny plants. A harvestable part of a plant can be
any useful part of a plant, for example, flowers, pollen,
seedlings, tubers, leaves, stems, fruit, seeds, roots and the like.
A part of a plant useful for propagation includes, for example,
seeds, fruits, cuttings, seedlings, tubers, rootstocks, and the
like.
[0098] A transgenic plant can be regenerated from a genetically
modified plant cell, i.e., a whole plant can be regenerated from a
plant cell; a group of plant cells; a protoplast; a seed or a piece
of a plant such as a leaf, a cotyledon or a cutting. Regeneration
from protoplasts varies among species of plants. For example, a
suspension of protoplasts can be made and, in certain species,
embryo formation can be induced from the protoplast suspension, to
the stage of ripening and germination. The culture media generally
contain various components necessary for growth and regeneration,
including, for example, hormones such as auxins and cytokinins; and
amino acids such as glutamic acid and proline, depending on the
particular plant species. Efficient regeneration will depend, in
part, on the medium, the genotype, and the history of the culture,
and is reproducible if these variables are controlled.
[0099] Regeneration can occur from plant callus, explants, organs
or plant parts. Transformation can be performed in the context of
organ or plant part regeneration. (see, Meth. Enzymol. Vol. 118;
Klee, et al., (1987) Ann. Rev. Plant Physiol. 38:467). Utilizing
the leaf disk-transformation-regeneration method, for example,
disks are cultured on selective media, followed by shoot formation
in about two to four weeks (see, Horsch, et al., supra, 1985).
Shoots that develop are excised from calli and transplanted to
appropriate root-inducing selective medium. Rooted plantlets are
transplanted to soil as soon as possible after roots appear. The
plantlets can be repotted as required, until reaching maturity.
This is the TO generation.
[0100] In seed-propagated crops, mature TO plants can be
self-pollinated. The resulting seeds can be grown and the progeny
plants tested for presence of the transgene, often by screening for
the expression of a linked marker gene. These transgenic plants
represent the T1 generation. Multiple generations (T2, T3, etc.)
may be produced to ensure that expression of the desired phenotypic
characteristic is stably maintained and inherited and seeds can be
harvested. In this manner, the present invention provides a
transformed seed (also referred to as a "transgenic seed") having a
polynucleotide of the invention, for example, an expression
cassette of the invention, stably incorporated into its genome.
Methods for further selfing, selection, and cross breeding of
plants having desirable characteristics or other characteristics of
interest include those disclosed herein and others well known to
plant breeders. Progeny, variants, and mutants of the regenerated
plants are also included within the scope of the invention,
provided that they comprise the introduced polynucleotides.
[0101] In various aspects of the present invention, one or more
transgenes is introduced into cells. When used in reference to a
transgene, the term "introducing" means transferring the exogenous
nucleic acid molecule into a cell. A nucleic acid molecule can be
introduced into a plant cell by a variety of methods. For example,
the transgene can be contained in a vector, can be introduced into
a plant cell using a direct gene transfer method such as
electroporation or microprojectile mediated transformation or using
Agrobacterium mediated transformation. As used herein, the term
"transformed" refers to a plant cell containing an exogenously
introduced nucleic acid molecule.
[0102] One or more exogenous nucleic acid molecules can be
introduced into plant cells using any of numerous well-known and
routine methods for plant transformation, including biological and
physical plant transformation protocols (see, e.g., Miki, et al.,
"Procedures for Introducing Foreign DNA into Plants"; In Methods in
Plant Molecular Biology and Biotechnology, Glick and Thompson, Eds.
(CRC Press, Inc., Boca Raton, 1993) pages 67-88). In addition,
expression vectors and in vitro culture methods for plant cell or
tissue transformation and regeneration of plants are routine and
well-known (see, e.g., Gruber, et al., "Vectors for Plant
Transformation"; Id. at pages 89-119).
[0103] Suitable methods of transforming plant cells include
microinjection, Crossway, et al., (1986) Biotechniques 4:320-334;
electroporation, Riggs, et al., (1986) Proc. Natl. Acad. Sci. USA
83:5602-5606; Agrobacterium-mediated transformation, see for
example, Townsend, et al., U.S. Pat. No. 5,563,055; direct gene
transfer, Paszkowski, et al., (1984) EMBO J. 3:2717-2722 and
ballistic particle acceleration, see for example, Sanford, et al.,
U.S. Pat. No. 4,945,050; Tomes, et al., (1995) in Plant Cell,
Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and
Phillips (Springer-Verlag, Berlin) and McCabe, et al., (1988)
Biotechnology 6:923-926. Also see, Weissinger, et al., (1988)
Annual Rev. Genet. 22:421-477; Sanford, et al., (1987) Particulate
Science and Technology 5:27-37 (onion); Christou, et al., (1988)
Plant Physiol. 87:671-674 (soybean); McCabe, et al., (1988)
Bio/Technology 6:923-926 (soybean); Datta, et al., (1990)
Biotechnology 8:736-740 (rice); Klein, et al., (1988) Proc. Natl.
Acad. Sci. USA 85:4305-4309 (maize); Klein, et al., (1988)
Biotechnology 6:559-563 (maize); Klein, et al., (1988) Plant
Physiol. 91:440-444 (maize); Fromm, et al., (1990) Biotechnology
8:833-839; Hooydaas-Van Slogteren, et al., (1984) Nature (London)
311:763-764; Bytebier, et al., (1987) Proc. Natl. Acad. Sci. USA
84:5345-5349 (Liliaceae); De Wet, et al., (1985) in The
Experimental Manipulation of Ovule Tissues, ed. Chapman, et al.,
(Longman, N.Y.), pp. 197-209 (pollen); Kaeppler, et al., (1990)
Plant Cell Reports 9:415-418 and Kaeppler, et al., (1992) Theor.
Appl. Genet. 84:560-566 (whisker-mediated transformation); D.
Halluin, et al., (1992) Plant Cell 4:1495-1505 (electroporation);
Li, et al., (1993) Plant Cell Reports 12:250-255 and Christou, et
al., (1995) Annals of Botany 75:407-413 (rice); Osjoda, et al.,
(1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium
tumefaciens); all of which are herein incorporated by
reference.
[0104] Agrobacterium-mediated transformation provides a useful
method for introducing a transgene into plants (Horsch, et al.,
(1985) Science 227:1229). A. tumefaciens and A. rhizogenes are
plant pathogenic soil bacteria that genetically transform plant
cells. The Ti and Ri plasmids of A. tumefaciens and A. rhizogenes,
respectively, carry genes responsible for genetic transformation of
the plant (see, e.g., Kado, (1991) Crit. Rev. Plant Sci. 10:1; see,
also, Moloney, et al., (1989) Plant Cell Reports 8:238; U.S. Pat.
No. 5,591,616; WO 1999/47552; Weissbach and Weissbach, "Methods for
Plant Molecular Biology" (Academic Press, NY 1988), section VIII,
pages 421-463; Grierson and Corey, "Plant Molecular Biology" 2d Ed.
(Blackie, London 1988), Chapters 7-9; see, also, Horsch, et al.,
supra, 1985).
[0105] With respect to A. tumefaciens, the wild type form contains
a Ti plasmid, which directs production of tumorigenic crown gall
growth on host plants. Transfer of the tumor-inducing T-DNA region
of the Ti plasmid to a plant genome requires the Ti plasmid-encoded
virulence genes as well as T-DNA borders, which are a set of direct
DNA repeats that delineate the region to be transferred. An
Agrobacterium based vector is a modified form of a Ti plasmid, in
which the tumor-inducing functions are replaced by a nucleotide
sequence of interest that is to be introduced into the plant host.
Methods of using Agrobacterium mediated transformation include
cocultivation of Agrobacterium with cultured isolated protoplasts;
transformation of plant cells or tissues with Agrobacterium; and
transformation of seeds, apices or meristems with Agrobacterium. In
addition, in planta transformation by Agrobacterium can be
performed using vacuum infiltration of a suspension of
Agrobacterium cells (Bechtold, et al., (1993) C.R. Acad. Sci. Paris
316:1194).
[0106] Agrobacterium-mediated transformation can employ cointegrate
vectors or binary vector systems, in which the components of the Ti
plasmid are divided between a helper vector, which resides
permanently in the Agrobacterium host and carries the virulence
genes, and a shuttle vector, which contains the gene of interest
bounded by T-DNA sequences. Binary vectors are well known in the
art (see, for example, De Framond, (1983) BioTechnology 1:262;
Hoekema, et al., (1983) Nature 303:179) and are commercially
available (Clontech; Palo Alto Calif.). For transformation,
Agrobacterium can be cocultured, for example, with plant cells or
wounded tissue such as leaf tissue, root explants, hypocotyls,
cotyledons, stem pieces or tubers (see, for example, Glick and
Thompson, "Methods in Plant Molecular Biology and Biotechnology"
(Boca Raton Fla., CRC Press 1993)). Wounded cells within the plant
tissue that have been infected by Agrobacterium can develop organs
de novo when cultured under the appropriate conditions; the
resulting transgenic shoots eventually give rise to transgenic
plants which contain the introduced polynucleotide.
[0107] Agrobacterium-mediated transformation has been used to
produce a variety of transgenic plants, including, for example,
transgenic cruciferous plants such as Arabidopsis, mustard,
rapeseed and flax; transgenic leguminous plants such as alfalfa,
pea, soybean, trefoil and white clover and transgenic solanaceous
plants such as eggplant, petunia, potato, tobacco and tomato (see,
for example, Wang, et al., "Transformation of Plants and Soil
Microorganisms" (Cambridge, University Press 1995)). In addition,
Agrobacterium mediated transformation can be used to introduce an
exogenous nucleic acid molecule into apple, aspen, belladonna,
black currant, carrot, celery, cotton, cucumber, grape,
horseradish, lettuce, morning glory, muskmelon, neem, poplar,
strawberry, sugar beet, sunflower, walnut, asparagus, rice, wheat,
sorghum, barley, maize and other plants (see, for example, Glick
and Thompson, supra, 1993; Hiei, et al., (1994) Plant J. 6:271-282;
Shimamoto, (1995) Science 270:1772-1773).
[0108] Suitable strains of A. tumefaciens and vectors as well as
transformation of Agrobacteria and appropriate growth and selection
media are well known in the art (GV3101, pMK90RK), Koncz, (1986)
Mol. Gen. Genet. 204:383-396; (C58C1, pGV3850kan), Deblaere, (1985)
Nucl. Acid Res. 13:4777; Bevan, (1984) Nucleic Acid Res. 12:8711;
Koncz, (1986) Proc. Natl. Acad. Sci. USA 86:8467-8471; Koncz,
(1992) Plant Mol. Biol. 20:963-976; Koncz, Specialized vectors for
gene tagging and expression studies. In: Plant Molecular Biology
Manual Vol. 2, Gelvin and Schilperoort (Eds.), Dordrecht, The
Netherlands: Kluwer Academic Publ. (1994), 1-22; European Patent
A-1 20 516; Hoekema: The Binary Plant Vector System,
Offsetdrukkerij Kanters B. V., Alblasserdam (1985), Chapter V;
Fraley, Crit. Rev. Plant. Sci., 4:1-46; An, (1985) EMBO J.
4:277-287).
[0109] As noted herein, the present invention provides vectors
capable of expressing genes of interest under the control of the
regulatory elements. In general, the vectors should be functional
in plant cells. At times, it may be preferable to have vectors that
are functional in E. coli (e.g., production of protein for raising
antibodies, DNA sequence analysis, construction of inserts,
obtaining quantities of nucleic acids). Vectors and procedures for
cloning and expression in E. coli are discussed in Sambrook, et al.
(supra).
[0110] The transformation vector, comprising the promoter of the
present invention operably linked to an isolated nucleotide
sequence in an expression cassette, can also contain at least one
additional nucleotide sequence for a gene to be co-transformed into
the organism. Alternatively, the additional sequence(s) can be
provided on another transformation vector.
[0111] Where the exogenous nucleic acid molecule is contained in a
vector, the vector can contain functional elements, for example
"left border" and "right border" sequences of the T-DNA of
Agrobacterium, which allow for stable integration into a plant
genome. Furthermore, methods and vectors that permit the generation
of marker-free transgenic plants, for example, where a selectable
marker gene is lost at a certain stage of plant development or
plant breeding, are known, and include, for example, methods of
co-transformation (Lyznik, (1989) Plant Mol. Biol. 13:151-161;
Peng, (1995) Plant Mol. Biol. 27:91-104) or methods that utilize
enzymes capable of promoting homologous recombination in plants
(see, e.g., WO 1997/08331; Bayley, (1992) Plant Mol. Biol.
18:353-361; Lloyd, (1994) Mol. Gen. Genet. 242:653-657; Maeser,
(1991) Mol. Gen. Genet. 230:170-176; Onouchi, (1991) Nucl. Acids
Res. 19:6373-6378; see, also, Sambrook, et al., supra, 1989).
[0112] Direct gene transfer methods also can be used to introduce
the desired transgene (or transgenes) into cells, including plant
cells that are refractory to Agrobacterium-mediated transformation
(see, e.g., Hiei, et al., (1994) Plant J. 6:271-282; U.S. Pat. No.
5,591,616). Such methods include direct gene transfer (see,
European Patent A 164 575), injection, electroporation, biolistic
methods such as particle bombardment, pollen-mediated
transformation, plant RNA virus-mediated transformation,
liposome-mediated transformation, transformation using wounded or
enzyme-degraded immature embryos or wounded or enzyme-degraded
embryogenic callus, and the like. Direct gene transfer methods
include microprojectile-mediated (biolistic) transformation
methods, wherein the transgene is carried on the surface of
microprojectiles measuring 1 to 4 mm. A vector, particularly an
expression vector containing the transgene(s) of interest, is
introduced into plant tissues with a biolistic device that
accelerates the microprojectiles to speeds of 300 to 600 m/s,
sufficient to penetrate plant cell walls and membranes (see, e.g.,
Sanford, et al., (1987) Part. Sci. Technol. 5:27; Sanford, (1988)
Trends Biotech. 6:299, Klein, et al., (1988) BioTechnology
6:559-563; Klein, et al., (1992) BioTechnology 10:268). In maize,
for example, several target tissues can be bombarded with
DNA-coated microprojectiles in order to produce transgenic plants,
including, for example, callus (Type I or Type II), immature
embryos, and meristem tissue.
[0113] Other methods for physical delivery of a transgene into
plants utilize sonication of the target cells (Zhang, et al.,
(1991) BioTechnology 9:996); liposomes or spheroplast fusion
(Deshayes, et al., (1985) EMBO J. 4:2731; Christou, et al., (1987)
Proc Natl. Acad. Sci., USA 84:3962); CaCl.sub.2 precipitation or
incubation with polyvinyl alcohol or poly-L-ornithine (Hain, et
al., (1985) Mol. Gen. Genet. 199:61; Draper, et al., (1982) Plant
Cell Physiol. 23:451) and electroporation of protoplasts and whole
cells and tissues (Donn, et al., (1990) In "Abstracts of VIIIth
International Congress on Plant Cell and Tissue Culture" IAPTC,
A2-38, pg. 53; D'Halluin, et al., (1992) Plant Cell 4:1495-1505;
Spencer, et al., (1994) Plant Mol. Biol. 24:51-61).
[0114] A direct gene transfer method such as electroporation can be
particularly useful for introducing exogenous nucleic acid
molecules into a cell such as a plant cell. For example, plant
protoplasts can be electroporated in the presence of a recombinant
nucleic acid molecule, which can be in a vector (Fromm, et al.,
(1985) Proc. Natl. Acad. Sci., USA 82:5824). Electrical impulses of
high field strength reversibly permeabilize membranes allowing the
introduction of the nucleic acid. Electroporated plant protoplasts
reform the cell wall, divide and form a plant callus.
Microinjection can be performed as described in Potrykus and
Spangenberg (eds.), Gene Transfer To Plants. Springer Verlag,
Berlin, N.Y. (1995). A transformed plant cell containing the
introduced recombinant nucleic acid molecule can be identified due
to the presence of a selectable marker included in the
construct.
[0115] As mentioned above, microprojectile mediated transformation
also provides a useful method for introducing exogenous nucleic
acid molecules into a plant cell (Klein, et al., (1987) Nature
327:70-73). This method utilizes microprojectiles such as gold or
tungsten, which are coated with the desired nucleic acid molecule
by precipitation with calcium chloride, spermidine or polyethylene
glycol. The microprojectile particles are accelerated at high speed
into a plant tissue using a device such as the BIOLISTIC PD-1000
particle gun (BioRad; Hercules Calif.). Microprojectile mediated
delivery ("particle bombardment") is especially useful to transform
plant cells that are difficult to transform or regenerate using
other methods. Methods for the transformation using biolistic
methods are well known (Wan, (1984) Plant Physiol. 104:37-48;
Vasil, (1993) BioTechnology 11:1553-1558; Christou, (1996) Trends
in Plant Science 1:423-431). Microprojectile mediated
transformation has been used, for example, to generate a variety of
transgenic plant species, including cotton, tobacco, corn, wheat,
oat, barley, sorghum, rice, hybrid poplar and papaya (see, Glick
and Thompson, supra, 1993; Duan, et al., (1996) Nature Biotech.
14:494-498; Shimamoto, (1994) Curr. Opin. Biotech. 5:158-162).
[0116] A rapid transformation regeneration system for the
production of transgenic plants such as a system that produces
transgenic wheat in two to three months (see, European Patent
Number EP 0709462 A2) also can be useful for producing a transgenic
plant according to a method of the invention, thus allowing more
rapid identification of gene functions. The transformation of most
dicotyledonous plants is possible with the methods described above.
Transformation of monocotyledonous plants also can be transformed
using, for example, biolistic methods as described above,
protoplast transformation, electroporation of partially
permeabilized cells, introduction of DNA using glass fibers,
Agrobacterium mediated transformation, and the like.
[0117] Plastid transformation also can be used to introduce a
nucleic acid molecule into a plant cell (U.S. Pat. Nos. 5,451,513,
5,545,817 and 5,545,818; WO 1995/16783; McBride, et al., (1994)
Proc. Natl. Acad. Sci., USA 91:7301-7305). Chloroplast
transformation involves introducing regions of cloned plastid DNA
flanking a desired nucleotide sequence, for example, a selectable
marker together with polynucleotide of interest, into a suitable
target tissue, using, for example, a biolistic or protoplast
transformation method (e.g., calcium chloride or PEG mediated
transformation). One to 1.5 kb flanking regions ("targeting
sequences") facilitate homologous recombination with the plastid
genome, and allow the replacement or modification of specific
regions of the plastome. Using this method, point mutations in the
chloroplast 16S rRNA and rps12 genes, which confer resistance to
spectinomycin and streptomycin and can be utilized as selectable
markers for transformation (Svab, et al., (1990) Proc. Natl. Acad.
Sci., USA 87:8526-8530; Staub and Maliga, (1992) Plant Cell
4:39-45), resulted in stable homopiasmic transformants, at a
frequency of approximately one per 100 bombardments of target
leaves. The presence of cloning sites between these markers allowed
creation of a plastid targeting vector for introduction of foreign
genes (Staub and Maliga, (1993) EMBO J. 12:601-606). Substantial
increases in transformation frequency are obtained by replacement
of the recessive rRNA or r-protein antibiotic resistance genes with
a dominant selectable marker, the bacterial aadA gene encoding the
spectinomycin-detoxifying enzyme
aminoglycoside-3'-adenyltransferase (Svab and Maliga, (1993) Proc.
Natl. Acad. Sci., USA 90:913-917). Approximately 15 to 20 cell
division cycles following transformation are generally required to
reach a homoplastidic state. Plastid expression, in which genes are
inserted by homologous recombination into all of the several
thousand copies of the circular plastid genome present in each
plant cell, takes advantage of the enormous copy number advantage
over nuclear-expressed genes to permit expression levels that can
readily exceed 10% of the total soluble plant protein.
[0118] The cells that have been transformed can be grown into
plants in accordance with conventional ways. See, for example,
McCormick, et al., (1986) Plant Cell Reports 5:81-84. These plants
can then be grown and pollinated with the same transformed strain
or different strains, and resulting plants having expression of the
desired phenotypic characteristic can then be identified. Two or
more generations can be grown to ensure that expression of the
desired phenotypic characteristic is stably maintained and
inherited.
[0119] A "subject plant" or "subject plant cell" is one in which
genetic alteration, such as transformation, has been affected as to
a gene of interest or is a plant or plant cell which is descended
from a plant or plant cell so altered and which comprises the
alteration. A "control" or "control plant" or "control plant cell"
provides a reference point for measuring changes in the subject
plant or plant cell.
[0120] A control plant or control plant cell may comprise, for
example: (a) a wild-type plant or plant cell, i.e., of the same
genotype as the starting material for the genetic alteration which
resulted in the subject plant or subject plant cell; (b) a plant or
plant cell of the same genotype as the starting material but which
has been transformed with a null construct (i.e., with a construct
which has no known effect on the trait of interest, such as a
construct comprising a marker gene); (c) a plant or plant cell
which is a non-transformed segregant among progeny of a subject
plant or subject plant cell; (d) a plant or plant cell genetically
identical to the subject plant or subject plant cell but which is
not exposed to conditions or stimuli that would induce expression
of the gene of interest or (e) the subject plant or subject plant
cell itself, under conditions in which the gene of interest is not
expressed.
[0121] In certain species, such as maize, the control and reference
plants may represent two hybrids, where the first hybrid is
produced from two parent inbred lines, and the second hybrid is
produced from the same two parental inbred lines except that one of
the parent inbred lines contains a recombinant DNA construct.
Performance of the second hybrid would typically be measured
relative to the first hybrid.
[0122] Further, where a plant comprising a recombinant DNA
construct is assessed or measured relative to a control plant not
comprising the recombinant DNA but otherwise having a comparable
genetic background to the plant, the control and reference plant
may share at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%
or 100% sequence identity of nuclear genetic material. There are
many laboratory-based techniques available for the analysis,
comparison and characterization of plant genetic backgrounds; among
these are isozyme electrophoresis, Restriction Fragment Length
Polymorphisms (RFLPs), Randomly Amplified Polymorphic DNAs (RAPDs),
Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNA
Amplification Fingerprinting (DAF), Sequence Characterized
Amplified Regions (SCARs), Amplified Fragment Length Polymorphisms
(AFLPs) and Simple Sequence Repeats (SSRs) which are also referred
to as microsatellites.
[0123] Plants suitable for purposes of the present invention can be
monocots or dicots and include, but are not limited to, maize,
wheat, barley, rye, sweet potato, bean, pea, chicory, lettuce,
cabbage, cauliflower, broccoli, turnip, radish, spinach, asparagus,
onion, garlic, pepper, celery, squash, pumpkin, hemp, zucchini,
apple, pear, quince, melon, plum, cherry, peach, nectarine,
apricot, strawberry, grape, raspberry, blackberry, pineapple,
avocado, papaya, mango, banana, soybean, tomato, sorghum,
sugarcane, sugar beet, sunflower, rapeseed, clover, tobacco,
carrot, cotton, alfalfa, rice, potato, eggplant, cucumber,
Arabidopsis thaliana, and woody plants such as coniferous and
deciduous trees. Thus, a transgenic plant or genetically modified
plant cell of the invention can be an angiosperm or gymnosperm.
[0124] Angiosperms are divided into two broad classes based on the
number of cotyledons, which are seed leaves that generally store or
absorb food; a monocotyledonous angiosperm has a single cotyledon,
and a dicotyledonous angiosperm has two cotyledons. Angiosperms
produce a variety of useful products including materials such as
lumber, rubber, and paper; fibers such as cotton and linen; herbs
and medicines such as quinine and vinblastine; ornamental flowers
such as roses and, where included within the scope of the present
invention, orchids; and foodstuffs such as grains, oils, fruits and
vegetables. Angiosperms encompass a variety of flowering plants,
including, for example, cereal plants, leguminous plants, oilseed
plants, hardwood trees, fruit-bearing plants and ornamental
flowers, which general classes are not necessarily exclusive.
Cereal plants, which produce an edible grain, include, for example,
corn, rice, wheat, barley, oat, rye, orchardgrass, guinea grass,
and sorghum. Leguminous plants include members of the pea family
(Fabaceae) and produce a characteristic fruit known as a legume.
Examples of leguminous plants include, for example, soybean, pea,
chickpea, moth bean, broad bean, kidney bean, lima bean, lentil,
cowpea, dry bean, and peanut, as well as alfalfa, birdsfoot
trefoil, clover and sainfoin. Oilseed plants, which have seeds that
are useful as a source of oil, include soybean, sunflower, rapeseed
(canola) and cottonseed. Angiosperms also include hardwood trees,
which are perennial woody plants that generally have a single stem
(trunk). Examples of such trees include alder, ash, aspen, basswood
(linden), beech, birch, cherry, cottonwood, elm, eucalyptus,
hickory, locust, maple, oak, persimmon, poplar, sycamore, walnut,
sequoia, and willow. Trees are useful, for example, as a source of
pulp, paper, structural material and fuel.
[0125] Angiosperms produce seeds enclosed within a mature, ripened
ovary. An angiosperm fruit can be suitable for human or animal
consumption or for collection of seeds to propagate the species.
For example, hops are a member of the mulberry family that are
prized for their flavoring in malt liquor. Fruit-bearing
angiosperms also include grape, orange, lemon, grapefruit, avocado,
date, peach, cherry, olive, plum, coconut, apple and pear trees and
blackberry, blueberry, raspberry, strawberry, pineapple, tomato,
cucumber and eggplant plants. An ornamental flower is an angiosperm
cultivated for its decorative flower. Examples of commercially
important ornamental flowers include rose, lily, tulip and
chrysanthemum, snapdragon, camellia, carnation and petunia plants,
and can include orchids. It will be recognized that the present
invention also can be practiced using gymnosperms, which do not
produce seeds in a fruit.
[0126] Certain embodiments of this invention overcome the problem
of maintenance of homozygous recessive reproductive traits when
using a transgenic restoration approach, while decreasing the
number of plants, plantings and steps needed for maintenance of
plants with such traits.
[0127] Homozygosity is a genetic condition existing when identical
alleles reside at corresponding loci on homologous chromosomes.
Heterozygosity is a genetic condition existing when different
alleles reside at corresponding loci on homologous chromosomes.
Hemizygosity is a genetic condition existing when there is only one
copy of a gene (or set of genes) with no allelic counterpart on the
sister chromosome.
[0128] Maintenance of the homozygous recessive condition for male
sterility is achieved by introducing into a plant a restoration
transgene construct that is linked to a sequence which interferes
with the formation, function or dispersal of male gametes of the
plant, to create a "maintainer" or "donor" plant. The restoring
transgene, upon introduction into a plant that is homozygous
recessive for the male sterility genetic trait, restores the
genetic function of that trait. Due to the linked gene driven by a
male-gamete-specific-promoter, all pollen containing the
restoration transgene is rendered nonviable. All viable pollen
produced contains a copy of the recessive allele but does not
contain the restoration transgene. The transgene is kept in the
hemizygous state in the maintainer plant.
[0129] The pollen from the maintainer can be used to fertilize
plants that are homozygous for the recessive trait, and the progeny
will therefore retain their homozygous recessive condition. The
maintainer plant containing the restoring transgene construct is
propagated by self-fertilization, with half of the resulting seed
used to produce further plants that are homozygous recessive for
the gene of interest and hemizygous for the restoring transgene
construct.
[0130] The maintainer plant serves as a pollen donor to the plant
having the homozygous recessive trait. The maintainer is optimally
produced from a plant having the homozygous recessive trait and
which also has nucleotide sequences introduced therein which would
restore the trait created by the homozygous recessive alleles.
Further, the restoration sequence is linked to nucleotide sequences
that interfere with the function, formation, or dispersal of male
gametes. The gene can operate to prevent formation of male gametes
or prevent function of the male gametes by any of a variety of
well-known modalities and is not limited to a particular
methodology. By way of example but not limitation, this can include
use of one or more genes which express a product cytotoxic to male
gametes (See for example, U.S. Pat. Nos. 5,792,853 and 5,689,049;
PCT/EP89/00495); inhibit product formation of another gene
important to male gamete formation, function, or dispersal (see,
U.S. Pat. Nos. 5,859,341 and 6,297,426); combine with another gene
product to produce a substance preventing gamete formation,
function or dispersal (see, U.S. Pat. Nos. 6,162,964; 6,013,859;
6,281,348; 6,399,856; 6,248,935; 6,750,868 and 5,792,853) are
antisense to or cause co-suppression of a gene critical to male
gamete formation, function or dispersal (see, U.S. Pat. Nos.
6,184,439; 5,728,926; 6,191,343; 5,728,558 and 5,741,684), or the
like.
[0131] Ordinarily, to produce more plants having the recessive
condition, one might cross the recessive plant with another
recessive plant, or self pollinate a recessive plant. This may not
be desirable for some recessive traits and may be impossible for
recessive traits affecting reproductive development. Alternatively,
one could cross the homozygous plant with a second plant having the
restoration gene, but this requires further crossing to segregate
away the restoring gene to once again reach the recessive
phenotypic state. Instead, in one embodiment the invention provides
a process in which the homozygous recessive condition can be
maintained, while crossing it with the maintainer plant. This
method can be used with any situation in which it is desired to
continue the recessive condition. This results in a relatively
simple, cost-effective system for maintaining a population of
homozygous recessive plants.
[0132] When the homozygous recessive condition is one that produces
male sterility, the maintainer plant, of necessity, must contain a
functional restoring transgene construct capable of complementing
the mutation and rendering the homozygous recessive plant able to
produce viable pollen. Linking this male fertility restoration gene
with a second functional nucleotide sequence which interferes with
the formation, function or dispersal of the male gametes of the
plant results in a maintainer plant that produces pollen containing
only the recessive allele of the restored gene at its native locus
due to the pollen-specific cytotoxic action of the second
nucleotide sequence. This viable pollen fraction is non-transgenic
with regard to the restoring transgene construct.
[0133] For example, it is desirable to produce male sterile female
plants for use in the hybrid production process which are sterile
as a result of being homozygous for a mutation in the MS45 gene, a
gene which is essential for male fertility. Such a mutant MS45
allele is designated as ms45. A plant that is homozygous for ms45
(represented by the notation ms45/ms45) displays the homozygous
recessive male sterility phenotype and produces no functional
pollen. See, U.S. Pat. Nos. 5,478,369; 5,850,014; 6,265,640 and
5,824,524. In both the inbred and hybrid production processes, it
is highly desired to maintain this homozygous recessive condition.
When sequences encoding the MS45 gene are introduced into a plant
having the homozygous condition, sporophytic restoration of male
fertility results. (Cigan, et al., (2001) Sex. Plant Repro.
14:135-142). By the method of the invention, a plant which is
ms45/ms45 homozygous recessive may have introduced into it a
functional MS45 gene, and thus male fertility is restored. This
gene can be linked to a second gene which operates to render pollen
nonfunctional or which prevents its formation, or which produces a
lethal product in pollen, and which is linked to a promoter
directing its expression in the male gametes. This results in a
plant which produces viable pollen containing ms45 without the
restoring transgene construct.
[0134] An example is a construct that includes the MS45 gene
operably linked to the 5126 promoter, a male tissue-preferred
promoter (see, U.S. Pat. No. 5,837,851) and further linked to the
cytotoxic DAM methylase gene under control of the PG47 promoter
(see, U.S. Pat. Nos. 5,792,853; 5,689,049). The resulting plant
produces pollen, but the only viable pollen contains the ms45 gene.
It can therefore be used as a pollinator to fertilize the
homozygous recessive plant (ms45/ms45), and 100% of the progeny
produced will continue to be male sterile as a result of
maintaining homozygosity for ms45. The progeny will not contain the
introduced restoring transgene construct.
[0135] Clearly, many variations on this method are available as it
relates to male sterility. Any other gene critical to male
fertility may be used in this system. For example and without
limitation, such genes can include the SBMu200 gene (also known as
SB200 or MS26) described at WO 2002/26789; the BS92-7 gene (also
known as BS7) described at WO 2002/063021; MS2 gene described at
Albertsen and Phillips, "Developmental Cytology of 13 Genetic Male
Sterile Loci in Maize" Canadian Journal of Genetics & Cytology
23:195-208 (January 1981); or the Arabadopsis MS2 gene described at
Aarts, et al., "Transposon Tagging of a Male Sterility Gene in
Arabidopsis", Nature, 363:715-717 (Jun. 24, 1993); and the
Arabidopsis gene MS1 described at Wilson, et al., "The Arabidopsis
MALE STERILITY1 (MS1) gene is a transcriptional regulator of male
gametogenesis, with homology to the PHD-finger family of
transcription factors", Plant J., 1:27-39 (Oct. 28, 2001).
[0136] A desirable result of the process of the invention is that
the plant having the restorer nucleotide sequence may be
self-fertilized; that is, pollen from the plant transferred to the
flower of the same plant to achieve the propagation of restorer
plants. (Note that "self fertilization" includes both the situation
where the plant producing the pollen is fertilized with that same
pollen and the situation where pollen from a plant, or from a group
of genetically identical plants, pollinates a plant which is a
genetically identical individual, or a group of such genetically
identical plants.) The restoring transgene construct will not be
present in the pollen, but it will be contained in 50% of the
ovules (the female gamete). The seed resulting from the
self-fertilization can be planted, and selection made for the seed
having the restoring transgene construct. The selection process can
occur by any one or more of many known processes, the most common
being where the restoration nucleotide sequence is linked to a
marker gene. The marker can be scorable or selectable, and allows
identification of the seed comprising the restoration sequence,
and/or of those plants produced from the seed having the
restoration sequence.
[0137] In an embodiment of the invention, it is possible to provide
that the promoter driving the restoration gene is inducible.
Additional control is thus allowed in the process, where so
desired, by providing that the plant having the restoration
nucleotide sequences is constitutively male sterile. This type of
male sterility is set forth the in U.S. Pat. No. 5,859,341. In
order for the plant to become fertile, the inducing substance must
be provided, and the plant will become fertile. Again, when
combined with the process of the invention as described supra, the
only pollen produced will not contain the restoration nucleotide
sequences.
[0138] In yet another embodiment of the invention, the gamete
controlling the transmission of the restoration nucleotide
sequences can be the female gamete, instead of the male gamete. The
process is the same as that described above, with the exception in
those instances where one also desires to maintain the plant having
the restoration nucleotide sequences by self fertilization. In that
case, it will be useful to provide that the promoter driving the
restoration gene is inducible, so that female fertility may be
triggered by exposure to the inducing substance, and seed can be
formed. Control of female fertility in such a manner is described
at U.S. Pat. No. 6,297,426. Examples of genes impacting female
fertility include the teosinte branched1 (Tb1) gene, which
increases apical dominance, resulting in multiple tassels and
repression of female tissue. Hubbard, et al., (2002) Genetics
162:1927-1935; Doebley, et al., (1997) Nature 386:485-488. Another
example is the so-called "barren 3" or "ba3". This mutant was
isolated from a mutant maize plant infected with wheat-streak
mosaic virus and is described at Pan and Peterson, (1992) J. Genet.
And Breed. 46:291-294. The plants develop normal tassels but do not
have any ear shoots along the stalks. Barren-stalk fastigiate is
described at Coe and Beckett, (1987) Maize Genet. Coop. Newslett.
61:46-47. Other examples include the barren stalkl gene
(Gallavotti, et al., (2004) Nature 432:630-635); lethal ovule
mutant (Vollbrecht, (1994) Maize Genetics Cooperation Newsletter
68:2-3); and defective pistil mutant (Miku and Mustyatsa, (1978)
Genetika 14(2):365-368).
[0139] Any plant-compatible promoter elements can be employed to
control expression of the regions of the restoring transgene
construct that encode specific proteins and functions. Those can be
plant gene promoters, such as, for example, the ubiquitin promoter,
the promoter for the small subunit of ribulose-1,5-bis-phosphate
carboxylase, or promoters from the tumor-inducing plasmids from
Agrobacterium tumefaciens, such as the nopaline synthase and
octopine synthase promoters or viral promoters such as the
cauliflower mosaic virus (CaMV) 19S and 35S promoters or the
figwort mosaic virus 35S promoter. See, Kay, et al., (1987) Science
236:1299 and European Patent Application Number 0 342 926. See,
International Application WO 1991/19806 for a review of
illustrative plant promoters suitably employed in the present
invention. The range of available plant-compatible promoters
includes tissue-specific and inducible promoters.
[0140] The invention contemplates the use of promoters providing
tissue-preferred expression, including promoters which
preferentially express to the gamete tissue, male or female, of the
plant. The invention does not require that any particular gamete
tissue-preferred promoter be used in the process, and any of the
many such promoters known to one skilled in the art may be
employed. By way of example, but not limitation, one such promoter
is the 5126 promoter, which preferentially directs expression of
the gene to which it is linked to male tissue of the plants, as
described in U.S. Pat. Nos. 5,837,851 and 5,689,051. Other examples
include the MS45 promoter described at U.S. Pat. No. 6,037,523; SF3
promoter described at U.S. Pat. No. 6,452,069; the BS92-7 or BS7
promoter described at WO 2002/063021; the SBMu200 promoter
described at WO 2002/26789; a SGB6 regulatory element described at
U.S. Pat. No. 5,470,359, and TA39 (Koltunow, et al., (1990) Plant
Cell 2:1201-1224; Goldberg, et al., (1993) Plant Cell 5:1217-1229
and U.S. Pat. No. 6,399,856. See also, Nadeau, et al., (1996) Plant
Cell 8(2):213-39; and Lu, et al., (1996) Plant Cell
8(12):2155-68.
[0141] The methods and constructs of the present invention may be
used for transformation of any plant species, including, but not
limited to, monocots and dicots. Examples of plant species of
interest include, but are not limited to, corn (Zea mays), Brassica
sp. (e.g., B. napus, B. rapa, B. juncea), particularly those
Brassica species useful as sources of seed oil, alfalfa (Medicago
sativa), rice (Oryza sativa), rye (Secale cereale), sorghum
(Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet
(Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail
millet (Setaria italica), finger millet (Eleusine coracana)),
sunflower (Helianthus annuus), safflower (Carthamus tinctorius),
wheat (Triticum aestivum), soybean (Glycine max), tobacco
(Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis
hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet
potato (Ipomoea batatus), cassaya (Manihot esculenta), coffee
(Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas
comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea
(Camellia sinensis), banana (Musa spp.), avocado (Persea
americana), fig (Ficus casica), guava (Psidium guajava), mango
(Mangifera indica), olive (Olea europaea), papaya (Carica papaya),
cashew (Anacardium occidentale), macadamia (Macadamia
integrifolia), almond (Prunus amygdalus), sugar beets (Beta
vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables,
ornamentals, grasses and conifers.
[0142] Vegetables include tomatoes (Lycopersicon esculentum),
lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris),
lima beans (Phaseolus limensis), peas (Lathyrus spp.) and members
of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C.
cantalupensis) and musk melon (C. melo). Ornamentals include azalea
(Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus
(Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.),
daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation
(Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima) and
chrysanthemum.
[0143] In specific embodiments, plants of the present invention are
crop plants (for example, corn (maize), alfalfa, sunflower,
Brassica, soybean, cotton, safflower, peanut, sorghum, wheat,
millet, tobacco, etc.). In certain embodiments, corn and soybean
plants are optimal, and in certain embodiments corn plants are
optimal.
[0144] Other plants of interest include grain plants that provide
seeds of interest, oil-seed plants and leguminous plants. Seeds of
interest include grain seeds, such as corn, wheat, barley, rice,
sorghum, rye, etc. Oil-seed plants include cotton, soybean,
safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc.
Leguminous plants include beans and peas. Beans include guar,
locust bean, fenugreek, soybean, garden beans, cowpea, mungbean,
lima bean, fava bean, lentils, chickpea, etc.
[0145] The P67 promoter set forth in SEQ ID NO: 1 is 1112
nucleotides in length. This promoter was isolated from a genomic
clone corresponding to a maize EST sequence. The sequence showed
limited homology to putative pectin methylesterase.
[0146] The pollen specificity of expression of P67 has been
confirmed by RT-PCR and Northern blot analyses of RNA samples from
different tissues including leaf, root, anther/mature pollen
grains, tassel at vacuole stage, spikelet, cob, husk, silk and
embryo. The results indicate a high level of specificity for
expression in developing pollen, particularly at the
mid-uninucleate stage.
[0147] Southern blot analysis has shown that the clone represents
single- or low-copy genes in the corn genome. Chromosome mapping
using the oat chromosome substitution line revealed that the
sequence is located at Chromosome 1 of maize.
[0148] The clone was used to screen a maize BAC library. Positive
BAC clones have been found and subcloned into pBluescript KS.
Subclones corresponding to the cDNA sequences have been identified
and sequenced. The transcriptional start site has been determined
using a RNA ligase-mediated rapid amplification of 5' end approach.
The promoter region was named P67.
[0149] The P95 promoter set forth in SEQ ID NO: 2 is 1092
nucleotides in length. This promoter was isolated from a genomic
clone corresponding to a maize EST sequence. The sequence showed
limited homology to putative L-ascorbate oxidase.
[0150] The pollen specificity of expression of P95 has been
confirmed by RT-PCR and Northern blot analyses of RNA samples from
different tissues including leaf, root, anther/mature pollen
grains, tassel at vacuole stage, spikelet, cob, husk, silk and
embryo. The results indicate a high level of specificity for
expression in developing pollen, particularly at the
mid-uninucleate stage.
[0151] Southern blot analysis has shown that the clone represents
single- or low-copy genes in the corn genome. Chromosome mapping
using the oat chromosome substitution line revealed that the
sequence is located at Chromosomes 6 and 8 of maize.
[0152] The clone was used to screen a maize BAC library. Positive
BAC clones have been found and subcloned into pBluescript KS.
Subclones corresponding to the cDNA sequences have been identified
and sequenced. The transcriptional start site has been determined
using a RNA ligase-mediated rapid amplification of 5' end approach.
The promoter region was named P95.
[0153] Using well-known techniques, additional promoter sequences
may be isolated based on their sequence homology to SEQ ID NO: 1 or
SEQ ID NO: 2. In these techniques, all or part of a known promoter
sequence is used as a probe which selectively hybridizes to other
sequences present in a population of cloned genomic DNA fragments
(i.e., genomic libraries) from a chosen organism. Methods that are
readily available in the art for the hybridization of nucleic acid
sequences may be used to obtain sequences which correspond to these
promoter sequences in species including, but not limited to, maize
(corn; Zea mays), canola (Brassica napus, Brassica rapa ssp.),
alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale
cereale), sorghum (Sorghum bicolor, Sorghum vulgare), sunflower
(Helianthus annuus), wheat (Triticum aestivum), soybean (Glycine
max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum),
peanuts (Arachis hypogaea), cotton (Gossypium hirsutum), sweet
potato (Ipomoea batatus), cassaya (Manihot esculenta), coffee
(Cofea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus),
citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia
sinensis), banana (Musa spp.), avocado (Persea americana), fig
(Ficus casica), guava (Psidium guajava), mango (Mangifera indica),
olive (Olea europaea), oats, barley, vegetables, ornamentals, and
conifers. Preferably, plants include maize, soybean, sunflower,
safflower, canola, wheat, barley, rye, alfalfa and sorghum.
[0154] The entire promoter sequence or portions thereof can be used
as a probe capable of specifically hybridizing to corresponding
promoter sequences. To achieve specific hybridization under a
variety of conditions, such probes include sequences that are
unique and are preferably at least about 10 nucleotides in length,
and most preferably at least about 20 nucleotides in length. Such
probes can be used to amplify corresponding promoter sequences from
a chosen organism by the well-known process of polymerase chain
reaction (PCR). This technique can be used to isolate additional
promoter sequences from a desired organism or as a diagnostic assay
to determine the presence of the promoter sequence in an organism.
Examples include hybridization screening of plated DNA libraries
(either plaques or colonies; see e.g., Innis, et al., (1990) PCR
Protocols, A Guide to Methods and Applications, eds., Academic
Press).
[0155] In general, sequences that correspond to a promoter sequence
of the present invention and hybridize to a promoter sequence
disclosed herein will be at least 50% homologous, 55% homologous,
60% homologous, 65% homologous, 70% homologous, 75% homologous, 80%
homologous, 85% homologous, 90% homologous, 95% homologous and even
98% homologous or more with the disclosed sequence.
[0156] Fragments of a particular promoter sequence disclosed herein
may operate to promote the pollen-preferred expression of an
operably-linked isolated nucleotide sequence. These fragments will
comprise at least about 20 contiguous nucleotides, preferably at
least about 50 contiguous nucleotides, more preferably at least
about 75 contiguous nucleotides, even more preferably at least
about 100 contiguous nucleotides of the particular promoter
nucleotide sequences disclosed herein. The nucleotides of such
fragments will usually comprise the TATA recognition sequence of
the particular promoter sequence. Such fragments can be obtained by
use of restriction enzymes to cleave the naturally-occurring
promoter sequences disclosed herein; by synthesizing a nucleotide
sequence from the naturally-occurring DNA sequence; or through the
use of PCR technology. See particularly, Mullis, et al., (1987)
Methods Enzymol. 155:335-350 and Erlich, ed. (1989) PCR Technology
(Stockton Press, New York). Again, variants of these fragments,
such as those resulting from site-directed mutagenesis, are
encompassed by the compositions of the present invention.
[0157] Thus, nucleotide sequences comprising at least about 20
contiguous nucleotides of the sequence set forth in SEQ ID NO: 1 or
SEQ ID NO: 2 are encompassed. These sequences can be isolated by
hybridization, PCR, and the like. Such sequences encompass
fragments capable of driving pollen-preferred expression, fragments
useful as probes to identify similar sequences, as well as elements
responsible for temporal or tissue specificity.
[0158] Biologically active variants of the promoter sequence are
also encompassed by the compositions of the present invention. A
regulatory "variant" is a modified form of a promoter wherein one
or more bases have been modified, removed or added. For example, a
routine way to remove part of a DNA sequence is to use an
exonuclease in combination with DNA amplification to produce
unidirectional nested deletions of double-stranded DNA clones. A
commercial kit for this purpose is sold under the trade name
Exo-Size.TM. (New England Biolabs, Beverly, Mass.). Briefly, this
procedure entails incubating exonuclease Ill with DNA to
progressively remove nucleotides in the 3' to 5' direction at 5'
overhangs, blunt ends or nicks in the DNA template. However,
exonuclease III is unable to remove nucleotides at 3', 4-base
overhangs. Timed digests of a clone with this enzyme produce
unidirectional nested deletions.
[0159] One example of a regulatory sequence variant is a promoter
formed by causing one or more deletions in a larger promoter.
Deletion of the 5' portion of a promoter up to the TATA box near
the transcription start site may be accomplished without abolishing
promoter activity, as described by Zhu, et al., (1995) The Plant
Cell 7:1681-89 (1995). Such variants should retain promoter
activity, particularly the ability to drive expression in specific
tissues. Biologically active variants include, for example, the
native regulatory sequences of the invention having one or more
nucleotide substitutions, deletions or insertions. Activity can be
measured by Northern blot analysis, reporter activity measurements
when using transcriptional fusions, and the like. See, for example,
Sambrook, et al., (1989) Molecular Cloning: A Laboratory Manual
(2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.),
herein incorporated by reference.
[0160] The nucleotide sequences for the pollen-preferred promoters
disclosed in the present invention, as well as variants and
fragments thereof, are useful in the genetic manipulation of any
plant when operably linked with an isolated nucleotide sequence
whose expression is to be controlled to achieve a desired
phenotypic response.
[0161] The nucleotide sequence operably linked to the regulatory
elements disclosed herein can be an antisense sequence for a
targeted gene. By "antisense DNA nucleotide sequence" is intended a
sequence that is in inverse orientation to the 5'-to-3' normal
orientation of that nucleotide sequence. When delivered into a
plant cell, expression of the antisense DNA sequence prevents
normal expression of the DNA nucleotide sequence for the targeted
gene. The antisense nucleotide sequence encodes an RNA transcript
that is complementary to and capable of hybridizing with the
endogenous messenger RNA (mRNA) produced by transcription of the
DNA nucleotide sequence for the targeted gene. In this case,
production of the native protein encoded by the targeted gene is
inhibited to achieve a desired phenotypic response. Thus the
regulatory sequences claimed herein can be operably linked to
antisense DNA sequences to reduce or inhibit expression of a native
or exogenous protein in the plant.
[0162] Many nucleotide sequences are known which inhibit pollen
formation or function or dispersal, and any sequences which
accomplish this inhibition will suffice. A discussion of genes
which can impact proper development or function is included at U.S.
Pat. No. 6,399,856 and includes dominant negative genes such as
cytotoxin genes, methylase genes, and growth-inhibiting genes.
Dominant negative genes include diphtheria toxin A-chain gene
(Czako and An, (1991) Plant Physiol. 95:687-692); cell cycle
division mutants such as CDC in maize (Colasanti, et al., (1991)
Proc. Natl. Acad. Sci. USA 88:3377-3381); the WT gene (Farmer, et
al., (1994) Hum. Mol. Genet. 3:723-728); and P68 (Chen, et al.,
(1991) Proc. Natl. Acad. Sci. USA 88, 315-319). A suitable gene may
also encode a protein involved in inhibiting pistil development,
pollen stigma interactions, pollen tube growth or fertilization, or
a combination thereof. In addition, genes that either interfere
with the normal accumulation of starch in pollen or affect osmotic
balance within pollen may also be suitable. These may include, for
example, the maize alpha-amylase gene, maize beta-amylase gene,
debranching enzymes such as Sugary1 and pullulanase, glucanase and
SacB.
[0163] In an illustrative embodiment, the DAM-methylase gene, the
expression product of which catalyzes methylation of adenine
residues in the DNA of the plant, is used. Methylated adenines will
not affect cell viability and will be found only in the tissues in
which the DAM-methylase gene is expressed, because such methylated
residues are not found endogenously in plant DNA. Examples of
so-called "cytotoxic" genes are discussed supra and can include,
but are not limited to pectate lyase gene pelE, from Erwinia
chrysanthermi (Kenn, et al., (1986) J. Bacteriol 168:595);
diphtheria toxin A-chain gene (Greenfield, et al., (1983) Proc.
Natl. Acad. Sci. USA 80:6853, Palmiter, et al., (1987) Cell
50:435); T-urf13 gene from cms-T maize mitochondrial genomes
(Braun, et al., (1990) Plant Cell 2:153; Dewey, et al., (1987)
Proc. Natl. Acad. Sci. USA 84:5374); CytA toxin gene from Bacillus
thuringiensis Israeliensis that causes cell membrane disruption
(McLean, et al., (1987) J. Bacteriol 169:1017, U.S. Pat. No.
4,918,006); DNAses, RNAses, (U.S. Pat. No. 5,633,441); proteases or
genes expressing anti-sense RNA.
[0164] Further, the methods of the invention are useful in
retaining the homozygous recessive condition of traits other than
those impacting plant fertility. The gene of interest which
restores the condition would be introduced into a plant linked to a
nucleotide sequence which inhibits the formation, function or
dispersal of pollen and which may be further linked to a male
gamete tissue-preferred promoter and a gene encoding a marker, for
example a seed-specific marker. Viable pollen produced by the plant
into which the construct is introduced contains only the recessive
allele of the gene of interest and none of the restoring transgene
sequences. Half of the female gametes of the hemizygous transgenic
plant contain the transgene and can be self-pollinated, or
pollinated by a plant comprising the recessive alleles. Half of the
seeds produced will carry the transgene and can be identified by
means of the linked marker. The hemizygous condition can be
maintained by selfing the hemizygous plant; half of the offspring
will contain the transgene and thus the trait of interest.
[0165] Genes of interest are reflective of the commercial markets
and interests of those involved in the development of the crop.
Crops and markets of interest change, and as developing nations
open up world markets, new crops and technologies will emerge also.
In addition, as our understanding of agronomic traits and
characteristics such as yield and heterosis increases, the choice
of genes for transformation will change accordingly.
[0166] Regulation of male fertility is necessarily measured in
terms of its effect on individual cells. For example, suppression
in 99.99% of pollen grains is required to achieve reliable
sterility for commercial use. However, successful suppression or
restoration of expression of other traits may be accomplished with
lower stringency. Within a particular tissue, for example,
expression in 98%, 95%, 90%, 80% or fewer cells may result in the
desired phenotype.
[0167] This invention has utility for a variety of genes, not
limited to those where affecting reproductive capacity. General
categories of genes of interest include, for example, those genes
involved in information, such as zinc fingers, those involved in
communication, such as kinases, and those involved in housekeeping,
such as heat shock proteins. More specific categories of
transgenes, for example, include genes encoding important traits
for agronomics, plant architecture, developmental timing and
initiation of reproductive growth, insect resistance, disease
resistance, herbicide resistance, sterility, grain characteristics
and commercial products. Genes of interest include, generally,
those involved in oil, starch, carbohydrate or nutrient metabolism
as well as those affecting kernel size, sucrose loading, and the
like. Agronomically important traits such as oil, starch and
protein content can be genetically altered in addition to using
traditional breeding methods. Modifications include increasing
content of oleic acid, saturated and unsaturated oils, increasing
levels of lysine and sulfur, providing essential amino acids, and
also modification of starch. Hordothionin protein modifications are
described in U.S. Pat. Nos. 5,703,049, 5,885,801, 5,885,802 and
5,990,389. Another example is lysine and/or sulfur rich seed
protein encoded by the soybean 2S albumin described in U.S. Pat.
No. 5,850,016 and the chymotrypsin inhibitor from barley, described
in Williamson, et al., (1987) Eur. J. Biochem. 165:99-106. Other
important genes encode growth factors and transcription
factors.
[0168] Agronomic traits can be improved by altering expression of
genes that: affect growth and development, especially during
environmental stress. These include, for example, genes encoding
cytokinin biosynthesis enzymes, such as isopentenyl transferase;
genes encoding cytokinin catabolic enzymes, such as cytokinin
oxidase; genes encoding polypeptides involved in regulation of the
cell cycle, such as CyclinD or cdc25; genes encoding cytokinin
receptors or sensors, such as CRE1, CKI1 and CKI2, histidine
phospho-transmitters or cytokinin response regulators.
[0169] Further examples include disease or herbicide resistance
(e.g., fumonisin detoxification genes (U.S. Pat. No. 5,792,931);
avirulence and disease resistance genes (Jones, et al., (1994)
Science 266:789; Martin, et al., (1993) Science 262:1432;
Mindrinos, et al., (1994) Cell 78:1089); acetolactate synthase
(ALS) mutants that lead to herbicide resistance such as the S4
and/or Hra mutations; inhibitors of glutamine synthase such as
phosphinothricin or basta (e.g., bar gene); and glyphosate
resistance (EPSPS gene)); carbon fixation, such as
phosphoenolpyruvate carboxylase (PepC) or ribulose-1,5-bisphosphate
carboxylase/oxygenase (Rubisco activase, RCA); traits desirable for
processing or process products such as high oil (e.g., U.S. Pat.
No. 6,232,529); modified oils (e.g., fatty acid desaturase genes
(U.S. Pat. No. 5,952,544; WO 1994/11516)); modified starches (e.g.,
ADPG pyrophosphorylases (AGPase), starch synthases (SS), starch
branching enzymes (SBE), and starch debranching enzymes (SDBE));
and polymers or bioplastics (e.g., U.S. Pat. No. 5,602,321;
beta-ketothiolase, polyhydroxybutyrate synthase, and
acetoacetyl-CoA reductase (Schubert, et al., (1988) J. Bacteriol.
170:5837-5847) facilitate expression of polyhydroxyalkanoates
(PHAs)); the disclosures of which are herein incorporated by
reference. The methods of the present invention could also be
combined with methods for transformation technology, such as cell
cycle regulation or gene targeting (e.g., WO 1999/61619, WO
2000/17364 and WO 1999/25821), the disclosures of which are herein
incorporated by reference.
[0170] Insect resistance genes may encode resistance to pests that
have great yield drag such as rootworm, cutworm, European Corn
Borer, and the like. Such genes include, for example: Bacillus
thuringiensis endotoxin genes, U.S. Pat. Nos. 5,366,892; 5,747,450;
5,737,514; 5,723,756; 5,593,881; Geiser, et al., (1986) Gene
48:109; lectins, Van Damme, et al., (1994) Plant Mol. Biol. 24:825;
and the like.
[0171] Genes encoding disease resistance traits include:
detoxification genes, such as against fumonisin (WO 1996/06175
filed Jun. 7, 1995); avirulence (avr) and disease resistance (R)
genes, Jones, et al., (1994) Science 266:789; Martin, et al.,
(1993) Science 262:1432; Mindrinos, et al., (1994) Cell 78:1089;
and the like.
[0172] Commercial traits can also be encoded on a gene(s) which
could alter or increase for example, starch for the production of
paper, textiles and ethanol, or provide expression of proteins with
other commercial uses. Another important commercial use of
transformed plants is the production of polymers and bioplastics
such as described in U.S. Pat. No. 5,602,321 issued Feb. 11, 1997.
Genes such as B-Ketothiolase, PHBase (polyhydroxybutyrate synthase)
and acetoacetyl-CoA reductase (see, Schubert, et al., (1988) J.
Bacteriol 170(12):5837-5847) facilitate expression of
polyhydroxyalkanoates (PHAs).
[0173] Exogenous products include plant enzymes and products as
well as those from other sources including prokaryotes and other
eukaryotes. Such products include enzymes, cofactors, hormones, and
the like. The level of seed proteins, particularly modified seed
proteins having improved amino acid distribution to improve the
nutrient value of the seed, can be increased. This is achieved by
the expression of such proteins having enhanced amino acid
content.
[0174] Expression cassettes of the invention, comprising a promoter
and isolated nucleotide sequence of interest, may also include, at
the 3' terminus of the isolated nucleotide sequence of interest, a
transcriptional and translational termination region functional in
plants. The termination region can be native with the promoter
nucleotide sequence of the cassette, can be native with the DNA
sequence of interest, or can be derived from another source.
[0175] Other convenient termination regions are available from the
Ti-plasmid of A. tumefaciens, such as the octopine synthase and
nopaline synthase termination regions. See also, Guerineau, et al.,
(1991) Mol. Gen. Genet. 262:141-144; Proudfoot, (1991) Cell
64:671-674; Sanfacon, et al., (1991) Genes Dev. 5:141-149; Mogen,
et al., (1990) Plant Cell 2:1261-1272; Munroe, et al., (1990) Gene
91:151-158; Ballas, et al., 1989) Nucleic Acids Res. 17:7891-7903;
Joshi, et al., (1987) Nucleic Acid Res. 15:9627-9639.
[0176] The expression cassettes can additionally contain 5' leader
sequences. Such leader sequences can act to enhance translation.
Translation leaders are known in the art and include: picornavirus
leaders, for example: EMCV leader (Encephalomyocarditis 5'
noncoding region), Elroy-Stein, et al., (1989) Proc. Nat. Acad.
Sci. USA 86:6126-6130; potyvirus leaders, for example, TEV leader
(Tobacco Etch Virus), Allison, et al., (1986); MDMV leader (Maize
Dwarf Mosaic Virus), Virology 154:9-20; human immunoglobulin
heavy-chain binding protein (BiP), Macejak, et al., (1991) Nature
353:90-94; untranslated leader from the coat protein mRNA of
alfalfa mosaic virus (AMV RNA 4), Jobling, et al., (1987) Nature
325:622-625); tobacco mosaic virus leader (TMV), Gallie, et al.,
(1989) Molecular Biology of RNA, pages 237-256; and maize chlorotic
mottle virus leader (MCMV) Lommel, et al., (1991) Virology
81:382-385. See also, Della-Cioppa, et al., (1987) Plant Physiology
84:965-968. The cassette can also contain sequences that enhance
translation and/or mRNA stability such as introns.
[0177] In those instances where it is desirable to have the
expressed product of the isolated nucleotide sequence directed to a
particular organelle, particularly the plastid, amyloplast or to
the endoplasmic reticulum or secreted at the cell's surface or
extracellularly, the expression cassette can further comprise a
coding sequence for a transit peptide. Such transit peptides are
well known in the art and include, but are not limited to: the
transit peptide for the acyl carrier protein, the small subunit of
RUBISCO, plant EPSP synthase, and the like.
[0178] In preparing the expression cassette, the various DNA
fragments can be manipulated, so as to provide for the DNA
sequences in the proper orientation and, as appropriate, in the
proper reading frame. Toward this end, adapters or linkers can be
employed to join the DNA fragments or other manipulations can be
involved to provide for convenient restriction sites, removal of
superfluous DNA, removal of restriction sites, or the like. For
this purpose, in vitro mutagenesis, primer repair, restriction
digests, annealing and resubstitutions such as transitions and
transversions, can be involved.
[0179] The following terms are used to describe the sequence
relationships between two or more nucleic acids or polynucleotides:
(a) "reference sequence", (b) "comparison window", (c) "percentage
of sequence identity", and (d) "substantial identity".
[0180] (a) As used herein, "reference sequence" is a defined
sequence used as a basis for sequence comparison. A reference
sequence may be a subset or the entirety of a specified sequence;
for example, a segment of a full-length promoter sequence or the
complete promoter sequence.
[0181] (b) As used herein, "comparison window" makes reference to a
contiguous and specified segment of a polynucleotide sequence,
wherein the polynucleotide sequence may be compared to a reference
sequence and wherein the portion of the polynucleotide sequence in
the comparison window may comprise additions or deletions (i.e.,
gaps) compared to the reference sequence (which does not comprise
additions or deletions) for optimal alignment of the two sequences.
Generally, the comparison window is at least 20 contiguous
nucleotides in length and optionally can be 30, 40, 50, 100 or more
contiguous nucleotides in length. Those of skill in the art
understand that to avoid a high similarity to a reference sequence
due to inclusion of gaps in the polynucleotide sequence, a gap
penalty is typically introduced and is subtracted from the number
of matches.
[0182] (c) As used herein, "percentage of sequence identity" means
the value determined by comparing two optimally aligned sequences
over a comparison window, wherein the portion of the polynucleotide
sequence in the comparison window may comprise additions or
deletions
[0183] (i.e., gaps) as compared to the reference sequence (which
does not comprise additions or deletions) for optimal alignment of
the two sequences. The percentage is calculated by determining the
number of positions at which the identical nucleic acid base occurs
in both sequences to yield the number of matched positions,
dividing the number of matched positions by the total number of
positions in the window of comparison and multiplying the result by
100 to yield the percentage of sequence identity.
[0184] (d) The term "substantial identity" of polynucleotide
sequences means that a polynucleotide comprises a sequence that has
at least 70% sequence identity, preferably at least 80%, more
preferably at least 90% and most preferably at least 95%, compared
to a reference sequence using one of the alignment programs
described using standard parameters.
[0185] Methods of aligning sequences for comparison are well known
in the art. Gene comparisons can be determined by conducting BLAST
(Basic Local Alignment Search Tool; Altschul, et al., (1993) J.
Mol. Biol. 215:403-410; see also, National Center for Biotechnology
Information of the National Institutes of Health) searches under
default parameters for identity to sequences contained in the BLAST
"GENEMBL" database. A sequence can be analyzed for identity to all
publicly available DNA sequences contained in the GENEMBL database
using the BLASTN algorithm under the default parameters.
[0186] For purposes of defining the present invention, GAP (Global
Alignment Program) is used. GAP uses the algorithm of Needleman and
Wunsch (J. Mol. Biol. 48:443-453, 1970) to find the alignment of
two complete sequences that maximizes the number of matches and
minimizes the number of gaps. Default gap creation penalty values
and gap extension penalty values in Version 10 of the Wisconsin
Package.RTM. (Accelrys, Inc., San Diego, Calif.) for protein
sequences are 8 and 2, respectively. For nucleotide sequences the
default gap creation penalty is 50 while the default gap extension
penalty is 3. Percent Similarity is the percent of the symbols that
are similar. Symbols that are across from gaps are ignored. A
similarity is scored when the scoring matrix value for a pair of
symbols is greater than or equal to 0.50, the similarity threshold.
The scoring matrix used in Version 10 of the Wisconsin Package.RTM.
(Accelrys, Inc., San Diego, Calif.) is BLOSUM62 (see, Henikoff and
Henikoff, (1989) Proc. Natl. Acad. Sci. USA 89:10915).
[0187] Large amounts of the nucleic acids of the present invention
may be produced by replication in a suitable host cell. Natural or
synthetic nucleic acid fragments coding for a desired fragment will
be incorporated into recombinant nucleic acid constructs, usually
DNA constructs, capable of introduction into and replication in a
prokaryotic or eukaryotic cell. Usually the nucleic acid constructs
will be suitable for replication in a unicellular host, such as
yeast or bacteria, but may also be intended for introduction to
(with and without integration within the genome) cultured mammalian
or plant or other eukaryotic cell lines. The purification of
nucleic acids produced by the methods of the present invention is
described, for example, in Sambrook, et al., Molecular Cloning. A
Laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory, Cold
Spring Harbor, N.Y. (1989) or Ausubel, et al., Current Protocols in
Molecular Biology, J. Wiley and Sons, NY (1992).
[0188] Nucleic acid constructs prepared for introduction into a
prokaryotic or eukaryotic host may comprise a replication system
recognized by the host, including the intended nucleic acid
fragment encoding the desired protein and will preferably also
include transcription and translational initiation regulatory
sequences operably linked to the protein encoding segment.
Expression vectors may include, for example, an origin of
replication or autonomously replicating sequence (ARS) and
expression control sequences, a promoter, an enhancer and necessary
processing information sites, such as ribosome-binding sites, RNA
splice sites, polyadenylation sites, transcriptional terminator
sequences, and mRNA stabilizing sequences. Secretion signals may
also be included where appropriate. Such vectors may be prepared by
means of standard recombinant techniques well known in the art and
discussed, for example, in Sambrook, et al., Molecular Cloning. A
Laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory, Cold
Spring Harbor, N.Y. (1989) or Ausubel, et al., Current Protocols in
Molecular Biology, J. Wiley and Sons, NY (1992).
[0189] Vectors for introduction of genes both for recombination and
for extrachromosomal maintenance are known in the art, and any
suitable vector may be used. Methods for introducing DNA into cells
such as electroporation, calcium phosphate co-precipitation, and
viral transduction are known in the art, and the choice of method
is within the competence of one skilled in the art (Robbins, Ed.,
Gene Therapy Protocols, Human Press, NJ (1997)).
[0190] Gene transfer systems known in the art may be useful in the
practice of the present invention. These include viral and
non-viral transfer methods. A number of viruses have been used as
gene transfer vectors, including polyoma, i.e., SV40 (Madzak, et
al., (1992) J. Gen. Virol., 73:1533-1536), adenovirus (Berkner,
(1992) Curr. Top. Microbiol. Immunol., 158:39-61; Berkner, et al.,
(1988) Bio Techniques, 6:616-629; Gorziglia, et al., (1992) J.
Virol., 66:4407-4412; Quantin, et al., (1992) Proc. Natl. Acad.
Sci. USA, 89:2581-2584; Rosenfeld, et al., (1992) Cell, 68:143-155;
Wilkinson, et al., (1992) Nucl. Acids Res. 20:2233-2239;
Stratford-Perricaudet, et al., (1990) Hum. Gene Ther. 1:241-256),
vaccinia virus (Mackett, et al., (1992) Biotechnology 24:495499),
adeno-associated virus (Muzyczka, (1992) Curr. Top. Microbiol.
Immunol. 158:91-123; Ohi, et al., (1990) Gene 89:279-282), herpes
viruses including HSV and EBV (Margolskee, (1992) Curr. Top.
Microbiol. Immunol. 158:67-90; Johnson, et al., (1992) J. Virol.,
66:2952-2965; Fink, et al., (1992) Hum. Gene Ther. 3:11-19;
Breakfield, et al., (1987) Mol. Neurobiol. 1:337-371; Fresse, et
al., (1990) Biochem. Pharmacol. 40:2189-2199), and retroviruses of
avian (Brandyopadhyay, et al., (1984) Mol. Cell Biol. 4:749-754;
Petropouplos, et al., (1992) J. Virol. 66:3391-3397), murine
(Miller, (1992) Curr. Top. Microbiol. Immunol. 158:1-24; Miller, et
al., (1985) Mol. Cell. Biol. 5:431-437; Sorge, et al., (1984) Mol.
Cell Biol. 4:1730-1737; Mann, et al., (1985) J. Virol. 54:401-407),
and human origin (Page, et al., (1990) J. Virol. 64:5370-5276;
Buchschalcher, et al., (1992) J. Virol. 66:2731-2739).
[0191] Non-viral gene transfer methods known in the art include
chemical techniques such as calcium phosphate coprecipitation
(Graham, et al., (1973) Virology 52:456-467; Pellicer, et al.,
(1980) Science 209:1414-1422), mechanical techniques, for example
microinjection (Anderson, et al., (1980) Proc. Natl. Acad. Sci. USA
77:5399-5403; Gordon, et al., (1980) Proc. Natl. Acad. Sci. USA
77:7380-7384; Brinster, et al., (1981) Cell 27:223-231;
Constantini, et al., (1981) Nature 294:92-94), membrane
fusion-mediated transfer via liposomes (Feigner, et al., (1987)
Proc. Natl. Acad. Sci. USA 84:7413-7417; Wang, et al., (1989)
Biochemistry, 28:9508-9514; Kaneda, et al., (1989) J. Biol. Chem.
264:12126-12129; Stewart, et al., (1992) Hum. Gene Ther. 3:267-275;
Nabel, et al., (1990) Science 249:1285-1288; Lim, et al., (1992)
Circulation 83:2007-2011) and direct DNA uptake and
receptor-mediated DNA transfer (Wolff, et al., (1990) Science
247:1465-1468; Wu, et al., (1991) BioTechniques 11:474-485; Zenke,
et al., (1990) Proc. Natl. Acad. Sci. USA 87:3655-3659; Wu, et al.,
(1989) J. Biol. Chem. 264:16985-16987; Wolff, et al., (1991)
BioTechniques 11:474485; Wagner, et al., (1990); Wagner, et al.,
(1991) Proc. Natl. Acad. Sci. USA 88:42554259; Cotton, et al.,
(1990) Proc. Natl. Acad. Sci. USA 87:4033-4037; Curiel, et al.,
(1991) Proc. Natl. Acad. Sci. USA 88:8850-8854; Curiel, et al.,
(1991) Hum. Gene Ther. 3:147-154).
[0192] One skilled in the art readily appreciates that the methods
described herein are applicable to other species not specifically
exemplified, including both plants and other non-human organisms.
The following examples are intended to illustrate but not limit the
invention.
Example 1
Promoter Hairpin RNA Expression Affects Plant Fertility
[0193] This example demonstrates that the fertility or fertility
potential of plants can be altered by expression of hairpin RNA
(hpRNA) molecules specific for the promoters of genes that encode
proteins involved in male fertility pathways.
[0194] Promoter hpRNA constructs were generated by linking a
ubiquitin promoter to an inverted repeat of the desired promoter,
including a NOS promoter segment between the inverted repeat
sequences. Expression of each construct generated a hpRNA specific
for one of the following promoters: MS45, 5126, BS7, SB200 and
PG47. Nucleic acid molecules and methods for preparing the
constructs and transforming maize were as previously described
(Cigan, et al., (2001) Sex Plant Reprod. 14:135-142). Progeny (T1
generation) of transformed (T0) plants were analyzed.
[0195] Of 32 transformation events comprising hpRNA specific for
the MS45 gene promoter, 29 produced T0 plants that were male
sterile.
[0196] Of 32 transformation events comprising hpRNA specific for
the 5126 gene promoter, 29 produced T0 plants that were male
sterile.
[0197] Of 32 transformation events comprising hpRNA specific for
the BS7 gene promoter, 23 produced T0 plants that either produced a
small amount of non-viable pollen ("breaker" phenotype) or were
male fertile but produced only a small amount of viable pollen
("shedder" phenotype).
[0198] Of 31 transformation events comprising hpRNA specific for
the SB200 gene promoter, 13 produced T0 plants of either the
breaker or shedder phenotype.
[0199] Of 24 transformation events comprising hpRNA specific for
the PG47 gene promoter linked to a construct for herbicide
resistance, 15 revealed no transmission of herbicide resistance to
the T1 seedling when using pollen from the primary transformants.
This is consistent with expected post-meiotic expression of
PG47.
[0200] Anther RNA from plants expressing the various hpRNAs was
analyzed by northern blot. For each target, six independent events
were analyzed in the T1 generation to determine whether hpRNA
expression reduced steady state RNA levels of the targeted genes.
Anthers were staged at tetrad release to early uninucleate stage of
microspore development. Poly A.sup.+ RNA was isolated, separated by
electrophoresis, transferred to membranes, and hybridized
sequentially with probes specific for MS45, 5126, BS7, SB200, NOS
and actin (RNA loading control). No MS45, 5126 or BS7 transcripts
were detected in plants expressing hpRNA specific for these
endogenous promoters. Only a slight reduction of SB200 RNA was
observed in plants expressing SB200 hpRNA.
[0201] Protein immunoblot analysis of anther proteins also was
performed essentially as described previously (Cigan, et al.,
(2001) Sex Plant Reprod. 14:135-142). For each target, six
independent events were analyzed in the T1 generation to determine
whether expression of the promoter hpRNA reduced steady-state
protein levels of the targeted genes. Anthers were staged as above,
ground in Laemelli buffer, separated by electrophoresis, and
reacted sequentially with antibodies specific for MS45, BS7, SB200
or 5126 protein. Similar to the northern blot results, no MS45,
5126 or BS7 proteins were detected in plants expressing hpRNA
specific for these endogenous promoters and only a slight reduction
of SB200 protein was observed for events comprising hpSB200.
[0202] These results demonstrate that expression of promoter hpRNA
can selectively suppress endogenous gene expression in plant cells.
In addition, the results demonstrate that suppression of different
genes involved in male sterility of plants can variously affect the
plant phenotype, including the degree of male fertility.
Example 2
Expression of Exogenous Ms45 Gene Product Restores Fertility
[0203] This example demonstrates that plants rendered male-sterile
by expression of an MS45 promoter hairpin construct can be restored
to fertility by expression of an exogenous MS45 gene construct.
[0204] Constructs were prepared containing the MS45 coding sequence
operably linked to a heterologous ubiquitin (UBI), 5126, SB200 or
BS7 promoter; these constructs were introduced into ms45 ms45 plant
cells. Regenerated plants and their progeny were fertile,
demonstrating that the native promoter of MS45 can be replaced with
either a constitutive or anther-preferred promoter to confer a
male-fertile phenotype to mutant ms45 maize. (See also, Cigan, et
al., (2001) Sex Plant Reprod. 14:135-142)
[0205] Further, plants containing the UBI:MS45 or 5126:MS45
construct were crossed to plants that were male sterile due to
expression of an MS45 gene promoter hpRNA. Progeny were tested by
PCR for presence of the hp construct and either UBI:MS45 or
5126:MS45. RNA hybridization analysis was conducted and fertility
phenotypes were scored.
[0206] Northern blot analysis of RNA obtained from leaves of the
progeny plants revealed that MS45 was expressed from the ubiquitin
promoter in 7 of 12 hp-containing progeny obtained from the
UBI:MS45 cross. Further, expression of MS45 from the UBI promoter
correlated with observed fertility in the progeny plants. These
results indicate that MS45 is expressed from the constitutive
ubiquitin promoter, and that constitutive expression of the MS45
gene product confers male fertility in the progeny plants.
[0207] Further, anther RNA from these MS45hp maize plants
containing 5126:MS45, BS7:MS45, or UBI:MS45 was analyzed. Anthers
were staged at tetrad release to early uninucleate stage of
microspore development, and poly A+ RNA was collected,
electrophoresed and hybridized sequentially with probes for MS45,
SB200 and BS7. MS45 was expressed in anthers of the male-fertile
progeny plants whether driven by the constitutive UBI promoter or
by the anther-specific 5126 or BS7 promoters, with timing of anther
collection likely affecting strength of the signal. No MS45 RNA was
observed in the male-sterile hairpin-only containing plants. These
results demonstrate that suppression of MS45 expression due to the
MS45 hpRNA can be overcome by expressing MS45 from a heterologous
promoter that drives expression at least in anther cells.
[0208] The promoter expressing the MS45 gene can be derived from a
source other than maize, and can be, for example, any plant
promoter capable of transcribing MS45 such that expression of the
transcription unit renders plants male fertile. For example, the
rice and Arabidopsis homologs of the maize MS45, 5126, BS7 and MS26
genes have been isolated and identified. See, FIG. 1 for
chromosomal coordinates providing sequence information for MS45,
MS26 and 5126 in rice and Arabidopsis and BS7 in Arabidopsis. For
BS7 in rice, see, SEQ ID NO: 3. Overall there is significant coding
sequence similarity between the species, with conservation of the
intronic regions. Importantly, the corresponding promoters of rice
and maize are approximately 50 to 60% identical overall, with
regions up to 85% identical, suggesting that these promoters may
function sufficiently in maize tapetum to transcribe the MS45
gene.
[0209] To test this, each of the rice MS45, rice 5126, rice BS7,
rice MS26 and Arabidopsis MS45, Arabidopsis 5126 and Arabidopsis
BS7 promoters was fused to the maize MS45 coding region and tested
for ability of the construct to confer fertility when transformed
into ms45 ms45 mutants. Using this test system, a high frequency of
male fertile plants was observed for all four constructs.
[0210] In certain respects, it is advantageous to use non-maize
promoters to express the MS45 gene. For example, where promoter
hpRNAs from the same species reduce target gene function such that
the plant is non-viable or non-reproductive, a promoter from a
different species can be used to transcriptionally express the
complementing gene function (e.g., MS45), thus circumventing this
potential problem. Moreover, an hpRNA construct can be generated to
target the non-maize promoter used in the MS45 expression cassette,
to suppress MS45 gene expression as a means to reduce or abolish
function and render the plant male sterile. For example, an ms45
homozygous recessive plant may be transformed with an MS45 rice
promoter homolog driving expression of the MS45 gene (MS45r::MS45),
rendering the plant male fertile. To suppress expression of this
MS45r::MS45 cassette, a second maize plant can be generated which
is heterozygous for the maize MS45 mutation and expresses an MS45r
promoter hpRNA. As there are no equivalent endogenous MS45 rice
promoter target sequences in this maize plant, this plant would be
male fertile. This second plant can be crossed onto the homozygous
ms45 plant containing the MS45r::MS45 construct, and ms45
homozygous recessive progeny screened for the MS45r::MS45 and the
MS45r hpRNA constructs. In this situation, MS45r::MS45 gene
function is suppressed by the presence and expression of the MS45r
hpRNA, resulting in a male-sterile plant.
[0211] Use of such constructs is supported by the finding that
expression of the rice 5126 promoter hp in maize does not result in
male sterile plants. This is in contrast to the results obtained
using a maize 5126 promoter hp (see, Example 1) and suggests that
expression of the rice 5126 promoter hairpin is incapable of
suppressing the endogenous maize 5126 gene.
Example 3
Promoter Specific Hairpin RNA Suppresses Transmission of Transgene
Mediated Herbicide Resistance
[0212] This example demonstrates that pollen of plants hemizygous
for a UBI:PG47 hairpin construct is non-viable as determined by
non-transmission of herbicide resistance to T1 outcrosses when a
herbicide resistance gene is linked to the PG47 hairpin
construct.
[0213] An hpRNA specific for the PG47 gene promoter comprising an
inverted repeat of the PG47 gene promoter driven by a ubiquitin
promoter (UBI:PG47hp), linked to a 35S:PAT construct, was
introduced into plant cells. Pollen from plants expressing the
transgene, representing 24 low- or single-copy transformation
events, was carried to ears of wild-type maize plants. Seed set on
the ears was very good, and comparable to that observed when
wild-type pollen was used. For each event, 32 seeds were planted in
soil, and seedlings were sprayed 5 days post-germination with
2.times. LIBERTY.TM. herbicide to detect transmission of UBI:PG47hp
linked to 35S:PAT.
[0214] It was expected that if PG47-specific hpRNA functioned at
the post-meiotic division of microspores, then viability would be
normal, and 50% of the pollen would carry the transgene, providing
herbicide resistance in 50% of the progeny. However, if PG47
function is required for pollen viability, and the hairpin
construct can suppress expression of the PG47 gene product, then
50% of the pollen grains would be non-viable; all viable pollen
would lack the transgene and be incapable of transmitting herbicide
resistance. Non-functioning UBI:PG47hp constructs would be
detectable by the presence of herbicide resistant plants.
[0215] Fifteen of 24 events tested were herbicide sensitive. This
result demonstrates that the UBI:PG47hp constructs suppress PG47
gene expression in pollen, rendering 50% of the pollen non-viable
and preventing transmission of herbicide resistance operably linked
to the suppression construct.
Example 4
Plants Containing Multiple Promoter-Specific Hairpin RNAs Suppress
Multiple Target Promoters
[0216] Plants containing 5126HP (i.e., a transgene encoding a 5126
promoter hpRNA) are used as pollen recipients for pollen from
BS7HP-expressing plants. In plants containing both 5126HP and
BS7HP, endogenous expression of 5126 and BS7 is suppressed, leading
to a stronger sterility phenotype than observed with either
construct alone. Plants are selected to contain either the 5126HP
or BS7HP or both and advanced to maturity, and the fertility
phenotypes of these resultant plants are determined.
[0217] Alternatively or in addition to crossing as a means to
combine hairpin constructs, one of said constructs, for example the
5126HP, can be placed under the transcriptional control of an
inducible promoter. In the absence of induction, these
BS7HP-containing plants are capable of producing enough pollen to
self. However, upon induction of the 5126HP, these plants are male
sterile, and can be used as females during hybrid production. This
process depends upon the combined expression of the hairpin
constructs (HPs) to render a plant infertile, while expression of
only one of the HPs does not impart sterility.
[0218] In certain embodiments, expression of both hpRNAs can be
placed under the transcriptional control of a single promoter. For
example, the 5126 promoter region can be juxtaposed to the BS7
promoter region and both are placed under the transcriptional
control of a single ubiquitin promoter or other constitutive,
developmental or tissue preferred promoter, resulting in the
expression of an RNA containing a 5126 and BS7 hybrid hairpin that
directs the suppression of both 5126 and BS7 endogenous genes. Any
combination and number of various promoters that target multiple
and different promoters can be used in the scheme. For example, a
promoter that regulates plant height genes and a promoter important
to a reproductive process can be combined, resulting in sterile
plants having short stature.
Example 5
Inbred Maintenance and Hybrid Production of Plants Containing
Promoter-Specific Hairpin RNAs Suppressing Target Promoters and
Complementation Constructs
[0219] This example demonstrates how an inbred plant containing two
constructs, a dominant hairpin RNA (hpRNA) construct specific for a
promoter and an MS45 gene expressed from a promoter, such as a
tissue-specific or constitutive promoter, can be maintained and
used in the production of male-sterile females for hybrid
production.
[0220] Inbred plants A1 and A2 are both homozygous recessive ms45
ms45. Fertility is restored to inbred A1 plants by introduction of
a transgene expressing the MS45 coding region operably linked to
the 5126 promoter. The A1 inbred plants also contain a
BS7HP-expressing construct. These plants can be selfed and the A1
line, homozygous for the transgene inserts, is maintained
independently of inbred A2. In inbred A2 plants, fertility is
restored by expressing the MS45 coding region operably linked to
the BS7 promoter. The A2 inbred plants also contain a
5126HP-expressing construct. These plants can be selfed and the A2
line, homozygous for the transgene inserts, is maintained
independently of inbred A1 plants.
[0221] In some embodiments comprised by this example, promoters
from the rice (Oryza sativa) orthologs of maize genes 5126, BS7
and/or MS45 are used. See Table 1 for examples. If no species is
indicated, maize is assumed.
TABLE-US-00001 TABLE 1 Plant A1 (ms45ms45) Plant A2 (ms45ms45)
Restoration construct rice5126::MS45 riceBS7::MS45 Hairpin
construct UBI::riceBS7pIR UBI::rice5126pIR OR Restoration construct
rice5126::MS45 riceMS45::MS45 Hairpin construct UBI::riceMS45pIR
UBI::rice5126pIR
[0222] To generate seed for female inbreds for hybrid production,
inbred A1 (containing homozygous transgene inserts) is detasseled
and fertilized with pollen from inbred A2 (containing homozygous
transgene inserts). The seed resulting from this cross is planted;
all of the progeny plants are male sterile due to the presence of
the homozygous ms45 alleles and the pIRs which suppress the
corresponding MS45 construct (e.g., riceMS45pIR suppresses
riceMS45::MS45 and the rice5126pIR suppresses rice5126::MS45). See,
FIG. 2. These plants are used as females in hybrid production and
pollinated with plants homozygous for the wild-type MS45 gene,
resulting in hybrid F1 seed. All plants derived from this seed are
heterozygous for the MS45 gene and are therefore male fertile.
[0223] This example demonstrates that plants containing both
dominant suppression and restoring constructs can be maintained and
used in a hybrid seed production strategy to generate sterile
female inbreds and fertile hybrid plants.
Example 6
Utility of Plants Containing Promoter-Specific Hairpin RNAs
Suppressing Target Pollen-Specific Promoters and Ms45
Complementation Constructs for Hybrid Production and Inbred
Maintenance
[0224] This example demonstrates how a method comprising the use of
two constructs, a dominant hairpin RNA (hpRNA) construct specific
for a pollen-specific promoter and a restoring transgene, allows
for the propagation of a plant having a homozygous recessive
reproductive trait without losing the homozygous recessive
condition in the resulting progeny, for use in the production of
sterile plants for hybrid production. This is accomplished by
introducing into a plant at least one restoring transgene
construct, operably linking a first nucleotide sequence comprising
a functional copy of a gene that complements the mutant phenotypic
trait produced by the homozygous recessive condition with a second
functional nucleotide sequence which interferes with the formation,
function or dispersal of the male gametes of the plant. This
construct is maintained in the hemizygous state and a plant
containing such a construct is referred to as a maintainer.
Interference with the formation, function, or dispersal of the male
gamete may be accomplished by linking the sequences interfering
with formation, function, or dispersal of the male gamete with a
gamete-tissue-preferred promoter. Since the transgene is in the
hemizygous state, only half of the pollen grains produced contain
the restoring transgene construct and none of these are viable due
to the action of the linked second gene that prevents the formation
of viable pollen. Therefore, when the maintainer plant containing
such a linked construct is used as a pollen donor to fertilize the
homozygous recessive plant, the only viable male gametes provided
to the homozygous recessive plant are those which contain the
recessive allele, but do not contain any component of the transgene
construct. The progeny resulting from such a sexual cross are non
transgenic with respect to this transgene construct.
[0225] While no viable pollen produced by the maintainer contains
the restoring transgene construct, 50% of the ovules (the female
gamete) will contain the restoring transgene construct. Therefore,
the maintainer can be propagated by self-fertilization, with the
restoring transgene construct segregating such that it will be
contained in 50% of the seed of a self fertilized maintainer. By
linking the restoring transgene construct with a selectable marker,
the 50% of the seed containing the transgene can be isolated to
propagate the maintainer population, which remains homozygous for
the recessive gene and hemizygous for the restoring transgene
construct. In this scenario, a single inbred can be maintained.
[0226] Inbred A1 is homozygous recessive for the fertility gene
ms45. Inbred A1 plants contain a construct in which male fertility
is restored by expressing the MS45 coding region using a tissue
specific promoter, for example the native MS45 promoter. Inbred A1
plants also contain a hairpin construct targeted to suppress a
pollen expressed promoter, in this example, a PG47HP expressing
construct operably linked to the MS45 restoring construct; and a
selectable or screenable marker, for example, a marker that confers
herbicide resistance and/or a construct that serves as a visual or
detectable marker for plant and/or seed screening. These plants are
fertile and can be selfed and maintained. The seed on these plants
will segregate 50:50 for the transgene because only non-transgenic
pollen is viable and capable of effecting fertilization of an
ovule, 50% of which contain the construct.
[0227] To generate seed for female inbreds for hybrid production,
in one row, only non-transgenic plants from inbred A1 are
maintained; these plants are homozygous recessive ms45 and male
sterile. In an adjacent row, both transgenic and non-transgenic
plants from inbred A1 are grown. Fertility in this row segregates
one to one (fertile to sterile); fertile plants are used to
pollinate the sterile plants in the adjacent row. The seed from
this cross is non-transgenic for the operably linked restorer, the
hpRNA and the screenable marker constructs, and all of the progeny
are male sterile due to the presence of the homozygous ms45 allele.
These plants are used as females in hybrid production and
pollinated with plants homozygous for the wild-type MS45 gene
resulting in hybrid F1 seed. All plants derived from this seed are
heterozygous for the MS45 gene and, therefore, male fertile.
[0228] This example demonstrates that plants containing a dominant
pollen suppression hairpin construct and a fertility restoring
construct can be maintained as inbreds and used in a hybrid seed
production strategy to generate sterile female inbreds and fertile
hybrid plants.
Example 7
Combinations
[0229] Two or more construct components described herein may be
combined in various ways to create systems for controlling gene
expression. Such combinations may be made by linking said
components within a single vector, by using multiple vectors in
simultaneous or sequential transformations, and/or by breeding of
plants comprising one or more components. Possible components are
described below and in Table 2. Table 3 provides representations of
illustrative, but not exhaustive, combinations useful in
controlling male fertility.
[0230] For example, the components may include promoters or coding
regions other than those listed, and the order of the components
within the constructs may be different than those shown. Further, a
construct could comprise individual promoter/coding sequence
combinations, or one promoter driving transcription of multiple
coding sequence components. As an example of the latter, a
construct could comprise a constitutive promoter driving
transcription of an MS45 coding sequence as well as a
polynucleotide encoding a gene product involved in producing or
regulating a screenable marker (for example, pigment) to create a
fusion product. This would allow screening for transformants using
any tissue of the plant, while expression of the MS45 coding
sequence results in male fertility.
[0231] Within any of the constructs, one or more promoter hairpin
components could be included, for example within an intron of any
of the encoded genes, or within a 5' or 3' non-coding region, or as
an initial or terminal extension. A hairpin may target a single
promoter, or two or more promoters, within a single transcribed
RNA. Pollen-promoter hairpin configurations, and/or polynucleotides
encoding pollen-disrupting polypeptides, can serve to prevent
transgene transmission through the male gametes.
[0232] Pollen-preferred or pollen-specific promoters ("Poll-P")
include, for example, PG47, P95 (onset between mid- and
late-uninucleate stages; see, SEQ ID NO: 2) and P67 (profile
similar to P95, more highly expressed at mid-uninucleate stage;
see, SEQ ID NO: 1).
[0233] Tapetum-specific ("Tisp-P") or tapetum-preferred ("Tap-P")
promoters include, for example, MS45 (U.S. Pat. No. 6,037,523);
5126 (U.S. Pat. No. 5,837,851); Bs7 (WO 2002/063021) and SB200 (WO
2002/26789).
[0234] Other tissue-specific or tissue-preferred promoters useful
in the invention include, for example, Br2 (Science 302(5642):71-2,
2003), CesA8 and LTP2 (Plant J 6:849-860, 1994).
[0235] Constitutive promoters ("ConstP") include, for example, the
CaMV .sup.35S promoter (WO 1991/04036 and WO 1984/02913) and the
maize ubiquitin promoter.
[0236] Male fertility genes ("MF") useful in the invention include,
for example, MS45 (Cigan, et al., (2001) Sex. Plant Repro.
14:135-142; U.S. Pat. No. 5,478,369) and MS26 (US Patent
Application Publication Number 2003/0182689, issued Dec. 19, 2006
as U.S. Pat. No. 7,151,205).
[0237] Pollen ablation genes ("Cytotox") useful in the invention
include DAM (GenBank J01600, Nucleic Acids Res. 11:837-851 (1983);
alpha-amylase (GenBank L25805, Plant Physiol. 105(2):759-760
(1994)); D8 (Physiol. Plant. 100(3):550-560 (1997)); SacB (Plant
Physiol. (2):355-363 (1996)), lipases and ribonucleases. In this
regard, a single polypeptide, or a fusion of two or more
polypeptides to generate a fusion product, is contemplated.
Selectable marker systems useful in the practice of the invention
include, for example, herbicide resistance conferred by PAT or
MoPAT.
[0238] Screenable marker systems useful in the practice of the
invention, for example in identifying transgenic seed among progeny
of a selfed maintainer line, include GFP (Gerdes, (1996) FEBS Lett.
389:44-47; Chalfie, et al., (1994) Science 263:802), RFP, DSred
(Dietrich, et al., (2002) Biotechniques 2(2):286-293), KN1 (Smith,
et al., (1995) Dev. Genetics 16(4):344-348), CRC, P, (Bruce, et
al., (2000) Plant Cell 12(1):65-79 and Sugary1 (Rahman, et al.,
(1998) Plant Physiol. 117:425-435; James, et al., (1995) Plant Cell
7:417-429; U18908).
[0239] Hairpin configurations may comprise, for example, PG47hp,
P95hp or P67 hp. A hairpin may target a single promoter or may
target two or more promoters by means of a single transcribed RNA.
The hairpin could be located in any appropriate position within the
construct, such as within an intron of any of the encoded genes or
within 5' or 3' non-coding regions.
TABLE-US-00002 TABLE 2 Symbol Description Example Poll-P Pollen
Promoter PG47, P95, P67 Tisp-P Tissue Specific Promoter Br2, CesA8,
LTP2 Tap-P Tapetum Promoter Ms45, 5126, Bs7, Sb200 ConstP
Constitutive Promoter 35S, Ubi MF Fertility Gene Ms45, Ms26 Cytotox
Cytotoxic Gene DAM, Alpha-Amylase, D8, SacB Herb R Herbicide
Resistance PAT, MoPAT Screen Screenable Marker RFP, GFP, KN1, CRC,
Su1 HP Hairpin PG47hp, P95hp, P67hp
TABLE-US-00003 TABLE 3 Description Components Single cytotox +
Selection Poll-P:Cytotox/Tap-P:MF/ConstP:Herb R Single cytotox +
Selection + Poll-P:Cytotox/Tap-P:MF/ConstP:Herb R/ Screen
Tisp-P:Screen Double cytotox + Selection
Poll-P:Cytotox/Poll-P:Cytotox/Tap- P:MF/ConstP:Herb R Single
cytotox + Screen Poll-P:Cytotox/Tap-P:MF/Tisp-P:Screen Double
cytotox + Screen Poll-P:Cytotox/Poll-P:Cytotox/Tap-P:MF/
Tisp-P:Screen Hairpin + Single cytotox +
ConstP:HP/Poll-P:Cytotox/Tap-P:MF/ Selection ConstP:Herb R Hairpin
+ Single cytotox + ConstP:HP/Poll-P:Cytotox/Tap-P:MF/ Screen
Tisp-P:Screen Hairpin + Selection ConstP:HP/Tap-P:MF/ConstP:Herb R
Hairpin + Screen ConstP:HP/Tap-P:MF/Tisp-P:Screen Hairpin/Male
fertile fusion + ConstP:HP + MF/Tisp-P:Screen Screen Hairpin/Male
fertile fusion + ConstP:HP + MF/ConstP:Herb R Selection Embedded
Hairpin/Male ConstP:MF Embedded HP/ConstP:Herb R fertile +
Selection Embedded Hairpin/Male ConstP:MF Embedded HP/Tisp-P:Screen
fertile + Screen Embedded Hairpin/Screen Tap-P:MF/ConstP:Screen
Embedded HP Single Cytotox Embedded
Poll-P:Cytotox/Tap-P:MF/ConstP:Screen Hairpin/Screen Embedded HP
Constitutive Fertility/Screen ConstP:(MF + Screen) Embedded HP with
Embedded Hairpin Tap-P:Cytotox/ConstP:(MF + Screen) Embedded HP
Example 8
Visual Marker-Based Selection
[0240] The experiments described below were designed to ask whether
the maize p1 gene, when expressed from various non-p1 promoters,
could be used as a visual marker for seed carrying a linked
transgene. As part of the experimental design, coloration of seed
from the transformed plant, as well as coloration of seed generated
by outcrossing pollen from the transformed plant, was tested to
examine inheritance of maternal and paternal p1 gene
expression.
[0241] The p1 gene of maize is a Myb-related transcriptional
activator demonstrated to regulate the a1 and c2 genes to produce
3-deoxy flavonoids, such as C-glycosyl flavones,
3-deoxyanthocyanins, flavan-4-ols and phlobaphenes (Grotewold, et
al., (1991) PNAS 88:4587-4591). Synthesis of these and related
compounds results in the coloration of floral organs including
pericarp, cob, silks, husks and tassel glumes (Cocciolone, et al.,
(2001) Plant J (5):467-478). Typically, expression of this gene is
maternal; that is, outcrossing of the p1 gene does not confer
coloration to reproductive parts until the next generation is grown
from seed. As the p1 gene has been shown to confer color to
non-reproductive maize tissues by constitutive expression in BMS
(Black Mexican Sweet) cells (Grotewold, et al., (1998) PI Cell),
expression of the p1 gene was investigated by placing the p1 gene
under the transcriptional control of the maize seed-preferred
promoters END2 and LTP2. Constitutive promoters rice Actin and
maize Ubiquitin were also used to transcriptionally regulate the p1
gene. These vectors would test whether expression of the p1 gene
would confer color differences sufficient for use as a visual
marker.
[0242] The following vectors were introduced into maize by
Agrobacterium transformation and tested for seed color of both the
transformed plant and ears pollinated with pollen from the
transformed plants.
[0243] 23030 End2:P1-UbimoPAT
[0244] 23066 Actin:P1-UBlmoPat
[0245] 23069 LTP2:P1-UBlmoPat
[0246] 23528 End2:P1-35SPAT
[0247] 23535 LTP2:P1-35S:PAT
[0248] 23537 UBI:P1-35S:PAT
[0249] Transformation with PHP23030 and PHP23069 has produced
plants demonstrating segregating colored seed both on ears of the
primary transformed plants and on ears pollinated by pollen from
these transformed plants. For PHP23030, 12 of the 14 independent
events used for outcrossing demonstrated brown colored kernels
segregating among the yellow kernels at nearly a 1:1 segregation
ratio. Ears on the primary transformants were pollinated with
pollen from non-transformed plants and the kernels on these ears
also segregated brown:yellow kernels at nearly a 1:1 ratio.
Identical results were observed with three of the four events
generated with PHP23069.
[0250] Brown and yellow seed from 5 single-copy PHP23030 events
were sorted and planted to test for germination of the brown seed
and co-segregation of the linked herbicide resistance marker,
35SPAT, with the colored kernels. In this small test, the majority
(>95%) of the brown seed produced herbicide resistant plants,
whereas 39 of the 40 seedlings germinated from yellow seed were
herbicide sensitive.
[0251] Close examination of the brown seed from PHP23030 revealed
that the aleurone layer fluoresced green, while the endosperm of
brown seed from PHP23069 showed strong green fluorescence when
compared to yellow segregating seed derived from the same ear. This
is consistent with the observation of green fluorescence observed
in BMS cells bombarded with 35S:P1 (Grotewold, et al., (1998) Plant
Cell 10(5):721-740). Moreover, examination of the transformed
callus with PHP23528 (End2:P1-35SPAT) and PHP23535
(LTP2:P1-35S:PAT) revealed, in contrast to untransformed GS3
callus, both PHP23528- and PHP23535-containing callus fluoresced
green. The observation of green fluorescence in these transformed
callus and the co-segregation of brown kernels with the herbicide
selectable marker in transformed plants indicates that expression
of p1 from at least seed-preferred promoters can be used as a
visual marker to identify transformed maize tissues.
Example 9
Alternatives for Pollen Cytotoxicity
[0252] As shown in Tables 2 and 3, disruption of pollen function
may be accomplished by any of numerous methods, including targeted
degradation of starch in the pollen grain or interference with
starch accumulation in developing pollen. For example, a construct
comprising the alpha-amylase coding region is operably linked to a
pollen specific promoter. The native secretory signal peptide
region may be present; may be removed; or may be replaced by an
amyloplastid-targeted signal peptide. In other embodiments, a
construct may comprise a pollen-specific promoter operably linked
to a coding region for beta-amylase; or for a debranching enzyme
such as Sugary1 (Rahman, et al., (1998) Plant Physiol. 117:425-435;
James, et al., (1995) Plant Cell 7:417-429; U18908) or pullulanase
(Dinges, et al., (2003) Plant Cell 15(3):666-680; Wu, et al.,
(2002) Archives Biochem. Biophys 406(1):21-32).
Example 10
Substituting Orthologous Promoters
[0253] Orthologous promoters from rice and Arabidopsis (see, FIG.
1) were isolated and tested for (1) their ability to regulate
transcription of the maize MS45 restorer gene, as described in
Example 2; (2) the effect of an ortholog-based pIR on endogenous
gene expression and (3) whether a pIR for an orthologous promoter
could effectively silence the MS45 transgene operably linked to
said orthologous promoter.
[0254] The isolated rice and Arabidopsis DNA sequences were
modified by PCR to accommodate construction of MS45 complementation
and inverted repeat vectors. Typically, HindIII and NcoI
restriction sites were introduced onto the 5' and 3' ends,
respectively, for the complementation vectors. For the promoter
inverted repeat vectors, NotI-NcoI ends and HindIII-EcoRI ends were
generated by PCR and subcloned into expression vectors as described
in Cigan, et. al., (2005) Plant Journal 43, 929-940.
[0255] (1) Ability to Drive the Maize MS45 Restorer Gene
[0256] Expression cassettes were constructed, each comprising a
promoter of the rice MS45, rice 5126, rice BS7, rice MS26,
Arabidopsis MS45, Arabidopsis 5126 or Arabidopsis BS7 gene,
operably linked to the maize MS45 coding region. Cells of
homozygous recessive ms45 ms45 maize were transformed and plants
were regenerated, according to methods known to those of skill in
the art. Typically, single plants from six to ten single-copy TO
transformants were evaluated for male fertility. In each case, a
high-frequency (>90%) of plants from independent TDNA insertions
demonstrated restoration of fertility by the orthologous promoter
driving MS45. Moreover, fertility restoration was maintained when
plants from these fertile events were analyzed in subsequent
generations, (T1, 3 plants per event and T2, 3 to 5 plants per
event).
[0257] (2) Effect of an Ortholog-Based pIR on Endogenous Gene
Expression
[0258] Constructs were created comprising the ubiquitin promoter
operably linked to a pIR based on each of the rice MS45, rice 5126,
rice BS7, Arabidopsis 5126 and Arabidopsis BS7 promoters. Wild-type
maize cells were transformed and plants regenerated. Typically,
single plants from six to ten single-copy T0 transformants were
evaluated for defects in either plant development or male
fertility. In each case, plants developed normally and defects in
fertility were not observed, indicating that the orthologous pIR
did not affect expression of the endogenous target gene.
[0259] (3) Effect of an Ortholog-Based pIR on Expression of Said
Orthologous Promoter Driving MS45
[0260] Male fertile, ms45 homozygous recessive plants containing
constructs described in (1) above were used to fertilize male
fertile Ms45/ms45 heterozygous plants containing the corresponding
promoter pIR described in (2) above. Progeny ms45-recessive plants
containing both an orthologous promoter operably linked to MS45,
and the corresponding pIR, were evaluated for male fertility. Each
pIR silenced expression of its corresponding promoter driving MS45
and resulted in male sterile plants due to the recessive nature of
ms45 and the inability of the promotor operably linked to the
transgenic copy of MS45 to direct transcription of this gene; for
example, a pIR for riceMS45 silenced riceMS45::MS45. Similar
results were obtained using the rice 5126 and the Arabidopsis 5126
and Arabidopsis BS7 promoters. See, FIG. 3.
Example 11
Allele Testing and Utilization
[0261] This example provides a method for evaluating functionality
of variant alleles of a gene of interest. Using an appropriate pIR,
the endogenous gene of interest is suppressed. A variant allele of
the gene of interest is expressed under the control of a non-target
promoter. The complementation and suppression elements may be
combined in a single vector. See, FIG. 4. In one embodiment of the
method, the variant allele is produced by gene shuffling.
Strategies for such DNA shuffling are known in the art. See, for
example, Stemmer, (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751;
Stemmer, (1994) Nature 370:389-391; Crameri, et al., (1997) Nature
Biotech. 15:436-438; Moore, et al., (1997) J. Mol. Biol.
272:336-347; Zhang, et al., (1997) Proc. Natl. Acad. Sci. USA
94:4504-4509; Crameri, et al., (1998) Nature 391:288-291 and U.S.
Pat. Nos. 5,605,793 and 5,837,458.
[0262] In further embodiments, a plant cell is transformed with an
expression cassette comprising a selected variant allele operably
linked to an appropriate promoter, and a transformed plant is
regenerated. The regenerated plant may display a phenotypic change.
In certain embodiments the phenotypic change is measurable only
when the plant or cell comprising the variant allele or its gene
product also comprises a second gene or gene product, such as a
reporter molecule or cofactor.
[0263] FIG. 5 presents one embodiment of the method as applied to
the MS45 male-fertility gene; however, the methods of the invention
may be employed with respect to a gene of interest selected from a
wide range of genes which encode a polypeptide involved in a
metabolic pathway affecting any of a variety of phenotypic traits,
including those listed elsewhere herein. In further embodiments,
the methods of this example are used in combination with other
methods described herein. For example, silencing of an endogenous
gene and transformation with a selected variant allele could be
combined with a method described in Example 5, such that the
selected variant allele is operably linked to a promoter in a first
plant; and a second plant comprises a pIR targeted to said
promoter, such that expression of the selected variant allele can
be controlled through crossing.
Example 12
Maintenance of Recessive Lethals
[0264] In a further embodiment of the complementation methods
incorporating pIRs, an orthologous promoter is employed to
complement expression of a mutant. In this way, plants comprising
recessive lethal mutants may be selfed. Crossing of plants
comprising corresponding transgene constructs (as shown in FIG. 6)
results in silencing of the complementing promoter, thereby
exposing the recessive mutation.
[0265] Methods used herein, such as for construction of expression
cassettes, transformation, plant regeneration, nucleic acid
isolation and analysis and scoring of male fertility, are known to
those of skill in the art; see, for example, Cigan, et al., (2005)
Plant J 43:929-940, and the references cited therein, including
Cigan, et al., (2001) Sex. Plant Repro. 14:135-142 and Unger, et
al., (2001) Transgenic Res. 10:409-422.
[0266] Although the invention has been described with reference to
the above example, it will be understood that modifications and
variations are encompassed within the spirit and scope of the
invention. Accordingly, the invention is limited only by the
claims.
[0267] All publications and patent herein referred to are hereby
incorporated by reference to the same extent as if each was
individually so incorporated.
Sequence CWU 1
1
311112DNAZea mayspromoter(1)...(1112)P67 1gacgcgactg ctgacaaccc
tagctagaaa caccctgaac actagttagg ttttcctctg 60ttatctgcgt tgtcgatgta
gttttcttta tctcgagcac cgatgtgcat ctgtgatcgg 120gagatcatgt
ctctggaaac tgttgtcttc gagatcctgt attaggagaa ggaaaataag
180gtttttgaga agcgtattca catgactact cacgttttcc ttgccatcga
ccacgtcgtc 240gaccctgcta gcttccacgt tgtcattcag tatgttcgat
cgcatcatct gatctaatct 300tataatgcag ttcatctgtt atggtagaag
tgtgtcgcat tcttataatt agcatgttag 360ggttacatgt taggtaacag
acaccgagat tatctctgta caccattgtt gccttcattg 420cctacgtcgt
ctctcacagc cacaggtgtc tgaatcatga ccctcttttt aggagtagtc
480tgtagagatg tgaggtaaag cagctttgca cgagaacgcc aatctcgcgt
gtttccgagt 540attttactgc tccatttgtg ggctacgcct gttgtttccg
ccacggatgt cggctgctca 600tcaccaaaaa tatgactact ttgaagttct
ggtagcagag tgggcccaga cgccgttgct 660tgattctggc tgggccaggc
tacgtgaggc cttcttatta gatcatttcc gctgaaaggc 720cgaaacgtga
gagcctggca aacttttcta gaaaaaaaaa attcgcaaac aaaatttttt
780ccgaacaaac gctacaccag tgaccgccgt ccgtcgtcgt tgcttggctc
tccctttact 840tcggctccaa cgccaatgca caaccgtccc tcttcgccat
gtcccagttt tgacgctgcc 900tgtagcgcag tataaaaaat cgtctcgatg
ctcttgctcg gtactccaat tcacaccaaa 960acatagagtg tcgacttttc
tattggtgtg attgggggca ctaaatacct accacattgc 1020actcagacta
catatactgt gtttgtgtgt tgtaagccgt aagcgtgtgt gagcttgcgc
1080aaattggaca tctaggccgt gcgtaccctg cg 111221092DNAZea
mayspromoter(1)...(1092)P95 2gcgacgtcga gatcacgaga ggctcgtacg
gggacaacgc gctaggtctc ttagtcagat 60cagttcaaat ctcttaattc ttgtcctcct
tctcagtcca gttcttacat ctatctgtct 120gatcccatta tttccaacac
cacttgaacc aatctgctct gatgccccgt tcctgatgtt 180gtcgtcgttg
tcactttctc gacgtgcgtt gtcgtccgac cctgacccct tctcgatgcc
240tcatctccga cagacgacga gtttagcaaa ccagcgagcg ttgattctct
gccgaaaagg 300ttgcctgacc ccgtctcctt cccgatggcc ctacacttcg
agaagatcac cacttcgaga 360agatcaccag atcaatatcc gaaaagatac
acatagttta gattcagtca gcaaaaagct 420aacattatgt ttgcttcttt
tattcatata gttttcttag catgaaattt aaattctata 480tagtactggt
tttttacgag cttacttaat tttattaggg ctaatttggt aaccacattt
540ttccacggaa tttcaatttt cctaaggaaa attagttaat tttcgcttgg
gaaaatagaa 600atttcatggg aaaatgcggt tcccaaacta gccttagcct
tataggtttt ttttagccca 660tgtgaattct cgtcaaaggg actcagtcca
cttcacagca ggtgaggtgg tttttgaatg 720cccaaataca gatctgttaa
ttaattttca gagggtcagg acgcggtcgc ccgaacgggc 780ggacgcgcga
acaatccgcc cgcccgcgcg cgcgacctgc cacttcgggc catggccagc
840acccagcatg cgtcgtccta aacgacgagc accgcccgtt ggcgctataa
agccccgcct 900cggcgtcccc ttgtcaattc gaagccttcc cggttacccc
ttcggcctcc acctatcacc 960acccgggacg tcttccaggg tctcctcgta
gtagaatagc tctatctcac cgcaacaact 1020cctcattaca tcctttagga
gaggctgatc gattggtaga tacgtactcg ggtggagcag 1080aacaacgaga ga
10923597DNAOryza sativapromoter(1)...(597)Rice BS7 promoter region
3agcttgtttt tggttcaaac aaaagcagca gcagcagcaa agaaccagag aaggctcctc
60ctgttaaagt tgatgaactt gcaaagaagg aagagcccaa gttccaagca ttttctggga
120cgagctactc gttgaaacgt tagctgctgc tattagggtt aaaagttttg
gaatcaatca 180tttgtttctt acttggagtt cgcctggtta ctctggcagc
tgtaaatgat tggtagcaat 240gtgtatcttt atcattttca gttctccctt
aataattcta gttattgtct tgctaattaa 300aagaattccg tggattacat
ggaacctgat actatttgct tgaccatatg tggagttttc 360ttgcaatgtc
aagcagaacg cattgctaat gtactcaacc aactccctac ctagagaaga
420ttctaactga atctaccctc aaccaacctg cttctccatc agttaattat
gatcacaaaa 480atgaggtgat gtacaacatt tcttggtcct cctcctctag
gatatttctt tgctgtgctt 540atatgagcag gttgatttgc ttcagagttc
aacatcatca cttccagttt gagaaac 597
* * * * *