U.S. patent application number 17/546990 was filed with the patent office on 2022-06-23 for disease resistant plant methods and compositions.
The applicant listed for this patent is Monsanto Technology LLC. Invention is credited to George J. Baley, Derek R. Drost, Hongwu Jia, Yule Pan, Jeffrey Michael Stein, Chongqing Xie, Hao Zhou.
Application Number | 20220192119 17/546990 |
Document ID | / |
Family ID | |
Filed Date | 2022-06-23 |
United States Patent
Application |
20220192119 |
Kind Code |
A1 |
Baley; George J. ; et
al. |
June 23, 2022 |
DISEASE RESISTANT PLANT METHODS AND COMPOSITIONS
Abstract
The present invention provides methods and compositions for
producing elite lines of corn exhibiting anthracnose stalk rot
(ASR) resistance. Also provided in the present invention are corn
plants exhibiting ASR resistance resulting from such methods, and
methods for breeding corn such that the ASR resistance traits may
be transferred to a desired genetic background.
Inventors: |
Baley; George J.; (St.
Louis, MO) ; Drost; Derek R.; (Penn Valley, CA)
; Jia; Hongwu; (Apex, NC) ; Pan; Yule;
(Chesterfield, MO) ; Stein; Jeffrey Michael;
(Wildwood, MO) ; Xie; Chongqing; (Johnston,
IA) ; Zhou; Hao; (Chesterfield, MO) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Monsanto Technology LLC |
St. Louis |
MO |
US |
|
|
Appl. No.: |
17/546990 |
Filed: |
December 9, 2021 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
16831282 |
Mar 26, 2020 |
11206777 |
|
|
17546990 |
|
|
|
|
16404570 |
May 6, 2019 |
10638685 |
|
|
16831282 |
|
|
|
|
14801618 |
Jul 16, 2015 |
10280433 |
|
|
16404570 |
|
|
|
|
62101292 |
Jan 8, 2015 |
|
|
|
62027153 |
Jul 21, 2014 |
|
|
|
International
Class: |
A01H 1/04 20060101
A01H001/04; C12Q 1/6895 20060101 C12Q001/6895; A01H 5/10 20060101
A01H005/10; A01H 6/46 20060101 A01H006/46; C12Q 1/6865 20060101
C12Q001/6865 |
Claims
1. A method of obtaining a corn plant with enhanced anthracnose
stalk rot resistance, said method comprising: a) obtaining a DNA
sample from at least one corn plant or part thereof from a
population of corn plants; b) detecting in the DNA sample the
presence of an anthracnose stalk rot resistance allele, wherein
said allele is within 5 cM of a "A" corresponding to position 151
of SEQ ID NO:106, and wherein the "A" at said position is
associated with enhanced anthracnose stalk rot resistance; c)
selecting at least a first plant comprising said allele and
enhanced anthracnose stalk rot resistance compared to a plant
lacking said allele; d) crossing the plant selected in step c) with
a second corn plant, wherein said second corn plant lacks or is
heterozygous for said anthracnose stalk rot resistance allele; e)
collecting seeds from the cross of step d); and f) growing at least
one progeny corn plant from the seeds of step e); wherein said
progeny corn plant comprises said allele and has enhanced
anthracnose stalk rot resistance compared to a corn plant lacking
said allele.
2. The method of claim 1, wherein said selecting comprises
detecting a polymorphism located in a chromosomal segment flanked
by marker loci AY107053 and umc1379.
3. The method of claim 2, wherein said polymorphism is located in a
chromosomal segment flanked by marker loci SEQ ID NO: 4 or 52 and
SEQ ID NO: 5.
4. The method of claim 2, wherein said polymorphism is located in a
chromosomal segment flanked by marker loci SEQ ID NO: 81 and SEQ ID
NO: 2 or 55.
5. The method of claim 4, wherein said chromosomal segment is
flanked by marker loci SEQ ID NO: 81 and SEQ ID NO: 54.
6. The method of claim 5, wherein said chromosomal segment is
flanked by marker loci SEQ ID NO: 82 and SEQ ID NO: 54.
7-32. (canceled)
33. The method of claim 1, wherein the selecting comprises
detecting enhanced anthracnose stalk rot resistance, wherein the
detecting enhanced anthracnose stalk rot resistance comprises
detecting a polynucleotide comprising SEQ ID NO: 106 in the DNA
sample.
Description
REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional of U.S. application Ser.
No. 16/831,282, filed Mar. 26, 2020, is a divisional of U.S.
application Ser. No. 16/404,570, filed May 6, 2019, now U.S. Pat.
No. 10,638,685, which is a divisional of U.S. application Ser. No.
14/801,618, filed Jul. 16, 2015, now U.S. Pat. No. 10,280,433,
which claims the benefit of U.S. Provisional Application No.
62/027,153, filed Jul. 21, 2014, and U.S. Provisional Application
No. 62/101,292, filed Jan. 8, 2015 each of which is herein
incorporated by reference in their entireties.
FIELD OF THE INVENTION
[0002] The present invention relates to the field of agricultural
biotechnology. More specifically, the invention relates to methods
for producing corn plants with resistance to fungi.
INCORPORATION OF SEQUENCE LISTING
[0003] A sequence listing contained in the file named
"MONS358US_ST25.txt" which is 40 bytes (measured in
MS-Windows.RTM.) and created on Jul. 16, 2015, and comprises 106
nucleotide sequences, is filed electronically herewith and
incorporated by reference in its entirety.
BACKGROUND OF THE INVENTION
[0004] Advances in molecular genetics have made it possible to
select plants based on genetic markers linked to traits of
interest, a process called marker-assisted selection (MAS). While
breeding efforts to date have provided a number of useful corn
lines and varieties with beneficial traits, there remains a need in
the art for selection of varieties with further improved traits and
methods for their production. In many cases, such efforts have been
hampered by difficulties in identifying and using alleles
conferring beneficial traits. These efforts can be confounded by
the lack of definitive phenotypic assays, and other issues such as
epistasis and polygenic or quantitative inheritance. In the absence
of molecular tools such as MAS, it may not be practical to attempt
to produce certain new genotypes of crop plants due to such
challenges.
SUMMARY OF THE INVENTION
[0005] In one aspect, the present invention provides a method for
obtaining a corn plant with enhanced anthracnose stalk rot
resistance comprising: a) providing a population of corn plants; b)
detecting in said plants an anthracnose stalk rot resistance allele
at a polymorphic locus in a chromosomal segment flanked by loci
IDP7601 and gpm426b on chromosome 6; c) selecting from said
population at least a first plant comprising said allele and
enhanced anthracnose stalk rot resistance compared to a plant
lacking said allele. In some embodiments, said segment is flanked
by marker loci umc2006 and chs562. In other embodiments, said
segment is flanked by marker loci umc2006 and SEQ ID NO: 8. In
further embodiments, said segment is flanked by marker loci SEQ ID
NO: 52 and SEQ ID NO: 8. In yet further embodiments, said segment
is flanked by marker loci SEQ ID NO: 4 and SEQ ID NO: 2. In other
embodiments, said segment is flanked by marker loci SEQ ID NO: 96
and SEQ ID NO: 106. In some embodiments, said polymorphic locus is
selected from the group consisting of: IDP7601, IDP62, 111,
IDP8090, umc2006, IDP8231, umc248b, SEQ ID NO: 10, pco136292, SEQ
ID NO: 3, IDP6025, IDP6010, SEQ ID NO: 1, SEQ ID NO: 7, agrr118a,
umc180 (pep), SEQ ID NO: 51, gpm74, TIDP3136, AY107053, SEQ ID NO:
4, SEQ ID NO: 52, IDP1699, pdi7, gpm869, SEQ ID NO: 81, ufg11, SEQ
ID NO: 82, umc1250, SEQ ID NO: 53, TIDP3356, SEQ ID NO: 83, SEQ ID
NO: 96, csu382a (cld), IDP2409, SEQ ID NO: 97, SEQ ID NO: 98, SEQ
ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID
NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, PCO146525,
SEQ ID NO: 8, csu225, bnl3.03, AI665560, SEQ ID NO: 54, pzb00414,
umc2141, SEQ ID NO: 55, SEQ ID NO: 2, AY110435, elfa5, SEQ ID NO:
5, umc1379, bnl15.37a, SEQ ID NO: 56, pza02478, IDP3886, c139957_1,
mmc0241, dup400 (pac), jpsb107b, chs562, gpm709b, SEQ ID NO: 6,
umc2321, bnlg1702, SEQ ID NO: 9, csu158b (eno), and gpm426b. In
further embodiments, the invention provides a corn plant produced
by the methods provided herein, or a plant part or seed of said
corn plant.
[0006] In another aspect, the present invention provides a method
of producing a corn plant with enhanced anthracnose stalk rot
resistance comprising: a) introgressing into a corn plant a genomic
segment comprising an anthracnose stalk rot resistance allele; and
b) selecting a plant based on the presence of said allele in at
least one polymorphic locus selected from the group consisting of:
IDP7601, IDP62, 111, IDP8090, umc2006, IDP8231, umc248b, SEQ ID NO:
10, pco136292, SEQ ID NO: 3, IDP6025, IDP6010, SEQ ID NO: 1, SEQ ID
NO: 7, agrr118a, umc180 (pep), SEQ ID NO: 51, gpm74, TIDP3136,
AY107053, SEQ ID NO: 4, SEQ ID NO: 52, IDP1699, pdi7, gpm869, SEQ
ID NO: 81, ufg11, SEQ ID NO: 82, umc1250, SEQ ID NO: 53, TIDP3356,
SEQ ID NO: 83, SEQ ID NO: 96, csu382a (cld), IDP2409, SEQ ID NO:
97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101,
SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ
ID NO: 106, PCO146525, SEQ ID NO: 8, csu225, bnl3.03, AI665560, SEQ
ID NO: 54, pzb00414, umc2141, SEQ ID NO: 55, SEQ ID NO: 2,
AY110435, elfa5, SEQ ID NO: 5, umc1379, bnl15.37a, SEQ ID NO: 56,
pza02478, IDP3886, c139957_1, mmc0241, dup400 (pac), jpsb107b,
chs562, gpm709b, SEQ ID NO: 6, umc2321, bnlg1702, SEQ ID NO: 9,
csu158b (eno), and gpm426b; wherein said allele confers enhanced
resistance to anthracnose stalk rot compared to a plant lacking
said allele. In further embodiments, the method further comprises:
c) crossing said corn plant with itself or a second plant to
produce one or more progeny plants; and d) selecting a progeny
plant comprising said allele. In some embodiments, step (d) of
selecting comprises marker-assisted selection. In other
embodiments, the progeny plant is an F2-F6 progeny plant. In
further embodiments, producing the progeny plant comprises
backcrossing. In yet further embodiments, backcrossing comprises
from 2-7 generations of backcrosses. In certain embodiments,
backcrossing comprises marker-assisted selection in at least two
generations. In further embodiments, the invention provides a corn
plant produced by the methods provided herein, or a plant part or
seed of said corn plant.
[0007] In yet another aspect, the invention provides a method of
producing a corn plant with enhanced anthracnose stalk rot
resistance comprising: a) crossing a first corn plant comprising an
anthracnose stalk rot resistance allele with a second corn plant of
a different genotype to produce one or more progeny plants; and b)
selecting a progeny plant based on the presence of said allele in
at least one polymorphic locus selected from the group consisting
of: IDP7601, IDP62, 111, IDP8090, umc2006, IDP8231, umc248b, SEQ ID
NO: 10, pco136292, SEQ ID NO: 3, IDP6025, IDP6010, SEQ ID NO: 1,
SEQ ID NO: 7, agrr118a, umc180 (pep), SEQ ID NO: 51, gpm74,
TIDP3136, AY107053, SEQ ID NO: 4, SEQ ID NO: 52, IDP1699, pdi7,
gpm869, SEQ ID NO: 81, ufg11, SEQ ID NO: 82, umc1250, SEQ ID NO:
53, TIDP3356, SEQ ID NO: 83, SEQ ID NO: 96, csu382a (cld), IDP2409,
SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID
NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO:
105, SEQ ID NO: 106, PCO146525, SEQ ID NO: 8, csu225, bnl3.03,
AI665560, SEQ ID NO: 54, pzb00414, umc2141, SEQ ID NO: 55, SEQ ID
NO: 2, AY110435, elfa5, SEQ ID NO: 5, umc1379, bnl15.37a, SEQ ID
NO: 56, pza02478, IDP3886, c139957_1, mmc0241, dup400 (pac),
jpsb107b, chs562, gpm709b, SEQ ID NO: 6, umc2321, bnlg1702, SEQ ID
NO: 9, csu158b (eno), and gpm426b; wherein said allele confers
enhanced resistance to anthracnose stalk rot compared to a plant
lacking said allele. In some embodiments, step (b) of selecting
comprises marker-assisted selection. In other embodiments, the
progeny plant is an F2-F6 progeny plant. In further embodiments,
producing the progeny plant comprises backcrossing. In yet further
embodiments, backcrossing comprises from 2-7 generations of
backcrosses. In some embodiments, backcrossing comprises
marker-assisted selection in at least two generations. In other
embodiments, the first corn plant is an inbred or a hybrid. In
further embodiments, the second corn plant is an agronomically
elite corn plant. In yet further embodiments, the agronomically
elite corn plant is an inbred or a hybrid. In further embodiments,
the invention provides a corn plant produced by the methods
provided herein, or a plant part or seed of said corn plant.
[0008] In some aspects, corn plants or methods disclosed herein are
used in combination with one or more pesticides including, but not
limited to, herbicides, fungicides, insecticides, microbicides,
nematicides, insect repellents, bactericides, and other substances
used to control pests. In other aspects, the corn plants or methods
disclosed herein are used in combination with one or more
triazoles, strobilurins, acylamino acids, pyrimidines, pyridines,
aryl phenyl ketones, amides, benzanilides, imidazoles,
dinitrophenols, morpholines, phenylsulfamides and organophosphorus
cpds, derivatives thereof and combinations thereof which may be
applied as seed, foliar, drench or drip treatments.
DESCRIPTION OF THE FIGURES
[0009] FIG. 1 shows first round fine-mapping of ASR-6.01 from
CV820914/CV391950 as also shown in Table 10. Bulk "f" shared at
least one same allele as the resistant inbred line (CV391950) at
the SNP positions represented by SEQ ID NO: 51, SEQ ID NO: 52 and
SEQ ID NO: 53 (highlighted by white cells). Bulk "f" shared the
same alleles as the susceptible inbred line (CV820914) at the SNP
positions represented by SEQ ID NO: 8, SEQ ID NO: 54, SEQ ID NO:
55, SEQ ID NO: 5 and SEQ ID NO: 56 (highlighted by grey cells).
Similar experiments were also conducted on BC1F2 kernels derived
from CV295879/CV391950. Bulk "f", "g", "i", "j", "p" and "o"
displayed significantly reduced ASR severity (highlighted by black
box, p-value <=0.05) compared with the bulk "b". Among these
resistant bulks, the same common SNP (SEQ ID NO: 53, highlighted by
black oval) was identified as the peak marker.
[0010] FIG. 2 shows first round fine-mapping of ASR-6.01 from
CV295879/CV391950 as also shown in Table 11.
[0011] FIG. 3 shows second round fine-mapping of ASR-6.01 from
CV005260/CV391950 as also shown in Table 14. For example, bulk "a"
shared the same alleles as the resistant inbred line, CV391950, at
the candidate QTL region (highlighted by white cells); bulk "b"
shared the same alleles as the susceptible inbred line, CV005260,
at the candidate QTL region (highlighted by grey cells).
DETAILED DESCRIPTION OF THE INVENTION
[0012] Anthracnose stalk rot (ASR) is caused by the fungal pathogen
Colletotrichum graminicola, and results in severe yield loss in
crop plants. Efforts to identify or produce plant lines resistant
to ASR have been hindered by a limited understanding of the genetic
loci controlling ASR resistance and a lack of available markers for
detecting and tracking ASR resistance in plants. Yield loss due to
ASR therefore remains a significant problem.
[0013] The present invention identifies previously-unknown genetic
loci which confer ASR resistance and provides novel molecular
markers linked to ASR resistance in plants. The invention further
provides methods for introgression of genetic loci conferring ASR
resistance into plant varieties previously lacking such loci,
thereby providing plants with a new or improved disease resistance.
The genetic loci, markers, and methods provided by the invention
therefore represent a significant advance in the art, enabling
production of new varieties exhibiting ASR resistance.
[0014] In some embodiments, the invention therefore provides
quantitative trait loci (QTL) that demonstrate significant
co-segregation with ASR resistance. The QTL of the invention can be
tracked during plant breeding or introgressed into a desired
genetic background in order to provide novel plants exhibiting ASR
resistance and one or more other beneficial traits. In particular
embodiments, the invention identifies for the first time a QTL on
chromosome 6 of the corn genome, designated ASR-6.01, which is
associated with ASR resistance.
[0015] In other embodiments, the invention provides molecular
markers linked to the QTL of the invention and methods of using the
markers for detection of and selection for ASR resistance.
Embodiments of the invention therefore include specific markers,
chromosome intervals comprising the markers, and methods of
detecting markers genetically linked to ASR-6.01 to identify
disease resistant plant lines. For example, the invention provides
a chromosome interval associated with ASR resistance which is
flanked by the markers IDP7601 and gpm426b, and which comprises
markers having SEQ ID NOs: 1-10, 51-56, 81-83, and 96-106, or any
of the markers listed in Table 17, and any other markers
genetically linked thereto. Also provided herein are markers that
are useful for detecting the presence or absence of disease
resistance alleles within the QTL of the invention that can be used
in marker assisted selection (MAS) breeding programs to produce
plants with improved resistance to ASR infection.
[0016] The invention further provides methods of using the markers
identified herein to introgress loci associated with ASR resistance
into plants. Thus, one skilled in the art can use the invention to
create novel maize plants with ASR resistance by crossing a donor
line comprising a QTL associated with ASR resistance into any
desired recipient line, with or without MAS. Resulting progeny can
be selected to be genetically similar to the recipient line except
for the ASR resistance QTL.
Quantitative Trait Loci
[0017] The term "chromosome interval" designates a contiguous
linear span of genomic DNA that resides on a single chromosome. A
chromosome interval may comprise a QTL linked with a genetic trait
and the QTL may comprise a single gene or multiple genes associated
with the genetic trait. The boundaries of a chromosome interval
comprising a QTL are drawn such that a marker that lies within the
chromosome interval can be used as a marker for the genetic trait,
as well as markers genetically linked thereto. Each interval
comprising a QTL comprises at least one gene conferring a given
trait, however knowledge of how many genes are in a particular
interval is not necessary to make or practice the invention, as
such an interval will segregate at meiosis as a linkage block. In
accordance with the invention, a chromosomal interval comprising a
QTL may therefore be readily introgressed and tracked in a given
genetic background using the methods and compositions provided
herein.
[0018] Identification of chromosomal intervals and QTL is therefore
beneficial for detecting and tracking a genetic trait, such as ASR
resistance, in plant populations. In some embodiments, this is
accomplished by identification of markers linked to a particular
QTL. The principles of QTL analysis and statistical methods for
calculating linkage between markers and useful QTL include
penalized regression analysis, ridge regression, single point
marker analysis, complex pedigree analysis, Bayesian MCMC,
identity-by-descent analysis, interval mapping, composite interval
mapping (CIM), and Haseman-Elston regression. QTL analyses may be
performed with the help of a computer and specialized software
available from a variety of public and commercial sources known to
those of skill in the art.
[0019] In some embodiments, the invention provides a chromosomal
interval comprising a QTL associated with ASR resistance. The
invention provides multiple markers associated with ASR resistance,
for example the markers having the sequence of SEQ ID NOs: 1-10,
51-56, 81-83, or 96-106. The invention therefore provides a plant
comprising a nucleic acid molecule selected from the group
consisting of SEQ ID NOs: 1-10, 51-56, 81-83, 96-106, fragments
thereof, or complements thereof. The present invention further
provides a plant comprising alleles of the chromosome interval
linked to ASR resistance or fragments and complements thereof as
well as any plant comprising any combination of one or more disease
resistance loci selected from the group consisting of SEQ ID NOs:
1-10, 51-56, 81-83 and 96-106. Plants provided by the invention may
be homozygous or heterozygous for such alleles.
[0020] In one embodiment, the chromosome interval associated with
ASR resistance contains SEQ ID NOs: 1-10, 51-56, 81-83 or 96-106,
and is flanked by the markers IDP7601 and gpm426b. This chromosome
interval encompasses markers that co-segregate with ASR resistance
in the populations studied at a p-value .ltoreq.0.05. An example of
a subinterval associated with ASR resistance includes the interval
flanked by umc2006 and chs562, which define a chromosome interval
encompassing markers that co-segregate with ASR resistance in
populations studied at a p-level .ltoreq.0.05. An example of a
subinterval associated with ASR resistance includes the interval
flanked by SEQ ID NO: 52 and SEQ ID NO: 8, which define a
chromosome interval encompassing markers that co-segregate with ASR
resistance in populations studied at a p-level .ltoreq.0.05. A
further example of a subinterval associated with ASR resistance
includes the interval flanked by SEQ ID NO: 53 and SEQ ID NO: 8,
that define a chromosome interval encompassing markers that
co-segregate with ASR resistance in the populations studied at a
p-level .ltoreq.0.05. Another example of a subinterval associated
with ASR resistance includes the interval flanked by SEQ ID NO: 96
and SEQ ID NO: 106, that define a chromosome interval encompassing
markers that co-segregate with ASR resistance in the populations
studied at a p-level .ltoreq.0.001.
[0021] Thus, one skilled in the art can use the invention to create
novel maize plants with ASR resistance by associating disease
resistance phenotypes with genotypes at previously unknown disease
resistance loci in the maize genome. Disclosed herein are
chromosome intervals that comprise alleles responsible for
phenotypic differences between ASR resistant and ASR susceptible
corn lines. The chromosome intervals of the invention are
characterized in specific embodiments by genomic regions including
and flanked by the markers IDP7601 and gpm426b, which comprise
markers within or closely linked to (within 20 cM of) ASR-6.01. The
invention also comprises other intervals whose borders fall
between, and including, those of IDP7601 and gpm426b, or any
interval closely linked to those intervals.
[0022] Examples of markers useful for this purpose comprise the SNP
markers listed in Table 16, or any marker linked thereto, including
a marker that maps within or is genetically linked to the
chromosome intervals described herein, including the termini of the
intervals. Such markers can be assayed simultaneously or
sequentially in a single sample or population of samples.
[0023] Accordingly, the compositions and methods of the present
invention can be utilized to guide MAS or breeding maize varieties
with a desired complement (set) of allelic forms of chromosome
intervals associated with superior agronomic performance
(resistance, along with any other available markers for yield,
disease resistance, etc.). Any of the disclosed marker alleles can
be introduced into a corn line via introgression, by traditional
breeding (or introduced via transformation, or both) to yield a
corn plant with superior agronomic performance. The number of
alleles associated with resistance that can be introduced or be
present in a corn plant of the present invention ranges from 1 to
the number of alleles disclosed herein, each integer of which is
incorporated herein as if explicitly recited.
[0024] MAS using additional markers flanking either side of the DNA
locus provide further efficiency because an unlikely double
recombination event would be needed to simultaneously break linkage
between the locus and both markers. Moreover, using markers tightly
flanking a locus, one skilled in the art of MAS can reduce linkage
drag by more accurately selecting individuals that have less of the
potentially deleterious donor parent DNA. Any marker linked to or
among the chromosome intervals described herein can thus find use
within the scope of this invention.
[0025] Similarly, by identifying plants lacking a desired marker
locus, susceptible or less resistant plants can be identified, and
eliminated from subsequent crosses. Similarly, these marker loci
can be introgressed into any desired genomic background, germplasm,
plant, line, variety, etc., as part of an overall MAS breeding
program designed to enhance disease resistance. The invention also
provides chromosome QTL intervals that find use in MAS to select
plants that demonstrate disease resistance or improved tolerance.
The QTL intervals can also be used to counter-select plants that
are susceptible or have reduced resistance to disease.
[0026] The present invention also extends to a method of making a
progeny corn plant and the resulting progeny corn plants. The
method comprises, in an embodiment, crossing a first parent corn
plant with a second corn plant and growing the female corn plant
parent under plant growth conditions to yield corn plant progeny.
Methods of crossing and growing corn plants are well within the
ability of those of ordinary skill in the art. Such corn plant
progeny can be assayed for alleles associated with ASR resistance
as disclosed herein and, thereby, the desired progeny selected.
Such progeny plants or seed thereof can be sold commercially for
corn production, used for food, processed to obtain a desired
constituent of the corn, or further utilized in subsequent rounds
of breeding. At least one of the first or second corn plants is a
corn plant of the present invention in that it comprises at least
one of the allelic forms of the markers of the present invention,
such that the progeny are capable of inheriting the allele.
[0027] Often, a method of the present invention may be applied to
at least one related corn plant such as from progenitor or
descendant line in the subject corn plants' pedigree such that
inheritance of the desired resistance allele can be traced. The
number of generations separating the corn plants being subjected to
the methods of the present invention may be, in specific
embodiments, from 1 to 20, commonly 1 to 5, and including 1, 2, or
3 generations of separation, and often a direct descendant or
parent of the corn plant will be subject to the method (i.e., one
generation of separation).
[0028] Thus, the invention permits one skilled in the art to detect
the presence or absence of disease resistance genotypes in the
genomes of corn plants as part of a MAS program. In one embodiment,
a breeder ascertains the genotype at one or more markers for a
disease resistant parent, which contains a disease resistance
allele, and the genotype at one or more markers for a susceptible
parent, which lacks the resistance allele. For example, the markers
of the present invention can be used in MAS in crosses involving
elite x exotic corn lines by subjecting the segregating progeny to
MAS to maintain disease resistance alleles, or alleles associated
with yield under disease conditions. A breeder can then reliably
track the inheritance of the resistance alleles through subsequent
populations derived from crosses between the two parents by
genotyping offspring with the markers used on the parents and
comparing the genotypes at those markers with those of the parents.
Depending on how tightly linked the marker alleles are with the
trait, progeny that share genotypes with the disease resistant
parent can be reliably predicted to express the resistant phenotype
and progeny that share genotypes with the disease susceptible
parent can be reliably predicted to express the susceptible
phenotype. Thus, the laborious, inefficient, and potentially
inaccurate process of manually phenotyping the progeny for disease
resistance is avoided.
[0029] By providing the positions in the maize genome of the
intervals and the disease resistance associated markers within,
this invention also allows one skilled in the art to identify and
use other markers within the intervals disclosed herein or linked
to the chromosome intervals disclosed herein. Having identified
such regions, these markers can be readily identified from public
linkage maps.
[0030] Closely linked markers flanking the locus of interest that
have alleles in linkage disequilibrium with a resistance allele at
that locus may be effectively used to select for progeny plants
with enhanced resistance to disease conditions. Thus, the markers
described herein, such as those listed in Table 16, as well as
other markers genetically linked to the same chromosome interval,
may be used to select for maize plants with enhanced resistance to
ASR. Often, a set of these markers will be used, (e.g., 2 or more,
3 or more, 4 or more, 5 or more) in the flanking regions of the
gene. Optionally, as described above, a marker flanking on either
side or within the actual gene and/or locus may also be used. The
parents and their progeny may be screened for these sets of
markers, and the markers that are polymorphic between the two
parents used for selection. In an introgression program, this
allows for selection of the gene or locus genotype at the more
proximal polymorphic markers and selection for the recurrent parent
genotype at the more distal polymorphic markers.
[0031] The choice of markers actually used to practice the
invention is not limited and can be any marker that is genetically
linked to the intervals described herein, which includes markers
mapping within the intervals. One example includes any marker
selected from SEQ ID NOs: 1-10, 51-56, 81-83, 96-106, or the
markers listed in Table 17. Furthermore, since there are many
different types of marker detection assays known in the art, it is
not intended that the type of marker detection assay used to
practice this invention be limited in any way.
Molecular Markers
[0032] "Marker," "genetic marker," "molecular marker," "marker
nucleic acid," and "marker locus" refer to a nucleotide sequence or
encoded product thereof (e.g., a protein) used as a point of
reference when identifying a linked locus. A marker can be derived
from genomic nucleotide sequence or from expressed nucleotide
sequences (e.g., from a spliced RNA, a cDNA, etc.), or from an
encoded polypeptide, and can be represented by one or more
particular variant sequences, or by a consensus sequence. In
another sense, a marker is an isolated variant or consensus of such
a sequence. The term also refers to nucleic acid sequences
complementary to or flanking the marker sequences, such as nucleic
acids used as probes or primer pairs capable of amplifying the
marker sequence. A "marker probe" is a nucleic acid sequence or
molecule that can be used to identify the presence of a marker
locus, e.g., a nucleic acid probe that is complementary to a marker
locus sequence. Alternatively, in some aspects, a marker probe
refers to a probe of any type that is able to distinguish (i.e.,
genotype) the particular allele that is present at a marker locus.
A "marker locus" is a locus that can be used to track the presence
of a second linked locus, e.g., a linked locus that encodes or
contributes to expression of a phenotypic trait. For example, a
marker locus can be used to monitor segregation of alleles at a
locus, such as a QTL, that are genetically or physically linked to
the marker locus. Thus, a "marker allele," alternatively an "allele
of a marker locus" is one of a plurality of polymorphic nucleotide
sequences found at a marker locus in a population that is
polymorphic for the marker locus.
[0033] "Marker" also refers to nucleic acid sequences complementary
to the genomic sequences, such as nucleic acids used as probes.
Markers corresponding to genetic polymorphisms between members of a
population can be detected by methods well-established in the art.
These include, e.g., PCR-based sequence specific amplification
methods, detection of restriction fragment length polymorphisms
(RFLP), detection of isozyme markers, detection of polynucleotide
polymorphisms by allele specific hybridization (ASH), detection of
amplified variable sequences of the plant genome, detection of
self-sustained sequence replication, detection of simple sequence
repeats (SSRs), detection of single nucleotide polymorphisms
(SNPs), or detection of amplified fragment length polymorphisms
(AFLPs). Well established methods are also know for the detection
of expressed sequence tags (ESTs) and SSR markers derived from EST
sequences and randomly amplified polymorphic DNA (RAPD).
[0034] A favorable allele of a marker is the allele of the marker
that co-segregates with a desired phenotype (e.g., disease
resistance). As used herein, a QTL marker has a minimum of one
favorable allele, although it is possible that the marker might
have two or more favorable alleles found in the population. Any
favorable allele of that marker can be used advantageously for the
identification and construction of disease resistant plant lines.
Optionally, one, two, three or more favorable allele(s) of
different markers are identified in, or introgressed into a plant,
and can be selected for or against during MAS. Desirably, plants or
germplasm are identified that have at least one such favorable
allele that positively correlates with disease resistance or
improved disease resistance. Alternatively, a marker allele that
co-segregates with disease susceptibility also finds use with the
invention, since that allele can be used to identify and counter
select disease susceptible plants. Such an allele can be used for
exclusionary purposes during breeding to identify alleles that
negatively correlate with resistance, to eliminate susceptible
plants or germplasm from subsequent rounds of breeding.
[0035] The more tightly linked a marker is with a DNA locus
influencing a phenotype, the more reliable the marker is in MAS, as
the likelihood of a recombination event unlinking the marker and
the locus decreases. Markers containing the causal mutation for a
trait, or that are within the coding sequence of a causative gene,
are ideal as no recombination is expected between them and the
sequence of DNA responsible for the phenotype.
[0036] Genetic markers are distinguishable from each other (as well
as from the plurality of alleles of any one particular marker) on
the basis of polynucleotide length and/or sequence. A large number
of corn molecular markers are known in the art, and are published
or available from various sources, such as the MaizeGDB internet
resource. In general, any differentially inherited polymorphic
trait (including a nucleic acid polymorphism) that segregates among
progeny is a potential genetic marker.
[0037] In some embodiments of the invention, one or more marker
alleles are selected for in a single plant or a population of
plants. In these methods, plants are selected that contain
favorable alleles from more than one resistance marker, or
alternatively, favorable alleles from more than one resistance
marker are introgressed into a desired germplasm. One of skill
recognizes that the identification of favorable marker alleles is
germplasm-specific. The determination of which marker alleles
correlate with resistance (or susceptibility) is determined for the
particular germplasm under study. One of skill recognizes that
methods for identifying the favorable alleles are routine and well
known in the art, and furthermore, that the identification and use
of such favorable alleles is well within the scope of this
invention. Furthermore still, identification of favorable marker
alleles in plant populations other than the populations used or
described herein is well within the scope of this invention.
Marker Detection
[0038] In some aspects, methods of the invention utilize an
amplification step to detect/genotype a marker locus, but
amplification is not always a requirement for marker detection
(e.g. Southern blotting and RFLP detection). Separate detection
probes can also be omitted in amplification/detection methods,
e.g., by performing a real time amplification reaction that detects
product formation by modification of the relevant amplification
primer upon incorporation into a product, incorporation of labeled
nucleotides into an amplicon, or by monitoring changes in molecular
rotation properties of amplicons as compared to unamplified
precursors (e.g., by fluorescence polarization).
[0039] "Amplifying," in the context of nucleic acid amplification,
is any process whereby additional copies of a selected nucleic acid
(or a transcribed form thereof) are produced. In some embodiments,
an amplification-based marker technology is used wherein a primer
or amplification primer pair is admixed with genomic nucleic acid
isolated from the first plant or germplasm, and wherein the primer
or primer pair is complementary or partially complementary to at
least a portion of the marker locus, and is capable of initiating
DNA polymerization by a DNA polymerase using the plant genomic
nucleic acid as a template. The primer or primer pair is extended
in a DNA polymerization reaction having a DNA polymerase and a
template genomic nucleic acid to generate at least one amplicon. In
other embodiments, plant RNA is the template for the amplification
reaction. In some embodiments, the QTL marker is a SNP type marker,
and the detected allele is a SNP allele, and the method of
detection is allele specific hybridization (ASH).
[0040] In general, the majority of genetic markers rely on one or
more properties of nucleic acids for their detection. Typical
amplification methods include various polymerase based replication
methods, including the polymerase chain reaction (PCR), ligase
mediated methods such as the ligase chain reaction (LCR) and RNA
polymerase based amplification (e.g., by transcription) methods. An
"amplicon" is an amplified nucleic acid, e.g., a nucleic acid that
is produced by amplifying a template nucleic acid by any available
amplification method (e.g., PCR, LCR, transcription, or the like).
A "genomic nucleic acid" is a nucleic acid that corresponds in
sequence to a heritable nucleic acid in a cell. Common examples
include nuclear genomic DNA and amplicons thereof. A genomic
nucleic acid is, in some cases, different from a spliced RNA, or a
corresponding cDNA, in that the spliced RNA or cDNA is processed,
e.g., by the splicing machinery, to remove introns. Genomic nucleic
acids optionally comprise non-transcribed (e.g., chromosome
structural sequences, promoter regions, enhancer regions, etc.)
and/or non-translated sequences (e.g., introns), whereas spliced
RNA/cDNA typically do not have non-transcribed sequences or
introns. A "template nucleic acid" is a nucleic acid that serves as
a template in an amplification reaction (e.g., a polymerase based
amplification reaction such as PCR, a ligase mediated amplification
reaction such as LCR, a transcription reaction, or the like). A
template nucleic acid can be genomic in origin, or alternatively,
can be derived from expressed sequences, e.g., a cDNA or an EST.
Details regarding the use of these and other amplification methods
can be found in any of a variety of standard texts. Many available
biology texts also have extended discussions regarding PCR and
related amplification methods and one of skill will appreciate that
essentially any RNA can be converted into a double stranded DNA
suitable for restriction digestion, PCR expansion and sequencing
using reverse transcriptase and a polymerase.
[0041] PCR detection and quantification using dual-labeled
fluorogenic oligonucleotide probes, commonly referred to as
"TaqMan.TM." probes, can also be performed according to the present
invention. These probes are composed of short (e.g., 20-25 base)
oligodeoxynucleotides that are labeled with two different
fluorescent dyes. On the 5' terminus of each probe is a reporter
dye, and on the 3' terminus of each probe a quenching dye is found.
The oligonucleotide probe sequence is complementary to an internal
target sequence present in a PCR amplicon. When the probe is
intact, energy transfer occurs between the two fluorophores and
emission from the reporter is quenched by the quencher by FRET.
During the extension phase of PCR, the probe is cleaved by 5'
nuclease activity of the polymerase used in the reaction, thereby
releasing the reporter from the oligonucleotide-quencher and
producing an increase in reporter emission intensity. TaqMan.TM.
probes are oligonucleotides that have a label and a quencher, where
the label is released during amplification by the exonuclease
action of the polymerase used in amplification, providing a real
time measure of amplification during synthesis. A variety of
TaqMan.TM. reagents are commercially available, e.g., from Applied
Biosystems as well as from a variety of specialty vendors such as
Biosearch Technologies.
[0042] In one embodiment, the presence or absence of a molecular
marker is determined simply through nucleotide sequencing of the
polymorphic marker region. This method is readily adapted to high
throughput analysis as are the other methods noted above, e.g.,
using available high throughput sequencing methods such as
sequencing by hybridization.
[0043] In alternative embodiments, in silico methods can be used to
detect the marker loci of interest. For example, the sequence of a
nucleic acid comprising the marker locus of interest can be stored
in a computer. The desired marker locus sequence or its homolog can
be identified using an appropriate nucleic acid search algorithm as
provided by, for example, in such readily available programs as
BLAST, or even simple word processors.
[0044] While the exemplary markers provided in the figures and
tables herein are either SNP markers, any of the aforementioned
marker types can be employed in the context of the invention to
identify chromosome intervals encompassing genetic element that
contribute to superior agronomic performance (e.g., disease
resistance or improved disease tolerance).
Probes and Primers
[0045] In general, synthetic methods for making oligonucleotides,
including probes, primers, molecular beacons, PNAs, LNAs (locked
nucleic acids), etc., are well known. For example, oligonucleotides
can be synthesized chemically according to the solid phase
phosphoramidite triester method described. Oligonucleotides,
including modified oligonucleotides, can also be ordered from a
variety of commercial sources.
[0046] Nucleic acid probes to the marker loci can be cloned and/or
synthesized. Any suitable label can be used with a probe of the
invention. Detectable labels suitable for use with nucleic acid
probes include, for example, any composition detectable by
spectroscopic, radioisotopic, photochemical, biochemical,
immunochemical, electrical, optical or chemical means. Useful
labels include biotin for staining with labeled streptavidin
conjugate, magnetic beads, fluorescent dyes, radio labels, enzymes,
and colorimetric labels. Other labels include ligands which bind to
antibodies labeled with fluorophores, chemiluminescent agents, and
enzymes. A probe can also constitute radio labeled PCR primers that
are used to generate a radio labeled amplicon. It is not intended
that the nucleic acid probes of the invention be limited to any
particular size.
[0047] In some embodiments, the molecular markers of the invention
are detected using a suitable PCR-based detection method, where the
size or sequence of the PCR amplicon is indicative of the absence
or presence of the marker (e.g., a particular marker allele). In
these types of methods, PCR primers are hybridized to the conserved
regions flanking the polymorphic marker region. As used in the art,
PCR primers used to amplify a molecular marker are sometimes termed
"PCR markers" or simply "markers." It will be appreciated that,
although many specific examples of primers are provided herein,
suitable primers to be used with the invention can be designed
using any suitable method. It is not intended that the invention be
limited to any particular primer or primer pair. In some
embodiments, the primers of the invention are radiolabelled, or
labeled by any suitable means (e.g., using a non-radioactive
fluorescent tag), to allow for rapid visualization of the different
size amplicons following an amplification reaction without any
additional labeling step or visualization step. In some
embodiments, the primers are not labeled, and the amplicons are
visualized following their size resolution, e.g., following agarose
gel electrophoresis. In some embodiments, ethidium bromide staining
of the PCR amplicons following size resolution allows visualization
of the different size amplicons. It is not intended that the
primers of the invention be limited to generating an amplicon of
any particular size. For example, the primers used to amplify the
marker loci and alleles herein are not limited to amplifying the
entire region of the relevant locus. The primers can generate an
amplicon of any suitable length that is longer or shorter than
those disclosed herein. In some embodiments, marker amplification
produces an amplicon at least 20 nucleotides in length, or
alternatively, at least 50 nucleotides in length, or alternatively,
at least 100 nucleotides in length, or alternatively, at least 200
nucleotides in length. Marker alleles in addition to those recited
herein also find use with the present invention.
Linkage Analysis
[0048] "Linkage", or "genetic linkage," is used to describe the
degree with which one marker locus is associated with another
marker locus or some other locus (for example, a resistance locus).
A marker locus may be located within a locus to which it is
genetically linked. For example, if locus A has genes "A" or "a"
and locus B has genes "B" or "b" and a cross between parent 1 with
AABB and parent 2 with aabb will produce four possible gametes
where the genes are segregated into AB, Ab, aB and ab. The null
expectation is that there will be independent equal segregation
into each of the four possible genotypes, i.e. with no linkage 1/4
of the gametes will of each genotype. Segregation of gametes into a
genotypes differing from 1/4 is attributed to linkage. As used
herein, linkage can be between two markers, or alternatively
between a marker and a phenotype. A marker locus may be genetically
linked to a trait, and in some cases a marker locus genetically
linked to a trait is located within the allele conferring the
trait. A marker may also be causative for a trait or phenotype, for
example a causative polymorphism. In a further example, a marker
locus can be associated with resistance or improved tolerance to a
plant pathogen when the marker locus is in linkage disequilibrium
with the resistance trait. The degree of linkage of a molecular
marker to a phenotypic trait (e.g., a QTL) is measured, e.g., as a
statistical probability of co-segregation of that molecular marker
with the phenotype.
[0049] As used herein, "closely linked" means that the marker or
locus is within about 20 cM, for instance within about 10 cM, about
5 cM, about 1 cM, about 0.5 cM, or less than 0.5 cM of the
identified locus associated with ASR resistance.
[0050] As used herein, the linkage relationship between a molecular
marker and a phenotype is given is the statistical likelihood that
the particular combination of a phenotype and the presence or
absence of a particular marker allele is random. Thus, the lower
the probability score, the greater the likelihood that a phenotype
and a particular marker will cosegregate. In some embodiments, a
probability score of 0.05 (p=0.05, or a 5% probability) of random
assortment is considered a significant indication of
co-segregation. However, the present invention is not limited to
this particular standard, and an acceptable probability can be any
probability of less than 50% (p<0.5). For example, a significant
probability can be less than 0.25, less than 0.20, less than 0.15,
or less than 0.1. The phrase "closely linked," in the present
application, means that recombination between two linked loci
occurs with a frequency of equal to or less than about 10% (i.e.,
are separated on a genetic map by not more than 10 cM). In one
aspect, any marker of the invention is linked (genetically and
physically) to any other marker that is at or less than 50 cM
distant. In another aspect, any marker of the invention is closely
linked (genetically and physically) to any other marker that is in
close proximity, e.g., at or less than 10 cM distant. Two closely
linked markers on the same chromosome can be positioned 9, 8, 7, 6,
5, 4, 3, 2, 1, 0.75, 0.5 or 0.25 cM or less from each other.
[0051] Classical linkage analysis can be thought of as a
statistical description of the relative frequencies of
cosegregation of different traits. Linkage analysis is the well
characterized descriptive framework of how traits are grouped
together based upon the frequency with which they segregate
together. That is, if two non-allelic traits are inherited together
with a greater than random frequency, they are said to be "linked."
The frequency with which the traits are inherited together is the
primary measure of how tightly the traits are linked, i.e., traits
which are inherited together with a higher frequency are more
closely linked than traits which are inherited together with lower
(but still above random) frequency. The further apart on a
chromosome the genes reside, the less likely they are to segregate
together, because homologous chromosomes recombine during meiosis.
Thus, the further apart on a chromosome the genes reside, the more
likely it is that there will be a crossing over event during
meiosis that will result in the marker and the DNA sequence
responsible for the trait the marker is designed to track
segregating separately into progeny. A common measure of linkage is
the frequency with which traits cosegregate.
[0052] Linkage analysis is used to determine which polymorphic
marker allele demonstrates a statistical likelihood of
co-segregation with the resistance phenotype (thus, a "resistance
marker allele"). Following identification of a marker allele for
co-segregation with the resistance phenotype, it is possible to use
this marker for rapid, accurate screening of plant lines for the
resistance allele without the need to grow the plants through their
life cycle and await phenotypic evaluations, and furthermore,
permits genetic selection for the particular resistance allele even
when the molecular identity of the actual resistance QTL is
unknown. Tissue samples can be taken, for example, from the
endosperm, embryo, or mature/developing plant and screened with the
appropriate molecular marker to rapidly determine determined which
progeny contain the desired genetics. Linked markers also remove
the impact of environmental factors that can often influence
phenotypic expression.
[0053] Because chromosomal distance is approximately proportional
to the frequency of crossing over events between traits, there is
an approximate physical distance that correlates with recombination
frequency. Marker loci are themselves traits and can be assessed
according to standard linkage analysis by tracking the marker loci
during segregation. Thus, in the context of the present invention,
one cM is equal to a 1% chance that a marker locus will be
separated from another locus (which can be any other trait, e.g.,
another marker locus, or another trait locus that encodes a QTL),
due to crossing over in a single generation.
[0054] When referring to the relationship between two genetic
elements, such as a genetic element contributing to resistance and
a proximal marker, "coupling" phase linkage indicates the state
where the "favorable" allele at the resistance locus is physically
associated on the same chromosome strand as the "favorable" allele
of the respective linked marker locus. In coupling phase, both
favorable alleles are inherited together by progeny that inherit
that chromosome strand. In "repulsion" phase linkage, the
"favorable" allele at the locus of interest (e.g., a QTL for
resistance) is physically linked with an "unfavorable" allele at
the proximal marker locus, and the two "favorable" alleles are not
inherited together (i.e., the two loci are "out of phase" with each
other).
Genetic Mapping
[0055] A "genetic map" is the relationship of genetic linkage among
loci on one or more chromosomes (or linkage groups) within a given
species, generally depicted in a diagrammatic or tabular form.
"Genetic mapping" is the process of defining the linkage
relationships of loci through the use of genetic markers,
populations segregating for the markers, and standard genetic
principles of recombination frequency. A "genetic map location" is
a location on a genetic map relative to surrounding genetic markers
on the same linkage group where a specified marker can be found
within a given species. In contrast, a physical map of the genome
refers to absolute distances (for example, measured in base pairs
or isolated and overlapping contiguous genetic fragments, e.g.,
contigs). A physical map of the genome does not take into account
the genetic behavior (e.g., recombination frequencies) between
different points on the physical map. A "genetic recombination
frequency" is the frequency of a crossing over event
(recombination) between two genetic loci. Recombination frequency
can be observed by following the segregation of markers and/or
traits following meiosis. In some cases, two different markers can
have the same genetic map coordinates. In that case, the two
markers are in such close proximity to each other that
recombination occurs between them with such low frequency that it
is undetected.
[0056] Genetic maps are graphical representations of genomes (or a
portion of a genome such as a single chromosome) where the
distances between markers are measured by the recombination
frequencies between them. Plant breeders use genetic maps of
molecular markers to increase breeding efficiency through MAS, a
process where selection for a trait of interest is not based on the
trait itself but rather on the genotype of a marker linked to the
trait. A molecular marker that demonstrates reliable linkage with a
phenotypic trait provides a useful tool for indirectly selecting
the trait in a plant population, especially when accurate
phenotyping is difficult, slow, or expensive.
[0057] In general, the closer two markers or genomic loci are on
the genetic map, the closer they lie to one another on the physical
map. A lack of precise proportionality between cM distances and
physical distances can exist due to the fact that the likelihood of
genetic recombination is not uniform throughout the genome; some
chromosome regions are cross-over "hot spots," while other regions
demonstrate only rare recombination events, if any.
[0058] Genetic mapping variability can also be observed between
different populations of the same crop species. In spite of this
variability in the genetic map that may occur between populations,
genetic map and marker information derived from one population
generally remains useful across multiple populations in
identification of plants with desired traits, counter-selection of
plants with undesirable traits and in guiding MAS.
[0059] As one of skill in the art will recognize, recombination
frequencies (and as a result, genetic map positions) in any
particular population are not static. The genetic distances
separating two markers (or a marker and a QTL) can vary depending
on how the map positions are determined. For example, variables
such as the parental mapping populations used, the software used in
the marker mapping or QTL mapping, and the parameters input by the
user of the mapping software can contribute to the QTL marker
genetic map relationships. However, it is not intended that the
invention be limited to any particular mapping populations, use of
any particular software, or any particular set of software
parameters to determine linkage of a particular marker or
chromosome interval with the disease resistance phenotype. It is
well within the ability of one of ordinary skill in the art to
extrapolate the novel features described herein to any gene pool or
population of interest, and using any particular software and
software parameters. Indeed, observations regarding genetic markers
and chromosome intervals in populations in addition to those
described herein are readily made using the teaching of the present
disclosure.
Association Mapping
[0060] Association or LD mapping techniques aim to identify
genotype-phenotype associations that are significant. It is
effective for fine mapping in outcrossing species where frequent
recombination among heterozygotes can result in rapid LD decay. LD
is non-random association of alleles in a collection of
individuals, reflecting the recombinational history of that region.
Thus, LD decay averages can help determine the number of markers
necessary for a genome-wide association study to generate a genetic
map with a desired level of resolution.
[0061] Large populations are better for detecting recombination,
while older populations are generally associated with higher levels
of polymorphism, both of which contribute to accelerated LD decay.
However, smaller effective population sizes tend to show slower LD
decay, which can result in more extensive haplotype conservation.
Understanding of the relationships between polymorphism and
recombination is useful in developing strategies for efficiently
extracting information from these resources. Association analyses
compare the plants' phenotypic score with the genotypes at the
various loci. Subsequently, any suitable maize genetic map (for
example, a composite map) can be used to help observe distribution
of the identified QTL markers and/or QTL marker clustering using
previously determined map locations of the markers.
Marker Assisted Selection
[0062] "Introgression" refers to the transmission of a desired
allele of a genetic locus from one genetic background to another.
For example, introgression of a desired allele at a specified locus
can be transmitted to at least one progeny via a sexual cross
between two parents of the same species, where at least one of the
parents has the desired allele in its genome. Alternatively, for
example, transmission of an allele can occur by recombination
between two donor genomes, e.g., in a fused protoplast, where at
least one of the donor protoplasts has the desired allele in its
genome. The desired allele can be, e.g., a selected allele of a
marker, a QTL, a transgene, or the like. In any case, offspring
comprising the desired allele can be repeatedly backcrossed to a
line having a desired genetic background and selected for the
desired allele, to result in the allele becoming fixed in a
selected genetic background.
[0063] A primary motivation for development of molecular markers in
crop species is the potential for increased efficiency in plant
breeding through MAS. Genetic markers are used to identify plants
that contain a desired genotype at one or more loci, and that are
expected to transfer the desired genotype, along with a desired
phenotype to their progeny. Genetic markers can be used to identify
plants containing a desired genotype at one locus, or at several
unlinked or linked loci (e.g., a haplotype), and that would be
expected to transfer the desired genotype, along with a desired
phenotype to their progeny. The present invention provides the
means to identify plants that are resistant, exhibit improved
resistance or are susceptible to ASR infection by identifying
plants having a specified allele that is linked to ASR-6.01.
[0064] In general, MAS uses polymorphic markers that have been
identified as having a significant likelihood of co-segregation
with a resistance trait. Such markers are presumed to map near a
gene or genes that give the plant its resistance phenotype, and are
considered indicators for the desired trait, and are termed QTL
markers. Plants are tested for the presence or absence of a desired
allele in the QTL marker.
[0065] Identification of plants or germplasm that include a marker
locus or marker loci linked to a resistance trait or traits
provides a basis for performing MAS. Plants that comprise favorable
markers or favorable alleles are selected for, while plants that
comprise markers or alleles that are negatively correlated with
resistance can be selected against. Desired markers and/or alleles
can be introgressed into plants having a desired (e.g., elite or
exotic) genetic background to produce an introgressed resistant
plant or germplasm. In some aspects, it is contemplated that a
plurality of resistance markers are sequentially or simultaneous
selected and/or introgressed. The combinations of resistance
markers that are selected for in a single plant is not limited, and
can include any combination of markers disclosed herein or any
marker linked to the markers disclosed herein, or any markers
located within the QTL intervals defined herein.
[0066] In some embodiments, a disease resistant first corn plant or
germplasm (the donor) can be crossed with a second corn plant or
germplasm (the recipient, e.g., an elite or exotic corn, depending
on characteristics that are desired in the progeny) to create an
introgressed corn plant or germplasm as part of a breeding program
designed to improve disease resistance of the recipient corn plant
or germplasm. In some aspects, the recipient plant can also contain
one or more disease resistant loci, which can be qualitative or
quantitative trait loci. In another aspect, the recipient plant can
contain a transgene.
[0067] In some embodiments, the recipient corn plant or germplasm
will typically display reduced resistance to disease conditions as
compared to the first corn plant or germplasm, while the
introgressed corn plant or germplasm will display an increased
resistance to disease conditions as compared to the second plant or
germplasm. An introgressed corn plant or germplasm produced by
these methods are also a feature of this invention.
[0068] MAS is a powerful shortcut to selecting for desired
phenotypes and for introgressing desired traits into cultivars
(e.g., introgressing desired traits into elite lines). MAS is
easily adapted to high throughput molecular analysis methods that
can quickly screen large numbers of plant or germplasm genetic
material for the markers of interest and is much more cost
effective than raising and observing plants for visible traits.
[0069] When a population is segregating for multiple loci affecting
one or multiple traits, e.g., multiple loci involved in resistance,
or multiple loci each involved in resistance or tolerance to
different diseases, the efficiency of MAS compared to phenotypic
screening becomes even greater, because all of the loci can be
evaluated in the lab together from a single sample of DNA.
Introgression of ASR Resistance Loci Using MAS
[0070] The introgression of one or more desired loci from a donor
line into another is achieved via repeated backcrossing to a
recurrent parent accompanied by selection to retain one or more ASR
resistance loci from the donor parent. Markers associated with ASR
resistance are assayed in progeny and those progeny with one or
more ASR resistance markers are selected for advancement. In
another aspect, one or more markers can be assayed in the progeny
to select for plants with the genotype of the agronomically elite
parent. This invention anticipates that trait introgression
activities will require more than one generation, wherein progeny
are crossed to the recurrent (agronomically elite) parent or
selfed. Selections are made based on the presence of one or more
ASR resistance markers and can also be made based on the recurrent
parent genotype, wherein screening is performed on a genetic marker
and/or phenotype basis. In another embodiment, markers of this
invention can be used in conjunction with other markers, ideally at
least one on each chromosome of the corn genome, to track the
introgression of ASR resistance loci into elite germplasm. In
another embodiment, QTLs associated with ASR resistance will be
useful in conjunction with SNP molecular markers of the present
invention to combine quantitative and qualitative ASR resistance in
the same plant. It is within the scope of this invention to utilize
the methods and compositions for trait integration of ASR
resistance. It is contemplated by the inventors that the present
invention will be useful for developing commercial varieties with
ASR resistance and an agronomically elite phenotype.
[0071] In an aspect, this invention could be used on any plant. In
another aspect, the plant is selected from the genus Zea. In
another aspect, the plant is selected from the species Zea mays. In
a further aspect, the plant is selected from the subspecies Zea
mays L. ssp. mays. In an additional aspect, the plant is selected
from the group Zea mays L. subsp. mays Indentata, otherwise known
as dent corn. In another aspect, the plant is selected from the
group Zea mays L. subsp. mays Indurata, otherwise known as flint
corn. In an aspect, the plant is selected from the group Zea mays
L. subsp. mays Saccharata, otherwise known as sweet corn. In
another aspect, the plant is selected from the group Zea mays L.
subsp. mays Amylacea, otherwise known as flour corn. In a further
aspect, the plant is selected from the group Zea mays L. subsp.
mays Everta, otherwise known as pop corn. Zea plants include
hybrids, inbreds, partial inbreds, or members of defined or
undefined populations.
[0072] In another aspect, a corn plant of the invention can show a
comparative resistance compared to a non-resistant control corn
plant. In this aspect, a control corn plant will preferably be
genetically similar except for the disease resistance allele or
alleles in question. Such plants can be grown under similar
conditions with equivalent or near equivalent exposure to the
pathogen.
Transgenic Plants
Transformation Constructs
[0073] Vectors used for plant transformation may include, for
example, plasmids, cosmids, YACs (yeast artificial chromosomes),
BACs (bacterial artificial chromosomes) or any other suitable
cloning system, as well as fragments of DNA therefrom. Thus when
the term "vector" or "expression vector" is used, all of the
foregoing types of vectors, as well as nucleic acid sequences
isolated therefrom, are included. It is contemplated that
utilization of cloning systems with large insert capacities will
allow introduction of large DNA sequences comprising more than one
selected gene. In accordance with the present disclosure, this
could be used to introduce genes corresponding to, e.g., an entire
biosynthetic pathway, into a plant.
[0074] Particularly useful for transformation are expression
cassettes which have been isolated from such vectors. DNA segments
used for transforming plant cells will generally comprise the cDNA,
gene, or genes which one desires to introduce into and have
expressed in the host cells. These DNA segments can further include
structures such as promoters, enhancers, polylinkers, or regulatory
genes as desired. The DNA segment or gene chosen for cellular
introduction will often encode a protein which will be expressed in
the resultant recombinant cells resulting in a screenable or
selectable trait and/or which will impart an improved phenotype to
the resulting transgenic plant.
[0075] Regulatory elements such as promoters, leaders, enhancers,
introns, and transcription termination regions (or 3' UTRs) can
play an integral part in the overall expression of genes in living
cells. The term "regulatory element," as used herein, refers to a
DNA molecule having gene-regulatory activity. The term
"gene-regulatory activity," as used herein, refers to the ability
to affect the expression of an operably linked transcribable DNA
molecule, for instance by affecting the transcription and/or
translation of the operably linked transcribable DNA molecule.
Regulatory elements, such as promoters, leaders, enhancers, and
introns that function in plants are therefore useful for modifying
plant phenotypes through genetic engineering.
[0076] As used herein, the term "intron" refers to a DNA molecule
that may be isolated or identified from the genomic copy of a gene
and may be defined generally as a region spliced out during
messenger RNA (mRNA) processing prior to translation. Alternately,
an intron may be a synthetically produced or manipulated DNA
element. An intron may contain enhancer elements that effect the
transcription of operably linked genes. An intron may be used as a
regulatory element for modulating expression of an operably linked
transcribable DNA molecule. A construct may comprise an intron, and
the intron may or may not be heterologous with respect to the
transcribable DNA molecule. Examples of introns in the art include
the rice actin intron and the corn HSP70 intron. In plants, the
inclusion of some introns in constructs leads to increased mRNA and
protein accumulation relative to constructs lacking the intron.
This effect has been termed "intron mediated enhancement" (IME) of
gene expression. Introns known to stimulate expression in plants
have been identified in maize genes (e.g., tubA1, Adh1, Sh1, and
Ubi1), in rice genes (e.g., tpi) and in dicotyledonous plant genes
like those from Petunia (e.g., rbcS), potato (e.g., st-ls1) and
from Arabidopsis thaliana (e.g., ubq3 and pat1). It has been shown
that deletions or mutations within the splice sites of an intron
reduce gene expression, indicating that splicing might be needed
for IME. However, that splicing per se is not required, as IME in
dicotyledonous plants has been shown by point mutations within the
splice sites of the pat1 gene from A. thaliana. Multiple uses of
the same intron in one plant have been shown to exhibit
disadvantages. In those cases, it is necessary to have a collection
of basic control elements for the construction of appropriate
recombinant DNA elements.
[0077] As used herein, the term "enhancer" or "enhancer element"
refers to a cis-acting regulatory element, a.k.a. cis-element,
which confers an aspect of the overall expression pattern, but is
usually insufficient alone to drive transcription, of an operably
linked DNA sequence. Unlike promoters, enhancer elements do not
usually include a transcription start site (TSS) or TATA box or
equivalent DNA sequence. A promoter or promoter fragment may
naturally comprise one or more enhancer elements that affect the
transcription of an operably linked DNA sequence. An enhancer
element may also be fused to a promoter to produce a chimeric
promoter cis-element, which confers an aspect of the overall
modulation of gene expression.
[0078] Regulatory elements may be characterized by their gene
expression pattern, e.g., positive and/or negative effects, such as
constitutive expression or temporal, spatial, developmental,
tissue, environmental, physiological, pathological, cell cycle,
and/or chemically responsive expression, and any combination
thereof, as well as by quantitative or qualitative indications. As
used herein, a "gene expression pattern" is any pattern of
transcription of an operably linked DNA molecule into a transcribed
RNA molecule. The transcribed RNA molecule may be translated to
produce a protein molecule or may provide an antisense or other
regulatory RNA molecule, such as a double-stranded RNA (dsRNA), a
transfer RNA (tRNA), a ribosomal RNA (rRNA), a microRNA (miRNA),
and the like.
[0079] As used herein, the term "protein expression" is any pattern
of translation of a transcribed RNA molecule into a protein
molecule. Protein expression may be characterized by its temporal,
spatial, developmental, or morphological qualities, as well as by
quantitative or qualitative indications.
[0080] A promoter is useful as a regulatory element for modulating
the expression of an operably linked transcribable DNA molecule. As
used herein, the term "promoter" refers generally to a DNA molecule
that is involved in recognition and binding of RNA polymerase II
and other proteins, such as trans-acting transcription factors, to
initiate transcription. A promoter may originate from the 5'
untranslated region (5' UTR) of a gene. Alternately, promoters may
be synthetically produced or manipulated DNA molecules. Promoters
may also be chimeric. As used herein, the term "chimeric" refers to
a single DNA molecule produced by fusing a first DNA molecule to a
second DNA molecule, where neither the first nor the second DNA
molecule would normally be contained in that configuration, i.e.,
fused to the other. The chimeric DNA molecule is thus a new DNA
molecule not otherwise normally contained in nature. As used
herein, the term "chimeric promoter" refers to a promoter produced
through such manipulation of DNA molecules. A chimeric promoter may
combine two or more DNA fragments, for example, the fusion of a
promoter to an enhancer element. Thus, the design, construction,
and use of chimeric promoters according to the methods disclosed
herein for modulating the expression of operably linked
transcribable DNA molecules are encompassed by the disclosure.
[0081] In specific embodiments, chimeric DNA molecules and any
variants or derivatives thereof as described herein, are further
defined as comprising promoter activity, i.e., are capable of
acting as a promoter in a host cell, such as in a transgenic plant.
In still further specific embodiments, a fragment may be defined as
exhibiting promoter activity possessed by the starting promoter
molecule from which it is derived, or a fragment may comprise a
"minimal promoter" which provides a basal level of transcription
and is comprised of a TATA box or equivalent DNA sequence for
recognition and binding of the RNA polymerase II complex for
initiation of transcription.
[0082] Exemplary promoters for expression of a nucleic acid
sequence include plant promoters such as the CaMV 35S promoter, or
others such as CaMV 19S, nos, Adh, sucrose synthase,
.alpha.-tubulin, actin, cab, PEPCase or those promoters associated
with the R gene complex. Tissue-specific promoters such as leaf
specific promoters, or tissue selective promoters (e.g., promoters
that direct greater expression in leaf primordia than in other
tissues), and tissue-specific enhancers are also contemplated to be
useful, as are inducible promoters such as ABA- and
turgor-inducible promoters. Any suitable promoters known in the art
may be used to express defensin or defensin-like coding sequences
in a plant. In an embodiment, the CaMV35S promoter may be used to
express defensin or defensin-like coding sequences in a plant. In
yet another embodiment, a disease or pathogen inducible promoter
can be used to express defensin or defensin like proteins. Examples
of disease or pathogen inducible promoters can be found in Kooshki
et al. Plant Science 165 (2003) 213-219, Koschmann et al. Plant
Physiology 160 (2012) 178-191, Rushton et al. The Plant Cell, 14
(2002) 749-762, and Kirsch et al. The Plant Journal (2001) 26
217-227.
[0083] The DNA sequence between the transcription initiation site
and the start of the coding sequence, i.e., the untranslated leader
sequence, can also influence gene expression. As used herein, the
term "leader" refers to a DNA molecule from the untranslated 5'
region (5' UTR) of a gene and defined generally as a DNA segment
between the transcription start site (TSS) and the protein coding
sequence start site. Alternately, leaders may be synthetically
produced or manipulated DNA elements. A leader can be used as a 5'
regulatory element for modulating expression of an operably linked
transcribable DNA molecule. Leader molecules may be used with a
heterologous promoter or with their native promoter. One may thus
wish to employ a particular leader sequence with a transformation
construct of the present disclosure. In an embodiment, leader
sequences are contemplated to include those which comprise
sequences predicted to direct optimum expression of the attached
gene, i.e., to include a consensus leader sequence which may
increase or maintain mRNA stability and prevent inappropriate
initiation of translation. The choice of such sequences will be
known to those of skill in the art in light of the present
disclosure. In some embodiments, sequences that are derived from
genes that are highly expressed in plants may be used for
expression of defensin or defensin-like coding sequences.
[0084] It is envisioned that defensin or defensin-like coding
sequences may be introduced under the control of novel promoters,
enhancers, etc., or homologous or tissue-specific or
tissue-selective, or pathogen or disease promoters or control
elements. Vectors for use in tissue-specific targeting of genes in
transgenic plants will typically include tissue-specific or
tissue-selective promoters and may also include other
tissue-specific or tissue-selective control elements such as
enhancer sequences. Promoters which direct specific or enhanced
expression in certain plant tissues will be known to those of skill
in the art in light of the present disclosure.
[0085] Transformation constructs prepared in accordance with the
present disclosure may further include a 3' end DNA sequence that
acts as a signal to terminate transcription and allow for the
polyadenylation of the mRNA produced by coding sequences operably
linked to a promoter. As used herein, the term "3' transcription
termination molecule," "3' untranslated region" or "3' UTR" herein
refers to a DNA molecule that is used during transcription to the
untranslated region of the 3' portion of an mRNA molecule. The 3'
untranslated region of an mRNA molecule may be generated by
specific cleavage and 3' polyadenylation, also known as a polyA
tail. A 3' UTR may be operably linked to and located downstream of
a transcribable DNA molecule and may include a polyadenylation
signal and other regulatory signals capable of affecting
transcription, mRNA processing, or gene expression. PolyA tails are
thought to function in mRNA stability and in initiation of
translation. Examples of 3' transcription termination molecules in
the art are the nopaline synthase 3' region; wheat hsp17 3' region,
pea rubisco small subunit 3' region, cotton E6 3' region, and the
coixin 3' UTR.
[0086] 3' UTRs typically find beneficial use for the recombinant
expression of specific DNA molecules. A weak 3' UTR has the
potential to generate read-through, which may affect the expression
of the DNA molecule located in the neighboring expression
cassettes. Appropriate control of transcription termination can
prevent read-through into DNA sequences (e.g., other expression
cassettes) localized downstream and can further allow efficient
recycling of RNA polymerase to improve gene expression. Efficient
termination of transcription (release of RNA Polymerase II from the
DNA) is prerequisite for re-initiation of transcription and thereby
directly affects the overall transcript level. Subsequent to
transcription termination, the mature mRNA is released from the
site of synthesis and template transported to the cytoplasm.
Eukaryotic mRNAs are accumulated as poly(A) forms in vivo, making
it difficult to detect transcriptional termination sites by
conventional methods. However, prediction of functional and
efficient 3' UTRs by bioinformatics methods is difficult in that
there are no conserved DNA sequences that would allow easy
prediction of an effective 3' UTR. In one embodiment, the native
terminator of a defensin or defensin-like coding sequence may be
used. Alternatively, a heterologous 3' end may enhance the
expression of sense or antisense defensin or defensin-like coding
sequences.
[0087] Sequences that are joined to the coding sequence of an
expressed gene, which are removed post-translationally from the
initial translation product and which facilitate the transport of
the protein into or through intracellular or extracellular
membranes, are termed transit or targeting peptide (usually into
vacuoles, vesicles, plastids and other intracellular organelles)
and signal peptide or sequences (usually to the endoplasmic
reticulum, Golgi apparatus, and outside of the cellular membrane).
By facilitating the transport of the protein into compartments
inside and outside the cell, these sequences may increase the
accumulation of gene products by protecting them from proteolytic
degradation. These sequences also allow for additional mRNA
sequences from highly expressed genes to be attached to the coding
sequence of the genes. Since mRNA being translated by ribosomes is
more stable than naked mRNA, the presence of translatable mRNA in
front of the gene may increase the overall stability of the mRNA
transcript from the gene and thereby increase synthesis of the gene
product. Since transit and signal sequences are usually
post-translationally removed from the initial translation product,
the use of these sequences allows for the addition of extra
translated sequences that may not appear on the final polypeptide.
It further is contemplated that targeting of certain proteins may
be desirable in order to enhance the stability of the protein.
[0088] Additionally, vectors may be constructed and employed in the
intracellular targeting of a specific gene product within the cells
of a transgenic plant or in directing a protein to the
extracellular environment. This generally will be achieved by
joining a DNA sequence encoding a transit or signal peptide
sequence to the coding sequence of a particular gene. The resultant
transit or signal peptide will transport the protein to a
particular intracellular or extracellular destination,
respectively, and will then be post-translationally removed.
[0089] By employing a selectable or screenable marker, one can
provide or enhance the ability to identify transformants. "Marker
genes" are genes that impart a distinct phenotype to cells
expressing the marker protein and thus allow such transformed cells
to be distinguished from cells that do not have the marker. Such
genes may encode either a selectable or screenable marker,
depending on whether the marker confers a trait which one can
"select" for by chemical means, i.e., through the use of a
selective agent (e.g., a herbicide, antibiotic, or the like), or
whether it is simply a trait that one can identify through
observation or testing, i.e., by "screening" (e.g., the green
fluorescent protein). Of course, many examples of suitable marker
proteins are known to the art and can be employed in the practice
of the present disclosure.
[0090] Selectable marker transgenes may also be used with the
present disclosure. As used herein the term "selectable marker
transgene" refers to any transcribable DNA molecule whose
expression in a transgenic plant, tissue or cell, or lack thereof,
can be screened for or scored in some way. Selectable marker genes,
and their associated selection and screening techniques, for use in
the practice of the present disclosure are known in the art and
include, but are not limited to, transcribable DNA molecules
encoding .beta.-glucuronidase (GUS), green fluorescent protein
(GFP), proteins that confer antibiotic resistance, and proteins
that confer herbicide resistance
Plant Cell Transformation Methods
[0091] Numerous methods for transforming chromosomes in a plant
cell with recombinant DNA are known in the art and are used in
methods of producing a transgenic plant cell and plant. Two
effective methods for such transformation are
Agrobacterium-mediated transformation and microprojectile
bombardment-mediated transformation. Microprojectile bombardment
methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S.
Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S.
Pat. No. 5,914,451 (soybean); U.S. Pat. No. 6,160,208 (corn); U.S.
Pat. No. 6,399,861 (corn); U.S. Pat. No. 6,153,812 (wheat) and U.S.
Pat. No. 6,365,807 (rice). Agrobacterium-mediated transformation
methods are described in U.S. Pat. No. 5,159,135 (cotton); U.S.
Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola);
U.S. Pat. No. 5,591,616 (corn); U.S. Pat. No. 5,846,797 (cotton);
U.S. Pat. No. 6,384,301 (soybean), U.S. Pat. No. 7,026,528 (wheat)
and U.S. Pat. No. 6,329,571 (rice), and US Patent Application
Publication Nos. US 2004/0087030 A1 (cotton), and US 2001/0042257
A1 (sugar beet), all of which are incorporated herein by reference
in their entirety. Transformation of plant material is practiced in
tissue culture on nutrient media, for example a mixture of
nutrients that allow cells to grow in vitro. Recipient cell targets
include, but are not limited to, meristem cells, shoot tips,
hypocotyls, calli, immature or mature embryos, and gametic cells
such as microspores, pollen, sperm and egg cells. Callus can be
initiated from tissue sources including, but not limited to,
immature or mature embryos, hypocotyls, seedling apical meristems,
microspores and the like. Cells containing a transgenic nucleus are
grown into transgenic plants.
[0092] In addition to direct transformation of a plant material
with a recombinant DNA, a transgenic plant can be prepared by
crossing a first plant comprising a recombinant DNA with a second
plant lacking the recombinant DNA. For example, recombinant DNA can
be introduced into a first plant line that is amenable to
transformation, which can be crossed with a second plant line to
introgress the recombinant DNA into the second plant line. A
transgenic plant with recombinant DNA providing an enhanced trait,
for example, enhanced yield, can be crossed with a transgenic plant
line having another recombinant DNA that confers another trait, for
example herbicide resistance or pest resistance or enhanced water
use efficiency, to produce progeny plants having recombinant DNA
that confers both traits. Typically, in such breeding for combining
traits the transgenic plant donating the additional trait is the
male line and the transgenic plant carrying the base traits is the
female line. The progeny of this cross will segregate such that
some of the plants will carry the DNA for both parental traits and
some will carry DNA for one parental trait; such plants can be
identified by markers associated with parental recombinant DNA, for
example, marker identification by analysis for recombinant DNA or,
in the case where a selectable marker is linked to the recombinant
DNA, by application using a selective agent such as a herbicide for
use with a herbicide resistance marker, or by selection for the
enhanced trait. Progeny plants carrying DNA for both parental
traits can be crossed back into the female parent line multiple
times, for example usually 6 to 8 generations, to produce a progeny
plant with substantially the same genotype as the original
transgenic parental line but for the recombinant DNA of the other
transgenic parental line.
[0093] In transformation, DNA is typically introduced into only a
small percentage of target plant cells in any one transformation
experiment. Marker genes are used to provide an efficient system
for identification of those cells that are stably transformed by
receiving and integrating a recombinant DNA molecule into their
genomes. Preferred marker genes provide selective markers which
confer resistance to a selective agent, such as an antibiotic or an
herbicide. Any of the herbicides to which plants of this disclosure
can be resistant is an agent for selective markers. Potentially
transformed cells are exposed to the selective agent. In the
population of surviving cells are those cells where, generally, the
resistance-conferring gene is integrated and expressed at
sufficient levels to permit cell survival. Cells can be tested
further to confirm stable integration of the exogenous DNA.
Commonly used selective marker genes include those conferring
resistance to antibiotics such as kanamycin and paromomycin
(nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin
(aac3 and aacC4) or resistance to herbicides such as glufosinate
(bar or pat), dicamba (DMO) and glyphosate (aroA or EPSPS).
Examples of such selectable markers are illustrated in U.S. Pat.
Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047. Markers which
provide an ability to visually screen transformants can also be
employed, for example, a gene expressing a colored or fluorescent
protein such as a luciferase or green fluorescent protein (GFP) or
a gene expressing a beta-glucuronidase or uidA gene (GUS) for which
various chromogenic substrates are known.
Transgenic Plants and Seeds
[0094] Transgenic plants derived from transgenic plant cells having
a transgenic nucleus of this disclosure are grown to generate
transgenic plants having an enhanced trait as compared to a control
plant, and produce transgenic seed and haploid pollen of this
disclosure. Such plants with enhanced traits are identified by
selection of transformed plants or progeny seed for the enhanced
trait. For efficiency a selection method is designed to evaluate
multiple transgenic plants (events) comprising the recombinant DNA,
for example multiple plants from 2 to 20 or more transgenic events.
Transgenic plants grown from transgenic seeds provided herein
demonstrate improved agronomic traits, such as resistance to
anthracnose stalk rot in maize.
Definitions
[0095] The definitions and methods provided define the present
invention and guide those of ordinary skill in the art in the
practice of the present invention. Unless otherwise noted, terms
are to be understood according to conventional usage by those of
ordinary skill in the relevant art. Examples of resources
describing many of the terms related to molecular biology used
herein can be found in in Alberts et al., Molecular Biology of The
Cell, 5.sup.th Edition, Garland Science Publishing, Inc.: New York,
2007; Rieger et al., Glossary of Genetics: Classical and Molecular,
5th edition, Springer-Verlag: New York, 1991; King et al, A
Dictionary of Genetics, 6th ed, Oxford University Press: New York,
2002; and Lewin, Genes Icorn, Oxford University Press: New York,
2007. The nomenclature for DNA bases as set forth at 37 CFR .sctn.
1.822 is used.
[0096] "Adjacent", when used to describe a nucleic acid molecule
that hybridizes to DNA containing a polymorphism, refers to a
nucleic acid that hybridizes to DNA sequences that directly abut
the polymorphic nucleotide base position. For example, a nucleic
acid molecule that can be used in a single base extension assay is
"adjacent" to the polymorphism.
[0097] "Allele" refers to an alternative nucleic acid sequence at a
particular locus; the length of an allele can be as small as 1
nucleotide base, but is typically larger. For example, a first
allele can occur on one chromosome, while a second allele occurs on
a second homologous chromosome, e.g., as occurs for different
chromosomes of a heterozygous individual, or between different
homozygous or heterozygous individuals in a population. A favorable
allele is the allele at a particular locus that confers, or
contributes to, an agronomically desirable phenotype, or
alternatively, is an allele that allows the identification of
susceptible plants that can be removed from a breeding program or
planting. A favorable allele of a marker is a marker allele that
segregates with the favorable phenotype, or alternatively,
segregates with susceptible plant phenotype, therefore providing
the benefit of identifying disease prone plants. A favorable
allelic form of a chromosome interval is a chromosome interval that
includes a nucleotide sequence that contributes to superior
agronomic performance at one or more genetic loci physically
located on the chromosome interval. "Allele frequency" refers to
the frequency (proportion or percentage) at which an allele is
present at a locus within an individual, within a line, or within a
population of lines. For example, for an allele "A," diploid
individuals of genotype "AA," "Aa," or "aa" have allele frequencies
of 1.0, 0.5, or 0.0, respectively. One can estimate the allele
frequency within a line by averaging the allele frequencies of a
sample of individuals from that line. Similarly, one can calculate
the allele frequency within a population of lines by averaging the
allele frequencies of lines that make up the population. For a
population with a finite number of individuals or lines, an allele
frequency can be expressed as a count of individuals or lines (or
any other specified grouping) containing the allele. An allele
positively correlates with a trait when it is linked to it and when
presence of the allele is an indictor that the desired trait or
trait form will occur in a plant comprising the allele. An allele
negatively correlates with a trait when it is linked to it and when
presence of the allele is an indicator that a desired trait or
trait form will not occur in a plant comprising the allele.
[0098] "Crossed" or "cross" means to produce progeny via
fertilization (e.g. cells, seeds or plants) and includes crosses
between plants (sexual) and self fertilization (selfing).
[0099] "Elite line" means any line that has resulted from breeding
and selection for superior agronomic performance. Numerous elite
lines are available and known to those of skill in the art of corn
breeding. An "elite population" is an assortment of elite
individuals or lines that can be used to represent the state of the
art in terms of agronomically superior genotypes of a given crop
species, such as corn. Similarly, an "elite germplasm" or elite
strain of germplasm is an agronomically superior germplasm.
[0100] "Exogenous nucleic acid" is a nucleic acid that is not
native to a specified system (e.g., a germplasm, plant, variety,
etc.), with respect to sequence, genomic position, or both. As used
herein, the terms "exogenous" or "heterologous" as applied to
polynucleotides or polypeptides typically refers to molecules that
have been artificially supplied to a biological system (e.g., a
plant cell, a plant gene, a particular plant species or variety or
a plant chromosome under study) and are not native to that
particular biological system. The terms can indicate that the
relevant material originated from a source other than a naturally
occurring source, or can refer to molecules having a non-natural
configuration, genetic location or arrangement of parts. In
contrast, for example, a "native" or "endogenous" gene is a gene
that does not contain nucleic acid elements encoded by sources
other than the chromosome or other genetic element on which it is
normally found in nature. An endogenous gene, transcript or
polypeptide is encoded by its natural chromosomal locus, and not
artificially supplied to the cell.
[0101] "Genetic element" or "gene" refers to a heritable sequence
of DNA, i.e., a genomic sequence, with functional significance. The
term "gene" can also be used to refer to, e.g., a cDNA and/or a
mRNA encoded by a genomic sequence, as well as to that genomic
sequence.
[0102] "Genotype" is the genetic constitution of an individual (or
group of individuals) at one or more genetic loci, as contrasted
with the observable trait (the phenotype). Genotype is defined by
the allele(s) of one or more known loci that the individual has
inherited from its parents. The term genotype can be used to refer
to an individual's genetic constitution at a single locus, at
multiple loci, or, more generally, the term genotype can be used to
refer to an individual's genetic make-up for all the genes in its
genome. A "haplotype" is the genotype of an individual at a
plurality of genetic loci. Typically, the genetic loci described by
a haplotype are physically and genetically linked, i.e., on the
same chromosome interval. The terms "phenotype," or "phenotypic
trait" or "trait" refers to one or more trait of an organism. The
phenotype can be observable to the naked eye, or by any other means
of evaluation known in the art, e.g., microscopy, biochemical
analysis, genomic analysis, an assay for a particular disease
resistance, etc. In some cases, a phenotype is directly controlled
by a single gene or genetic locus, i.e., a "single gene trait." In
other cases, a phenotype is the result of several genes.
[0103] "Germplasm" refers to genetic material of or from an
individual (e.g., a plant), a group of individuals (e.g., a plant
line, variety or family), or a clone derived from a line, variety,
species, or culture. The germplasm can be part of an organism or
cell, or can be separate from the organism or cell. In general,
germplasm provides genetic material with a specific molecular
makeup that provides a physical foundation for some or all of the
hereditary qualities of an organism or cell culture. As used
herein, germplasm includes cells, seed or tissues from which new
plants may be grown, or plant parts, such as leaves, stems, pollen,
or cells that can be cultured into a whole plant.
[0104] "Linkage disequilibrium" refers to a non-random segregation
of genetic loci or traits (or both). In either case, linkage
disequilibrium implies that the relevant loci are within sufficient
physical proximity along a length of a chromosome so that they
segregate together with greater than random (i.e., non-random)
frequency (in the case of co-segregating traits, the loci that
underlie the traits are in sufficient proximity to each other).
Linked loci co-segregate more than 50% of the time, e.g., from
about 51% to about 100% of the time. The term "physically linked"
is sometimes used to indicate that two loci, e.g., two marker loci,
are physically present on the same chromosome. Advantageously, the
two linked loci are located in close proximity such that
recombination between homologous chromosome pairs does not occur
between the two loci during meiosis with high frequency, e.g., such
that linked loci cosegregate at least about 90% of the time, e.g.,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.75%, or more
of the time.
[0105] "Locus" a chromosome region where a polymorphic nucleic
acid, trait determinant, gene or marker is located. The loci of
this invention comprise one or more polymorphisms in a population;
i.e., alternative alleles are present in some individuals. A "gene
locus" is a specific chromosome location in the genome of a species
where a specific gene can be found.
[0106] "Marker Assay" means a method for detecting a polymorphism
at a particular locus using a particular method, e.g. measurement
of at least one phenotype (such as seed color, flower color, or
other visually detectable trait), restriction fragment length
polymorphism (RFLP), single base extension, electrophoresis,
sequence alignment, allelic specific oligonucleotide hybridization
(ASO), random amplified polymorphic DNA (RAPD), microarray-based
technologies, and nucleic acid sequencing technologies, etc.
"Marker Assisted Selection" (MAS) is a process by which phenotypes
are selected based on marker genotypes.
[0107] "Molecular phenotype" is a phenotype detectable at the level
of a population of one or more molecules. Such molecules can be
nucleic acids, proteins, or metabolites. A molecular phenotype
could be an expression profile for one or more gene products, e.g.,
at a specific stage of plant development, in response to an
environmental condition or stress, etc.
[0108] "Operably linked" refers to the association of two or more
nucleic acid elements in a recombinant DNA construct, e.g. as when
a promoter is operably linked with DNA that is transcribed to RNA
whether for expressing or suppressing a protein. Recombinant DNA
constructs can be designed to express a protein which can be an
endogenous protein, an exogenous homologue of an endogenous protein
or an exogenous protein with no native homologue. Alternatively,
recombinant DNA constructs can be designed to suppress the level of
an endogenous protein, e.g. by suppression of the native gene. Such
gene suppression can be effectively employed through a native RNA
interference (RNAi) mechanism in which recombinant DNA comprises
both sense and anti-sense oriented DNA matched to the gene targeted
for suppression where the recombinant DNA is transcribed into RNA
that can form a double-strand to initiate an RNAi mechanism. Gene
suppression can also be effected by recombinant DNA that comprises
anti-sense oriented DNA matched to the gene targeted for
suppression. Gene suppression can also be effected by recombinant
DNA that comprises DNA that is transcribed to a microRNA matched to
the gene targeted for suppression.
[0109] "Percent identity" or "% identity" means the extent to which
two optimally aligned DNA or protein segments are invariant
throughout a window of alignment of components, for example
nucleotide sequence or amino acid sequence. An "identity fraction"
for aligned segments of a test sequence and a reference sequence is
the number of identical components that are shared by sequences of
the two aligned segments divided by the total number of sequence
components in the reference segment over a window of alignment
which is the smaller of the full test sequence or the full
reference sequence.
[0110] "Phenotype" means the detectable characteristics of a cell
or organism which can be influenced by genotype.
[0111] "Plant" refers to a whole plant any part thereof, or a cell
or tissue culture derived from a plant, comprising any of: whole
plants, plant components or organs (e.g., leaves, stems, roots,
etc.), plant tissues, seeds, plant cells, and/or progeny of the
same. A plant cell is a biological cell of a plant, taken from a
plant or derived through culture from a cell taken from a
plant.
[0112] "Polymorphism" means the presence of one or more variations
in a population. A polymorphism may manifest as a variation in the
nucleotide sequence of a nucleic acid or as a variation in the
amino acid sequence of a protein. Polymorphisms include the
presence of one or more variations of a nucleic acid sequence or
nucleic acid feature at one or more loci in a population of one or
more individuals. The variation may comprise but is not limited to
one or more nucleotide base changes, the insertion of one or more
nucleotides or the deletion of one or more nucleotides. A
polymorphism may arise from random processes in nucleic acid
replication, through mutagenesis, as a result of mobile genomic
elements, from copy number variation and during the process of
meiosis, such as unequal crossing over, genome duplication and
chromosome breaks and fusions. The variation can be commonly found
or may exist at low frequency within a population, the former
having greater utility in general plant breeding and the latter may
be associated with rare but important phenotypic variation. Useful
polymorphisms may include single nucleotide polymorphisms (SNPs),
insertions or deletions in DNA sequence (Indels), simple sequence
repeats of DNA sequence (SSRs), a restriction fragment length
polymorphism, and a tag SNP. A genetic marker, a gene, a
DNA-derived sequence, a RNA-derived sequence, a promoter, a 5'
untranslated region of a gene, a 3' untranslated region of a gene,
microRNA, siRNA, a resistance locus, a satellite marker, a
transgene, mRNA, ds mRNA, a transcriptional profile, and a
methylation pattern may also comprise polymorphisms. In addition,
the presence, absence, or variation in copy number of the preceding
may comprise polymorphisms.
[0113] A "population of plants" or "plant population" means a set
comprising any number, including one, of individuals, objects, or
data from which samples are taken for evaluation, e.g. estimating
QTL effects. Most commonly, the terms relate to a breeding
population of plants from which members are selected and crossed to
produce progeny in a breeding program. A population of plants can
include the progeny of a single breeding cross or a plurality of
breeding crosses, and can be either actual plants or plant derived
material, or in silico representations of the plants. The
population members need not be identical to the population members
selected for use in subsequent cycles of analyses or those
ultimately selected to obtain final progeny plants. Often, a plant
population is derived from a single biparental cross, but may also
derive from two or more crosses between the same or different
parents. Although a population of plants may comprise any number of
individuals, those of skill in the art will recognize that plant
breeders commonly use population sizes ranging from one or two
hundred individuals to several thousand, and that the highest
performing 5-20% of a population is what is commonly selected to be
used in subsequent crosses in order to improve the performance of
subsequent generations of the population.
[0114] "Resistance" or "improved resistance" in a plant to disease
conditions is an indication that the plant is more able to reduce
disease burden than a non-resistant or less resistant plant.
Resistance is a relative term, indicating that a "resistant" plant
is more able to reduce disease burden compared to a different (less
resistant) plant (e.g., a different corn line) grown in similar
disease conditions. One of skill will appreciate that plant
resistance to disease conditions varies widely, and can represent a
spectrum of more-resistant or less-resistant phenotypes. However,
by simple observation, one of skill can generally determine the
relative resistance of different plants, plant lines, or plant
families under disease conditions, and furthermore, will also
recognize the phenotypic gradations of "resistant."
[0115] "Resistance locus" means a locus that contributes
resistance, tolerance, or susceptibility to anthracnose stalk
rot.
[0116] "Resistance allele" means the nucleic acid sequence
associated with resistance or tolerance to disease.
[0117] "Tolerance locus" means a locus associated with tolerance or
resistance to disease. For instance, a tolerance locus according to
the present invention may, in one embodiment, control tolerance or
susceptibility for one or more races of Colletotrichum
graminicola.
[0118] "Tolerance allele" means the nucleic acid sequence
associated with tolerance or resistance to disease.
[0119] "Recombinant" in reference to a nucleic acid or polypeptide
indicates that the material (e.g., a recombinant nucleic acid,
gene, polynucleotide, polypeptide, etc.) has been altered by human
intervention. The term recombinant can also refer to an organism
that harbors recombinant material, e.g., a plant that comprises a
recombinant nucleic acid is considered a recombinant plant.
[0120] "Tolerance" or "improved tolerance" in a plant to disease
conditions is an indication that the plant is less affected by
disease conditions with respect to yield, survivability and/or
other relevant agronomic measures, compared to a less resistant,
more "susceptible" plant. Tolerance is a relative term, indicating
that a "tolerant" plant survives and/or produces better yields in
disease conditions compared to a different (less tolerant) plant
(e.g., a different corn line strain) grown in similar disease
conditions. One of skill will appreciate that plant tolerance to
disease conditions varies widely, and can represent a spectrum of
more-tolerant or less-tolerant phenotypes. However, by simple
observation, one of skill can generally determine the relative
tolerance or susceptibility of different plants, plant lines or
plant families under disease conditions, and furthermore, will also
recognize the phenotypic gradations of "tolerant."
[0121] "Transgenic plant" refers to a plant that comprises within
its cells a heterologous polynucleotide. Generally, the
heterologous polynucleotide is stably integrated within the genome
such that the polynucleotide is passed on to successive
generations. The heterologous polynucleotide may be integrated into
the genome alone or as part of a recombinant expression cassette.
"Transgenic" is used herein to refer to any cell, cell line,
callus, tissue, plant part or plant, the genotype of which has been
altered by the presence of heterologous nucleic acid including
those transgenic organisms or cells initially so altered, as well
as those created by crosses or asexual propagation from the initial
transgenic organism or cell. The term "transgenic" as used herein
does not encompass the alteration of the genome (chromosomal or
extrachromosomal) by conventional plant breeding methods (e.g.,
crosses) or by naturally occurring events such as random
cross-fertilization, non-recombinant viral infection,
non-recombinant bacterial transformation, non-recombinant
transposition, or spontaneous mutation.
[0122] "Vector" is a polynucleotide or other molecule that
transfers nucleic acids between cells. Vectors are often derived
from plasmids, bacteriophages, or viruses and optionally comprise
parts which mediate vector maintenance and enable its intended use.
A "cloning vector" or "shuttle vector" or "subcloning vector"
contains operably linked parts that facilitate subcloning steps
(e.g., a multiple cloning site containing multiple restriction
endonuclease sites). The term "expression vector" as used herein
refers to a vector comprising operably linked polynucleotide
sequences that facilitate expression of a coding sequence in a
particular host organism (e.g., a bacterial expression vector or a
plant expression vector).
[0123] "Yield" is the culmination of all agronomic traits as
determined by the productivity per unit area of a particular plant
product of commercial value. "Agronomic traits," include the
underlying genetic elements of a given plant variety that
contribute to yield over the course of growing season.
EXAMPLES
Example 1. Field Studies A, B and C
Biparental Mapping Populations
[0124] Parental lines were selected from resistant inbred lines:
CV820914, CV094802 and CV594360, and susceptible inbred lines:
CV391950, 1294213 and 1283669. CV391950 is described in U.S. Pat.
Nos. 7,718,859; 1,294,213 is described in U.S. Pat. Nos. 7,166,779;
and 1,283,669 is described in U.S. Pat. No. 7,414,181. Number of
lines derived were 168 doubled-haploid from CV820914/CV391950, 180
BC1F3 inbred from CV094802/1294213*2 and 178 BC1F2 inbred from
I283669*2/CV594360. 168 hybrid lines were also derived from the
cross of (CV820914/CV391950) BC1F3 and testers that are
modest-resistant or neutral to ASR (Table 1).
TABLE-US-00001 TABLE 1 Mapping populations Field Resistant
Susceptible Population Number Study Mapping Population Line Line
Type Gender of Lines A CV820914/CV391950 CV820914 CV391950 DH M 168
A CV820914/CV391950 CV820914 CV391950 (BC1F3XTester)F1 M 168 B
CV094802/I294213*2 CV094802 I294213 BC1F3 F 180 C
I283669*2/CV594360 CV594360 I283669 BC1F2 M 178
Inoculation and Rating Scale of Phenotypes
[0125] Corn plants grown in a field were inoculated 14 days after
the mid-silk stage, i.e. the point when 50% of the plants within a
given row had reached the R1 (silking) growth stage, by injecting
5.times.105 Colletotrichum graminicola spores suspended in 1 mL of
distilled water. Thirty days after inoculation, the severity of
anthracnose stalk rot in plants was visually assessed by splitting
each stalk longitudinally to expose the pith. Each pith was
examined to determine 1) the total number of internodes that
displayed visual legions characteristic of the disease, and 2) the
total number of internodes wherein visual legions had infected
>75% of the tissue within the internode, as summarized in Table
2. These two numbers were then summed into a disease score
phenotype for each plant, with scores of 10 converted to 9 to fit a
scale ranging from 1 (highly resistant) to 9 (highly susceptible).
Twelve to fourteen plants were ranged per row and the space between
each row was 0.80 m in field. The individual plant scores of each
row were then averaged and the average was reported as a final
score for the row. Two populations (CV820914/CV391950 and
CV094802/I294213*2) were measured in two field replicates and one
population (I283669*2/CV594360) was measured in three field
replicates for ASR resistance at different research sites using
methods described in the art and the rating scale in Table 2.
Phenotype Analysis
[0126] After statistical procedures for phenotype quality control,
a mixed model was run to estimate the variance components and to
compute the heritability for ASR resistance. The heritability was
0.40 for inbred per se and 0.60 for hybrid for the population
CV820914/CV391950, 0.46 for inbred per se for the population
CV094802/I294213*2, and 0.30 for inbred per se for the population
I283669*2/CV594360.
TABLE-US-00002 TABLE 2 Rating Scale of relative ASR infection
resistance phenotypes No. No. Internodes Internodes >75%
Infected Infected Score Rating 1 0 1 Highly resistant 1 1 2 Highly
resistant 2 1 3 Resistant 2 2 4 Resistant 3 2 5 Intermediate 3 3 6
Susceptible 4 3 7 Susceptible 4 4 8 Highly susceptible 5 4 9 Highly
susceptible 5 4 or 5 9 Highly susceptible
Primers and Probes Useful for Detecting ASR Resistance
Genotypes
[0127] These plants were then genotyped using SNP markers that
collectively spanned each chromosome in the maize genome. Loci that
were monomorphic in the subject populations were eliminated from
further analysis.
[0128] The primer sequences for amplifying exemplary SNP marker
loci linked to ASR-6.01 QTL and the probes used to genotype the
corresponding SNP sequences are provided in Table 3. One of skill
in the art will recognize that sequences to either side of the
given primers can be used in place of the given primers, so long as
the primers can amplify a region that includes the allele to be
detected. The precise probe to be used for detection can vary,
e.g., any probe that can identify the region of a marker amplicon
to be detected can be substituted for those probes exemplified
herein. Also, configuration of the amplification primers and
detection probes can, of course, vary. Thus, the invention is not
limited to the primers, probes, or marker sequences specifically
recited herein.
TABLE-US-00003 TABLE 3 Primers and probes used for detecting SNPs
linked to ASR-6.01 in field studies SEQ ID NO. SEQ SNP Fwd Rev ID
NO. Pos. Primer Primer Probe 1 Probe 2 1 433 11 21 31 41 2 381 12
22 32 42 3 221 13 23 33 43 4 130 14 24 34 44 5 373 15 25 35 45 6
301 16 26 36 46 7 463 17 27 37 47 8 618 18 28 38 48 9 148 19 29 39
49 10 469 20 30 40 50
[0129] Illustrative ASR resistance marker DNA sequences SEQ ID NOs:
1 can be amplified using the primers described in Table 3 as SEQ ID
NOs: 11 (forward primer) and 21 (reverse primer), and detected with
probes as SEQ ID NOs: 31 (probe 1) and 41 (probe 2).
Marker-Trait Association Study
[0130] Marker-trait association studies were performed using both
single-marker analysis (SMA) and CIM. For each marker, the
thresholds of Likelihood ratio between full and null models for CIM
were based on 1000 random permutation tests and the thresholds
(p-value) for SMA were based on 10,000 random permutation tests
(Churchill and Doerge 1994). The CIM analysis revealed a strong QTL
associated with ASR resistance on chromosome 6. The QTL was
confirmed in multiple genetic backgrounds and multi-year phenotypes
for both inbred per se and hybrid populations. The QTL peaks from
these three populations were located on chromosome 6 within 54 to
62 cMon the Monsanto's internal consensus genetic map as shown in
Table 4. Combining the data from three mapping populations, the
interval for this QTL was 48.8-67.9 cM. This QTL is designated as
"ASR-6.01". The QTL effect for one copy of favorable allele was
0.75 rating score and 1.5 rating score for homozygotes on average.
The phenotypic variance explained (R2) by this QTL was 24%.
TABLE-US-00004 TABLE 4 Summary of the CIM analysis from field
studies A, B, and C. Field Population Resistant QTL P- QTL Total
Study Mapping Population Type #Mk Parent Chr Peak Left Right val
Additive R.sup.2 R.sup.2 A CV820914/CV391950 Inbred 146 CV391950 6
53.9 48.8 65.1 0.01 0.75 0.24 0.48 A CV820914/CV391950 Hybrid 146
CV391950 6 54.9 49.9 67.9 0.01 1.16 0.55 0.66 B CV094802/I294213*2
Inbred 194 CV094802 6 55.7 49.7 57.5 0.01 0.77 0.11 0.35 C
I283669*2/CV594360 Inbred 140 CV594360 6 62.5 56.8 66.6 0.01 0.61
0.11 0.22 *P-value is based on 1,000 permutation tests
[0131] Each row provides field study ID, mapping population,
population type, number of markers used, resistant parent,
chromosome position, the peak of the Likelihood ratio corresponds
to ASR resistance, QTL interval where left and right flanking
positions are shown, additive effect, phenotypic variance of
individual QTL R.sup.2 and total R.sup.2.
[0132] Table 5 lists the effect estimates on ASR resistance
phenotype ratings associated with each marker (SEQ ID NO) measured
by single marker association (SMA) analysis in field study A, B and
C. Each row provides the SEQ ID NO of the marker, and genetic map
loci are represented in cM, with position zero being the first
(most distal) marker known at the beginning of the chromosome on
the internal consensus genetic map, mapping population, Genetic
source of favorable allele, favorable allele, unfavorable allele, F
statistical value and the estimated effect that the marker
polymorphism had on the ASR phenotype. The statistical significance
(p-value) of the association between the marker and the ASR
resistance rating in each case was p-value .ltoreq.0.01 on 10,000
permutation tests.
TABLE-US-00005 TABLE 5 Statistical associations of markers
associated with ASR-6.01 in field studies A, B and C. Genetic
Source of Permutation Single SEQ MON Favorable Favorable
Unfavorable testing Allele ID NO. Map cM Mapping Population Allele
allele allele Fstat Probability Effect 1 49.7 I283669*2/CV594360
CV594360 A T 14.1 0.01 0.51 2 62.5 I283669*2/CV594360 CV594360 T C
23.4 0.001 0.63 3 49.6 CV820914/CV391950 CV391950 C T 19.4 0.001
0.54 4 53.9 CV820914/CV391950 CV391950 A G 45.3 0.001 0.77 5 63.1
CV820914/CV391950 CV391950 T C 23.6 0.001 0.59 6 68.3
CV820914/CV391950 CV391950 G A 21.2 0.001 0.56 7 49.7
CV094802/I294213*2 CV094802 T C 17.2 0.005 0.76 8 58.6
CV094802/I294213*2 CV094802 C G 17.6 0.005 0.78 9 69
CV094802/I294213*2 CV094802 G A 19.4 0.001 0.81 *P-value is based
on 10,000 permutation tests
[0133] For example, SEQ ID NO: 3 was associated with a 0.54 change
in ASR resistance rating by one copy of the favorable allele. SEQ
ID NO: 5 was associated with a 0.59 change in ASR resistance rating
by one copy of the favorable allele. ASR resistance ratings were
generated using the methods described in Example 1.
Example 2. Field Study D
[0134] 180 BC1F4 plants were derived from BC1F3 CV094802/I294213*2
as shown in Table 6. Corn plants were inoculated as described in
Example 1 and then measured for ASR resistance at research site
using methods described in the art and the rating scale in Table 2.
These plants were genotyped using SNP markers that collectively
spanned each chromosome in the maize genome. To note, the SNP
markers used in this field study overlapped yet varied from the SNP
markers used in the prior field studies.
TABLE-US-00006 TABLE 6 Mapping populations of field study D Field
Resistant Susceptible Population Number Study Mapping Population
Parent parent Type Gender of Lines D CV094802/I294213*2 CV094802
I294213 BC1F4 F 180
Marker-Trait Association Study
[0135] Marker-trait association studies were performed using both
SMA and CIM. For each marker, the thresholds of Likelihood ratio
between full and null models for CIM were based on 1000 random
permutation tests and the thresholds (p-value) for SMA were based
on 10,000 random permutation tests (Churchill and Doerge 1994). The
CIM analysis from field study D confirmed the QTL region associated
with ASR resistance in Example 1. The QTL peak was mapped to 58.9
cM on chromosome 6 on the internally-derived genetic map as shown
in Table 7. The QTL interval was 52.5-66.3 cM. The phenotypic
variance explained (R.sup.2) by this QTL was 15%.
TABLE-US-00007 TABLE 7 Summary of the CIM analysis from field study
D Field Population Resistant QTL P- QTL Total Study Type #Mk Parent
Chr Peak Left Right value Additive R.sup.2 R.sup.2 D Inbred 178
CV094802 6 58.9 52.5 66.3 0.01 0.54 0.15 0.38 *P-value is based on
1,000 permutation tests
[0136] Table 7 provides the population type, number of markers
used, resistant parent, chromosome location, the peak of the
Likelihood ratio corresponds to ASR resistance, QTL interval where
left and right flanking positions are shown, additive effect,
phenotypic variance of individual QTL or Total (R.sup.2).
[0137] Table 8 lists the effect estimates on ASR resistance
phenotype ratings of each marker (SEQ ID NO) linked to ASR-6.01
measured by single marker association (SMA) analysis from field
study D. Each row provides the SEQ ID NO of the marker, genetic map
loci are represented in cM, with position zero being the first
(most distal) marker known at the beginning of the chromosome on
the internal consensus genetic map, mapping population, genetic
source of favorable allele, favorable allele, unfavorable allele, F
statistical value and the estimated effect that the marker
polymorphism had on the ASR phenotype. The statistical significance
(p-value) of the association between the marker and the ASR
resistance rating in each case was p-value .ltoreq.0.01 on 10,000
permutation tests.
TABLE-US-00008 TABLE 8 Estimate effects of markers associated with
ASR-6.01 from field study D. Genetic Source of Permutation Single
SEQ MON Favorable Favorable Unfavorable testing Allele ID NO. Map
cM Mapping Population Allele allele allele Fstat Probability Effect
10 49.5 CV094802/I294213*2 CV094802 A G 23.81 0.001 0.584 4 53.9 A
G 28.18 0.001 0.618 2 62.5 T C 29.14 0.001 0.625 *P-value is based
on 10,000 permutation tests
[0138] For example, SEQ ID NO: 10 was associated with a 0.584
change in ASR resistance rating by one copy of the favorable
allele. SEQ ID NO: 4 was associated with a 0.618 change in ASR
resistance rating by one copy of the favorable allele. ASR
resistance ratings were generated using the methods described in
Example 1.
Example 3. First Round of Fine-Mapping of ASR Resistance QTL on
Chromosome 6
[0139] In order to obtain additional recombinants,
CV820914/CV391950 derived F1 lines were selected, self-crossed, and
harvested. The resulting segregating F2 kernels were chipped and
genotyped with 8 SNP markers within 51-65 cM on Monsanto's internal
consensus genetic map (Table 9).
TABLE-US-00009 TABLE 9 Primers and probes used for detecting SNPs
linked to ASR-6.01 in first round fine-mapping SEQ ID NO. SEQ SNP
Fwd Rev ID NO. Pos. Primer Primer Probe 1 Probe 2 51 118 57 63 69
75 52 74 58 64 70 76 53 89 59 65 71 77 8 618 18 28 38 48 54 101 60
66 72 78 55 291 61 67 73 79 5 373 15 25 35 45 56 100 62 68 74
80
[0140] Kernels were bulked based on their haplotypes within this
QTL region. These bulks (10-20 plants) were then planted and
subsequently screened for ASR resistance via progeny test in the
greenhouse. In Table 10, grey cells indicated that the bulk carried
the same alleles as the susceptible inbred line at the specific SNP
position. White cells indicated that the bulk carried at least one
copy of the same allele as the resistant inbred line at the
specific SNP position. Lines which were homozygous or heterozygous
for the resistant allele were grouped together in this analysis.
Bulk "b" shared the same candidate QTL region as the susceptible
inbred line, CV820914. The individual plant scores of each bulk
were averaged. The average was reported as a final score for the
bulk and then compared with that of bulk "b". Bulk "f", "g", "h",
"i", "j", "p" and "o" displayed significantly reduced ASR severity
(highlighted by black box, p-value <0.05). Based on the common
SNP (highlighted by black oval) of these bulks, SEQ ID NO: 53 was
identified as the peak marker. The two closest markers flanking SEQ
ID NO: 53 are SEQ ID NO: 52 and SEQ ID NO: 8.
[0141] For example, bulk "f" shared at least one same allele as the
resistant inbred line (CV391950) at the SNP positions represented
by SEQ ID NO: 51, SEQ ID NO: 52 and SEQ ID NO: 53 (highlighted by
white cells). Bulk "f" shared the same alleles as the susceptible
inbred line (CV820914) at the SNP positions represented by SEQ ID
NO: 8, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 5 and SEQ ID NO: 56
(highlighted by grey cells).
[0142] Similar experiments were also conducted on BC1F2 kernels
derived from CV295879/CV391950. Bulk "f", "g", "i", "j", "p" and
"o" displayed significantly reduced ASR severity (highlighted by
black box, p-value <=0.05) compared with the bulk "b". Among
these resistant bulks, the same common SNP (SEQ ID NO: 53,
highlighted by black oval) was identified as the peak marker, as
shown in Table 11.
[0143] The QTL region associated with ASR resistance was
fine-mapped to 53.9-58.6 cM on chromosome 6 based on the
internally-derived genetic map (Table 12).
TABLE-US-00010 TABLE 12 Summary of first round fine-mapping results
SEQ ID NO. MON Map cM Marker Profile 52 53.9 Left flanking marker
53 56.8 QTL peak 8 58.6 Right flanking marker
Example 4. Second Round Fine-Mapping of ASR Resistance QTL on
Chromosome 6
[0144] In order to further fine-map the QTL region,
CV005260/CV391950 derived F2 lines were selected, self-crossed, and
harvested. CV005260 was the susceptible inbred line and CV391950
was the resistant inbred line. The resulting segregating F3 kernels
were chipped and genotyped with 6 SNP markers within 54-59 cM on
the internally-derived genetic map (Table 13). Primer and probe
synthesis is within the skill of the art once the SNP position in
the corn genome is provided. One of skill in the art will also
immediately recognize that other sequences to either side of the
given primers can be used in place of the given primers, so long as
the primers can amplify a region that includes the allele to be
detected. Further, it will be appreciated that the precise probe to
be used for detection can vary, e.g., any probe that can identify
the region of a marker amplicon to be detected can be substituted
for those examples provided herein. Also, configuration of the
amplification primers and detection probes can, of course, vary.
Thus, the invention is not limited to the primers, probes, or
marker sequences specifically recited herein.
TABLE-US-00011 TABLE 13 Primers and probes used for detecting SNPs
linked to ASR- 6.01 in second round fine-mapping from
CV005260/CV391950 SEQ ID NO. SEQ SNP Fwd Rev ID NO. Pos. Primer
Primer Probe 1 Probe 2 4 130 14 24 34 44 81 101 84 87 90 93 82 101
85 88 91 94 53 89 59 65 71 77 83 101 86 89 92 95 8 618 18 28 38
48
[0145] Kernels were bulked based on their haplotypes within this
QTL region. These bulks (9-19 plants/bulk) were then planted and
subsequently screened for ASR resistance via progeny test in the
greenhouse. In Table 14, grey cells indicated that the bulk shared
the same alleles as the susceptible inbred line at the specific SNP
positions. White cells indicated that the bulk shared the same
alleles as the resistant inbred line at the specific SNP positions.
The individual plant scores of each bulk were averaged and the
average was reported as a final score for the bulk. Bulk "i", "j",
"k", "1" and "m" displayed significantly reduced ASR severity with
mean values less than 2 (highlighted by black box). Based on the
common SNP (highlighted by black oval) of these bulks, SEQ ID NO:
83 was identified as the peak marker.
[0146] For example, bulk "a" shared the same alleles as the
resistant inbred line, CV391950, at the candidate QTL region
(highlighted by white cells); bulk "b" shared the same alleles as
the susceptible inbred line, CV005260, at the candidate QTL region
(highlighted by grey cells).
[0147] The two closest markers flanking SEQ ID NO: 83 are SEQ ID
NO: 53 and SEQ ID NO: 8. The QTL region associated with ASR
resistance was further fine-mapped to 56.8-58.6 cM on chromosome 6
based on the internally-derived genetic map (Table 15).
TABLE-US-00012 TABLE 15 Summary of second round fine-mapping
results SEQ ID NO. MON Map cM Marker Profile 53 56.8 Left flanking
marker 83 57.1 QTL peak 8 58.6 Right flanking marker
Example 5. Further Fine-Mapping Using Genotype-by-Sequencing (GBS)
Method
[0148] SNP markers were specifically designed for
CV005260/CV391950-derived plants via genotype-by-sequencing method
within ASR-6.01 interval. One hundred and twenty-seven BC1F2 inbred
plants were genotyped and measured for ASR resistance. SMA analysis
identified the top 11 SNP markers associated with ASR resistance.
Each row in Table 16 provides the SEQ ID NO of the marker, genetic
map positions of the marker, SNP position, favorable allele,
unfavorable allele, marker effect, p-value and phenotypic variance
(R.sup.2) of the marker. Genetic map loci are represented in cM,
with position zero being the first (most distal) marker known at
the beginning of the chromosome on Monsanto's internal consensus
genetic map.
TABLE-US-00013 TABLE 16 Further Fine-Mapping of ASR-6.01 via GBS
Method SEQ MON SNP Favorable Unfavorable Marker ID NO. Map cM
position allele allele Effect p-value R.sup.2 96 57.1 101 C T 1
0.0001 0.12 97 58 151 T C 0.94 0.0007 0.09 98 58 151 T C 0.97
0.0002 0.11 99 58 151 T G 0.98 0.0001 0.11 100 58 151 A G 0.98
0.0001 0.11 101 58 151 T G 0.98 0.0001 0.11 102 58 151 C A 0.98
0.0001 0.11 103 58 151 C T 0.97 0.0002 0.11 104 58.2 151 A G 1.93
0.0003 0.1 105 58.2 151 T A 0.75 0.0006 0.09 106 58.6 151 A G 0.71
0.0002 0.1
[0149] Chromosome intervals according to the invention and
comprising markers closely linked to the ASR-6.01 QTL are disclosed
in Table 17. Genetic map loci are represented in cM, with position
zero being the first (most distal) marker known at the beginning of
the chromosome on both an internal consensus genetic map (MON) and
the Neighbors 2008 maize genomic map (IBM2008), which is freely
available to the public from the Maize GDB website and commonly
used by those skilled in the art. Also disclosed in Table 17 are
the physical locations of loci as they are reported on the B73
RefGen_v2 sequence public assembly by the Arizona Genomics
Institute, available on the internet.
TABLE-US-00014 TABLE 17 Genetic and physical map positions of
markers and chromosome intervals associated with ASR-6.01. Relative
Genetic Map Position.dagger. MON IBM2008 Physical Map
Position.dagger..dagger. Marker/Locus Map cM Map IcM Contig Chr
Start Chr End IDP7601 38.2 200.7 AC204522.4 107366978 107368801
IDP62 38.9 206.2 AC208541.3 107736319 107737212 l11 43.1 216 -- --
-- IDP8090 44.6 219.5 AC201909.4 109532609 109539045 umc2006 48.7
228.9 -- -- -- IDP8231 49.1 229.9 AC206946.2 113039145 113042824
umc248b 49.1 230 -- -- -- SEQ ID NO: 10 49.5 231.1 -- -- --
pco136292 49.6 231.3 -- -- -- SEQ ID NO: 3 49.6 231.3 -- -- --
IDP6025 49.7 231.5 AC212465.3 115308486 115310063 IDP6010 49.7
231.5 AC209367.3 116123817 116124980 SEQ ID NO: 1 49.7 231.6 -- --
-- SEQ ID NO: 7 49.7 231.6 -- -- -- agrr118a 50.1 232.6 -- -- --
umc180(pep) 50.2 232.9 -- -- -- SEQ ID NO: 51 50.7 234.3 -- -- --
gpm74 51.1 235.3 -- -- -- TIDP3136 52.5 239.1 AC209629.2 118788679
118790325 AY107053 53.7 242.3 -- -- -- SEQ ID NO: 4 53.9 242.7 --
-- -- SEQ ID NO: 52 53.9 242.7 -- -- -- IDP1699 54.1 243.3
AC197533.3 120878064 120883418 pdi7 54.9 245.3 -- -- -- gpm869 55.3
246.2 -- -- -- SEQ ID NO: 81 55.9 247.6 -- -- -- ufg11 56.1 248.1
-- -- -- SEQ ID NO: 82 56.3 251.3 -- -- -- umc1250 56.6 254.5
AC194965.4 127445565 127446395 SEQ ID NO: 53 56.8 255.2 -- -- --
TIDP3356 57 255.9 AC203836.3 128061342 128063001 SEQ ID NO: 83 57.1
256.3 -- -- -- SEQ ID NO: 96 57.1 256.3 -- -- -- csu382a(cld) 57.3
257.1 -- -- -- IDP2409 57.8 258.9 AC189055.3 129901107 129902196
SEQ ID NO: 97 58 259.6 -- -- -- SEQ ID NO: 98 58 259.6 -- -- -- SEQ
ID NO: 99 58 259.6 -- -- -- SEQ ID NO: 100 58 259.6 -- -- -- SEQ ID
NO: 101 58 259.6 -- -- -- SEQ ID NO: 102 58 259.6 -- -- -- SEQ ID
NO: 103 58 259.6 -- -- -- SEQ ID NO: 104 58.2 260.4 -- -- -- SEQ ID
NO: 105 58.2 260.4 -- -- -- SEQ ID NO: 106 58.6 262.3 -- -- --
PCO146525 58.6 262.3 -- -- -- SEQ ID NO: 8 58.6 262.3 -- -- --
csu225 58.7 262.8 -- -- -- bnl3.03 58.9 264 -- -- -- AI665560 61.1
273.2 AC195903.3 132064031 132064497 SEQ ID NO: 54 61.5 274.4 -- --
-- pzb00414 61.7 275.2 -- -- -- umc2141 62.5 295.4 AC204295.3
134846202 134846710 SEQ ID NO: 55 62.5 295.4 -- -- -- SEQ ID NO: 2
62.5 295.4 -- -- -- AY110435 62.8 296.3 AC200260.3 137078584
137079677 elfa5 63.1 297.1 -- -- -- SEQ ID NO: 5 63.1 297.1 -- --
-- umc1379 63.1 297.1 AC214298.3 138536487 138537038 bnl15.37a 64.2
303 -- -- -- SEQ ID NO: 56 64.3 303.4 -- -- -- pza02478 64.3 303.5
-- -- -- IDP3886 65 306 AC205030.3 141412746 141415456 cl39957_1
65.6 308 -- -- -- mmc0241 66.2 312.8 -- -- -- dup400(pac) 66.4
313.4 -- -- -- jpsb107b 66.6 314 -- -- -- chs562 67.9 317.5 -- --
-- gpm709b 68.3 318.6 -- -- -- SEQ ID NO: 6 68.3 318.7 -- -- --
umc2321 68.4 319 AC208555.3 147911766 147912501 bnlg1702 69 320.7
-- -- -- SEQ ID NO: 9 69 320.7 -- -- -- csu158b(eno) 69.2 321.6 --
-- -- gpm426b 77.9 350.6 -- -- -- .dagger.cM = centiMorgans, IcM =
map units of the IBM2 2008 Neighbors Genetic Map.
.dagger..dagger.Arizona Genomics Institute B73 RefGen_v2 sequence.
* Exact coordinates not known. Coordinates can be estimated based
on nearest flanking loci with known coordinates.
[0150] In Table 17, "IcM" refers to the map units of the IBM2 2008
Neighbors Genetic Map, which was generated with an intermated
recombinant inbred population (syn 4) that resulted in
approximately a four-fold increase in the number of meiosies as
compared to the typical recombination experiment that is used to
generate centiMorgan (cM) distances (Lee et al., 2002, Plant Mol
Biol 48:453 and the Maize Genetics and Genomics Database). "cM"
refers to the classical definition of a centimorgan wherein one cM
is equal to a 1% chance that a trait at one genetic locus will be
separated from a trait at another locus due to crossing over in a
single generation (meaning the traits cosegregate 99% of the time
during meiosis), and this definition is used herein to delineate
map locations pertaining to this invention. Any markers within the
identified region, including those disclosed herein or publicly
known, could be used for detection of and selection for ASR
resistance in accordance with the methods of the present
invention.
Example 6. Annotated Genes within ASR-6.01
[0151] Table 18 lists annotated coding sequences within ASR-6.01
region. Each row provides gene ID, gene annotation, chromosome
location, genetic position on Monsanto internal consensus map and
physical position based on Arizona Genomics Institute B73 RefGen_v2
sequence which is publicly available. Transgenic maize resistant to
anthracnose stalk rot can be created using these annotated genes as
described in the specification.
TABLE-US-00015 TABLE 18 Annotated coding sequences within ASR-6.01
region. MON Map Physical Map Position bp .dagger..dagger. Gene ID
Annotation Chr cM .dagger. Start End 1 Putative uncharacterized
protein Sb10g013040 n = 2 Tax = Andropogoneae RepID = C5Z298_SORBI
(4e-20) 6 53.9 121384232 121384851 2 Delta zein storage protein n =
6 Tax = Zea mays RepID = C7AIP8_MAIZE (3e-22) 6 53.9 121390345
121391190 3 S-layer domain protein n = 2 Tax = Cyanothece RepID =
B7K1E8_CYAP8 (1e-19); GO_CC:GO:0009507, chloroplast# (3e-73) 6 53.9
121497243 121506368 4 ZCN11 n = 1 Tax = Zea mays RepID =
A8WES3_MAIZE (5e-82); PBP: Phosphatidylethanolamine-binding protein
6 53.9 121537244 121538748 (9.1e-43); GO_BP:GO:0030154, cell
differentiation# (3e-34); GO_CC:GO:0005737, cytoplasm# (2e-46) 5
Protein binding protein n = 1 Tax = Zea mays RepID = B6SVM4_MAIZE
(1e-103); GO_MF:GO:0046872, metal 6 53.9 121553074 121554257 ion
binding# (1e-103); GO_BP:GO:0007229, integrin-mediated signaling
pathway# (7e-25); GO_CC:GO:0005622, intracellular# (7e-35) 6 ELMO
domain-containing protein 2 n = 3 Tax = Zea mays RepID =
B6T7G4_MAIZE (4e-23); 6 53.9 121554918 121556006 GO_BP:GO:0006909,
IMP#phagocytosis# (4e-23); GO_CC:GO:0005856, cytoskeleton# (4e-23)
7 SMC4 protein n = 3 Tax = Oryza sativa RepID = Q8L6H8_ORYSA
(1e-104); GO_MF:GO:0005524, ATP binding# (1e-104); 6 53.9 121556779
121559923 GO_BP:GO:0051276, chromosome organization# (1e-104);
GO_CC:GO:0005694, chromosome# (1e-104) 8 Pollen-specific protein
NTP303 n = 4 Tax = Zea mays RepID = B6U4I6_MAIZE (9e-60);
Cu-oxidase: Multicopper 6 53.9 121566108 121567043 oxidase
(0.0056); GO_MF:GO:0016491, oxidoreductase activity# (9e-60);
GO_BP:GO:0055114, oxidation reduction# (9e-60); GO_CC:GO:0005576,
extracellular region# (5e-34) 9 AlphaSNBP(B)-like n = 3 Tax = Oryza
sativa RepID = Q651K5_ORYSJ (1e-125); DFDF: DFDF motif (3.4e-07); 6
53.9 121688996 121698144 FFD_TFG: FFD and TFG box motifs (1e-20) 10
Histone mRNA exonuclease 1 n = 2 Tax = Zea mays RepID =
B6T5F9_MAIZE (0.0); Exonuc_X-T: Exonuclease 6 53.9 121757218
121777486 (8e-05); GO_MF:GO:0004527, exonuclease activity# (0.0);
GO_BP:GO:0031125, rRNA 3'-end processing# (2e-24);
GO_CC:GO:0005622, intracellular# (2e-26) 11 Aluminum-activated
malate transporter-like n = 2 Tax = Oryza sativa RepID =
Q6EPG5_ORYSJ (7e-11); GO_BP:GO:0010044, 6 53.9 121766949 121767251
response to aluminum ion# (7e-11) 12 Putative polyprotein n = 1 Tax
= Zea mays RepID = Q8SA93_MAIZE (5e-45); Exo_endo_phos: 6 53.9
121770395 121775874 Endonuclease/Exonuclease/phosphatase family
(0.074); GO_MF:GO:0003964, RNA-directed DNA polymerase, group II
intron encoded# (5e-45); GO_BP:GO:0015074, DNA integration#
(5e-45); GO_CC:GO:0005634, nucleus# (5e-45) 13 DNA helicase
homolog, putative n = 1 Tax = Musa acuminata RepID = Q1EPC6_MUSAC
(1e-17); GO_MF:GO:0004386, 6 53.9 121779361 121796764 helicase
activity# (1e-17) 14 B-cell receptor-associated protein 31-like
containing protein n = 2 Tax = Andropogoneae RepID = B6TG43_MAIZE 6
53.9 121926217 121928807 (8e-20); GO_MF:GO:0004872, receptor
activity# (8e-20); GO_BP:GO:0006886, intracellular protein
transport# (2e-50); GO_CC:GO:0016021, integral to membrane# (2e-50)
15 Reticulon n = 3 Tax = Andropogoneae RepID = B6TG01_MAIZE
(1e-135); Reticulon: Reticulon (6.5e-58); 6 53.9 121943435
121946102 GO_MF:GO:0003676, nucleic acid binding# (2e-97);
GO_BP:GO:0006313, transposition, DNA-mediated# (8e-89);
GO_CC:GO:0005783, IDA#endoplasmic reticulum# (1e-135) 16
OSJNBa0029H02.21 protein n = 1 Tax = Oryza sativa RepID =
Q7XT72_ORYSA (1e-09); Ribosomal_L23: 6 53.9 122086378 122086631
Ribosomal protein L23 (0.0023); GO_MF:GO:0003735, structural
constituent of ribosome# (2e-09); GO_BP:GO:0006412, translation#
(2e-09); GO_CC:GO:0030529, ribonucleoprotein complex# (2e-09) 17
V-type proton ATPase 16 kDa proteolipid subunit c4 n = 52 Tax =
Embryophyta RepID = VATL4_ARATH (2e-26); 6 53.9 122086738 122090981
GO_MF:GO:0015078, hydrogen ion transmembrane transporter activity#
(2e-26); GO_BP:GO:0015992, proton transport# (2e-26);
GO_CC:GO:0033179, proton-transporting V-type ATPase, V0 domain#
(2e-26) 18 Putative uncharacterized protein n = 2 Tax = Zea mays
RepID = B6U525_MAIZE (5e-10) 6 53.9 122093288 122093569 19
Tesmin-like n = 2 Tax = Oryza sativa Japonica Group RepID =
Q69WH4_ORYSJ (1e-145); CXC: Tesmin/TSO1- 6 53.9 122095245 122102827
like CXC domain (5.9e-16); CXC: Tesmin/TSO1-like CXC domain
(1.4e-21); GO_MF:GO:0005515, protein binding# (1e-68);
GO_BP:GO:0045449, regulation of transcription# (2e-74);
GO_CC:GO:0031523, IDA#Myb complex# (8e-33) 20 Fiber protein Fb34 n
= 2 Tax = Andropogoneae RepID = B4FVT6_MAIZE (7e-36); DUF1218:
Protein of unknown 6 53.9 122116076 122116865 function (DUF1218)
(2.2e-11) 21 Protein kinase family protein n = 2 Tax = Eumusa RepID
= Q1EPA3_MUSAC (1e-146); Pkinase: Protein kinase 6 53.9 122247935
122249667 domain (8.9e-36); Pkinase_Tyr: Protein tyrosine kinase
(2.1e-36); APH: Phosphotransferase enzyme family (0.028);
GO_MF:GO:0005524, ATP binding# (1e-179); GO_BP:GO:0006468, protein
amino acid phosphorylation# (1e-179); GO_CC:GO:0016459, myosin
complex# (1e-179) 22 Putative Potential phospholipid-transporting
ATPase 8 n = 2 Tax = Oryza sativa RepID = Q67VX1_ORYSJ 6 53.9
122254921 122264424 (0.0); E1-E2_ATPase: E1-E2 ATPase (9.6e-05);
Hydrolase: haloacid dehalogenase-like hydrolase (0.0033);
GO_MF:GO:0016820, hydrolase activity, acting on acid anhydrides,
catalyzing transmembrane movement of substances# (0.0);
GO_BP:GO:0016820, hydrolase activity, acting on acid anhydrides,
catalyzing transmembrane movement of substances# (0.0);
GO_CC:GO:0016021, integral to membrane# (0.0) 23 Retrotransposon
protein, putative, unclassified n = 1 Tax = Oryza sativa Japonica
Group RepID = 6 53.9 122304131 122304529 Q2QRU0_ORYSJ (1e-10);
RVT_2: Reverse transcriptase (RNA-dependent DNA pol (0.0023);
GO_MF:GO:0003676, nucleic acid binding# (2e-10); GO_BP:GO:0015074,
DNA integration# (4e-10) 24 Retrotransposon protein, putative,
unclassified n = 2 Tax = Oryza sativa Japonica Group RepID = 6 53.9
122311854 122312338 Q10HG0_ORYSJ (3e-30); GO_MF:GO:0004523,
ribonuclease H activity# (3e-30); GO_BP:GO:0006278, RNA-dependent
DNA replication# (3e-30) 25
Pyrophosphate-fructose-6-phosphate1-phosphotransferase alpha
subunit (Fragment) n = 2 Tax = Saccharum 6 53.9 122322616 122325389
officinarum complex RepID = A1E380_SACSP (5e-24); GO_MF:GO:0003872,
6-phosphofructokinase activity# (1e-24); GO_BP:GO:0006096,
glycolysis# (1e-24); GO_CC:GO:0005945, 6-phosphofructokinase
complex# (1e-24) 26 Pho1-like protein n = 1 Tax = Populus
trichocarpa RepID = B9HWP3_POPTR (0.0); SPX: SPX domain 6 53.9
122394825 122399345 (2.2e-26); EXS: EXS family (2.3e-144);
GO_MF:GO:0004872, receptor activity# (0.0); GO_BP:GO:0004872,
receptor activity# (0.0); GO_CC:GO:0016021, integral to membrane#
(0.0) 27 PpPPR_77 protein n = 1 Tax = Physcomitrella patens RepID =
Q5W963_PHYPA (1e-106); PPR: PPR 6 53.9 122404713 122406776 repeat
(0.26); PPR: PPR repeat (0.94); PPR: PPR repeat (0.0071); PPR: PPR
repeat (3.6e-05); PPR: PPR repeat (6.1e-09); PPR: PPR repeat
(0.057); PPR: PPR repeat (0.7); GO_MF:GO:0005488, binding# (4e-94);
GO_CC:GO:0009536, plastid# (8e-99) 28 Putative uncharacterized
protein 9C20.7 n = 1 Tax = Zea mays RepID = Q5NKP3_MAIZE (1e-12) 6
53.9 122421193 122421729 29 DEAD-box ATP-dependent RNA helicase 14
n = 4 Tax = Oryza sativa RepID = RH14_ORYSJ (2e-49); DEAD: 6 53.9
122524854 122525657 DEAD/DEAH box helicase (0.087);
GO_MF:GO:0016787, hydrolase activity# (2e-49); GO_BP:GO:0042254,
ribosome biogenesis# (2e-49); GO_CC:GO:0005634, nucleus# (2e-49) 30
Putative uncharacterized protein n = 1 Tax = Zea mays RepID =
B6SM34_MAIZE (2e-13) 6 53.9 122555403 122555864 31
Pentatricopeptide repeat-containing protein, putative n = 1 Tax =
Ricinus communis RepID = B9SV96_RICCO 6 53.9 122582468 122585135
(1e-173); PPR: PPR repeat (0.0007); PPR: PPR repeat (0.0031); PPR:
PPR repeat (9.6e-05); PPR: PPR repeat (5e-11); PPR: PPR repeat
(0.0066); PPR: PPR repeat (0.036); PPR: PPR repeat (7e-10); PPR:
PPR repeat (0.18); PPR: PPR repeat (8.7e-08); GO_MF:GO:0030528,
transcription regulator activity# (0.0); GO_BP:GO:0045449,
regulation of transcription# (0.0); GO_CC:GO:0009536, plastid#
(1e-173) 32 MADS-box transcription factor 31 n = 3 Tax =
Andropogoneae RepID = B6TW19_MAIZE (6e-14); 6 53.9 122587039
122588859 GO_MF:GO:0043565, sequence-specific DNA binding# (6e-14);
GO_BP:GO:0045449, regulation of transcription# (6e-14);
GO_CC:GO:0005634, nucleus# (6e-14) 33 Probable calcium-binding
protein CML30 n = 3 Tax = Oryza sativa RepID = CML30_ORYSJ (1e-54);
efhand: EF 6 53.9 122664103 122665029 hand (0.0013); efhand: EF
hand (0.006); efhand: EF hand (1.4e-06); efhand: EF hand (4e-08);
GO_MF:GO:0005509, calcium ion storage activity# (1e-105);
GO_BP:GO:0009409, IEP#response to cold# (5e-21); GO_CC:GO:0005737,
cytoplasm# (5e-21) 34 Alkaline alpha galactosidase 2 n = 1 Tax =
Zea mays RepID = Q575Z7_MAIZE (0.0); Raffinose_syn: Raffinose 6
53.9 122727878 122731414 synthase or seed imbibition protein Sip1
(0); GO_MF:GO:0047274, galactinol-sucrose galactosyltransferase
activity# (0.0); GO_BP:GO:0009409, IEP#response to cold# (0.0);
GO_CC:GO:0009507, chloroplast# (0.0) 35 26S protease regulatory
subunit 6A homolog n = 12 Tax = Poaceae RepID = PRS6A_ORYSJ
(2e-37); 6 53.9 122797640 122807850 GO_MF:GO:0016765, transferase
activity, transferring alkyl or aryl (other than methyl) groups#
(2e-37); GO_BP:GO:0030163, protein catabolic process# (8e-36);
GO_CC:GO:0005737, cytoplasm# (8e-36) 36 26S protease regulatory
subunit 6A homolog n = 12 Tax = Poaceae RepID = PRS6A_ORYSJ
(1e-135); AAA_2: 6 53.9 122836036 122838395 ATPase family
associated with various (0.0093); AAA: ATPase family associated
with various cellular activities (AAA) (1.2e-89); AAA_3: ATPase
family associated with various (0.011); AAA_5: ATPase family
associated with various (0.00017); GO_MF:GO:0017111,
nucleoside-triphosphatase activity# (1e-130); GO_BP:GO:0030163,
protein catabolic process# (1e-130); GO_CC:GO:0005737, cytoplasm#
(1e-130) 37 Putative uncharacterized protein n = 2 Tax = Zea mays
RepID = B6TTZ4_MAIZE (0.0); Dev_Cell_Death: 6 53.9 122889105
122892158 Development and cell death domain (1e-63);
GO_MF:GO:0003677, DNA binding# (5e-33) 38 Longin-like n = 1 Tax =
Medicago truncatula RepID = A4Q7K9_MEDTR (2e-77); Synaptobrevin:
Synaptobrevin 6 53.9 122950872 122954048 (1.1e-39);
GO_MF:GO:0005515, protein binding# (7e-45); GO_BP:GO:0016192,
vesicle-mediated transport# (1e-104); GO_CC:GO:0016021, integral to
membrane# (1e-104) 39 Clathrin assembly protein AP180 short
form-like n = 2 Tax = Oryza sativa RepID = Q69SJ3_ORYSJ 6 53.95
122961662 122968145 (1e-169); ANTH: ANTH domain (5.7e-112); ENTH:
ENTH domain (6.1e-05); GO_MF:GO:0030276, clathrin binding# (0.0);
GO_BP:GO:0048268, IDA#clathrin coat assembly# (0.0);
GO_CC:GO:0030118, clathrin coat# (0.0) 40 Receptor serine-threonine
protein kinase, putative n = 1 Tax = Ricinus communis RepID =
B9S1N3_RICCO 6 54 122994729 122996638 (1e-138); Pkinase: Protein
kinase domain (7.9e-31); Pkinase_Tyr: Protein tyrosine kinase
(4.3e-31); GO_MF:GO:0005524, ATP binding# (0.0); GO_BP:GO:0006468,
protein amino acid phosphorylation# (0.0) 41 Cytochrome b-c1
complex subunit 8 n = 1 Tax = Solanum tuberosum RepID = QCR8_SOLTU
(2e-20); 6 54.1 123080089 123083460 GO_MF:GO:0016491,
oxidoreductase activity# (2e-16); GO_BP:GO:0022900, electron
transport chain# (2e-20); GO_CC:GO:0070469, respiratory chain#
(2e-20) 42 Putative iron/ascorbate-dependent oxidoreductase n = 1
Tax = Oryza sativa Japonica Group 6 54.1 123156144 123157022 RepID
= Q658E2_ORYSJ (7e-78); 2OG-FeII_Oxy: 2OG-Fe(II) oxygenase
superfamily (1.1e-30); GO_MF:GO:0016491, oxidoreductase activity#
(1e-80); GO_BP:GO:0055114, oxidation reduction# (1e-80) 43
OSJNBa0029H02.21 protein n = 1 Tax = Oryza sativa RepID =
Q7XT72_ORYSA (6e-22); Ribosomal_L23eN: 6 54.1 123201331 123203345
Ribosomal protein L23, N-terminal domain (2.4e-18);
GO_MF:GO:0003735, structural constituent of ribosome# (7e-22);
GO_BP:GO:0006412, translation# (7e-22); GO_CC:GO:0030529,
ribonucleoprotein complex# (7e-22) 44 Putative uncharacterized
protein Sb01g049710 n = 1 Tax = Sorghum bicolor RepID =
C5X128_SORBI (1e-23) 6 54.1 123335141 123335768 45
Pyrophosphate-energized vacuolar membrane proton pump n = 12 Tax =
Poaceae RepID = AVP_HORVU (0.0); 6 54.1 123336536 123341421
H_PPase: Inorganic H+ pyrophosphatase (0); OPT: OPT oligopeptide
transporter protein (0.084); BCCT: BCCT family transporter (0.062);
GO_MF:GO:0016787, hydrolase activity# (0.0); GO_BP:GO:0015992,
proton transport# (0.0); GO_CC:GO:0016021, integral to membrane#
(0.0) 46 Heparanase-like protein 3 n = 3 Tax = Andropogoneae RepID
= B6SXU7_MAIZE (0.0); Glyco_hydro_79n: 6 54.1 123344114 123346798
Glycosyl hydrolase family 79, N-terminal domain (2.4e-88);
GO_MF:GO:0016798, hydrolase activity, acting on glycosyl bonds#
(0.0); GO_BP:GO:0055085, transmembrane transport# (2e-50);
GO_CC:GO:0016020, membrane# (0.0) 47 Jp18 n = 1 Tax = Citrus
trifoliata RepID = Q8H6R4_PONTR (3e-17) 6 54.1 123370995 123372142
48 Nodulin-like protein n = 2 Tax = Oryza sativa RepID =
Q8H613_ORYSJ (0.0); Nodulin-like: Nodulin-like 6 54.1 123372572
123376208 (2.8e-117); MFS_1: Major Facilitator Superfamily
(0.049);
GO_MF:GO:0016798, hydrolase activity, acting on glycosyl bonds#
(1e-153); GO_BP:GO:0055085, transmembrane transport# (0.0);
GO_CC:GO:0016020, membrane# (1e-153) 49 Putative villin n = 1 Tax =
Oryza sativa Japonica Group RepID = Q65XP6_ORYSJ (0.0); Gelsolin:
Gelsolin 6 54.1 123383577 123388905 repeat (3.6e-11); Gelsolin:
Gelsolin repeat (0.00013); Gelsolin: Gelsolin repeat (5.4e-05);
Gelsolin: Gelsolin repeat (2e-05); Gelsolin: Gelsolin repeat
(0.064); Gelsolin: Gelsolin repeat (0.13); GO_MF:GO:0003779, actin
binding# (0.0); GO_BP:GO:0007010, cytoskeleton organization# (0.0);
GO_CC:GO:0015629, actin cytoskeleton# (0.0) 50 Tryptophan
aminotransferase n = 2 Tax = Zea mays RepID = B5ATU2_MAIZE (0.0);
Alliinase_C: Allinase, C- 6 54.2 123432761 123435867 terminal
domain (8.5e-198); Aminotran_1_2: Aminotransferase class I and II
(0.00013); GO_MF:GO:0030170, pyridoxal phosphate binding# (0.0);
GO_BP:GO:0080022, IMP#primary root development# (7e-91);
GO_CC:GO:0005737, cytoplasm# (2e-89) 51 OSJNBa0053K19.25 protein n
= 2 Tax = Oryza sativa RepID = Q7XPP8_ORYSJ (6e-26) 6 54.8
123669647 123669987 52 OSJNBa0053K19.25 protein n = 2 Tax = Oryza
sativa RepID = Q7XPP8_ORYSJ (3e-46); DUF1682: Protein of 6 54.85
123660711 123671949 unknown function (DUF1682) (0.0022);
GO_CC:GO:0016021, integral to membrane# (2e-17) 53 OSJNBa0053K19.25
protein n = 2 Tax = Oryza sativa RepID = Q7XPP8_ORYSJ (8e-18);
GO_CC:GO:0005739, 6 54.9 123671681 123672761 mitochondrion# (2e-14)
54 2,3-bisphosphoglycerate-independent phosphoglycerate mutase n =
6 Tax = Poaceae RepID = PMGI_MAIZE 6 54.9 123673484 123674700
(3e-99); iPGM_N: BPG-independent PGAM N-terminus (iPGM (9.4e-16);
GO_MF:GO:0046872, metal ion binding# (3e-99); GO_BP:GO:0008152,
metabolic process# (3e-99); GO_CC:GO:0005737, cytoplasm# (3e-99) 55
Cyclic nucleotide-gated ion channel 2 (Fragment) n = 1 Tax =
Hordeum vulgare subsp. vulgare 6 54.9 123676263 123676490 RepID =
Q4VDM4_HORVD (3e-15); GO_MF:GO:0005216, ion channel activity#
(5e-12); GO_BP:GO:0055085, transmembrane transport# (5e-12);
GO_CC:GO:0016021, integral to membrane# (5e-12) 56 CENP-E like
kinetochore protein n = 1 Tax = Zea mays RepID = B6SHI8_MAIZE
(0.0); KIP1: KIP1-like protein 6 54.9 123677322 123687963
(2.6e-38); DUF2051: Double stranded RNA binding protein ((0.079);
Pox_A_type_inc: Viral A-type inclusion protein repeat (57);
Pox_A_type_inc: Viral A-type inclusion protein repeat (77);
Pox_A_type_inc: Viral A-type inclusion protein repeat (0.79);
Pox_A_type_inc: Viral A-type inclusion protein repeat (12);
Cenp-F_leu_zip: Leucine-rich repeats of kinetochore p (0.053);
Pox_A_type_inc: Viral A-type inclusion protein repeat (27);
GO_MF:GO:0016301, kinase activity# (1e-132); GO_BP:GO:0016301,
kinase activity# (1e-132); GO_CC:GO:0005886, plasma membrane#
(1e-21) 57 NHP2-like protein 1 n = 7 Tax = Andropogoneae RepID =
B6TBE1_MAIZE (5e-24); GO_MF:GO:0005515, protein 6 54.9 123706476
123707839 binding# (5e-19); GO_BP:GO:0042254, ribosome biogenesis#
(5e-24); GO_CC:GO:0030529, ribonucleoprotein complex# (5e-24) 58
Integral membrane protein like n = 1 Tax = Zea mays RepID =
B6SMU5_MAIZE (1e-139); UAA: UAA transporter 6 54.9 123729619
123734039 family (0.011); Nuc_sug_transp: Nucleotide-sugar
transporter (0.022); DUF6: Integral membrane protein DUF6 (0.037);
TPT: Triose-phosphate Transporter family (4.5e-49);
GO_BP:GO:0009624, IEP#response to nematode# (5e-36);
GO_CC:GO:0016021, integral to membrane# (1e-125) 59
Aminotransferase y4uB n = 2 Tax = Andropogoneae RepID =
B6T579_MAIZE (9e-27); GO_MF:GO:0030170, 6 54.9 123741189 123741689
pyridoxal phosphate binding# (9e-27); GO_BP:GO:0055114, oxidation
reduction# (9e-12) 60 Aminotransferase y4uB n = 2 Tax =
Andropogoneae RepID = B6T579_MAIZE (1e-62); GO_MF:GO:0030170, 6
54.9 123741701 123742472 pyridoxal phosphate binding# (1e-62) 61
Putative uncharacterized protein Sb09g005000 n = 2 Tax =
Andropogoneae RepID = C5Z118_SORBI (1e-111); 6 54.9 123748498
123751787 GO_BP:GO:0006979, response to oxidative stress# (2e-78)
62 Transcription factor BIM2 n = 3 Tax = Andropogoneae RepID =
B6SVP6_MAIZE (7e-11); GO_MF:GO:0030528, 6 54.9 123753813 123761545
transcription regulator activity# (7e-11); GO_BP:GO:0045449,
regulation of transcription# (7e-11); GO_CC:GO:0005634, nucleus#
(7e-11) 63 AP2 domain-containing transcription factor n = 1 Tax =
Populus trichocarpa RepID = B9GNL6_POPTR (4e-22); 6 54.9 123763332
123764175 GO_MF:GO:0003700, transcription factor activity# (7e-23);
GO_BP:GO:0045449, regulation of transcription# (7e-23);
GO_CC:GO:0005634, nucleus# (7e-23) 64 Catalytic/hydrolase n = 2 Tax
= Zea mays RepID = B6TIK5_MAIZE (1e-120); GO_MF:GO:0016787,
hydrolase 6 54.9 123766758 123770464 activity# (1e-120);
GO_BP:GO:0008152, metabolic process# (1e-120) 65 Germin-like
protein n = 4 Tax = Andropogoneae RepID = Q6TM44_MAIZE (1e-117);
Cupin_1: Cupin (3.6e-34); 6 54.9 123777183 123778314 Cupin_2: Cupin
domain (6.8e-07); GO_MF:GO:0046872, metal ion binding# (8e-97);
GO_BP:GO:0055114, oxidation reduction# (1e-71); GO_CC:GO:0048046,
IDA#apoplast# (8e-97) 66 Ribulose bisphosphate carboxylase large
chain n = 4 Tax = BEP clade RepID = B8Y2Y5_FESAR (9e-63); 6 55.1
123912742 123913547 RuBisCO_large_N: Ribulose bisphosphate
carboxylase large chain, N-terminal domain (1e-79);
GO_MF:GO:0016984, ribulose-bisphosphate carboxylase activity#
(4e-62); GO_BP:GO:0055114, oxidation reduction# (4e-62);
GO_CC:GO:0009536, plastid# (4e-62) 67 Putative uncharacterized
protein n = 1 Tax = Zea mays RepID = B8A1X9_MAIZE (3e-81) 6 55.1
123914152 123915257 68 Auxin Efflux Carrier family protein n = 1
Tax = Zea mays RepID = B6SVJ1_MAIZE (7e-29); 6 55.1 123949237
123949664 GO_BP:GO:0055085, transmembrane transport# (7e-29);
GO_CC:GO:0016021, integral to membrane# (7e-29) 69
Armadillo/beta-catenin-like repeat family protein n = 1 Tax = Zea
mays RepID = B6U4A9_MAIZE (5e-32); 6 55.1 123952012 123952497
GO_MF:GO:0005488, binding# (5e-32) 70 Kelch-like protein n = 3 Tax
= Oryza sativa RepID = Q84S70_ORYSJ (7e-82); Dev_Cell_Death:
Development 6 55.1 124019830 124042554 and cell death domain
(7.1e-40); Kelch_1: Kelch motif (0.095); Kelch_1: Kelch motif
(1.3e-16); Kelch_2: Kelch motif (6.9e-05); Kelch_1: Kelch motif
(4.2e-08); Kelch_2: Kelch motif (8.6); Kelch_1: Kelch motif
(5.5e-11); Kelch_2: Kelch motif (0.00044); Kelch_1: Kelch motif
(8.5e-14); Kelch_2: Kelch motif (1.5e-05); Kelch_1: Kelch motif
(4.4e-05); Kelch_2: Kelch motif (2.3); GO_MF:GO:0005515, protein
binding# (5e-40); GO_BP:GO:0050807, IGI#regulation of synapse
organization# (7e-38); GO_CC:GO:0005575, cellular_component#
(7e-38) 71 Kelch-like protein n = 3 Tax = Oryza sativa RepID =
Q84S70_ORYSJ (4e-44); Dev_Cell_Death: Development 6 55.1 124104544
124110586 and cell death domain (2.8e-74); Kelch_2: Kelch motif
(21); Kelch_1: Kelch motif (0.11); Kelch_1: Kelch motif (0.23);
Kelch_2: Kelch motif (15); Kelch_1: Kelch motif (5.4e-12); Kelch_2:
Kelch motif (2.3); Kelch_1: Kelch motif (1.2e-12); Kelch_2: Kelch
motif (9.9e-06); Kelch_1: Kelch motif (0.004); Kelch_2: Kelch motif
(2.4); GO_MF:GO:0005515, protein binding# (1e-26);
GO_BP:GO:0046529, IGI#imaginal disc fusion, thorax closure#
(6e-26); GO_CC:GO:0031463, IPI#Cul3-RING ubiquitin ligase complex#
(6e-26) 72 Erg28 like protein n = 4 Tax = Andropogoneae RepID =
B6U3K5_MAIZE (9e-68); Erg28: Erg28 like protein 6 55.1 124135063
124140932 (1.6e-36); GO_BP:GO:0016126, IGI#sterol biosynthetic
process# (1e-45); GO_CC:GO:0016021, integral to membrane# (9e-68)
73 Putative uncharacterized protein Sb02g010980 n = 1 Tax = Sorghum
bicolor RepID = C5X573_SORBI (6e-22) 6 55.1 124156120 124156572 74
DNA binding protein n = 1 Tax = Zea mays RepID = B6U8E0_MAIZE
(1e-123); HLH: Helix-loop-helix DNA- 6 55.1 124197455 124198967
binding domain (3.5e-07); GO_MF:GO:0030528, transcription regulator
activity# (1e-123); GO_BP:GO:0045449, regulation of transcription#
(1e-123); GO_CC:GO:0005634, nucleus# (1e-123) 75 DNA helicase
homolog, putative n = 1 Tax = Musa acuminata RepID = Q1EPC6_MUSAC
(6e-10); 6 55.1 124205879 124207211 GO_MF:GO:0004386, helicase
activity# (6e-10) 76 RuBisCo subunit binding-protein beta subunit
(Fragment) n = 1 Tax = Zea mays RepID = Q6B7Q9_MAIZE 6 55.1
124214939 124216073 (5e-62); GO_MF:GO:0005524, ATP binding#
(7e-60); GO_BP:GO:0044267, cellular protein metabolic process#
(7e-60); GO_CC:GO:0009536, plastid# (7e-60) 77 Ulp1 protease
family, C-terminal catalytic domain containing protein n = 2 Tax =
Oryza sativa Japonica Group 6 55.1 124218673 124221589 RepID =
Q109R5_ORYSJ (4e-37); Peptidase_C48: Ulp1 protease family,
C-terminal catalytic domain (4.9e-13); GO_MF:GO:0008234,
cysteine-type peptidase activity# (1e-158); GO_BP:GO:0006508,
proteolysis# (1e-158) 78 Transposon protein, putative, CACTA,
En/Spm sub-class n = 1 Tax = Oryza sativa Japonica Group 6 55.15
124153890 124156112 RepID = Q2QWY8_ORYSJ (1e-128);
GO_MF:GO:0004803, transposase activity# (2e-57); GO_BP:GO:0006313,
transposition, DNA-mediated# (2e-57) 79 Glutaryl-CoA dehydrogenase
n = 1 Tax = Zea mays RepID = B6TNB5_MAIZE (0.0); Acyl-CoA_dh_N:
Acyl-CoA 6 55.2 124146431 124151926 dehydrogenase, N-terminal
domain (7e-30); Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle
domain (1.7e-22); Acyl-CoA_dh_1: Acyl-CoA dehydrogenase, C-terminal
do (2.8e-25); Acyl-CoA_dh_2: Acyl-CoA dehydrogenase, C-terminal do
(0.0014); GO_MF:GO:0050660, FAD binding# (0.0); GO_BP:GO:0055114,
oxidation reduction# (0.0); GO_CC:GO:0009514, glyoxysome# (0.0) 80
PHD finger transcription factor-like n = 2 Tax = Oryza sativa RepID
= Q5JJV7_ORYSJ (1e-153); PHD: PHD-finger 6 55.3 124296440 124300947
(1.8e-10); Acetyltransf_1: Acetyltransferase (GNAT) family (0.074);
GO_MF:GO:0046872, metal ion binding# (1e-153); GO_BP:GO:0008152,
metabolic process# (1e-153) 81 Growth inhibition and
differentiation-related protein 88 n = 2 Tax = Andropogoneae RepID
= B6TKU0_MAIZE 6 55.9 124363443 124366224 (1e-140); RNA_bind: RNA
binding domain (0.027); GO_MF:GO:0046872, metal ion binding#
(1e-140); GO_BP:GO:0006402, mRNA catabolic process# (1e-140);
GO_CC:GO:0005737, cytoplasm# (1e-140) 82 Putative uncharacterized
protein n = 1 Tax = Zea mays RepID = B4FS85_MAIZE (4e-14) 6 55.9
124471043 124472524 83 Putative uncharacterized protein n = 3 Tax =
Zea mays RepID = B6U549_MAIZE (4e-66) 6 55.9 124489396 124490221 84
Nucleolar complex protein 4 n = 1 Tax = Zea mays RepID =
B6SWX2_MAIZE (5e-43); DUF947: Domain of 6 55.9 124525406 124526646
unknown function (DUF947) (0.018); CBF: CBF/Mak21 family (2.7e-05);
GO_MF:GO:0005515, protein binding# (1e-19); GO_BP:GO:0006364, rRNA
processing# (4e-15); GO_CC:GO:0016020, membrane# (4e-34) 85
Fructose-6-phosphate-2-kinase/fructose-2,6-bisphosphatase n = 4 Tax
= Andropogoneae RepID = Q947C1_MAIZE 6 55.9 124531369 124550954
(0.0); CBM_20: Starch binding domain (0.0071); 6PF2K:
6-phosphofructo-2-kinase (2.6e-121); PGAM: Phosphoglycerate mutase
family (1.6e-33); GO_MF:GO:0030246, carbohydrate binding# (0.0);
GO_BP:GO:0016301, kinase activity# (0.0); GO_CC:GO:0043540,
IDA#6-phosphofructo-2-kinase/fructose- 2,6-biphosphatase 1 complex#
(8e-97) 86 RING-H2 finger protein ATL3F n = 2 Tax = Zea mays RepID
= B6U6T9_MAIZE (2e-75); PHD: PHD-finger 6 55.9 124551008 124551883
(0.066); zf-C3HC4: Zinc finger, C3HC4 type (RING finger) (2.8e-08);
GO_MF:GO:0046872, metal ion binding# (2e-75); GO_BP:GO:0010200,
IEP#response to chitin# (1e-15); GO_CC:GO:0016021, integral to
membrane# (1e-15) 87 Putative CCR4-associated factor 1 n = 2 Tax =
Oryza sativa RepID = Q5VPG5_ORYSJ (4e-72); CAF1: CAF1 6 55.9
124603474 124604545 family ribonuclease (8.7e-63);
GO_MF:GO:0003676, nucleic acid binding# (4e-72); GO_BP:GO:0045449,
regulation of transcription# (3e-45); GO_CC:GO:0005634, nucleus#
(4e-72) 88 Protein binding protein, putative n = 1 Tax = Ricinus
communis RepID = B9S0N5_RICCO (2e-33); PHD: PHD- 6 56 124658046
124668099 finger (0.019); zf-C3HC4: Zinc finger, C3HC4 type (RING
finger) (3.6e-07); GO_MF:GO:0046872, metal ion binding# (0.0) 89
PHD finger protein n = 4 Tax = Andropogoneae RepID = B4FK95_MAIZE
(1e-107); C1_3: C1-like domain 6 56.1 124705685 124710899 (0.091);
PHD: PHD-finger (3.4e-10); GO_MF:GO:0046872, metal ion binding#
(1e-107); GO_BP:GO:0046961, proton-transporting ATPase activity,
rotational mechanism# (2e-54); GO_CC:GO:0005634, nucleus# (4e-58)
90 Arginyl-tRNA synthetase n = 2 Tax = Zea mays RepID =
B4FMR1_MAIZE (0.0); Arg_tRNA_synt_N: Arginyl 6 56.2 124736591
124745075 tRNA synthetase N terminal do (1e-18); tRNA-synt_1d: tRNA
synthetases class I (R) (9.5e-117); DALR_1: DALR anticodon binding
domain (3.7e-48); GO_MF:GO:0016874, ligase activity# (0.0);
GO_BP:GO:0006420, arginyl-tRNA aminoacylation# (0.0);
GO_CC:GO:0005737, cytoplasm# (0.0) 91 Fasciclin-like
arabinogalactan protein 8 n = 2 Tax = Zea mays RepID = B6SL10_MAIZE
(1e-108); Fasciclin: 6 56.45 124803296 124805408 Fasciclin domain
(4.3e-18); GO_CC:GO:0046658, anchored to plasma membrane# (2e-36)
92 Arginine/serine-rich splicing factor, putative n = 1 Tax =
Ricinus communis RepID = B9SGV2_RICCO (1e-39); 6 56.8 124861967
124863604 zf-CCHC: Zinc knuckle (1.4e-05); zf-CCHC: Zinc knuckle
(6.9e-06); GO_MF:GO:0046872, metal ion binding# (1e-39);
GO_BP:GO:0008380, RNA splicing# (2e-32) 93 Putative receptor-like
protein kinase n = 2 Tax = Oryza sativa RepID = Q75IR9_ORYSJ (0.0);
Pkinase: Protein 6 56.8 124877371 124878770 kinase domain
(1.9e-32); Pkinase_Tyr: Protein tyrosine kinase (2.3e-23);
GO_MF:GO:0016301, kinase activity# (0.0); GO_BP:GO:0016301, kinase
activity# (0.0); GO_CC:GO:0016021, integral to membrane# (1e-141)
94 Aspartic proteinase oryzasin-1 n = 3 Tax = Zea mays RepID =
B6TSQ9_MAIZE (3e-51); GO_MF:GO:0016787, 6 56.8 124956620 124957402
hydrolase activity# (3e-51); GO_BP:GO:0006629, lipid metabolic
process# (3e-51); GO_CC:GO:0005773, IDA#vacuole# (1e-41) 95
Peroxidase (Fragment) n = 6 Tax = Zea mays RepID = Q6RFK0_MAIZE
(0.0); peroxidase: Peroxidase (2.4e-134); 6 56.8 125011395
125012945 GO_MF:GO:0046872, metal ion binding# (0.0);
GO_BP:GO:0055114, oxidation reduction# (0.0); GO_CC:GO:0016021,
integral to membrane# (2e-84) 96 Peroxidase (Fragment) n = 6 Tax =
Zea mays RepID = Q6RFK0_MAIZE (1e-157); peroxidase: Peroxidase 6
56.8 125155203 125156888 (4.3e-134); GO_MF:GO:0046872, metal ion
binding# (0.0); GO_BP:GO:0055114, oxidation reduction# (0.0);
GO_CC:GO:0016021, integral to membrane# (5e-86) 97 Chloroplast RelA
homologue 2 n = 2 Tax = Oryza sativa Japonica Group RepID =
Q9AYT4_ORYSJ (0.0); 6 56.8 125187331 125190275 RelA_SpoT: Region
found in RelA/SpoT proteins (6.3e-46); efhand: EF hand (0.0012);
efhand: EF hand (0.043); GO_MF:GO:0005509, calcium ion storage
activity# (0.0); GO_BP:GO:0015969, guanosine tetraphosphate
metabolic process# (0.0); GO_CC:GO:0009507, chloroplast# (1e-149)
98 Dihydrolipoyl dehydrogenase n = 3 Tax = Poaceae RepID =
B9FML1_ORYSJ (1e-61); Pyr_redox_2: Pyridine 6 56.8 125286546
125310756 nucleotide-disulphide oxidored (0.0013); Pyr_redox:
Pyridine nucleotide-disulphide oxidore (8.3e-16); GO_MF:GO:0050660,
FAD binding# (1e-61); GO_BP:GO:0055114, oxidation reduction#
(1e-61); GO_CC:GO:0005737, cytoplasm# (1e-61) 99 Retrotransposon
protein, putative, unclassified n = 1 Tax = Oryza sativa Japonica
Group RepID = Q2QSA6_ORYSJ 6 56.8 125334886 125345192 (1e-70);
GO_MF:GO:0003677, DNA binding# (1e-70); GO_BP:GO:0015074, DNA
integration# (1e-70); GO_CC:GO:0005634, nucleus# (7e-67) 100
Alpha-L-fucosidase 2 n = 3 Tax = Zea mays RepID = B6TDT3_MAIZE
(0.0); Lipase_GDSL: GDSL-like 6 56.8 125454576 125459572
Lipase/Acylhydrolase (9.8e-76); GO_MF:GO:0016788, hydrolase
activity, acting on ester bonds# (0.0); GO_BP:GO:0006629, lipid
metabolic process# (0.0); GO_CC:GO:0005576, extracellular region#
(8e-88) 101 Ubiquitin-protein ligase, putative n = 1 Tax = Ricinus
communis RepID = B9RZW1_RICCO (1e-114); HECT: 6 56.8 125545211
125554393 HECT-domain (ubiquitin-transferase) (4.5e-53);
GO_MF:GO:0016881, acid-amino acid ligase activity# (1e-123);
GO_BP:GO:0006464, protein modification process# (1e-123);
GO_CC:GO:0005622, intracellular# (1e-123) 102 Ubiquitin-protein
ligase, putative n = 1 Tax = Ricinus communis RepID = B9RZW1_RICCO
(2e-32); 6 56.8 125612410 125613737 GO_MF:GO:0016881, acid-amino
acid ligase activity# (7e-46); GO_BP:GO:0006464, protein
modification process# (7e-46); GO_CC:GO:0005622, intracellular#
(7e-46) 103 Putative aldose reductase-related protein n = 1 Tax =
Zea mays RepID = Q7FS90_MAIZE (2e-19); Kelch_1: 6 56.8 125628803
125629340 Kelch motif (1.6e-06); Kelch_2: Kelch motif (0.00097);
GO_MF:GO:0005515, protein binding# (5e-46); GO_BP:GO:0055114,
oxidation reduction# (2e-19) 104 Protein phosphatase 2C 35 n = 2
Tax = Oryza sativa RepID = P2C35_ORYSJ (5e-40); GO_MF:GO:0046872, 6
56.8 125630885 125631928 metal ion binding# (5e-40);
GO_BP:GO:0006952, defense response# (5e-40); GO_CC:GO:0016020,
membrane# (5e-40) 105 Replication protein A 70 kDa DNA-binding
subunit n = 3 Tax = Zea mays RepID = B6SL03_MAIZE (1e-141); 6 56.8
125632605 125635951 Rep_fac-A_C: Replication factor-A C terminal
domain (4e-66); GO_MF:GO:0003677, DNA binding# (1e-141);
GO_BP:GO:0006260, DNA replication# (1e-141); GO_CC:GO:0005634,
nucleus# (1e-141) 106 Retrotransposon protein, putative, Ty1-copia
subclass n = 1 Tax = Oryza sativa Japonica Group 6 56.8 125879055
125879270 RepID = Q2R0F7_ORYSJ (8e-17); GO_MF:GO:0003677, DNA
binding# (8e-17); GO_BP:GO:0015074, DNA integration# (8e-17) 107
Gibberellin 2-oxidase n = 1 Tax = Zea mays RepID = B6U889_MAIZE
(1e-139); 2OG-FeII_Oxy: 2OG-Fe(II) 6 56.8 125881243 125886353
oxygenase superfamily (0.008); GO_MF:GO:0016491, oxidoreductase
activity# (1e-139); GO_BP:GO:0055114, oxidation reduction#
(1e-139); GO_CC:GO:0016020, membrane# (3e-42) 108 Putative gag-pol
polyprotein n = 1 Tax = Oryza sativa Japonica Group RepID =
Q6UUN3_ORYSJ (4e-33); 6 56.8 125909464 125910136 GO_MF:GO:0004190,
penicillopepsin activity# (4e-33); GO_BP:GO:0015074, DNA
integration# (4e-33); GO_CC:GO:0005634, nucleus# (9e-29) 109 ATP
citrate lyase b-subunit n = 3 Tax = Papilionoideae RepID =
Q93YH3_LUPAL (6e-21); GO_MF:GO:0005524, 6 56.8 126000743 126001820
ATP binding# (6e-23); GO_BP:GO:0006085, NAS#acetyl-CoA biosynthetic
process# (1e-19) 110 Putative aspartic proteinase nepenthesin I n =
1 Tax = Oryza sativa Japonica Group RepID = Q69IP6_ORYSJ 6 56.8
126012128 126013728 (9e-45); Asp: Eukaryotic aspartyl protease
(1.6e-05); GO_MF:GO:0004190, penicillopepsin activity# (9e-45);
GO_BP:GO:0006508, proteolysis# (9e-45); GO_CC:GO:0005576,
extracellular region# (4e-41) 111 Transposon protein, putative,
CACTA, En/Spm sub-class n = 1 Tax = Oryza sativa Japonica Group 6
56.8 126014170 126016932 RepID = Q10BK1_ORYSJ (5e-59);
GO_MF:GO:0004803, transposase activity# (4e-92); GO_BP:GO:0006313,
transposition, DNA-mediated# (4e-92); GO_CC:GO:0016020, membrane#
(1e-33) 112 Putative uncharacterized protein n = 1 Tax = Zea mays
RepID = C0PP88_MAIZE (3e-32) 6 56.8 126063923 126064225 113
Putative uncharacterized protein Sb09g004490 n = 1 Tax = Sorghum
bicolor RepID = C5Z0L6_SORBI (4e-18); 6 56.8 126090413 126091289
GO_MF:GO:0030528, transcription regulator activity# (7e-10);
GO_BP:GO:0045449, regulation of transcription# (7e-10);
GO_CC:GO:0005634, nucleus# (7e-10) 114 Putative uncharacterized
protein n = 1 Tax = Zea mays RepID = C4JC40_MAIZE (8e-11) 6 56.8
126126609 126126863 115 CID11 n = 3 Tax = Andropogoneae RepID =
B4FZ16_MAIZE (1e-41); GO_MF:GO:0003676, nucleic acid 6 56.8
126130008 126133974 binding# (1e-41); GO_BP:GO:0006397, mRNA
processing# (4e-20); GO_CC:GO:0005634, nucleus# (4e-20) 116 USP
family protein n = 4 Tax = Andropogoneae RepID = B6TC12_MAIZE
(4e-65); Usp: Universal stress protein 6 56.8 126146579 126149276
family (1.6e-20); GO_MF:GO:0016818, hydrolase activity, acting on
acid anhydrides, in phosphorus-containing anhydrides# (1e-55);
GO_BP:GO:0006950, response to stress# (4e-65); GO_CC:GO:0005634,
nucleus# (1e-55) 117 DNA-directed RNA polymerase II 19 kDa
polypeptide n = 2 Tax = Andropogoneae RepID = B4FXC7_MAIZE 6 56.8
126149278 126152151 (2e-98); RNA_pol_Rpb7_N: RNA polymerase Rpb7,
N-terminal domain (6.2e-13); RNA_pol_Rbc25: RNA polymerase III
subunit Rpc25 (0.059); GO_MF:GO:0003899, DNA-directed RNA
polymerase III activity# (2e-98); GO_BP:GO:0006350, transcription#
(2e-98); GO_CC:GO:0080137, IPI#DNA-directed RNA polymerase V
complex# (1e-48) 118 Putative uncharacterized protein Sb10g005530 n
= 1 Tax = Sorghum bicolor RepID = C5Z5H0_SORBI (6e-25) 6 56.8
126152259 126152825 119 Pyrophosphate-energized vacuolar membrane
proton pump n = 2 Tax = Andropogoneae RepID = B6UEE8_MAIZE 6 56.8
126196881 126200082 (0.0); H_PPase: Inorganic H+ pyrophosphatase
(0); OPT: OPT oligopeptide transporter protein (0.048); DUF540:
Protein of unknown function (DUF540) (0.096); GO_MF:GO:0009678,
hydrogen-translocating pyrophosphatase activity# (0.0);
GO_BP:GO:0015992, proton transport# (0.0); GO_CC:GO:0016020,
membrane# (0.0) 120 Putative uncharacterized protein n = 1 Tax =
Zea mays RepID = B6U5J9_MAIZE (2e-16) 6 56.8 126286798 126287445
121 Putative polyprotein n = 1 Tax = Oryza sativa Japonica Group
RepID = Q65XD2_ORYSJ (2e-16); 6 56.8 126290188 126291608
GO_MF:GO:0004190, penicillopepsin activity# (2e-16);
GO_BP:GO:0015074, DNA integration# (2e-16); GO_CC:GO:0005634,
nucleus# (8e-16) 122 Polyprotein n = 1 Tax = Oryza sativa Japonica
Group RepID = Q8W150_ORYSJ (1e-30); GO_MF:GO:0003964, 6 56.8
126292009 126292632 RNA-directed DNA polymerase, group II intron
encoded# (1e-30); GO_BP:GO:0015074, DNA integration# (1e-30);
GO_CC:GO:0005634, nucleus# (1e-30) 123 Putative SMEK homolog 3 n =
2 Tax = Mus musculus RepID = SMEK3_MOUSE (8e-19); GO_MF:GO:0005488,
6 56.8 126343969 126349725 binding# (2e-47) 124 Putative
polyprotein n = 1 Tax = Zea mays RepID = Q8SA93_MAIZE (1e-160);
DUF625: Protein of unknown 6 56.8 126358241 126418203 function
(DUF625) (8.6e-57); GO_MF:GO:0003964, RNA-directed DNA polymerase,
group II intron encoded# (1e-160); GO_BP:GO:0015074, DNA
integration# (1e-160); GO_CC:GO:0005634, nucleus# (1e-160) 125
OSJNBa0065O17.7 protein n = 1 Tax = Oryza sativa Japonica Group
RepID = Q7XPS4_ORYSJ (2e-40); 6 56.8 126362377 126368009
GO_MF:GO:0003964, RNA-directed DNA polymerase, group II intron
encoded# (2e-40); GO_BP:GO:0015074, DNA integration# (2e-40) 126
Tubulin gamma-1 chain n = 28 Tax = Embryophyta RepID = TBG1_ARATH
(0.0); Tubulin: Tubulin/FtsZ family, 6 56.8 126579166 126583379
GTPase domain (3.7e-94); Tubulin_C: Tubulin/FtsZ family, C-terminal
domain (1.2e-58); GO_MF:GO:0005525, GTP binding# (0.0);
GO_BP:GO:0051641, IMP#cellular localization# (0.0);
GO_CC:GO:0043234, protein complex# (0.0) 127 Putative
uncharacterized protein Sb01g009200 n = 3 Tax = Andropogoneae RepID
= C5WLY8_SORBI (1e-26); 6 56.8 126648784 126649020
GO_MF:GO:0008375, acetylglucosaminyltransferase activity# (1e-11);
GO_CC:GO:0016020, membrane# (1e-11) 128 Chaperone protein dnaJ,
putative n = 1 Tax = Ricinus communis RepID = B9RNG7_RICCO
(1e-141); DnaJ: DnaJ 6 56.8 126678899 126686639 domain (1e-36);
DnaJ_C: DnaJ C terminal region (1.6e-18); GO_MF:GO:0051082,
unfolded protein binding# (1e-145); GO_BP:GO:0006457, protein
folding# (1e-145); GO_CC:GO:0005886, plasma membrane# (1e-139) 129
Putative uncharacterized protein Sb02g029480 n = 2 Tax =
Andropogoneae RepID = C5X5A3_SORBI (8e-23); 6 56.8 126761961
126762272 GO_MF:GO:0005515, protein binding# (5e-16);
GO_CC:GO:0005737, cytoplasm# (5e-16) 130 Protein disulfide
isomerase n = 2 Tax = Andropogoneae RepID = Q5EUD6_MAIZE (0.0);
Thioredoxin: 6 56.8 126779705 126784442 Thioredoxin (2.5e-49);
AhpC-TSA: AhpC/TSA family (0.034); Thioredoxin: Thioredoxin
(2.9e-57); ERp29: Endoplasmic reticulum protein ERp29, C-te
(3.3e-46); GO_MF:GO:0016853, isomerase activity# (0.0);
GO_BP:GO:0045454, cell redox homeostasis# (0.0); GO_CC:GO:0005783,
IDA#endoplasmic reticulum# (0.0) 131 Retrotransposon protein,
putative, unclassified n = 2 Tax = Oryza sativa Japonica Group
RepID = Q2QZV1_ORYSJ 6 56.8 126790130 126790810 (2e-26);
GO_MF:GO:0003964, RNA-directed DNA polymerase, group II intron
encoded# (2e-29); GO_BP:GO:0006278, RNA-dependent DNA replication#
(2e-29); GO_CC:GO:0005634, nucleus# (4e-21) 132 Gamma-tubulin
complex component, putative n = 1 Tax = Ricinus communis RepID =
B9SAS5_RICCO (0.0); 6 56.8 126812997 126837059 Spc97_Spc98:
Spc97/Spc98 family (9.1e-144); GO_MF:GO:0005515, protein binding#
(0.0); GO_BP:GO:0000226, microtubule cytoskeleton organization#
(0.0); GO_CC:GO:0005815, microtubule organizing center# (0.0) 133
Putative AC transposase n = 1 Tax = Zea mays RepID = TRA1_MAIZE
(0.0); zf-BED: BED zinc finger (4.4e-05); 6 56.8 126822114
126824371 hATC: hAT family dimerisation domain (1.2e-38);
GO_MF:GO:0046983, protein dimerization activity# (0.0);
GO_BP:GO:0032196, transposition# (0.0) 134 Putative polyprotein n =
1 Tax = Zea mays RepID = Q8SA93_MAIZE (2e-26); GO_MF:GO:0003964,
RNA- 6 56.8 126826110 126831487 directed DNA polymerase, group II
intron encoded# (2e-26); GO_BP:GO:0015074, DNA integration#
(2e-26); GO_CC:GO:0005634, nucleus# (2e-26) 135 F6D8.18 protein n =
11 Tax = rosids RepID = Q9SSR2_ARATH (1e-22); GO_MF:GO:0008233,
peptidase activity# 6 56.8 126872786 126877517 (1e-24);
GO_BP:GO:0006508, proteolysis# (1e-24); GO_CC:GO:0016020, membrane#
(1e-24) 136 Ulp1 protease family, C-terminal catalytic domain
containing protein n = 2 Tax = Oryza sativa Japonica Group 6 56.8
126877369 126879300 RepID = Q109R5_ORYSJ (5e-34); Peptidase_C48:
Ulp1 protease family, C-terminal catalytic domain (5.8e-13);
GO_MF:GO:0008234, cysteine-type peptidase activity# (1e-129);
GO_BP:GO:0006508, proteolysis# (1e-129) 137 VIP2 protein n = 1 Tax
= Avena fatua RepID = Q9M4C5_AVEFA (1e-171); zf-C3HC4: Zinc finger,
C3HC4 type 6 56.8 126957235 126967077 (RING finger) (4.8e-05);
zf-RING-like: RING-like domain (0.095); GO_MF:GO:0046872, metal ion
binding# (1e-171); GO_BP:GO:0004842, NAS#ubiquitin-protein ligase
activity# (2e-43) 138 Putative ABI3-interacting protein 2 n = 1 Tax
= Oryza sativa Japonica Group RepID = Q6K486_ORYSJ (5e-09); 6 56.8
126982783 126983154 GO_BP:GO:0000226, microtubule cytoskeleton
organization# (5e-09); GO_CC:GO:0005874, microtubule# (5e-09) 139
ATP binding protein n = 2 Tax = Andropogoneae RepID = B6SXM5_MAIZE
(0.0); Kinesin: Kinesin motor domain 6 56.8 127109946 127127395
(1.2e-125); GO_MF:GO:0005524, ATP binding# (0.0); GO_BP:GO:0007018,
microtubule-based movement# (0.0); GO_CC:GO:0005874, microtubule#
(0.0) 140 Putative polyprotein n = 1 Tax = Zea mays RepID =
Q8SA93_MAIZE (2e-62); RVT_1: Reverse transcriptase 6 56.8 127112084
127116226 (RNA-dependent DN (0.00015); GO_MF:GO:0003964,
RNA-directed DNA polymerase, group II intron encoded# (2e-62);
GO_BP:GO:0015074, DNA integration# (2e-62); GO_CC:GO:0005634,
nucleus# (2e-62) 141 Putative polyprotein n = 1 Tax = Zea mays
RepID = Q8SA93_MAIZE (1e-28); GO_MF:GO:0003964, RNA- 6 56.8
127116846 127117349
directed DNA polymerase, group II intron encoded# (1e-28);
GO_BP:GO:0006355, regulation of transcription, DNA-dependent#
(1e-34); GO_CC:GO:0005634, nucleus# (1e-34) 142 Putative
polyprotein n = 1 Tax = Zea mays RepID = Q8SA93_MAIZE (6e-62);
GO_MF:GO:0003964, RNA- 6 56.8 127129438 127130136 directed DNA
polymerase, group II intron encoded# (6e-62); GO_BP:GO:0015074, DNA
integration# (6e-62); GO_CC:GO:0005634, nucleus# (6e-62) 143
Serine/threonine-protein phosphatase n = 2 Tax = Andropogoneae
RepID = C5Z0J0_SORBI (1e-175); Metallophos: 6 56.8 127199789
127203947 Calcineurin-like phosphoesterase (1.3e-44);
GO_MF:GO:0016787, hydrolase activity# (1e-163); GO_BP:GO:0004721,
phosphoprotein phosphatase activity# (1e-163); GO_CC:GO:0016459,
myosin complex# (1e-128) 144 Putative uncharacterized protein n = 1
Tax = Zea mays RepID = B6UAL2_MAIZE (2e-23) 6 56.8 127262064
127265900 145 Putative uncharacterized protein n = 1 Tax = Zea mays
RepID = B6UAL2_MAIZE (3e-17) 6 56.8 127283052 127283372 146 HAT
family dimerisation domain containing protein n = 1 Tax = Oryza
sativa Japonica Group 6 56.8 127360096 127364045 RepID =
Q8LNK9_ORYSJ (0.0); zf-BED: BED zinc finger (9.6e-08); hATC: hAT
family dimerisation domain (4.6e-39); GO_MF:GO:0046983, protein
dimerization activity# (0.0); GO_BP:GO:0006468, protein amino acid
phosphorylation# (3e-92) 147 Ribosomal protein L18 n = 16 Tax =
Poaceae RepID = Q5WMY3_ORYSJ (3e-99); Ribosomal_L18e: Eukaryotic 6
56.8 127372821 127376997 ribosomal protein L18 (7.2e-127);
GO_MF:GO:0003735, structural constituent of ribosome# (3e-99);
GO_BP:GO:0006412, translation# (3e-99); GO_CC:GO:0030529,
ribonucleoprotein complex# (3e-99) 148 Ethylene receptor protein n
= 1 Tax = Musa acuminata AAA Group RepID = A1IIY0_MUSAC (0.0); GAF:
GAF 6 56.8 127377761 127381836 domain (1.6e-07); HisKA: His Kinase
A (phosphoacceptor) domain (6.3e-20); HATPase_c: Histidine kinase-,
DNA gyrase B-, and HSP90-like ATPase (4.6e-31); GO_MF:GO:0016772,
transferase activity, transferring phosphorus-containing groups#
(0.0); GO_BP:GO:0018106, peptidyl-histidine phosphorylation# (0.0);
GO_CC:GO:0016020, membrane# (0.0) 149 Putative uncharacterized
protein Sb09g004315 (Fragment) n = 1 Tax = Sorghum bicolor RepID =
C5Z0J6_SORBI 6 56.8 127445565 127447307 (1e-14); GO_MF:GO:0046872,
metal ion binding# (2e-09); GO_BP:GO:0006355, regulation of
transcription, DNA-dependent# (2e-09) 150 Importin subunit alpha-1b
n = 5 Tax = Poaceae RepID = IMA1B_ORYSJ (0.0); IBB: Importin beta
binding domain 6 56.8 127496705 127501662 (8.7e-27); Arm:
Armadillo/beta-catenin-like repeat (4); HEAT: HEAT repeat (30);
Arm: Armadillo/beta-catenin- like repeat (5.1e-11); HEAT: HEAT
repeat (5.1); Arm: Armadillo/beta-catenin-like repeat (1.3e-14);
HEAT: HEAT repeat (8.1e-05); Arm: Armadillo/beta-catenin-like
repeat (4.5e-08); Arm: Armadillo/beta-catenin-like repeat
(1.1e-06); HEAT: HEAT repeat (1.5); Arm:
Armadillo/beta-catenin-like repeat (2.1e-10); HEAT: HEAT repeat
(1.5); Arm: Armadillo/beta-catenin-like repeat (8e-11); HEAT: HEAT
repeat (9.3); Arm: Armadillo/beta- catenin-like repeat (1.7e-13);
HEAT: HEAT repeat (30); Arm: Armadillo/beta-catenin-like repeat
(4.5e-07); HEAT: HEAT repeat (37); GO_MF:GO:0008565, protein
transporter activity# (0.0); GO_BP:GO:0015031, protein transport#
(0.0); GO_CC:GO:0048471, ISS#perinuclear region of cytoplasm# (0.0)
151 WRKY67-superfamily of TFs having WRKY and zinc finger domains n
= 2 Tax = Zea mays 6 56.8 127590782 127592172 RepID = B6T4Y9_MAIZE
(7e-51); FAR1: FAR1 family (0.0056); WRKY: WRKY DNA-binding domain
(7.5e-36); GO_MF:GO:0043565, sequence-specific DNA binding#
(4e-81); GO_BP:GO:0045449, regulation of transcription# (4e-81);
GO_CC:GO:0005634, nucleus# (4e-81) 152 Putative uncharacterized
protein Sb05g019580 n = 1 Tax = Sorghum bicolor RepID =
C5Y395_SORBI (2e-10) 6 56.8 127598820 127599045 153 Putative
uncharacterized protein n = 2 Tax = Zea mays RepID = B6SQA8_MAIZE
(8e-56) 6 56.8 127633793 127634935 154 H0103C06.4 protein n = 1 Tax
= Oryza sativa RepID = Q259H8_ORYSA (4e-28); GO_MF:GO:0046983,
protein 6 56.8 127659907 127661365 dimerization activity# (3e-28)
155 Alpha-L-fucosidase 2 n = 2 Tax = Zea mays RepID = B6TLP8_MAIZE
(2e-66); Lipase_GDSL: GDSL-like 6 56.8 127663965 127666621
Lipase/Acylhydrolase (3.5e-07); Gp_dh_N: Glyceraldehyde 3-phosphate
dehydrogenase, (1.3e-07); GO_MF:GO:0016788, hydrolase activity,
acting on ester bonds# (1e-113); GO_BP:GO:0006629, lipid metabolic
process# (1e-113); GO_CC:GO:0005576, extracellular region# (2e-49)
156 Putative uncharacterized protein n = 2 Tax = Zea mays RepID =
B6SQA8_MAIZE (2e-81) 6 56.8 127687297 127688865 157
OSJNBa0040D17.12 protein n = 2 Tax = Oryza sativa Japonica Group
RepID = Q7XX95_ORYSJ (1e-148); 6 56.8 127714984 127716689
Transferase: Transferase family (1.6e-40); GO_MF:GO:0016747,
transferase activity, transferring acyl groups other than
amino-acyl groups# (1e-146) 158 Putative uncharacterized protein
Sb09g005695 n = 3 Tax = Andropogoneae RepID = C5YU84_SORBI
(1e-180); 6 56.8 127766680 127770452 GO_MF:GO:0004803, transposase
activity# (2e-43); GO_BP:GO:0006313, transposition, DNA-mediated#
(2e-43) 159 BZIP transcription factor bZIP109 n = 3 Tax = Glycine
max RepID = Q0GPG4_SOYBN (5e-49); DUF1664: Protein 6 56.8 127774370
127787122 of unknown function (DUF1664) (3.1e-67) 160 Putative
uncharacterized protein Sb08g000780 n = 1 Tax = Sorghum bicolor
RepID = C5YQ53_SORBI (3e-20) 6 56.8 127859677 127860013 161 FACT
complex subunit SSRP1-B n = 3 Tax = Oryza sativa RepID =
SSP1B_ORYSJ (0.0); SSrecog: Structure- 6 56.8 127883928 127890893
specific recognition protein (4.6e-144); Rtt106: Histone chaperone
Rttp106-like (1.2e-56); HMG_box: HMG (high mobility group) box
(3.2e-22); GO_MF:GO:0003677, DNA binding# (0.0); GO_BP:GO:0045449,
regulation of transcription# (0.0); GO_CC:GO:0005694, chromosome#
(0.0) 162 Tetratricopeptide repeat domain protein n = 1 Tax =
Microcoleus chthonoplastes PCC 7420 6 56.8 127893148 127895627
RepID = B4VZS1_9CYAN (6e-15); TPR_2: Tetratricopeptide repeat
(0.072); TPR_2: Tetratricopeptide repeat (4.7); TPR_2:
Tetratricopeptide repeat (28); GO_MF:GO:0005488, binding# (1e-160);
GO_BP:GO:0019684, photosynthesis, light reaction# (2e-15);
GO_CC:GO:0009941, IDA#chloroplast envelope# (5e-27) 163
Bifunctional protein tilS/hprT n = 3 Tax = Andropogoneae RepID =
B6SSV8_MAIZE (3e-85); Pribosyltran: 6 56.8 127898464 127901020
Phosphoribosyl transferase domain (2.3e-24); GO_MF:GO:0016740,
transferase activity# (3e-85); GO_BP:GO:0009116, nucleoside
metabolic process# (3e-85); GO_CC:GO:0005737, cytoplasm# (3e-85)
164 3'-N-debenzoyltaxol N-benzoyltransferase-like n = 2 Tax = Oryza
sativa RepID = Q9LGF6_ORYSJ (1e-170); 6 56.8 128052937 128055250
Transferase: Transferase family (1.5e-49); GO_MF:GO:0016747,
transferase activity, transferring acyl groups other than
amino-acyl groups# (0.0) 165 60S ribosomal protein L13 n = 14 Tax =
Poaceae RepID = Q7XJB4_ORYSJ (1e-60); Ribosomal_L13e: Ribosomal 6
56.8 128062357 128064852 protein L13e (1.6e-90); GO_MF:GO:0003735,
structural constituent of ribosome# (1e-60); GO_BP:GO:0006412,
translation# (1e-60); GO_CC:GO:0030529, ribonucleoprotein complex#
(1e-60) 166 PRP38 pre-mRNA processing factor 38 domain containing B
n = 3 Tax = Andropogoneae 6 56.8 128201353 128207921 RepID =
B6TSE1_MAIZE (1e-112); PRP38: PRP38 family (1.4e-26); DUF1777:
Protein of unknown function (DUF1777) (0.022); GO_MF:GO:0004437,
inositol or phosphatidylinositol phosphatase activity# (9e-37);
GO_BP:GO:0009651, IEP#response to salt stress# (1e-110);
GO_CC:GO:0005681, spliceosomal complex# (4e-38) 167 Macrophage
erythroblast attacher n = 2 Tax = Andropogoneae RepID =
B6TF70_MAIZE (1e-133); 6 56.85 125268872 125272587
GO_MF:GO:0003779, actin binding# (2e-40); GO_BP:GO:0051301, cell
division# (2e-40); GO_CC:GO:0016363, nuclear matrix# (2e-40) 168
Protein TOC75, chloroplastic n = 3 Tax = Oryza sativa RepID =
TOC75_ORYSJ (2e-22); GO_MF:GO:0015450, 6 56.9 125224666 125225259
P--P-bond-hydrolysis-driven protein transmembrane transporter
activity# (3e-19); GO_BP:GO:0015031, protein transport# (2e-22);
GO_CC:GO:0019867, outer membrane# (2e-22) 169 Ribosomal protein
S27a, isoform CRA_c n = 9 Tax = Euteleostomi RepID = B2RDW1_HUMAN
(4e-59); ubiquitin: 6 56.9 125241154 125242015 Ubiquitin family
(2.9e-38); Ribosomal_S27: Ribosomal protein S27a (4.2e-30);
GO_MF:GO:0003735, structural constituent of ribosome# (1e-57);
GO_BP:GO:0006412, translation# (1e-57); GO_CC:GO:0005840, ribosome#
(1e-57) 170 Retrotransposon protein, putative, Ty3-gypsy subclass n
= 2 Tax = Oryza sativa RepID = Q7XGB8_ORYSJ (8e-10); 6 56.9
125241943 125247539 GO_MF:GO:0008270, zinc ion binding# (8e-10);
GO_BP:GO:0015074, DNA integration# (8e-10) 171 Retrotransposon
protein, putative, unclassified n = 1 Tax = Oryza sativa Japonica
Group RepID = Q2R3U8_ORYSJ 6 56.9 125247227 125248186 (7e-66);
GO_MF:GO:0003677, DNA binding# (7e-66); GO_BP:GO:0015074, DNA
integration# (7e-66) 172 WD-repeat protein, putative n = 1 Tax =
Ricinus communis RepID = B9RVD2_RICCO (3e-33); 6 56.9 125265027
125267222 GO_BP:GO:0010072, IGI#primary shoot apical meristem
specification# (2e-33); GO_CC:GO:0005829, IDA#cytosol# (3e-33) 173
Putative uncharacterized protein n = 1 Tax = Zea mays RepID =
B6T0R3_MAIZE (4e-13); DVL: DVL family 6 56.9 128132458 128133047
(1.1e-08) 174 Protein binding protein n = 2 Tax = Andropogoneae
RepID = B6TV66_MAIZE (0.0); PHD: PHD-finger (0.048); zf- 6 56.9
128159679 128163410 C3HC4: Zinc finger, C3HC4 type (RING finger)
(6.8e-09); GO_MF:GO:0046872, metal ion binding# (0.0);
GO_CC:GO:0005886, plasma membrane# (5e-23) 175 Putative
serine/threonine protein phosphatase 2A (PP2A) regulatory subunit
B' (B'gamma) n = 1 Tax = Oryza 6 56.9 128299646 128308939 sativa
Japonica Group RepID = Q5VRD6_ORYSJ (0.0); B56: Protein phosphatase
2A regulatory B subunit (B56 family) (7.4e-224); GO_MF:GO:0008601,
protein phosphatase type 2A regulator activity# (0.0);
GO_BP:GO:0008601, protein phosphatase type 2A regulator activity#
(0.0); GO_CC:GO:0000159, protein phosphatase type 2A complex# (0.0)
176 Gibberellin 3-beta-dioxygenase 2-2 n = 4 Tax = Zea mays RepID =
B6UAD7_MAIZE (0.0); 2OG-FeII_Oxy: 2OG- 6 56.9 128315121 128316850
Fe(II) oxygenase superfamily (3.8e-29); GO_MF:GO:0016702,
oxidoreductase activity, acting on single donors with incorporation
of molecular oxygen, incorporation of two atoms of oxygen# (0.0);
GO_BP:GO:0055114, oxidation reduction# (0.0); GO_CC:GO:0005737,
cytoplasm# (1e-51) 177 Ankyrin repeat family protein-like n = 2 Tax
= Oryza sativa RepID = Q69TB9_ORYSJ (4e-66); Ank: Ankyrin 6 56.9
128318222 128321074 repeat (11); Ank: Ankyrin repeat (0.41); Ank:
Ankyrin repeat (0.23); Ank: Ankyrin repeat (0.0015); Ank: Ankyrin
repeat (2.9); Ank: Ankyrin repeat (0.006); GO_MF:GO:0008234,
cysteine-type peptidase activity# (4e-66); GO_BP:GO:0006508,
proteolysis# (4e-66) 178 Cytokinin-O-glucosyltransferase 1 n = 2
Tax = Zea mays RepID = B4FAT6_MAIZE (0.0); UDPGT: UDP- 6 57
128420330 128421841 glucoronosyl and UDP-glucosyl transferase
(3e-07); GO_MF:GO:0016758, transferase activity, transferring
hexosyl groups# (0.0); GO_BP:GO:0008152, metabolic process# (0.0);
GO_CC:GO:0016021, integral to membrane# (1e-104) 179 Probable
cellulose synthase A catalytic subunit 1 [UDP-forming] n = 15 Tax =
Poaceae RepID = CESA1_ORYSJ 6 57.05 128560617 128567283 (0.0); PHD:
PHD-finger (0.011); zf-C3HC4: Zinc finger, C3HC4 type (RING finger)
(0.05); Cellulose_synt: Cellulose synthase (0); GO_MF:GO:0046872,
metal ion binding# (0.0); GO_BP:GO:0030244, cellulose biosynthetic
process# (0.0); GO_CC:GO:0016021, integral to membrane# (0.0) 180
Putative uncharacterized protein n = 1 Tax = Zea mays RepID =
B6TYR3_MAIZE (2e-39); GO_MF:GO:0005488, 6 57.1 128455019 128455534
binding# (9e-11) 181 Putative uncharacterized protein n = 2 Tax =
Zea mays RepID = B6SN58_MAIZE (5e-31); GO_MF:GO:0005488, 6 57.1
128465318 128466183 binding# (1e-09) 182 Putative uncharacterized
protein Sb09g005320 n = 2 Tax = Andropogoneae RepID = C5Z157_SORBI
(1e-20) 6 57.1 128467513 128484308 183 17.5 kDa class II heat shock
protein n = 1 Tax = Zea mays RepID = B6U175_MAIZE (3e-52); HSP20: 6
57.1 128470652 128471159 Hsp20/alpha crystallin family (0.0014);
GO_MF:GO:0051082, unfolded protein binding# (9e-11);
GO_BP:GO:0006950, response to stress# (3e-52); GO_CC:GO:0005737,
cytoplasm# (1e-35) 184 Putative uncharacterized protein Sb04g007000
n = 1 Tax = Sorghum bicolor RepID = C5XXW4_SORBI (2e-10) 6 57.1
128501719 128502463 185 Putative wall-associated serine/threonine
kinase n = 1 Tax = Oryza sativa Japonica Group 6 57.1 128520533
128525078 RepID = Q6ZK05_ORYSJ (1e-177); Pkinase: Protein kinase
domain (2.2e-39); Pkinase_Tyr: Protein tyrosine kinase (3.6e-34);
GO_MF:GO:0016301, kinase activity# (1e-177); GO_BP:GO:0016301,
kinase activity# (1e-177) 186 Lactoylglutathione lyase n = 1 Tax =
Zea mays RepID = B6UGW8_MAIZE (2e-92); Glyoxalase: 6 57.1 128580829
128583989 Glyoxalase/Bleomycin resistance protein/Dioxygenase
superfamily (7e-07); GO_MF:GO:0016829, lyase activity# (2e-92) 187
Isoform 2 of Probable protein phosphatase 2C 48 n = 1 Tax = Oryza
sativa Japonica Group RepID = Q6L482-2 6 57.2 128601099 128602653
(3e-10); GO_MF:GO:0046872, metal ion binding# (4e-10);
GO_BP:GO:0004721, phosphoprotein phosphatase activity# (4e-10) 188
Transposon protein, putative, CACTA, En/Spm sub-class n = 1 Tax
=
Oryza sativa Japonica Group 6 57.2 128635663 128637800 RepID =
Q10N80_ORYSJ (2e-50); GO_MF:GO:0004803, transposase activity#
(2e-50); GO_BP:GO:0006313, transposition, DNA-mediated# (2e-50);
GO_CC:GO:0005783, IDA#endoplasmic reticulum# (2e-27) 189 Nucleotide
sugar translocator BT2A n = 4 Tax = Zea mays RepID = B2LWG5_MAIZE
(0.0); Mito_carr: 6 57.2 128638388 128642377 Mitochondrial carrier
protein (6.6e-26); Mito_carr: Mitochondrial carrier protein
(1.1e-34); Mito_carr: Mitochondrial carrier protein (5.9e-33);
GO_MF:GO:0005488, binding# (0.0); GO_BP:GO:0055085, transmembrane
transport# (0.0); GO_CC:GO:0016021, integral to membrane# (0.0) 190
Putative uncharacterized protein n = 1 Tax = Zea mays RepID =
B6SUB9_MAIZE (4e-99) 6 57.3 128663003 128666303 191 OSJNBa0053K19.6
protein n = 5 Tax = Poaceae RepID = Q7X809_ORYSJ (1e-58);
GO_MF:GO:0016491, 6 57.3 128667645 128669160 oxidoreductase
activity# (1e-58); GO_BP:GO:0055114, oxidation reduction# (1e-58);
GO_CC:GO:0005777, IDA#peroxisome# (1e-44) 192 Phospholipase D alpha
1 n = 7 Tax = Poaceae RepID = PLDA1_ORYSJ (0.0); C2: C2 domain
(7.6e-06); PLDc: 6 57.4 128722429 128725039 Phospholipase D. Active
site motif (1.2e-09); PLDc: Phospholipase D. Active site motif
(1.4e-08); GO_MF:GO:0005509, calcium ion storage activity# (0.0);
GO_BP:GO:0046470, phosphatidylcholine metabolic process# (0.0);
GO_CC:GO:0016020, membrane# (0.0) 193 Putative uncharacterized
protein n = 1 Tax = Zea mays RepID = B4FWV4_MAIZE (4e-69) 6 57.4
128734831 128736354 194 CDPK-related protein kinase n = 1 Tax = Zea
mays RepID = B6SYP7_MAIZE (2e-67); Pkinase: Protein kinase 6 57.5
128754439 128759348 domain (3.2e-09); Pkinase_Tyr: Protein tyrosine
kinase (3.5e-06); WD40: WD domain, G-beta repeat (0.011); WD40: WD
domain, G-beta repeat (0.0046); GO_MF:GO:0016740, transferase
activity# (9e-87); GO_BP:GO:0016301, kinase activity# (9e-87);
GO_CC:GO:0005886, plasma membrane# (1e-55) 195 Putative
uncharacterized protein n = 2 Tax = Zea mays RepID = Q5GAU8_MAIZE
(9e-27) 6 57.5 128781974 128782353 196 NBS-LRR class disease
resistance protein n = 1 Tax = Oryza sativa Japonica Group RepID =
B5UBC0_ORYSJ 6 57.5 128790205 128798880 (0.0); NB-ARC: NB-ARC
domain (1.1e-35); GO_MF:GO:0017111, nucleoside-triphosphatase
activity# (0.0); GO_BP:GO:0006952, defense response# (0.0) 197
Putative uncharacterized protein n = 2 Tax = Zea mays RepID =
B6TX07_MAIZE (1e-112); IQ: IQ calmodulin- 6 57.6 128819708
128821261 binding motif (7.9e-05); IQ: IQ calmodulin-binding motif
(0.0012) 198 Putative Mlal n = 1 Tax = Sorghum bicolor RepID =
Q8LJZ8_SORBI (1e-143); NB-ARC: NB-ARC domain 6 57.6 128825273
128833947 (1.4e-57); NACHT: NACHT domain (0.036); LRR_1: Leucine
Rich Repeat (9); LRR_1: Leucine Rich Repeat (2.4); LRR_1: Leucine
Rich Repeat (1.6); LRR_1: Leucine Rich Repeat (45); LRR_1: Leucine
Rich Repeat (3e+02); LRR_1: Leucine Rich Repeat (43);
GO_MF:GO:0005524, ATP binding# (1e-149); GO_BP:GO:0006952, defense
response# (1e-149) 199 Putative RGH1A n = 1 Tax = Oryza sativa
Japonica Group RepID = Q6Z021_ORYSJ (1e-16); 6 57.6 128827662
128828455 GO_MF:GO:0005524, ATP binding# (1e-16); GO_BP:GO:0006952,
defense response# (1e-16) 200 Putative serine/threonine protein
kinase (Fragment) n = 1 Tax = Oryza sativa Japonica Group 6 57.6
128927057 128927892 RepID = Q84P73_ORYSJ (9e-16); GO_MF:GO:0005524,
ATP binding# (4e-17); GO_BP:GO:0016567, IGI#protein ubiquitination#
(4e-17); GO_CC:GO:0000151, ubiquitin ligase complex# (4e-17) 201
Putative Avr9/Cf-9 rapidly elicited protein n = 1 Tax = Oryza
sativa Japonica Group RepID = 6 57.6 129025487 129026094
Q6EUK7_ORYSJ (1e-09); GO_MF:GO:0005488, binding# (1e-09);
GO_BP:GO:0016567, IGI#protein ubiquitination# (1e-09);
GO_CC:GO:0000151, ubiquitin ligase complex# (1e-09) 202 H0716A07.11
protein n = 1 Tax = Oryza sativa RepID = Q01MA7_ORYSA (0.0);
Inhibitor_I9: Peptidase inhibitor 6 57.6 129031227 129036927 I9
(1.2e-19); Peptidase_S8: Subtilase family (3.6e-10); PA: PA domain
(9.8e-05); GO_MF:GO:0043086, negative regulation of catalytic
activity# (0.0); GO_BP:GO:0043086, negative regulation of catalytic
activity# (0.0); GO_CC:GO:0009505, IDA#expansin# (1e-153) 203
Inositol-3-phosphate synthase n = 16 Tax = Magnoliophyta RepID =
INO1_ORYSJ (1e-27); GO_MF:GO:0016853, 6 57.6 129042421 129042715
isomerase activity# (1e-27); GO_BP:GO:0008654, phospholipid
biosynthetic process# (1e-27); GO_CC:GO:0005737, cytoplasm# (1e-27)
204 Inositol-3-phosphate synthase n = 16 Tax = Magnoliophyta RepID
= INO1_ORYSJ (1e-108); NAD_binding_5: 6 57.6 129042809 129044242
Myo-inositol-1-phosphate synthase (3.4e-08); Inos-1-P_synth:
Myo-inositol-1-phosphate synthase (2.2e-61); GO_MF:GO:0016853,
isomerase activity# (1e-108); GO_BP:GO:0008654, phospholipid
biosynthetic process# (1e-108); GO_CC:GO:0005737, cytoplasm#
(1e-108) 205 Leaf senescence related protein-like n = 2 Tax = Oryza
sativa RepID = Q69RQ8_ORYSJ (2e-18); IBB: Importin 6 57.6 129045552
129049517 beta binding domain (0.076); GO_MF:GO:0008565, protein
transporter activity# (1e-14); GO_BP:GO:0015031, protein transport#
(1e-14); GO_CC:GO:0048471, ISS#perinuclear region of cytoplasm#
(1e-14) 206 Xylanase inhibitor protein 1 n = 1 Tax = Zea mays RepID
= B6U2X8_MAIZE (1e-170); Glyco_hydro_18: Glycosyl 6 57.6 129086009
129087210 hydrolases family 18 (1.2e-19); GO_MF:GO:0043169, cation
binding# (1e-170); GO_BP:GO:0045493, xylan catabolic process#
(1e-170); GO_CC:GO:0005576, extracellular region# (2e-87) 207
Putative uncharacterized protein n = 1 Tax = Oryza sativa Indica
Group RepID = A2YUK8_ORYSI (1e-15) 6 57.6 129126147 129126488 208
Putative transposon protein n = 1 Tax = Oryza sativa Japonica Group
RepID = Q8H801_ORYSJ (3e-31); 6 57.6 129127693 129129065
Transposase_23: TNP1/EN/SPM transposase (6.2e-05) 209 Putative
uncharacterized protein Sb05g026840 n = 1 Tax = Sorghum bicolor
RepID = C5Y811_SORBI (0.0); 6 57.6 129138400 129140529 DUF594:
Protein of unknown function, DUF594 (1.6e-30); GO_MF:GO:0046872,
metal ion binding# (1e-115); GO_BP:GO:0006278, RNA-dependent DNA
replication# (1e-51) 210 Retrotransposon protein, putative,
unclassified n = 1 Tax = Oryza sativa Japonica Group RepID =
Q2QQR5_ORYSJ 6 57.6 129142269 129144473 (3e-33); zf-CCHC: Zinc
knuckle (0.015); GO_MF:GO:0008270, zinc ion binding# (2e-49);
GO_BP:GO:0006278, RNA-dependent DNA replication# (3e-40) 211 HAT
family dimerisation domain containing protein n = 1 Tax = Oryza
sativa Japonica Group 6 57.7 129169527 129171992 RepID =
Q2R0F0_ORYSJ (1e-107); zf-BED: BED zinc finger (1.4e-09); hATC: hAT
family dimerisation domain (1.5e-28); GO_MF:GO:0046983, protein
dimerization activity# (1e-116); GO_BP:GO:0006350, transcription#
(1e-33) 212 Triose phosphate/phosphate translocator, non-green
plastid, chloroplast, putative n = 1 Tax = Ricinus communis 6 57.7
129222041 129225144 RepID = B9RB11_RICCO (1e-116); UAA: UAA
transporter family (0.0016); DUF6: Integral membrane protein DUF6
(1.2e-11); DUF6: Integral membrane protein DUF6 (0.0068); TPT:
Triose-phosphate Transporter family (3.5e-52); GO_MF:GO:0005215,
transporter activity# (1e-146); GO_BP:GO:0006810, transport#
(1e-146); GO_CC:GO:0016021, integral to membrane# (1e-146) 213
Putative transcription regulatory protein n = 2 Tax = Oryza sativa
RepID = Q94LQ9_ORYSJ (2e-68); U-box: 6 57.7 129243446 129247172
U-box domain (0.0089); GO_MF:GO:0016301, kinase activity# (2e-79);
GO_BP:GO:0016301, kinase activity# (2e-79); GO_CC:GO:0000151,
ubiquitin ligase complex# (3e-25) 214 NADH-ubiquinone
oxidoreductase 10.5 kDa subunit n = 4 Tax = Andropogoneae RepID =
B6TDN0_MAIZE 6 57.8 129361190 129365442 (2e-31); L51_S25_CI-B8:
Mitochondrial ribosomal protein L51/S25/CI-B8 domain (2e-15);
GO_MF:GO:0016491, oxidoreductase activity# (4e-18);
GO_BP:GO:0055114, oxidation reduction# (4e-18); GO_CC:GO:0045271,
IDA#respiratory chain complex I# (4e-21) 215 Putative
uncharacterized protein n = 1 Tax = Zea mays RepID = B6TDS4_MAIZE
(1e-09) 6 57.9 129437152 129437697 216 Putative receptor protein
kinase n = 1 Tax = Oryza sativa Japonica Group RepID = Q65XS7_ORYSJ
(0.0); 6 57.95 129472709 129517525 LRRNT_2: Leucine rich repeat
N-terminal domain (6.8e-13); LRR_1: Leucine Rich Repeat (3.2);
LRR_1: Leucine Rich Repeat (0.91); LRR_1: Leucine Rich Repeat
(0.11); LRR_1: Leucine Rich Repeat (5.8); LRR_1: Leucine Rich
Repeat (12); LRR_1: Leucine Rich Repeat (41); LRR_1: Leucine Rich
Repeat (1.2); LRR_1: Leucine Rich Repeat (4.3); LRR_1: Leucine Rich
Repeat (0.09); LRR_1: Leucine Rich Repeat (2.5); LRR_1: Leucine
Rich Repeat (0.11); LRR_1: Leucine Rich Repeat (1.2); LRR_1:
Leucine Rich Repeat (0.21); LRR_1: Leucine Rich Repeat (2.3);
LRR_1: Leucine Rich Repeat (2.8); LRR_1: Leucine Rich Repeat
(0.13); LRR_1: Leucine Rich Repeat (0.1); LRR_1: Leucine Rich
Repeat (0.29); LRR_1: Leucine Rich Repeat (0.13); LRR_1: Leucine
Rich Repeat (0.44); LRR_1: Leucine Rich Repeat (1.7); LRR_1:
Leucine Rich Repeat (0.041); LRR_1: Leucine Rich Repeat (0.26);
LRR_1: Leucine Rich Repeat (0.21); LRR_1: Leucine Rich Repeat
(0.96); LRR_1: Leucine Rich Repeat (14); LRR_1: Leucine Rich Repeat
(0.94); LRR_1: Leucine Rich Repeat (0.092); LRR_1: Leucine Rich
Repeat (0.25); LRR_1: Leucine Rich Repeat (5.5); LRR_1: Leucine
Rich Repeat (6); LRR_1: Leucine Rich Repeat (12); LRR_1: Leucine
Rich Repeat (0.33); LRR_1: Leucine Rich Repeat (5.1); LRR_1:
Leucine Rich Repeat (0.078); LRR_1: Leucine Rich Repeat (2.2);
LRR_1: Leucine Rich Repeat (3.4); LRR_1: Leucine Rich Repeat
(0.56); LRR_1: Leucine Rich Repeat (1.2); LRR_1: Leucine Rich
Repeat (3.3); LRR_1: Leucine Rich Repeat (2.7); LRR_1: Leucine Rich
Repeat (47); LRR_1: Leucine Rich Repeat (0.85); GO_MF:GO:0016301,
kinase activity# (0.0); GO_BP:GO:0016301, kinase activity# (0.0);
GO_CC:GO:0016021, integral to membrane# (0.0) 217 BEL1-related
homeotic protein 30 n = 2 Tax = Andropogoneae RepID = B6SWM4_MAIZE
(1e-64); 6 58 129501726 129502856 GO_MF:GO:0043565,
sequence-specific DNA binding# (1e-64); GO_BP:GO:0045449,
regulation of transcription# (1e-64); GO_CC:GO:0005634, nucleus#
(1e-64) 218 HAT family dimerization domain protein n = 2 Tax =
Oryza sativa RepID = D0UZH7_ORYSJ (6e-94); 6 58 129520475 129521414
GO_MF:GO:0046983, protein dimerization activity# (3e-86) 219
Putative uncharacterized protein n = 1 Tax = Zea mays RepID =
C0PP88_MAIZE (1e-46) 6 58 129538411 129540061 220 Putative
uncharacterized protein Sb01g027800 n = 1 Tax = Sorghum bicolor
RepID = C5WQN1_SORBI (3e-13) 6 58 129581574 129582554 221 Alliin
lyase n = 3 Tax = Zea mays RepID = B6TK37_MAIZE (0.0);
Aminotran_1_2: Aminotransferase class I and II 6 58 129661095
129664534 (0.006); Alliinase_C: Allinase, C-terminal domain
(4.8e-199); GO_MF:GO:0030170, pyridoxal phosphate binding# (0.0);
GO_BP:GO:0080022, LMP#primary root development# (9e-82);
GO_CC:GO:0005737, cytoplasm# (9e-82) 222 O-sialoglycoprotein
endopeptidase, putative n = 2 Tax = rosids RepID = B9T542_RICCO
(1e-164); 6 58 129670272 129674945 Peptidase_M22: Glycoprotease
family (6.3e-73); GO_MF:GO:0008270, zinc ion binding# (0.0);
GO_BP:GO:0006508, proteolysis# (0.0); GO_CC:GO:0005737, cytoplasm#
(1e-125) 223 HAT family dimerisation domain containing protein n =
2 Tax = Oryza sativa Japonica Group 6 58 129679558 129681972 RepID
= Q7XE06_ORYSJ (1e-44); hATC: hAT family dimerisation domain
(1e-11); GO_MF:GO:0046983, protein dimerization activity# (7e-52);
GO_BP:GO:0006350, transcription# (7e-52) 224 Nonspecific
lipid-transfer protein n = 2 Tax = Zea mays RepID = B6SZZ6_MAIZE
(6e-29); Tryp_alpha_amyl: 6 58 129703134 129703976 Protease
inhibitor/seed storage/LTP f (8.5e-10); GO_MF:GO:0008289, lipid
binding# (3e-13); GO_BP:GO:0006869, lipid transport# (6e-29) 225
Stem 28 kDa glycoprotein n = 1 Tax = Zea mays RepID = B6T003_MAIZE
(1e-147); Acid_phosphat_B: HAD 6 58.2 129792745 129795009
superfamily, subfamily IIIB (Acid (3.6e-90); GO_MF:GO:0003993, acid
phosphatase activity# (1e-147); GO_BP:GO:0003993, acid phosphatase
activity# (1e-147); GO_CC:GO:0005886, plasma membrane# (1e-51) 226
Serine-threonine protein kinase, plant-type, putative n = 1 Tax =
Ricinus communis RepID = B9RKF0_RICCO 6 58.3 129841439 129842719
(1e-105); LRRNT_2: Leucine rich repeat N-terminal domain (2.6e-06);
LRR_1: Leucine Rich Repeat (3.9); LRR_1: Leucine Rich Repeat (1.8);
LRR_1: Leucine Rich Repeat (5.4); LRR_1: Leucine Rich Repeat (32);
LRR_1: Leucine Rich Repeat (2.1e+02); LRR_1: Leucine Rich Repeat
(70); LRR_1: Leucine Rich Repeat (0.72); LRR_1: Leucine Rich Repeat
(0.23); LRR_1: Leucine Rich Repeat (1.4e+02); GO_MF:GO:0005515,
protein binding# (1e-141); GO_BP:GO:0055114, oxidation reduction#
(1e-105); GO_CC:GO:0009505, IDA#expansin# (2e-68) 227 Putative
uncharacterized protein n = 4 Tax = Zea mays RepID = B6U1N7_MAIZE
(7e-24) 6 58.3 129880459 129880719 228 Retrotransposon protein,
putative, Ty1-copia subclass n = 2 Tax = Oryza sativa RepID =
Q7XH58_ORYSJ (6e-28); 6 58.3 129887372 129887779 GO_MF:GO:0003677,
DNA binding# (6e-28); GO_BP:GO:0015074, DNA integration# (6e-28)
229 OSJNBa0064G10.18 protein n = 3 Tax = Oryza sativa RepID =
Q7XKB3_ORYSJ (7e-94); WD40: WD domain, G- 6 58.35 129888300
129891431 beta repeat (1.6); WD40: WD domain, G-beta repeat
(0.016); WD40: WD domain, G-beta repeat (3e-09); WD40: WD domain,
G-beta repeat (3.4e-12); WD40: WD domain, G-beta repeat (2.6e-10);
GO_MF:GO:0016740, transferase activity# (5e-92); GO_BP:GO:0016905,
myosin heavy chain
kinase activity# (2e-84); GO_CC:GO:0005874, microtubule# (1e-89)
230 SIN3 component, histone deacetylase complex n = 1 Tax = Populus
trichocarpa RepID = B9HU88_POPTR (2e-15); 6 58.4 129892633
129892893 GO_MF:GO:0016564, transcription repressor activity#
(1e-12); GO_BP:GO:0006355, regulation of transcription,
DNA-dependent# (5e-21); GO_CC:GO:0005634, nucleus# (5e-21) 231
L-lactate dehydrogenase n = 3 Tax = Oryza sativa RepID =
Q0E4Q5_ORYSJ (1e-51); Ldh_1_C: lactate/malate 6 58.4 129892886
129893304 dehydrogenase, alpha/b (7.2e-05); GO_MF:GO:0016616,
oxidoreductase activity, acting on the CH--OH group of donors, NAD
or NADP as acceptor# (1e-51); GO_BP:GO:0055114, oxidation
reduction# (1e-51); GO_CC:GO:0005737, cytoplasm# (1e-51) 232
Derlin-1.2 n = 2 Tax = Zea mays RepID = DER12_MAIZE (1e-137); DER1:
Der1-like family (2.5e-56); 6 58.4 129897727 129902466
GO_MF:GO:0005515, protein binding# (3e-35); GO_BP:GO:0006950,
response to stress# (1e-137); GO_CC:GO:0016021, integral to
membrane# (1e-137) 233 Putative uncharacterized protein n = 1 Tax =
Zea mays RepID = B6UF52_MAIZE (1e-14) 6 58.5 129955339 129955661
234 OSJNBa0036E02.10 protein n = 2 Tax = Oryza sativa RepID =
Q7F7E1_ORYSJ (7e-35); IQ: IQ calmodulin- 6 58.5 129963265 129965399
binding motif (0.0013); IQ: IQ calmodulin-binding motif (0.006) 235
Hexokinase-1 n = 2 Tax = Zea mays RepID = B6TL75_MAIZE (0.0);
Hexokinase_1: Hexokinase (2.9e-09); 6 58.5 129979002 129982104
Hexokinase_2: Hexokinase (4e-79); GO_MF:GO:0016773,
phosphotransferase activity, alcohol group as acceptor# (0.0);
GO_BP:GO:0016301, kinase activity# (0.0); GO_CC:GO:0005737,
cytoplasm# (1e-152) 236 Retrotransposon protein, putative,
unclassified n = 1 Tax = Oryza sativa Japonica Group RepID =
Q7XE51_ORYSJ 6 58.5 129986022 129989105 (7e-30); zf-CCHC: Zinc
knuckle (0.0013); zf-CCHC: Zinc knuckle (0.16); GO_MF:GO:0008270,
zinc ion binding# (7e-44); GO_BP:GO:0006278, RNA-dependent DNA
replication# (4e-35) 237 IAA16-auxin-responsive Aux/IAA family
member n = 2 Tax = Zea mays RepID = B6TT61_MAIZE (5e-89); 6 58.6
130004376 130008214 AUX_IAA: AUX/IAA family (2.4e-19);
GO_MF:GO:0046983, protein dimerization activity# (5e-89);
GO_BP:GO:0045449, regulation of transcription# (5e-89);
GO_CC:GO:0005634, nucleus# (5e-89) 238 Os07g0695700 protein n = 1
Tax = Oryza sativa Japonica Group RepID = Q0D3B3_ORYSJ (1e-12) 6
58.6 130011779 130011936 239 Histidine-containing phosphotransfer
protein 4 n = 2 Tax = Andropogoneae RepID = B6SRE6_MAIZE (2e-50); 6
58.6 130159712 130161359 Hpt: Hpt domain (1.7e-08);
GO_MF:GO:0004871, signal transducer activity# (7e-65);
GO_BP:GO:0004871, signal transducer activity# (7e-65);
GO_CC:GO:0005737, cytoplasm# (2e-38) 240 OSJNBa0027O01.13 protein n
= 3 Tax = Oryza sativa RepID = Q7XXC5_ORYSJ (0.0); NCD3G: Nine
Cysteines 6 58.6 130239488 130245375 Domain of family 3 GPC
(0.093); GO_CC:GO:0005773, IDA#vacuole# (0.0) 241 Putative
polyprotein n = 1 Tax = Zea mays RepID = Q8SA93_MAIZE (3e-59);
GO_MF:GO:0003964, RNA- 6 58.6 130257021 130258701 directed DNA
polymerase, group II intron encoded# (3e-59); GO_BP:GO:0015074, DNA
integration# (3e-59); GO_CC:GO:0005634, nucleus# (3e-59) .dagger.
cM = centiMorgans. .dagger..dagger. bp = base pair of Arizona
Genomics Institute B73 RefGen_v2 sequence.
[0152] As various modifications could be made in the constructions
and methods herein described and illustrated without departing from
the scope of the invention, it is intended that all matter
contained in the foregoing description or shown in the accompanying
drawings shall be interpreted as illustrative rather than limiting.
The breadth and scope of the present invention should not be
limited by any of the above-described exemplary embodiments, but
should be defined only in accordance with the following claims
appended hereto and their equivalents. All patent and non-patent
documents cited in this specification are incorporated herein by
reference in their entireties.
Sequence CWU 1
1
1061668DNAZea maysmisc_feature(433)..(433)n is a, c, g, or
tmisc_feature(448)..(456)n is a, c, g, or
tmisc_feature(542)..(551)n is a, c, g, or
tmisc_feature(565)..(576)n is a, c, g, or
tmisc_feature(578)..(578)n is a, c, g, or
tmisc_feature(580)..(585)n is a, c, g, or
tmisc_feature(587)..(591)n is a, c, g, or
tmisc_feature(593)..(594)n is a, c, g, or
tmisc_feature(601)..(618)n is a, c, g, or
tmisc_feature(623)..(631)n is a, c, g, or
tmisc_feature(636)..(667)n is a, c, g, or t 1ccaagcccta ctgcctcaat
ggtaacactt ctaataaaag caactgcgcc tgtcaaacaa 60gaaatgaaac tgtcgttgtt
agtggtatgg atgatggtgt caccatcaaa cagttcatag 120taccactgca
taatcacaat tccagcagaa atgctagctg acataatttg tatattttct
180acactatata tctatcttta cctctttgca ttcccttgag caatttccga
tccttcttgt 240agcttttgat gggcaacgag accaactttc tggtccctga
accaacagca actagtgatc 300ttattggagg aagccctttt agcaatttgt
gcacctagac aacagatact tcagttcaga 360ctaagggggg attaattcat
aaatcaagtg gaaatatagt attttctctg tatttgcaca 420agcaaatcaa
aanattatat atatattnnn nnnnnncttt ttctgctatc aagtttttac
480atgttccgtg tccctcatgc aaaagcatac atgtctgaga gtacaggtgc
acaaggggag 540annnnnnnnn natttttaga aatgnnnnnn nnnnnntncn
nnnnnannnn ntnncctatg 600nnnnnnnnnn nnnnnnnncc cannnnnnnn
ncatgnnnnn nnnnnnnnnn nnnnnnnnnn 660nnnnnnna 6682876DNAZea
maysmisc_feature(381)..(381)n is a, c, g, or t 2atttttgccg
gccctgtctc cggtaagacg gattccgatt ccgttgtttt cttgccaaat 60ccttcgcagc
ttgggggcgg tttcgctccg gttcttgcgc ttcggctcca ggccatggag
120cagcggaggt ggctcgcggt agccgttttg atgtgcctgc tggtgctttg
ctccgggaga 180ggtgggttgt tggcccttct ttggtcctcc cgtttctcgc
tgccggaaag gaaaaaaatt 240gtcttttgaa tcggtttccc ctaccgtttc
gtgcaagcgg actctgcctg ccggttgatt 300ttccttagtt tatgtattgc
acatttcatc agattcttat tttacccgta ccttttggat 360tcagaactga
agaccaaaca ngtgcccata tatgacccag tgctggcccg gacacttgct
420gaatatactt ctgctgtgag ttcacctgac cttcttgatg ctgtcatcat
tcacatccac 480atccacgttg gattatgtta ttgttgaata cgtccttttt
ctagtgaaat atgctgcatt 540catcgtggag ttgaacttgg tgcttttgtg
caggtctata ctgctgacct tacccaactg 600tttacatgga catgtgagag
atgttgtgac ttaacagagg tattttatat ttgtcatcac 660catctgacat
tctataattt taccaatggt tttcaaattc acatttggct tggtttgaaa
720tcttcattaa atttatttgg tagctcaggg gttcgaggtg atagagctga
ttgttgatgt 780gaaaaattgc ttacaggtta ctgcttctgc cagtgcacct
gaaccgtttt ctttttacct 840agtaataggc ttttgattat attgatgatg atgtgt
8763473DNAZea maysmisc_feature(221)..(221)n is a, c, g, or t
3ggtactgaca tcataacaga atgtgcactc gccaaaagtt tttagcaatt caactctagt
60caattcagtt gaactattgc cacaaaattc ataggtttcc accgaatgat ctccaacagc
120aaacaggcac tgagggaggg aagcttgaac tccttgccgc aagttattgt
tcaagaagtg 180attaccaagg tttgaatcat ctgaaatatt gtttccggcg
nggtagtatt catcaagttt 240aatttgggca attgatgcct tgagccttac
attttttgga taagtctgca gatatcaaca 300agaaaaaata tcaaatacca
agcttggtga aactaaaatg atgcatggac taagaagccc 360tgatgtacca
gtaccagtac agacaaaatg aatacctgta gatcaagatg aatgttctca
420cacttggctt tgagatgatg catatttaag ctggaagctg tagcaggaga taa
4734374DNAZea maysmisc_feature(130)..(130)n is a, c, g, or t
4tctgctgttc aagaaaatgc tggcattaaa ggtttggcct accaatgcga cgtattcttg
60catcctgaag gtgtttgata cgcccgattt gctatccgtt ggaatgcaac ttcatggctg
120cttgctgaan atgggaacgg aggttgacac tgctttgggg actgccttga
tgacgatgta 180tggcaggtgt ggtggagttg atgagatacc taggttggct
tgtcgtataa ggcatgatgc 240gctttcgagg actgccctgc ttggcgctta
tgcacgtact ggatacaatg cagaggcaat 300tggtgttttc aaggagatga
tcatgaaaaa tatggcaatt gaccagtcag ctatgactgg 360tatgctgcag gttt
3745705DNAZea maysmisc_feature(373)..(373)n is a, c, g, or
tmisc_feature(492)..(492)n is a, c, g, or
tmisc_feature(596)..(596)n is a, c, g, or
tmisc_feature(608)..(608)n is a, c, g, or
tmisc_feature(642)..(643)n is a, c, g, or
tmisc_feature(646)..(646)n is a, c, g, or
tmisc_feature(648)..(652)n is a, c, g, or
tmisc_feature(694)..(694)n is a, c, g, or
tmisc_feature(696)..(696)n is a, c, g, or
tmisc_feature(698)..(700)n is a, c, g, or
tmisc_feature(703)..(703)n is a, c, g, or t 5gctccttttc aagtgccttt
tgggcgtata tagtagatgg gccttataca ctttataaca 60tcaatataaa tataattgtc
tcaaattaca aatgctaaca cattcctttt cttaaagata 120tgcattacaa
atccatgtta ctacctttca tttatctgac catatcaacc tatcaccacc
180agattccaaa tattaccaac ataggtttga cagcacggaa aattaaaaag
gcagctatcg 240ttgggggtgg tctaatggga tccggaattg caacaatact
gatattgaac aactttaatg 300ttgtcttgaa agaagtaaat gaacagttct
tatctgctgg cattaacaga attaaaggta 360cacttttatt tgntgcactt
tttttttgga attgccttca tagttcctca gaagtttgtt 420ctcttgtgtt
cagtgaattt gcaaagtctt gtcagaaagg gtcaacttac tgaagaagat
480tatgaaaaga anctttctct gctatgtggt gctcttgact atgaacagtt
cagagataca 540gatgtagtaa ttgaggtaga cccagtttct attatattca
ccactctctg attaanatga 600gacagcgntg cttattcagc tttgtcacct
atatagagac anntancnnn nntatatcat 660gtgcataggt ataactagtt
atgtcttata acancngnnn cantc 7056700DNAZea
maysmisc_feature(111)..(111)n is a, c, g, or
tmisc_feature(136)..(136)n is a, c, g, or
tmisc_feature(166)..(166)n is a, c, g, or
tmisc_feature(202)..(202)n is a, c, g, or
tmisc_feature(301)..(301)n is a, c, g, or
tmisc_feature(411)..(412)n is a, c, g, or
tmisc_feature(445)..(445)n is a, c, g, or
tmisc_feature(464)..(464)n is a, c, g, or
tmisc_feature(535)..(535)n is a, c, g, or
tmisc_feature(546)..(546)n is a, c, g, or
tmisc_feature(597)..(597)n is a, c, g, or
tmisc_feature(600)..(600)n is a, c, g, or t 6cctccagtat caggtcatgc
agggtcccgg tcaccacctg ccgcttggat ttgagcaccc 60tagtaaactc caaagcggcg
ccctgtacaa gaaaattctc caaatattat naactcggaa 120gaaactcagc
gtggcngtgg gggtacatac atctacggag agatgngaga tcatgccact
180aatatgagaa aatacaagtt cnaccattaa ccgaaacgtt gattctagca
aatctagtag 240gtcactcccc caaagagttg agacctaagt ttaaggaccc
ctgcaagttg atgcaactgg 300naagcccgtt agcgaatcca tggacccaac
tcttttcccc tctcgggagt gaaacttcat 360tgacctaatt aggtggcgtc
acctcgtaag tcaatgcaat tcactctctc nnatggtagt 420acataccaag
agtccacacg ctganggaat tggtatcggc aggntggaga gacgaggagg
480gaggcgcaca cctggttctt gttgtagtgg gcgacggcga agcgagcggc
gtccncggcc 540tcggcncgct cgcggagcgc ggcgagcaca cccctcacga
gaccgctctc gtccccnccn 600aggtgaaacc cggagaccgc ggcggcggag
gccgcgagga gcaccgcggc gaagagaagg 660gcgcggcgag gcatcatcgt
cagcgcggcg aacctactac 7007519DNAZea maysmisc_feature(463)..(463)n
is a, c, g, or t 7caagtgaacg tcgtgcccga cttactggat tgaagcaggc
agaggacata aagaagttag 60agatgtcagc aacgccgacc acaacagtgt gtatttcatc
ggtagagcaa cagggagctg 120cttctttaag tgcgaagatt accaatgctt
ctgtttctga aggacagaag aatcctggaa 180attatatgcc ttctgccatt
tcaattcccg tggggagcca tgttctgggc ctgggcgcaa 240caagtattga
agaaacaact gccactatga taactcaggc tcctgcagtt tcaaaatcag
300aacgaagaaa acttccagga ggcagtcaac aaggtattat ttattctact
cagatcatga 360tcaattttct tggtccagat gagaagagtg gcataatctt
tgctattatt ttccatggta 420acagtaacag tggctgacat gacttgtaca
tgttattgtt ttnccttttt cgtaggtatt 480cagtttgaga gttcagcatc
aaaaacaaag atggtatca 51981343DNAZea maysmisc_feature(6)..(10)n is
a, c, g, or tmisc_feature(70)..(70)n is a, c, g, or
tmisc_feature(73)..(76)n is a, c, g, or tmisc_feature(94)..(94)n is
a, c, g, or tmisc_feature(292)..(292)n is a, c, g, or
tmisc_feature(311)..(311)n is a, c, g, or
tmisc_feature(315)..(315)n is a, c, g, or
tmisc_feature(317)..(318)n is a, c, g, or
tmisc_feature(320)..(320)n is a, c, g, or
tmisc_feature(404)..(404)n is a, c, g, or
tmisc_feature(618)..(618)n is a, c, g, or
tmisc_feature(998)..(998)n is a, c, g, or
tmisc_feature(1040)..(1040)n is a, c, g, or
tmisc_feature(1122)..(1122)n is a, c, g, or
tmisc_feature(1176)..(1176)n is a, c, g, or
tmisc_feature(1282)..(1282)n is a, c, g, or
tmisc_feature(1309)..(1311)n is a, c, g, or
tmisc_feature(1320)..(1328)n is a, c, g, or t 8tctgtnnnnn
ctatctctcc ttctccgtct ctttcttctg tgttcttcct ccattgctct 60gtacttattn
atnnnngcgc gctgcctttt caancagggg caagatcctc gaggtgctca
120agaactggcc cgagaggagc atccaggtca tcgtcgtcac cgacggcgag
cgcatcctcg 180gcctcggtga tctcggttgc caggggatgg gaattcccgt
tggcaagctc tccctctaca 240ctgccctcgg aggtgttcgc ccgtcagctg
taagtgctgc tcacaatgct cnttcttcag 300tattactact nctgntnngn
aataaacttg tagcactagt cgtagtagga aagatttgga 360atcgattttt
tttcttcagt attactacta cttcagtatt attngtcgta ataatgttta
420cgctgctgca gtgcctgccc atcacaattg atgtcggcac caacaacgag
gccttgctca 480aggacgagtt ctacatcggc ctccgccaga ggcgtgccac
cggcgaggtc agcaactcat 540ctgcaatccc ctccattgat ttagttctac
ccctacatgg ctgttctgtt cacccacttg 600cagctggtga ttttgttnaa
cctgtaacca gtctcttgtc tggattattg agacgtggct 660tgtgtttttg
atggttcaca ggagtaccat gaacttcttg aagagttcat gaccgccgtc
720aagcaaaact acggcgagaa ggtcctcacc caggtcagtc tcagtggacc
agccacagat 780actaccagct gttggttttc gcctttttgg ccgaactttc
tctcatcctg gatctgaaat 840ggatgttctt tttgacctct gaccgtgcag
ttcgaagact tcgccaacca caacgccttt 900gacctgctcg agaagtacag
ggagagccat ctcgtcttca acgacgatat ccaggtaggc 960taggctttcc
ttgtgacagc gcatcacagg caaacagnag caccatggat gccaagttca
1020gaacaggggc ctgcctgttn tgtgctcgtt ccgtcgtccg tttctttcca
ccgtgctgaa 1080cgaaaacgat gcggatgtgt gtgattgctg cagggaacag
cntccgtggt cctcgctggc 1140ctcctggcgg cgctcaaggt ggtcggcggg
acactngcgg accacactta cctgttcctc 1200ggcgccggcg aggtcggtcg
atttgacttg ctagtatact gcatcagtgt taccctatct 1260tttctttgcc
gatcaaagct tnggatcact cgcggcctca ttcttttcnn ngattacgtn
1320nnnnnnnnca tctgcaggcc ggg 13439402DNAZea
maysmisc_feature(148)..(148)n is a, c, g, or
tmisc_feature(389)..(394)n is a, c, g, or t 9ttgaatttct ttgattccat
ttcttgacag cataagcatc cacctgtgga tgtgtcctcc 60aggagaaaac atgtgaaccc
gccgagcatt catttcaaac ttcaaaatag ggccatcatg 120gagggagaga
aacgttatga cgaagtanac aaatctgtcg ctgtcaccgt cttcattacc
180attgcctaaa gcaaaatcat cttctctgaa catcaattca gtcattgaag
cccatgtgta 240cctccatttc cttgacaaga gacatgttct tacagcttct
tttattggca aacagcagag 300aattttatct ttaataacat caggtagatt
actgatgatg tcaacatttg taacagattt 360atgtcttttc ttttgagaac
ctccacgann nnnngggtat ac 40210584DNAZea
maysmisc_feature(469)..(469)n is a, c, g, or t 10agcaagaaca
tactgggaaa aggtggcttt ggatacgtct acagagggca gttccctgac 60ggaactcttg
tggccgtcaa gcgactcaag gacggcaacg ccgcgggcgg cgaggcccag
120tttcaaaccg aggtcgagat gatcagcctg gcactgcaca gaaaccttct
caggctctat 180gggttctgca tgaccgccac agagaggttg ctggtctatc
catacatggc taatggaagc 240gtcgcgtccc gcctcagagg taagcttttt
tttttcttct tcttcttctc aagattccaa 300tgtgaacttg cagtagtgca
gaacagattc tctcttcttc ttcggaaagt gactggaatc 360ggattctagc
tagcacttcc ttattcttcc ttccagttga caaatgttgg cacagctagc
420agtaccacaa gcatacgatt cctatcctca ctttattcca caatgatcnc
tacgcctaca 480gggaagccac ctctggactg ggtgacgagg aagaggatag
ctctcggggc agggaggggg 540ctgctgtacc tgcacgagca gtgcgacccc
aagatcatac acag 5841127DNAZea mays 11gggattaatt cataaatcaa gtggaaa
271225DNAZea mays 12ccgtaccttt tggattcaga actga 251328DNAZea mays
13tgttcaagaa gtgattacca aggtttga 281423DNAZea mays 14cgatttgcta
tccgttggaa tgc 231525DNAZea mays 15tgctggcatt aacagaatta aaggt
251622DNAZea mays 16tttaaggacc cctgcaagtt ga 221725DNAZea mays
17acagtggctg acatgacttg tacat 251821DNAZea mays 18tgttctgttc
acccacttgc a 211925DNAZea mays 19catcatggag ggagagaaac gttat
252025DNAZea mays 20cagtaccaca agcatacgat tccta 252126DNAZea mays
21acggaacatg taaaaacttg atagca 262226DNAZea mays 22acagcagaag
tatattcagc aagtgt 262323DNAZea mays 23gtaaggctca aggcatcaat tgc
232420DNAZea mays 24ccccaaagca gtgtcaacct 202523DNAZea mays
25gaggaactat gaaggcaatt cca 232620DNAZea mays 26ggtccatgga
ttcgctaacg 202726DNAZea mays 27gatgctgaac tctcaaactg aatacc
262822DNAZea mays 28caagccacgt ctcaataatc ca 222924DNAZea mays
29gcaatggtaa tgaagacggt gaca 243020DNAZea mays 30ccagaggtgg
cttccctgta 203114DNAZea mays 31agcaaatcaa aaaa 143219DNAZea mays
32catatatggg cacgtgttt 193321DNAZea mays 33cttgatgaat actaccgcgc c
213417DNAZea mays 34cttgctgaaa atgggaa 173516DNAZea mays
35aaaagtgcag caaata 163613DNAZea mays 36caactggaaa gcc 133715DNAZea
mays 37tgttttccct ttttc 153815DNAZea mays 38caggttgaac aaaat
153916DNAZea mays 39acgaagtaaa caaatc 164018DNAZea mays
40cacaatgatc actacgcc 184117DNAZea mays 41aagcaaatca aaatatt
174218DNAZea mays 42atatatgggc acatgttt 184320DNAZea mays
43ttgatgaata ctaccacgcc 204417DNAZea mays 44cttgctgaag atgggaa
174514DNAZea mays 45agtgcaacaa ataa 144614DNAZea mays 46tgcaactggg
aagc 144717DNAZea mays 47ttgtttttcc tttttcg 174815DNAZea mays
48caggttcaac aaaat 154915DNAZea mays 49cgaagtagac aaatc
155017DNAZea mays 50acaatgatcg ctacgcc 1751367DNAZea
maysmisc_feature(118)..(118)n is a, c, g, or
tmisc_feature(357)..(363)n is a, c, g, or t 51gagctgtatc tgtaagcagc
tgcacagtag cagcagcatc acgaacccga tgatgcagtc 60ggtcttgtac tgcatgttgc
cggcgcaacg caagtacttc gctcaggctt tcccacanga 120tccaaacagg
cgcagcttct ctgctacaac agctttcatt gcctctttag cagacgccat
180cacctgaatc aagtcctttt ctggctttct gagggacgcc aggtagctgt
tccgaacctc 240ggtgttcaca ttgaattttc tcacgcccaa gtctatgcac
tcctgctcca gaaattagtg 300cactgttata gcgcctacac gataagtttt
atcctaataa tacttgagat atggccnnnn 360nnntagc 36752487DNAZea
maysmisc_feature(74)..(74)n is a, c, g, or tmisc_feature(95)..(95)n
is a, c, g, or tmisc_feature(105)..(105)n is a, c, g, or
tmisc_feature(119)..(119)n is a, c, g, or
tmisc_feature(126)..(126)n is a, c, g, or
tmisc_feature(151)..(151)n is a, c, g, or
tmisc_feature(170)..(170)n is a, c, g, or
tmisc_feature(172)..(172)n is a, c, g, or
tmisc_feature(189)..(189)n is a, c, g, or
tmisc_feature(197)..(197)n is a, c, g, or
tmisc_feature(202)..(202)n is a, c, g, or
tmisc_feature(232)..(232)n is a, c, g, or
tmisc_feature(238)..(238)n is a, c, g, or
tmisc_feature(253)..(253)n is a, c, g, or
tmisc_feature(256)..(428)n is a, c, g, or
tmisc_feature(454)..(454)n is a, c, g, or t 52actactgatg ccattggcta
ccatgaaccc atggatgcag tactgcatga agcaacaggg 60ggttgccaac ttgntagcgt
ggccgaccct gatgntgcag caacngttgg cctcaccgnt 120tcagcngtgc
cagatgccaa tgatgatgcc nggtatgatg ccaccgatgn cnatgatgcc
180gatgccgant atgatgncat cnatgatggt gccgactatg atgtcaccaa
tnacgatngc 240tagtatgatg ccnccnnnnn nnnnnnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 300nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 360nnnnnnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 420nnnnnnnnca
gtgccacaat gttactctga ttcnatctcg cacattatac aacaacaaca 480attacca
48753226DNAZea maysmisc_feature(89)..(89)n is a, c, g, or
tmisc_feature(217)..(218)n is a, c, g, or t 53tttgtcttgt tagttgttac
cacatctgaa tctaacaaca ttaatccatt ccatggtgca 60acaatataat gtaatatcat
gtctctttnc ctttttcttg tatgtatgtt cccaggcctt 120cacaaatggg
aaggtgataa gcgtccggca cagggtaatt gcaagctcga gcagggcgag
180gctgtcaacg atctacttcg ctgcgccgcc actgcannca cgaatt
22654201DNAZea maysmisc_feature(101)..(101)n is a, c, g, or
tmisc_feature(150)..(150)n is a, c, g, or
tmisc_feature(160)..(160)n is a, c, g, or
tmisc_feature(197)..(197)n is a, c, g, or t 54tgcttgatac agcataaatc
catcgcccag ctgaaactaa aaccaagttg tcattggcca 60ctttattgtt tgactgcaaa
gaataaaggc acgtcactca ngagaagtgc tataggaaac 120atcaattgca
ttatttatca acttatgatn tctcagaaan tagaaaatgc attgtgcgca
180cagaccataa catgcanctg t 20155616DNAZea
maysmisc_feature(291)..(291)n is a, c, g, or
tmisc_feature(554)..(555)n is a, c, g, or
tmisc_feature(565)..(566)n is a, c, g, or
tmisc_feature(578)..(578)n is a, c, g, or
tmisc_feature(589)..(593)n is a, c, g, or
tmisc_feature(602)..(602)n is a, c, g, or
tmisc_feature(604)..(612)n is a, c, g, or t 55atcttaaaag cactgaagtt
atcgaacatc catatgtcca ggtaatagca gttcaactgc 60tccagtttga ctaatattcc
ctgttttatt tggagtgcta agtctctctt ttgctcctat 120tcagatattt
aatgaaggac atcaaaatgt tcttgtagag atgttggaaa tcataacagt
180aatttgtgaa gagctcaaac tacccatagc tcagacttgg gtgccatgca
aataccaaaa 240tttattgata cattgtggtg gtgaaaataa gagttgcttc
gatattcatg naagttgtgc 300ccaagaacta tgcatgtcaa caagtgctgt
tatgtttcat attatcgatg ctcatatgtg 360gggcttccga gatgcctgtg
tagagcacca cctgaagaag ggacaagggg tttctggaaa 420ggcttttatc
ctacgtaggc cttgctttac gaaagatgtt actagattct ctaaaatgga
480gtaccccctt gttcactatg ctcgtatgtt tggattagct ggctgttttt
cgatatgctt 540gcaaagtgct tatnntagaa atgannacta tgtattgnag
ttcttcttnn nnnctgattg 600tngnnnnnnn nntgag 61656655DNAZea
maysmisc_feature(4)..(18)n is a, c, g, or
tmisc_feature(100)..(100)n is a, c, g, or
tmisc_feature(573)..(575)n is a, c, g, or
tmisc_feature(577)..(578)n is a, c, g, or
tmisc_feature(586)..(587)n is a, c, g, or
tmisc_feature(593)..(598)n is a, c, g, or
tmisc_feature(607)..(609)n is a, c, g, or
tmisc_feature(618)..(623)n is a, c, g, or
tmisc_feature(625)..(648)n is a, c, g, or t 56gtgnnnnnnn nnnnnnnntt
ggtaactcca gctctggagt agaagatgga tgtcgagaag 60gaacatgaaa gtagagcatc
tgtaaagtta tcatagaaan ctatattcat ttttgctctg 120gacacaagag
agctatgtat tttgtataaa ttcaagagag aaaagggaga agagtaaagc
180cacaatcatt ttaagttgcc atagagcaga atattaggtg gtcacaaaat
ccaagtgacc 240atgcagcaac gatggaacag aacaaaactc tgtaagagta
aaaattaaga gtacacctgt 300gggatttaaa tgataccgaa accacacttt
ttggaactta ttttgtagaa ctaaacaaac 360tttttttcct tcaaaaaaaa
agaactaaac aaacttcggc catactatct caaagctaca 420tgtttgcaaa
aaccattagg ttggacagca actgaaaggg gtttcaaagc atgtagtttt
480gaactacgtt aaagcaacta aactaaaagt acttcatttc atgatattgc
accatgttgg 540ttggaaggca aaagtgcaag gtaacaatgg tcnnngnngg
tcctgnntgt ttnnnnnnaa 600aaacaannnt cgtagctnnn nnncnnnnnn
nnnnnnnnnn nnnnnnnnag cctgc 6555719DNAZea mays 57ggcgcaacgc
aagtacttc 195822DNAZea mays 58tgaacccatg gatgcagtac tg 225925DNAZea
mays 59cattaatcca ttccatggtg caaca 256024DNAZea mays 60ggccacttta
ttgtttgact gcaa 246125DNAZea mays 61gtggtggtga aaataagagt tgctt
256227DNAZea mays 62gaaggaacat gaaagtagag catctgt 276325DNAZea mays
63caatgaaagc tgttgtagca gagaa 256421DNAZea mays 64ccaacagttg
ctgcatcatc a 216524DNAZea mays 65aaggcctggg aacatacata caag
246623DNAZea mays 66ctgtgcgcac aatgcatttt cta 236725DNAZea mays
67agcacttgtt gacatgcata gttct 256829DNAZea mays 68ctcccttttc
tctcttgaat ttatacaaa 296914DNAZea mays 69cccacacgat ccaa
147014DNAZea mays 70acgctagcaa gttg 147118DNAZea mays 71atgtctcttt
cccttttt 187217DNAZea mays 72acgtcactca ggagaag 177318DNAZea mays
73cacaactttc atgaatat 187421DNAZea mays 74caaaaatgaa tatagttttc t
217516DNAZea mays 75ttcccacatg atccaa 167614DNAZea mays
76cgctaacaag ttgg 147718DNAZea mays 77atgtctcttt tccttttt
187817DNAZea mays 78acgtcactca agagaag 177916DNAZea mays
79cacaacttcc atgaat 168020DNAZea mays 80caaaaatgaa tatagctttc
2081201DNAZea maysmisc_feature(17)..(17)n is a, c, g, or
tmisc_feature(27)..(27)n is a, c, g, or tmisc_feature(101)..(101)n
is a, c, g, or t 81ttccatcatt gcttctntgt aggttgnggg ctcatcattg
tccaacaata atatgtcatg 60atgctctatg gctaggatta tcaactattg agttgctcga
ngttcccttg tagacttatg 120ttggactggt gcttcatcaa tagagtgcac
aacatcttgt ataagttcag tgggcgctga 180aatattttag gtgtttatcg a
20182201DNAZea maysmisc_feature(31)..(31)n is a, c, g, or
tmisc_feature(101)..(101)n is a, c, g, or t 82ttaattaaaa caagtgaaat
ttaatttgct nctctactca aatcgcatcg atcggtagcc 60ccaactttga tgcaccgacc
accaaagctg tcagactacg ntttgagttc cctctgctgc 120tttaaaaaaa
ctctctatca aaagatatca caagaagaat ctaatgaaac aagcttagtt
180agtgttagac agctcacagc a 20183201DNAZea
maysmisc_feature(101)..(101)n is a, c, g, or
tmisc_feature(187)..(187)n is a, c, g, or
tmisc_feature(194)..(194)n is a, c, g, or t 83ggataagttt tcaggtagca
aaatttgatt ccatcgggat tccagattgt tggatgagag 60ctgacatggc aattcagact
aactagtgtg ctatgtaccc ntatgttttc tttggtcttg 120ctattatgtt
tggcaaaagg atggaatggt tgagcaaata aagtaattcc agattgagaa
180atatttncag cganggtatt c 2018425DNAZea mays 84gtcatgatgc
tctatggcta ggatt 258517DNAZea mays 85gcaccgacca ccaaagc
178623DNAZea mays 86atgagagctg acatggcaat tca 238724DNAZea mays
87gcaccagtcc aacataagtc taca 248826DNAZea mays 88gagttttttt
aaagcagcag agggaa 268925DNAZea mays 89ccattccatc cttttgccaa acata
259018DNAZea mays 90agttgctcga tgttccct 189117DNAZea mays
91tcagactacg atttgag 179220DNAZea mays 92tgctatgtac ccatatgttt
209315DNAZea mays 93tgctcgacgt tccct 159417DNAZea mays 94tcagactacg
gtttgag 179520DNAZea mays 95tgctatgtac ccttatgttt 2096201DNAZea
mays 96ctgtatgaca tacatatgcc atatgacatg gccaytttca ttgtggtaaa
aaaaattacg 60tgcagtgaac agaatgttag ttagatttat gtgcagtgaa yggaatgtta
gttccttagt 120gtgcaccatc gaaatcatac tagcttcgct atttccctgt
tgattttagt yggtaaaaaa 180attctagcaa actatccggt g 20197301DNAZea
mays 97gattatattt tcctttccag ttcatgcacg caaaaaattg gatggcatga
gtcacataga 60gcataaattc ttatacaaca tccaataaat acttacaaat ctggcattta
tgaacataaa 120tgatttgatt ttttatgata attacgaaca ycataaatca
agaaattatc tttccaatgt 180gtatgcaaaa aatatgcatg cagcatactg
atataggaac ttcgttttca agcataaaat 240agtacaattt ttagcgtaaa
taatatatgt ggtaggcata aaatataata atcgaaaaya 300a 30198301DNAZea
mays 98aggaagctgg caatttayag gatccaccac aatgaagata tattcaaaaa
tttgctgtcc 60tcgatccagt acctcagtgg ttattcactc caaactyttt taatcgttga
tgagtcatct 120gaattcttca agaccctgga gtcaatgtcg ycatcccatc
taactgacct gagagctctg 180gagctgtctg gcaaattgct ttaccttcca
aagtggctcg acactcttca acatcttgtg 240aagttaacgc tttcagcaac
agccctatgc yctgataact ttttggtcyt cagaaaactg 300a 30199301DNAZea
mays 99acctctatct ctactkctat aaaacaccac ttttcctggt ttctaccttg
gtcccttttc 60aaaaagtcat cacaattatt tttaatttaa ackacggtct aaacatcaac
tttaacgtkc 120acgcccaccg gtttgcacgt ttatgcaaaa ktaaggtaaa
attgtgcata agkcagagtt 180cgaacttggt tgttgtctcc aacagaacac
acatttttgt gcttttttaa aacaaataca 240tatggcatat agaaaccata
gtgatgcacg ggcatttgac tagttaatta atatatacaa 300c 301100301DNAZea
mays 100ataaaccttt gttgtagtga cataaggagt ttcgaaattg caaggaattt
taaatttgaa 60tatttttcag tgagatgttg aggttgataa ttttaatctt tgtgcactaa
tatgttgtag 120aaagtagttt gttcaccgtt gcaacgcacg rgcatgtacc
tagtatatat atatgaaatt 180attgaagtgt gttatgttat tacaggatac
aaatattcat gaggctcaca tgacgtgtaa 240atatgaatca gtgccacatg
aaaaagctag ttagtctaga catccaatac ggtaatatgt 300a 301101301DNAZea
mays 101gttcgcggtc tacgtcgtgg tgcccatgtg gcctgagggc atcccggaga
gcggctccgt 60gcaggccatc ctcgactggc agaggaggac catggagatg atgtacaccg
acatcgcaca 120ggcgatccag gccaagggka tcgacgccaa kcccagggac
tacctkacct tcttctgcct 180cggcaaccgg gaggcgaaga agccagggga
gtacgtgccc acggaggagg ctgagcctga 240cactggctac atcaaggccc
agcaaaacag aaggttcatg atctatgtcc acaccaagat 300g 301102301DNAZea
mays 102gttcgcggtc tacgtcgtgg tgcccatgtg gcctgagggc atcccggaga
gcggctccgt 60gcaggccatc ctcgactggc agaggaggac catggagatg atgtacaccg
acatcgcaca 120ggcgatccag gccaagggma tcgacgccaa mcccagggac
tacctmacct tcttctgcct 180cggcaaccgg gaggcgaaga agccagggga
gtacgtgccc acggaggagg ctgagcctga 240cactggctac atcaaggccc
agcaaaacag aaggttcatg atctatgtcc acaccaagat 300g 301103301DNAZea
mays 103tggaaggtcc accccctcct cctcctctcc ccaaatcgtg catccgccgc
gccctcaaat 60cccgctggcc ttcaactcta tctctgcagc ggatgcgccc gcggatggaa
ggtaccagac 120ctcttctcgc cattaccgcg cccgccccgt yaattcccat
atctcttctc gccatcctct 180cggatcgtcc actgccattc atggacggca
gccgattcca tcctctcggt tcatggacag 240caaacttgta tctatttaaa
aacccctaat cgatccatac gccatatgcc agtgaagcca 300c 301104301DNAZea
mays 104actctcctac atcatcacca ttgcaaagta cgggccaaca aaacacaaca
agargarctg 60gatcgggcac accgcacaca gggatctctg aagcttaccc gatggagaag
gtggtcatgg 120agctatcctc cgtcgtcggt gtagagcgtc rcgctgtggg
tcgtgaagac ccgggaatcg 180agggggtcat cgcgagcggc gtcaggcagg
tggatgacgg crgctgtctc gcaggcgggt 240aggcaagggg gacgggtgcg
gcggtccctg aggggatgac gatgcatgcg ggggttgaga 300a 301105301DNAZea
mays 105gcccataaag atctctgatg tgtactcgtc catagccctc ttactatctc
ccacgtacgg 60cacatactgc atgcaacaaa tgagtggcaa gtttcaatgt aaatctacgt
ttaaactgct 120gcatgtgcca tctttttaaa gaggtggaag wtcagctaac
agaccttgat gacaacaaca 180tgatcgggat gctcgccggg cccatagaga
atggcattgc ttgagacaat gtcatccacc 240acgttgctct tggagatctc
cttggacctg aatgtttgag gggcagacag gttcatgccg 300t 301106301DNAZea
mays 106atacccgaag ccatgcttag catagtaggg gaggttggag agcgtcgtct
catcgacgtc 60gaacacccag acctccttgc cttggccggt gaggttgagg ccctcggcgt
aggcgatggc 120ctcgttggcg acggctcggg agtcgctgcg rtagtgcccg
ccgagcatgt agttgccgac 180gtacttctcg cagcgggctg ggacagtgtc
ccagtcgcgg agggtgttgg tctccacagc 240gaaccgccag ctgtcgcacg
gcacgcggcc gcgccggccg aggtcgccgc crgaatgcag 300c 301
* * * * *