A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice.
ABSTRACT The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.
[show abstract] [hide abstract]
ABSTRACT: Physical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant region on the long arm of chromosome 5B. This distally located region accounts for 4% of the physical size of the long arm and at least 30% of the recombination along the entire chromosome. Multiple crossovers occurred within this region, and the degree of recombination is at least 11-fold greater than the genomic average. Characteristics of the region such as gene order and frequency of recombination appear to be conserved throughout the evolution of the Triticeae. The region is more prone to chromosome breakage by gametocidal gene action than gene-poor regions, and evidence for genomic instability was implied by loss of gene collinearity for six loci among the homeologous regions. These data suggest that a unique level of chromatin organization exists within gene-rich recombination hot spots. The many agronomically important genes in this region should be accessible by positional cloning.Genetics 03/2000; 154(2):823-35. · 4.01 Impact Factor
Article: Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat.[show abstract] [hide abstract]
ABSTRACT: We studied the distribution of genes and recombination in wheat (Triticum aestivum) group 1 chromosomes by comparing high-density physical and genetic maps. Physical maps of chromosomes 1A, 1B, and 1D were generated by mapping 50 DNA markers on 56 single-break deletion lines. A consensus physical map was compared with the 1D genetic map of Triticum tauschii (68 markers) and a Triticeae group 1 consensus map (288 markers) to generate a cytogenetic ladder map (CLM). Most group 1 markers (86%) were present in five clusters that encompassed only 10% of the group 1 chromosome. This distribution may reflect that of genes because more than half of the probes were cDNA clones and 30% were PstI genomic. All 14 agronomically important genes in group 1 chromosomes were present in these clusters. Most recombination occurred in gene-cluster regions. Markers fell at an average distance of 244 kb in these regions. The CLM involving the Triticeae consensus genetic map revealed that the above distribution of genes and recombination is the same in other Triticeae species. Because of a significant number of common markers, our CLM can be used for comparative mapping and to estimate physical distances among markers in many Poaceae species including rice and maize.Genetics 01/1997; 144(4):1883-91. · 4.01 Impact Factor
Copyright 2004 by the Genetics Society of America
A 2600-Locus Chromosome Bin Map of Wheat Homoeologous Group 2 Reveals
Interstitial Gene-Rich Islands and Colinearity With Rice
E. J. Conley,* V. Nduati,* J. L. Gonzalez-Hernandez,*,1A. Mesfin,* M. Trudeau-Spanjers,*
S. Chao,†,2G. R. Lazo,†D. D. Hummel,†O. D. Anderson,†L. L. Qi,‡B. S. Gill,‡B. Echalier,‡
A. M. Linkiewicz,§,3J. Dubcovsky,§E. D. Akhunov,§J. Dvor ˇa ´k,§J. H. Peng,¶
N. L. V. Lapitan,¶M. S. Pathan,&H. T. Nguyen,&X.-F. Ma,&Miftahudin,&
J. P. Gustafson,** R. A. Greene,††M. E. Sorrells,††K. G. Hossain,‡‡
V. Kalavacharla,‡‡S. F. Kianian,‡‡D. Sidhu,§§M. Dilbirligi,§§
K. S. Gill,§§D. W. Choi,¶¶,4R. D. Fenton,¶¶T. J. Close,¶¶
P. E. McGuire,&&C. O. Qualset&&and J. A. Anderson*,5
*Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108,†U.S. Department of Agriculture-
Agricultural Research Center (USDA-ARS) Western Regional Research Center, Albany, California 94710-1105,‡Department of Plant
Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas 66506-5502,§Department of Agronomy
and Range Science, University of California, Davis, California 95616,¶Department of Soil and Crop Sciences, Colorado State
University, Fort Collins, Colorado 80523-1170,&Department of Agronomy, University of Missouri, Columbia,
Missouri 65211, **USDA-ARS Plant Genetics Research Unit, Department of Agronomy, University of Missouri,
Columbia, Missouri 65211,††Department of Plant Breeding, Cornell University, Ithaca, New York 14853,
‡‡Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105,
§§Department of Crop and Soil Sciences, Washington State University, Pullman,
Washington 99164-6420,¶¶Department of Botany and Plant Sciences,
University of California, Riverside, California 92521 and
&&Genetic Resources Conservation Program, University of
California, Davis, California 95616
Manuscript received December 15, 2003
Accepted for publication June 1, 2004
The complex hexaploid wheat genome offers many challenges for genomics research. Expressed se-
quence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers
for mapping and comparison with model organisms. The objectives of this study were to construct a high-
density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the
distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns
of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map.
A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern
hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed
of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins
and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively
gene-poor regions on both the short and long arms and having good synteny with rice were discovered.
The map locations of two ESTs indicated the possible presence of a small pericentric inversion on
chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes
4 and 7.
The hexaploid wheat genome is composed of three
EXAPLOID commonwheat (Triticumaestivum L.)
related diploid genomes designated A, B, and D with
seven chromosomes each (2n ? 6x ? 42). Extensive
genetic and cytogenetic characterization of diploid, tet-
raploid, and hexaploid wheat relatives has made it a
model system for the study of allopolyploid evolution.
whole-genome sequencing is not currently feasible for
gene discovery and genome evolution analysis in hexa-
ploid wheat. Expressed sequence tags (ESTs) are seg-
1Present address: Department of Plant Sciences, North Dakota State
University, Fargo, ND 58105-5051.
2Present address:USDA-ARS Biosciences ResearchLaboratory, Fargo,
3Present address: Plant Breeding and Acclimatization Institute, Radzi-
kow 05-870 Blonie, Poland.
4Present address:Eugentech, 52Oun-Dong, Yusong,Taeson, 305-333,
Republic of Korea.
5Corresponding author: Department ofAgronomy and Plant Genetics,
411 Borlaug Hall, University of Minnesota, St. Paul, MN 55108.
Genetics 168: 625–637 (October 2004)
626E. J. Conley et al.
ments of sequences from cDNA clones that correspond
to mRNA (Adams et al. 1991). The EST sequencing
approach targets sequencing of the expressed portions
of the genome and is particularly useful for gene discov-
ESTs can be isolated from a broad range of libraries to
maximize the number of genes identified. As of January
2004, 577,538 wheat ESTs were cataloged in the public
database at NCBI (http:/ /www.ncbi.nlm.nih.gov/dbEST/
dbEST_summary.html). Large-scale EST mapping pro-
vides valuable insights into the structure and evolution
of genomes. EST mapping studies can be used to assess
gene density and distribution, duplication, structural
rearrangements, colinearity with related species, and
function through comparative genomics (Akhunov et
al. 2003a; Sorrells et al. 2003; Qi et al. 2004).
The triplication of genomic content allows wheat to
tolerate the loss of chromosomes, arms, and segments
(Sears 1954, 1966; Sears and Sears 1978; Endo and
Gill 1996). The use of nullisomic-tetrasomic, ditelo-
somic, and deletion lines missing successive terminal
segments allows for the mapping of molecular markers
to chromosomes, arms, and chromosome bins within
been used extensively in mapping studies (Anderson et
al. 1992; Gill et al. 1993, 1996a,b; Delany et al. 1995;
Faris et al. 2000; Qi and Gill 2001; Sandhu et al. 2001;
Weng and Lazar 2002; Akhunov et al. 2003a; Qi et al.
2004). A high proportion of DNA fragments can be
mapped within subchromosomalregions using deletion
lines because intragenomic polymorphism is not re-
quired. Deletion bins along the chromosome arms have
been defined as chromosome segments lying between
the breakpoints of two deletion lines (Endo and Gill
1996). A National Science Foundation-funded wheat
EST project was undertaken with a goal of mapping
10,000 ESTs to chromosome bins in the wheat genome
by Southern hybridization using nullisomic-tetrasomic,
types detailing breakpoints and chromosome bins for
the cytogenetic stocks used in the wheat EST mapping
project can be found online at http:/ /wheat.pw.usda.
The rice (Oryza sativa L.) genome sequence (Goff et
al. 2002; Yu et al. 2002; http:/ /rgp.dna.affrc.go.jp/cgi-
bin/statusdb/irgsp-status.cgi; http:/ /www.gramene.org/)
provides a useful reference for comparative genomics
in the cereals. The deletion mapping system of wheat
provides a tool to examine colinearity with rice at the
a whole-genome comparative mapping study of wheat
and rice using wheat EST and rice sequence data and
found that BAC/PAC clones from one or a few rice
chromosomes have homology to each wheat homoeolo-
gous chromosome group.
The group 2 chromosomes contain several genes of
great agronomic importance, including the photope-
riod response genes Ppd1, Ppd2, and Ppd3 (Scarth and
Law 1983), numerous genes conferring resistance to
tosh et al. 2003), the two semidwarfing genes Rht 7
(Worland et al. 1980) and Rht 8 (Worland and Law
1986), the gametocidal genes Gc1-B1a and Gc1-B1b
in resistance to preharvest sprouting (Anderson et al.
The objectives of this study were to (1) construct a
high-density EST chromosome bin map of wheat homo-
eologous group 2 chromosomes, (2) analyze the distri-
bution of EST loci among the genomes and along the
chromosome arms, (3) construct a consensus map of
group 2, (4) investigate synteny among the group 2
(6) assess the colinearity of ESTs mapped on the group
2 consensus map with the rice genome sequence.
MATERIALS AND METHODS
Wheat ESTs were sequenced at the U.S. Department of
Agriculture-Agricultural Research Service Western Regional
senting a wide range of tissues, developmental stages, and
environmental stresses and distributed to the 10 mapping
laboratories. Information on the cDNA libraries is available
in Zhang et al. (2004) and the development of EST singletons
chromosome bin locations on the chromosomes via Southern
analysis using a set of deletion lines (Endo and Gill 1996;
Qi et al. 2003). DNA for the Southern blots was digested with
EcoRI enzyme. The group 2 cytogenetic stocks used were the
Chinese Spring nullisomic-tetrasomic (N2AT2B, N2BT2D,
and N2DT2A), ditelosomic (Dt2AS, Dt2BL, Dt2DS, Dt2DL),
and 11 deletion lines (2AS5, 2AL1, 2BS1, 2BS4/2BL4, 2BS3,
2 chromosomes into 18 bins (Figure 1). Bins are designated
by their bounding breakpoints, which in turn are designated
by fraction length (FL) values derived from the ratio of the
arm with the deletion to the whole chromosome arm (Gill
et al. 1996a). Chromosome bin mapping and data verification
procedures have been described by Lazo et al. (2004). Loci
mapped to group 2 chromosomes by any of the 10 mapping
labs were confirmed by the University of Minnesota lab on
the basis of the autoradiogram image available in the online
database (http:/ /wheat.pw.usda.gov/cgi-bin/westsql/map_locus.
Gene distribution among the genomes and within the chro-
mosome arms: Tests for random distribution of EST loci
among the three genomes and along the chromosome arms
were assessed by chi-square analysis of the confirmed set of
loci mapping to the chromosomes of homoeologous group 2
(mapping data are available online at http:/ /wheat.pw.usda.
gov/cgi-bin/westsql/map_locus.cgi). The analysis was re-
peated using the subset of 986 loci generated from the 337
group 2 ESTs having all restriction fragments mapped to re-
duce any bias due to unmapped restriction fragments and
different intergenomic polymorphism frequencies. The null
hypothesis assumed a proportional distribution of EST loci
among each of the three group 2 chromosomes on the basis
of their physical length (Gill et al. 1991). Expected values
for the number of EST loci between the long and short arms
were calculated on the basis of the arm ratio values (1.3,
627Group 2 Chromosome Bin Map
1.2, and 1.3 for 2A, 2B, and 2D, respectively) from physical
measurement of C-banded mitotic chromosomes (Gill et al.
1991). Analysis of the distribution of EST loci between the
long and short arms was performed on the subset of 965 loci
mapped to chromosome arms or bins (excluding loci mapped
only to chromosomes), generated from only those ESTs with
all restriction fragments mapped. Analysis of EST distribution
along the chromosome arms was performed on the subset of
854 EST loci mapped to chromosome bins (excluding loci
mapped only to chromosomes or chromosome arms); gener-
ated from only those ESTs with all restriction fragments
mapped. To assess EST locus distribution along the chromo-
some arms, the expected number of EST loci per micrometer
for each group 2 chromosome was calculated by dividing the
total number of EST loci in the data subset mapping to the
These expectation values were multiplied by the physical
length of each bin to determine the expected number of EST
the observed number of EST loci in a particular chromosome,
arm, or bin by the expected number.
Construction of group 2 consensus EST map: ESTs mapped
to bins in two or three group 2 chromosomes were assigned
to 14 consensus bins, designated CS, 1S, 2S, 3S, 4S, 5S, and
6S on the short arm and CL, 1L, 2L, 3L, 4L, 5L, and 6L on
the long arm from the centromere to the telomere (Figure
2; see also supplemental online materials at http:/ /wheat.
pw.usda.gov/pubs/2004/Genetics/). Deletion bins were or-
The consensus bins were defined by ESTs sharing a common
mapping pattern, on the basis of restriction fragments from
the different genomes being located in syntenous bins. For
example, consensus bin CS was defined by ESTs mapped to
chromosome deletion bins C-2AS5-0.78, C-2BS1-0.53, and
C-2DS1-0.33, while neighboring consensus bin 1S was defined
by ESTs mapped to chromosome deletion bins C-2AS5-0.78,
C-2BS1-0.53, and 2DS1-0.33-0.47. Some ESTs with loci in only
two group 2 chromosomes were mapped to combined consen-
sus bins if the map locations of the loci spanned more than
one consensus bin. For example, an EST having mapped loci
in chromosome bins C-2AS5-0.78 and C-2BS1-0.53, but no
map location for chromosome 2D, could map to consensus
bins CS, 1S, or 2S and was therefore assigned to the combined
bin CS-2S. However, an EST with mapped loci in chromosome
bins C-2BS1-0.53 and C-2DS1-0.33, but no 2A location, could
still be assigned to bin CS, because the map locations in 2B
and 2D are entirely contained within the bin C-2AS5-0.78.
Because all consensus bins, except 4S, were bounded by the
superimposed fraction lengths of the chromosome deletion
bins onto a single consensus group 2 chromosome (Figure
imposed breakpoints of the deletion bins among the three
group 2 chromosomes. Distribution of EST loci along the
consensus map was assessed by chi-square analysis using the
from ESTs having all restriction fragments mapped to reduce
bias due to unmapped fragments. The expected density of
EST loci for each consensus bin was calculated by multiplying
the total number of loci assigned to all consensus bins by the
proportional length of the bin.
Detecting anomalies: ESTs that did not fit into consensus
bins due to nonsyntenous map locations among the group 2
raphy images were examined for clarity and for unmapped
fragments that could confound the interpretation of the
for possible explanations, such as (i) unmapped restriction
fragments, (ii) structural rearrangement, or (iii) technical
error. In the first case, the unmapped restriction fragments
ous mapped fragments may have been interbin duplication
Duplications: ESTs with mapped loci in two different bins
events. These were assigned to the consensus map if at least
two chromosomes had loci in syntenous bins. ESTs with a
to a non-group 2 location were considered interchromosome
duplication events. This analysis did not take into account
differences in hybridization intensity among the restriction
fragments. Among ESTs having at least one fragment mapped
to a group 2 chromosome and at least one fragment mapped
to another homoeologous group, the total number of loci
for each non-group 2 bin throughout the hexaploid wheat
genome was counted. Chi-square analysis was used to test the
randomness of distribution of group 2 ESTs duplicated in
the other homoeologous groups. The null hypothesis was a
proportional distribution of duplicate EST loci among the
other homoeologous groups, such that the number of dupli-
cate loci would be based on the physical size of each chromo-
some group. Chi-square analysis was also used to test the ran-
domness of the distribution of duplicates among non-group
2 chromosome bins. The null hypothesis was that the fre-
quency of duplicate loci from group 2 in each bin would be
equal to the total frequency of all loci mapped to that bin.
plying the frequency of all loci occurring in that bin by the
total number of duplicate loci mapping to non-group 2 chro-
mosomes. Chi-square analysis was used to test the probability
of finding the observed number of duplicate loci in each bin
under the null hypothesis.
mosome group 2 consensus map were used to analyze wheat-
rice colinearity. The wheat EST nucleotide sequences were
compared against the rice BAC/PAC DNA sequences using
blastN at NCBI. The statistics of all the high-scoring pairs for
any given query-subject pair were calculated and summarized,
with the following cutoff parameters: E-value ? 1E?15, and
80% sequence identity over at least 100 bp. A binomial distri-
bution was used to test the probability of finding the observed
number of matches under the null hypothesis. The null hy-
pothesis was no colinearity (i.e., the matches to rice would be
randomly distributed throughout the rice genome). For each
bin, the rice chromosome with the largest number of matches
was identified. To test for the possibility of colinearity with
more than one rice chromosome within a wheat bin, the
binomial calculation was repeated for the rice chromosome
with the second highest number of matches, after eliminating
ing an equal probability of matches occurring on each of the
remaining 11 chromosomes.
Distribution of EST loci among the three homoeolo-
gous group 2 chromosomes: As of March 17, 2003, 1110
ESTs generating 2600 confirmed loci were mapped to
homoeologous group 2 chromosomes (available online
at http:/ /wheat.pw.usda.gov/cgi-bin/westsql/map_locus.
cgi), of which 2239 were mapped to specific chromo-
some bins, with the remaining 361 mapped to chromo-
somes or chromosome arms. Of the 2600 confirmed
loci mapping to homoeologous group 2 chromosomes,
628E. J. Conley et al.
Number and distribution of EST loci among group 2 chromosomes in wheat
All ESTs ESTs with all fragments mapped
Item2A2B2D Total 2A 2B2DTotal
** and ***, significant at 0.01 and 0.001 probability levels, respectively.
aBased on the assumption of proportional distribution of ESTs among the group 2 chromosomes based on
their physical length (Gill et al. 1991).
bProbability of a departure from the expected number of loci.
cRatio of observed to expected number of loci.
769 loci (29.6%) from 651 EST probes mapped to 2A,
959 loci (36.9%) from 728 probes mapped to 2B, and
872 loci (33.5%) from 725 probes mapped to 2D (Table
1). The chi-square analysis using the confirmed set of
data mapping to the chromosomes of homoeologous
group 2 indicated a highly significant (P ? 0.001) non-
random distribution of EST loci among the three chro-
mosomes of homoeologous group 2 on the basis of
the assumption of proportional distribution of EST loci
among the three group 2 chromosomes based on their
physical length. Chromosome 2D had a larger than ex-
pected number of loci, while 2A had a smaller number.
The chi-square analysis was repeated using the subset
of 986 confirmed loci generated from the 337 ESTs
having all restriction fragments mapped. A total of 302
loci from 253 EST probes mapped to 2A, 360 loci from
265 probes mapped to 2B, and 324 loci from 266 probes
mapped to 2D (Table 1). Density ratios and chi-square
analyses were similar to the analysis using all ESTs.
Distribution of EST loci between the chromosome
arms: Chi-square analysis of the subset of 965 confirmed
EST loci having all restriction fragments mapped re-
vealed significant deviations from the expectation that
the number of loci on long vs. short chromosome arms
was proportional to their physical lengths (Gill et al.
1991; Table 2). EST loci mapped to a chromosome but
not to an arm or bin were excluded from this analysis,
reducing the data subset from 986 to 965 loci. Some
ESTs mapping to homoeologous group 2 were hybrid-
ized to a mapping filter that did not include N2AT2B.
Therefore, any EST loci located in the C-2AS5-0.78 bin,
which spans the majority of the short arm, could not be
mapped. Loci in the C-2AL1-0.85 bin could be mapped
due to the presence of ditelosomic 2AS on the mapping
filters. The missing N2AT2B stock could have skewed
the results of the EST distribution between the arms of
2A and in the bins along the short arm of 2A. For this
reason, the 337 group 2 ESTs having all restriction frag-
ments mapped were used to analyze EST distributions
between and along the chromosome arms. Ratios of
mapped loci on the long vs. short arms were 1.8, 1.6,
and 1.8 for chromosomes 2A, 2B, and 2D, respectively.
All three group 2 chromosomes had higher than ex-
pected numbers of EST loci on the long arm with sig-
nificance levels of P ? 0.01 for 2A and 2D and P ? 0.05
Distribution of EST loci along the chromosome arms:
Analysis of the subset of 854 confirmed group 2 loci,
mapped to chromosome bins from the ESTs having all
restriction fragments mapped, revealed highly signifi-
cant (P ? 0.001) deviations from the expected number
of EST loci for 10 of the 18 group 2 chromosome bins
(Figure 1, Table 2). EST loci mapped to a chromosome
or chromosome arm but not to a chromosome bin were
excluded from this analysis, resulting in a data set of
854 loci. Gene densities were expressed as a ratio of
observed vs. expected loci on the basis of physical
length. The interstitial bin 2BL2-0.36-0.50 had the high-
est gene density with a ratio of 3.01. The most distal
bins of both arms for all three group 2 chromosomes
had high EST densities (P ? 0.001), ranging from ratios
of 1.74 to 2.63, with the exception of 2DS5-0.47-1.00,
which did not differ significantly from the expectation.
ESTs: C-2AS5-0.78, C-2BS1-0.53, C-2DS1-0.33, C-2BL2-
0.36, and C-2DL3-0.49 had fewer loci than expected
(P ? 0.01). The centromeric bin C-2AL1-0.85, spanning
85% of the fraction length of the long arm, did not
differ significantly from the expectation.
Group 2 consensus EST map: Of the 1110 ESTs with
mapped loci, 552 ESTs mapped to overlapping chromo-
some bins in two or three genomes were assigned to
consensus bins with 225 ESTs located on the short arm
and 327 on the long arm (see supplemental online mater-
ials at http:/ /wheat.pw.usda.gov/pubs/2004/Genetics/).
Of the 552 ESTs assigned to the consensus map, 376
629Group 2 Chromosome Bin Map
Distribution of EST loci between the group 2 chromosome arms and among the chromosome bins
No. of loci
*, **, and ***, significant at 0.05, 0.01, and 0.001 probability levels, respectively.
aFrom Endo and Gill (1996).
bDetermined from arm ratio value (Gill et al. 1991) for arms and from the physical length of the bin for
cRatio of observed to expected number of loci.
dTest for probability of departure of observed from expected number of loci.
eA total of 965 EST loci mapped to chromosome arms generated from only those ESTs having all restriction
fA total of 854 EST loci mapped to chromosome bins generated from only those ESTs having all restriction
were mapped to specific consensus bins, with 151 and
225 ESTs located to bins in the short and long arms,
respectively. An additional 176 ESTs were mapped to
larger, combined bins due to missing data in one of the
interval, but not the specific bin, to be identified.
The consensus bin 4S was bounded by nonoverlap-
ping fractions between chromosomes 2A and 2B. One
EST, BF482723, with loci mapped to bins C-2AS5-0.78
and 2BS4-0.75-0.84, fit into the expected fraction (0.75–
0.78); however, this EST had a highly complex banding
pattern, with 14 total loci mapping to four different
homoeologous groups and seven unmapped fragments.
This EST was treated as an anomaly, while the 37 ESTs
mapping to the syntenous bins of nonoverlapping frac-
tions 2AS5-0.78-1.00, 2BS1-0.53-0.75, and 2DS5-0.47-1.00
defined consensus bin 4S. For the purpose of this study,
the consensus bin 4S was defined by the 2BS1 0.75 break-
point at its proximal end and the 2AS5 0.78 breakpoint
at its distal end.
Chi-square analysis was performed using loci gener-
ated from ESTs havingall restriction fragments mapped
and assigned to specific consensus bins to analyze fur-
ther the distribution of loci contained in smaller inter-
vals (Figure 2, Table 3). Small interstitial consensus bins
on the long arm (2L, estimated FL 0.49-0.50) and on
the shortarm (4S, estimatedFL 0.75-0.78) hadthe high-
est EST density ratios of 34.6 and 7.8, respectively (P ?
mapped to consensus bins, yet constituted only ?1%
of the physical arm. This bin was flanked by bins 1L
(estimated FL 0.36-0.49) and 3L (estimated FL 0.50-
630E. J. Conley et al.
Figure 1.—Distribution of EST loci among group 2 chromosome bins. Italicized numbers indicate the gene density ratios
(mean over all bins is 1.0); numbers outside parentheses are the observed number of loci; within parentheses are the expected
number based on the physical size of the bin. The bin fraction is indicated to the right of each chromosome. The solid horizontal
bands on each chromosome depict heterochromatic regions. Hatched horizontal bands are heterochromatic regions not consis-
tently observed (Gill et al. 1991). The figure is based on 854 loci generated from only those ESTs having all restriction fragments
mapped and assigned to chromosome bins.
0.76), which contained significantly fewer than expected
for ?3% of the length of the arm. Adjacent bin 3S
(estimated FL 0.53-0.75) was extremely sparse (P ?
0.001) with a gene density ratio of only 0.10. The other
neighboring consensus bin also had a low density ratio
of 0.58, although there were only a small number of
loci discovered. The most distal bins, 6S and 6L, had
significantly higher than expected numbers of EST loci
(P ? 0.01 and P ? 0.001, respectively). Consensus bin
4L, with estimated fraction length 0.76–0.85, was also
highly EST rich (P ? 0.001). Both centromeric consen-
sus bins CS and CL were regions of lower than expected
EST density (P ? 0.001).
Anomalies: Sixty-seven ESTs (6.0%) that mapped to
two or three homoeologous group 2 chromosomes
could not be assigned to consensus bins because they
some bins in the different genomes. These 67 ESTs
detected 30 different types of anomaly, of which 43 had
unmapped restriction fragments. Furthermore, nearly
one-half of anomalous ESTs had more than six restric-
tion fragments, and approximately one-third had frag-
ments mapped to other homoeologous groups. There-
fore, many of these anomalies occurred in higher-copy
ESTs with complex patterns of duplication. One-half of
the various types of anomalies were detected by only
one EST. One such anomaly, BE604879, had fragments
mapped to bins 2BS3-0.84-1.00, 6AS5-0.65-1.00, and
the possible presence of a 6BS-2BS translocation.
Structural rearrangements: A possible pericentric in-
version on chromosome 2B was detected by two ESTs:
BE404630 and BE500625. Missing restriction fragments
in N2BT2D, N2AT2B, and N2DT2A and ditelosomic
lines indicated map locations on the opposite arm of
chromosome 2B vs. 2A and 2D. Due to the absence of
restriction fragments in the group 2 nullisomic-tet-
rasomic and ditelosomic lines and the presence of all
loci in all group 2 deletion lines, the loci were mapped
to bins nearest the centromere. The two EST probes
involved in the possible inversion constitute 2.9% of the
70 EST probes that detected loci in the centromeric
consensus bins, including probes mapped to consensus
bins CS and CL, plus the two probes involved in the
631Group 2 Chromosome Bin Map
plication analysis was restricted to duplication to other
group 2 bins and to other homoeologous groups. Only
25 ESTs (2.3%, based on the confirmed set of ESTs with
loci mapping to homoeologous group 2 chromosomes)
detected loci in two or more bins within a homoeolo-
gous group 2 chromosome, 15 of which involved dupli-
cation to bins on opposite arms. The 25 ESTs generated
eight duplicate loci on 2A, 14 on 2B, and 6 on 2D.
Three hundred sixty ESTs (32.4%) had at least one
locus mappedto ahomoeologous group2 chromosome
and at least one locus mapped to a different homoeolo-
gous group chromosome. On a whole-chromosome ba-
sis, no significant deviations from random distribution
were detected by chi-square analysis (see supplemen-
tal online materials at http:/ /wheat.pw.usda.gov/pubs/
On a chromosome-bin basis, the number of duplicate
loci mapping within each non-group 2 bin ranged from
0 to 20. No highly significant pattern of duplication to
non-group 2 chromosome bins was found. However,
significant duplication (P ? 0.01) was found in the
chromosome bin C-1BL6-0.32, with 14 duplicated loci
generated from 10 EST probes. Eight additional chro-
mosome bins had more duplicate loci than expected
with a significance level of P ? 0.05 (see supplemen-
tal online materials at http:/ /wheat.pw.usda.gov/pubs/
Wheat-rice comparisons: The sequences of the 552
ESTs assigned to the consensus map were compared
against the rice BAC/PAC sequences at NCBI using
blastN for analysis of wheat-rice colinearity. Highly sig-
nificant colinearity was found between the short arm of
the wheat consensus group 2 chromosome (W2) and
rice chromosome 7 (R7) and between the long arm of
W2 and rice chromosome 4 (R4) (Table 4). Of the 122
short-arm ESTs having matches to rice, 70.5% matched
the most distal consensus bin on the short arm of W2
(6S) had highly significant colinearity with R4, but also
had significant colinearity with R7. Of the 18 matches
in bin 6S, 10 went to R4 and 5 went to R7. Colinearity
between the ESTs of W2 and R7 extended into the
proximal region of the long arm of W2 with consensus
bin CL having good colinearity with the short arm of
R7 and bin CS having good colinearity with both the
short- and long-arm centromeric regions of R7. Of the
31 matches in bin CL (estimated FL C-0.36) and com-
bined bin CL-1L (estimated FL C-0.49), 16 matched
sequences on R7 and 9 matched sequences on R4. The
majority of disruptions in colinearity occurred in the
most distal bins of the consensus map. Although the
order of wheat ESTs within bins is unknown, those ESTs
mapped to specific consensus bins with matches to rice
chromosomes determined to have significant colinear-
ity were assigned to putative orders within bins on the
basis of comparison with the ordered rice BAC/PAC
Figure 2.—Distribution of EST loci on the group 2 consen-
sus map. Italicized numbers indicate the gene density ratios;
within parentheses are the expected numbers based on the
physical size of the bin. Consensus bin designations are indi-
cated to the left of the chromosome, and bin fraction is indi-
cated to the right. The figure is based on the subset of ESTs
having all restriction fragments mapped and assigned to spe-
cific consensus bins.
fragments detected by an EST probe to the same bin
could be due to duplication of genetic material or to
other factors such as intragenic restriction sites. These
factors confound the analysis of duplication of genetic
material within chromosome bins. For this reason, du-
632E. J. Conley et al.
Distribution of EST loci along the group 2 chromosome consensus map
No. of loci
Only loci from ESTs with all restriction fragments mapped and assigned to specific consensus bins were
included in this analysis. *, **, and ***, significant at 0.05, 0.01, and 0.001 probability levels, respectively.
aFrom Gill et al. (1991).
bNumber of loci based on the physical length of the bin.
cRatio of observed to expected number of loci.
dTest for departure of observed from expected number of loci.
mental online materials http:/ /wheat.pw.usda.gov/pubs/
2004/Genetics/). ESTs mapped to combined bins were
excluded from Figure 3. Of the 146 ESTs mapped to
specific consensus bins having matches to rice colinear
chromosomes 4 and 7, 6 were excluded from the figure
because the rice BACs that they matched were not in-
cluded in the map of ordered rice BACs (http:/ /www.
All&markerSource?All; http:/ /www.tigr.org/tigr-scripts/
All). Of the 140 ESTs (11.4%) included in Figure 3, 16
detected disruptions in wheat-rice synteny at the W2
consensus bin level. Of the 5 ESTs with matches to R4
in bin CL, 3 showed disruptions in synteny. Distal bin 6S
contained four synteny disruptions, and 6L contained
three. Wheat consensus bins tended to correspond to
blocks of ordered rice BACs/PACs.
heterochromatic of the group 2 chromosomes (Gill et
al. 1991; Figure 1).
As reported elsewhere (Akhunov et al. 2003a; Qi et
al. 2004), chi-square analysis revealed numerous bins
with significantly higher or lower densities than ex-
pected. The tendency for deletion line breakpoints to
coincide with interstitial gene-rich clusters (Endo and
Gill 1996), possibly due to loose packing of transcrip-
tionally active regions, has been reported for wheat
group 1 (Gill et al. 1996b; Sandhu et al. 2001) and
group 5 (Gill et al. 1996a; Faris et al. 2000). Consensus
bins 4S and 2L were defined by breakpoints in neigh-
boring regions between the A and B and B and D ge-
nomes, respectively. The extremely high gene density
in these small consensus bins provided additional sup-
porting evidence for the coincidence of deletion line
breakpoints and gene-rich clusters. The long-arm chro-
mosome bin 2BL2-0.36-0.50 was unique due to its ex-
tremely high gene density ratio, ?3.0, despite its loca-
tion in the proximal one-half of the chromosome arm.
0.49–0.50 had a gene density ratio exceeding 34 times
sus map location (2L, estimated FL 0.49-0.50), the ma-
jority (85%) of the loci mapping to 2BL2-0.36-0.50 were
concentrated around the distal 1% of the bin. There
appeared to be an inaccuracy in the measurement of
deletion fraction lengths involving consensus bin 4S, as
evidenced by the 37 ESTs having loci in syntenous bins
with nonoverlapping breakpoint fractions between
chromosomes 2A and 2B. The bin 2BS4-0.75-0.84 was
Distribution of EST loci: Chromosome 2D is a highly
EST-rich chromosome with an overall density ratio of
1.18 (1.16 using the subset of data having all restriction
fragments mapped). Although chromosome 2B had
more EST loci than 2A or 2D, analysis showed that, on
the basis of its size, it had the expected number of EST
loci. Therefore, the larger physical size of chromosome
2B accounted for its large number of EST loci. It is
notable that chromosome 2B had an average gene den-
sity, while 2A had fewer loci than expected, especially
in light of the fact that chromosome 2B is the most
633 Group 2 Chromosome Bin Map
Colinearity between the wheat group 2 consensus map and the rice genome
123456789 10 11 12match
11 1011 16 14
383 193 25
992011420 1048040 10 272280
Underlining indicates rice chromosomes with greatest colinearity with each wheat consensus bin.
aNumbers within each column are the number of ESTs with significant matches between the wheat consensus bin and the
bBinomial probability of finding the observed number of ESTs in the rice chromosome showing the greatest colinearity in
cBinomial probability of finding the observed number of ESTs in the rice chromosome showing the second greatest colinearity.
an EST-poor region (the gene density ratio was 0.39).
This is inconsistent with the finding that part of this bin
was contained in an EST-rich region (gene density ratio
was 7.78) on the consensus map. The bin 2BS1-0.53-
0.75 had a slightly above-average gene density (1.29).
This evidence, as well as the large number of ESTs
exhibiting the mapping pattern 2AS5-0.78-1.00; 2BS1-
0.53-0.75; 2DS5-0.47-1.00, supported the adjustment of
the 2AS5 breakpoint from 0.78 to the vicinity of 0.75.
For the purpose of this article, the 37 ESTs were placed
into consensus bin 4S, and the breakpoint for 2AS5 was
thus assumed to be somewhat proximal of 0.78. The
extreme concentration of EST loci into very small frac-
tions of the group 2 consensus map provided evidence
stitial gene-rich islands, surrounded by large, gene-poor
oceans. Such gene islands provide potential targets for
sequencing, mapping, and gene discovery, and BAC
clones from dense, syntenous regions can be used in
blast searches (i) to design molecular markers, (ii) to
assess function on the basis of sequence comparison,
and (iii) for genomic evolutionary studies.
634E. J. Conley et al.
Figure 3.—Depiction of wheat consensus group 2 and rice syntenous blocks. Wheat group 2 ESTs are listed in their putative
order within consensus bins on the basis of comparison with ordered rice BAC/PAC clones. The wheat EST consensus map
showing loci with matches to the rice colinear chromosomes is flanked by the genetic maps of rice BAC/PAC clones for rice
chromosomes 4 (left) and 7 (right). Solid lines connect syntenous blocks between wheat ESTs and rice BAC/PAC clones. Dotted
lines indicate significant blast matches between a wheat EST and rice BAC/PAC showing synteny disruptions at the consensus
bin level. ESTs involved in synteny disruptions are shown in boldface, underlined type. Thin solid lines connect EST-rice BAC/
PAC matches that are syntenous at the bin level, but have only one match to the syntenous region in rice. Centromeres are
indicated by thick solid horizontal lines. Cumulative centimorgan distances are given on the side of each rice chromosome.
Information on genetic mapping of rice chromosomes 4 and 7 BAC/PAC clones was obtained at http:/ /www.tigr.org/tigr-scripts/
IRGSP/assignMap.pl?chr?4&site?All&markerSource?All and http:/ /www.tigr.org/tigr-scripts/IRGSP/assignMap.pl?chr?7&
635Group 2 Chromosome Bin Map
Consensus bins provided a higher resolution frame-
work than individual chromosome deletion bins did
for ordering blocks of ESTs along the chromosomes.
However, our mapping data have shown that the homo-
eologous group 2 chromosomes were not perfectly con-
served (see Structural rearrangements in the results and
discussion) and, given the resolution of the chromo-
some deletion bins (two to four per chromosome arm),
it is likely that many deviations in gene order and con-
tent have remained undetected.
While the number of predicted genes in eukaryotic
organisms has been shown to be relatively constant,
genome sizes are known to vary over five orders of mag-
nitude (Gregory 2001). The main difference in ge-
nome structure between species with large and small
genomesappearsto bethesizeof thegene-poorregions
separating gene-rich islands. It has been estimated that
?80% of genomic content in the Triticeae consists of
repetitive DNA sequences (Smith and Flavell 1975).
A comparative study of the Sh2/A1 orthologous region
in rice, sorghum (Sorghum vulgare L.), maize (Zea mays
L.), and the Triticeae revealed massive expansions in
certain intergenic regions in the Triticeae. The inter-
genic distances of wheat in comparison with rice varied
from 4-fold for one gene pair to an estimated 195-fold
for another gene pair (Li and Gill 2002). Therefore,
we conclude that genome expansion in the Triticeae
did not occur uniformly throughout the genome.
Genome expansion events caused by insertions of
repetitive sequences such as retrotransposable elements
(RTEs) are subject to natural selection (SanMiguel et
al. 1996) and would be dependent on the availability of
nondeleterious insertion sites (Petrov 2001). In maize,
periodic insertions of retrotransposons usually occur
within other RTEs (SanMiguel et al. 1998; Gaut et
al. 2000). Walbot and Petrov (2001) theorized that
periodic retrotransposable element expansions, tem-
pered locally by tolerance for insertions, were highly
likely to produce the observed extreme unevenness in
gene density due to the preferential accumulation of
insertions in less gene-dense regions. Thus, the cluster-
ing of genes on small, interstitial islands within each
group 2 chromosome arm, surrounded by vast regions
of noncoding DNA, could reduce the probability that
deleterious mutations will occur within coding regions.
Wheat-rice comparisons: The results of the wheat-rice
colinearity analysis were consistent with the findings of
good colinearity between wheat homoeologous group
2 and rice chromosomes 4 and 7 by Sorrells et al.
(2003) and with previous RFLP-based comparative maps
of wheat and rice (Kurata et al. 1994; Van Deynze et
al. 1995). The consensus bins along the homoeologous
group 2 consensus map also had generally good colin-
earity with blocks of ordered BACs/PACs matching
ESTs in each bin. At the bin level, the highest frequency
of synteny disruptions occurred in the most distal con-
sensus bins, 6S and 6L. These results were consistent
with previous findings that synteny levels tend to de-
crease with distance from the centromere (Akhunov et
al. 2003b). However, disruptions in synteny were also
observed in the centromeric bin CL, which will be dis-
cussed in the next section. Bennetzen et al. (1998)
observed the maintenance of colinearity in gene-rich
regions of rice and sorghum, despite their evolutionary
distance of ?50 million years. Similarly, the highly EST-
rich consensus bins 4S and 2L appeared to have the
best overall synteny with rice with a large number of
ESTs matching with blocks of rice-ordered BAC/PAC
clones and no synteny disruptions observed at the bin
Structural rearrangements: The detection of a small
putative pericentric inversion in chromosome 2B was
and to ourknowledge has not beenpreviously reported.
Due to its small size and close proximity to the centro-
mere, a region of low recombination, this inversion
would have been difficult to detect using genetic map-
ping systems that rely on intragenic polymorphism.
Akhunov et al. (2003b) reported decreased synteny lev-
els with increased distance from the centromere, corre-
lating with higher levels of recombination. However,
they also reported that a greater number of unique loci
occur in the proximal region of the B genome than in
the same regions of the A and D genomes. Figure 3
indicates disruptionsin syntenyin thecentromeric bins,
as well as significant colinearity with both rice chromo-
somes 7 and 4 for consensus bin CL (Table 4). The EST
BE404630 involved in the inversion had a significant
blast match to the rice BAC AP004384 in the block
colinear with consensus bin CS. Because this EST was
an anomaly, with loci mapped to the centromeric chro-
mosome bins in 2AL, 2DL, and 2BS, it was not placed
on the consensus map and was not included in Figure
3. In Figure 3, three of the five ESTs with matches to
rice chromosome 4 and mapped to CL showed bin-level
synteny disruptions. Additionally, Figure 3 shows two
disruptions in synteny between consensus bin CS and
rice chromosome 7 and one for consensus bin CL. The
lack of synteny in the centromeric region among the
homoeologous group 2 chromosomes detected by the
two wheat ESTs involved in the pericentric inversion,
as well as the disruptions in synteny between consensus
bin CL and rice, suggest that this has been a region
subject to rearrangement during the evolution of the
A translocation involving the short arms of chromo-
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basis of genetic mapping data (Devos et al. 1993). This
rearrangement also was reported in tetraploid wheat
(T. turgidum L.) from the mapping of the cDNA clone
PSR899 with orthologous loci on 6S–2BS (Blanco et al.
1998). However, deletion mapping revealed markers
Xpsr899-6A and Xpsr899-6D to be physically located in
636E. J. Conley et al.
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Comparison of homoeologous
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The telocentric chromosomes
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Communicating editor: J. P. Gustafson