Yu et al.

BMC Genomics 2011, 12:15

http://www.biomedcentral.com/1471-2164/12/15

RESEARCH ARTICLE Open Access

Genome structure of cotton revealed by a

genome-wide SSR genetic map constructed from
a BC1 population between gossypium hirsutum
and G. barbadense
Yu Yu1,2, Daojun Yuan1, Shaoguang Liang1, Ximei Li1, Xiaqing Wang1, Zhongxu Lin1*, Xianlong Zhang1

Abstract
Background: Cotton, with a large genome, is an important crop throughout the world. A high-density genetic
linkage map is the prerequisite for cotton genetics and breeding. A genetic map based on simple polymerase
chain reaction markers will be efficient for marker-assisted breeding in cotton, and markers from transcribed
sequences have more chance to target genes related to traits. To construct a genome-wide, functional marker-
based genetic linkage map in cotton, we isolated and mapped expressed sequence tag-simple sequence repeats
(EST-SSRs) from cotton ESTs derived from the A1, D5, (AD)1, and (AD)2 genome.
Results: A total of 3177 new EST-SSRs developed in our laboratory and other newly released SSRs were used to
enrich our interspecific BC1 genetic linkage map. A total of 547 loci and 911 loci were obtained from our EST-SSRs
and the newly released SSRs, respectively. The 1458 loci together with our previously published data were used to
construct an updated genetic linkage map. The final map included 2316 loci on the 26 cotton chromosomes,
4418.9 cM in total length and 1.91 cM in average distance between adjacent markers. To our knowledge, this map
is one of the three most dense linkage maps in cotton. Twenty-one segregation distortion regions (SDRs) were
found in this map; three segregation distorted chromosomes, Chr02, Chr16, and Chr18, were identified with 99.9%
of distorted markers segregating toward the heterozygous allele. Functional analysis of SSR sequences showed that
1633 loci of this map (70.6%) were transcribed loci and 1332 loci (57.5%) were translated loci.
Conclusions: This map lays groundwork for further genetic analyses of important quantitative traits, marker-
assisted selection, and genome organization architecture in cotton as well as for comparative genomics between
cotton and other species. The segregation distorted chromosomes can be a guide to identify segregation
distortion loci in cotton. The annotation of SSR sequences identified frequent and rare gene ontology items on
each chromosome, which is helpful to discover functions of cotton chromosomes.

Background map is a foundation in genetic dissection of economically

Cotton (Gossypium spp.) is the most important fiber crop
in the world and one of the most important oilseed
crops. Within the genus Gossypium, two cultivated allo-
tetraploid species, G. hirsutum L. and G. barbadense L.,
account for 90% and 8% of the world cotton production
respectively [1]. The construction of a molecular genetic
* Correspondence: linzhongxu@mail.hzau.edu.cn
1
National Key Laboratory of Crop Genetic Improvement & National Centre of
Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan
430070, Hubei, PR China
Full list of author information is available at the end of the article
important traits, marker-assisted selection (MAS), and
map-based cloning. It provides new insights into genome
structure and chromosomal architecture of the cotton
genome. However, the allotetraploid (2n = 4x = 46) spe-
cies has a large genome size of ~ 2246 Mb [2], which has
hindered the development of a high-density map.
To explore the cotton genome structure and to
identify quantitative trait loci (QTLs) for agronomically
important traits which can facilitate MAS in cotton,
several genetic maps have been constructed including
high-density interspecific [3-8] and intraspecific maps

© 2011 Yu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
Yu et al. BMC Genomics 2011, 12:15
http://www.biomedcentral.com/1471-2164/12/15
[9-13]. The early cotton genetic maps were comprised of
only restriction fragment length polymorphisms (RFLPs)
[2]; later, polymerase chain reaction (PCR)-based mar-
kers were widely adopted, including random amplified
polymorphic DNA (RAPD), amplified fragment length
polymorphism (AFLP), simple sequence repeat (SSR),
sequence-related amplified polymorphism (SRAP), and
target region amplification polymorphism (TRAP) [1].
Among the molecular markers, SSRs have become pop-
ular markers of choice for cotton genetic analysis and
mapping.
SSRs, consisting of a variable number of tandem
repeats, are mainly characterized by their high
frequency, even distribution, co-dominance, reproduci-
bility, and high polymorphism [14,15]. Because of these
characteristics, microsatellites have become the most
favoured genetic markers for plant breeding and genet-
ics such as genetic diversity assessment, genetic map
construction, QTL mapping, and marker aided selection,
etc [16]. In general, SSRs are identified from either
genomic DNA or cDNA sequences. The usual source
sequences for SSRs have included SSR-enriched library
clones, expressed sequence tags (ESTs), and bacterial
artificial chromosome end sequences [17-19]. However,
conventional SSR marker development (from enriched
libraries) is costly and time consuming [20]. In recent
years, with the rapid increase of ESTs in public
databases and the advent of bioinformatics tools, SSR
marker development has become easier and more cost-
effective. Mining SSRs from ESTs is becoming popular
for SSR development.
Thanks to global efforts, 11938 SSR markers have
been released (CMD website, http://www.cottonmarker.
org) up to 2009. Among these SSRs, more than half are
EST-SSRs. However, compared to the huge ESTs tank
of cotton, only ~25% of the cotton ESTs is applied to
SSR development. Cotton ESTs are still a valuable
resource for SSR marker development, especially for
gene-derived SSRs. It is worth mentioning that the
genetic map constructed by Guo et al. contains 71.96%
functional marker loci, of which 87.11% are EST-SSR
loci [7]. High-density genetic maps of EST-SSR markers
are an essential tool for enhanced genome analysis.
They represent the transcript part of the genome and
can be links between genetic and physical maps [21].
Moreover, as EST-SSRs target coding regions of the
genome, they may be useful in association with genes of
known function to facilitate the dissection of complex
traits [22].
With an endless effort to construct a high-density
genetic map of cotton in our laboratory, we have tried
RAPDs, SRAPs, and SSRs when no sufficient easy-to-use
markers such as SSRs in cotton were available [5,23].
In the last 5 years, the cotton EST project and genome
Page 2 of 14
sequencing project generated a great number of
sequences that could promote the marker development,
and thousands of EST-SSRs and BAC-end SSRs have
been developed. Benefited from these projects, we con-
structed an SSR-based genetic map using SSRs available
in 2008 [8]. Thereafter, 700 new Gh-prefixed SSRs [24],
new NAU-prefixed SSRs [7,25], and more recently 2937
genomic SSRs (gSSRs) (Monsanto Company) [26] have
been released. In this study, we enriched our SSR-based
map by these new SSRs; we also isolated and mapped
SSRs from ESTs with BLAST hits to known genes, from
newly released ESTs of G. hirsutum by Yuxian Zhu
(GenBank, December 31, 2007), and from newly
developed ESTs of G. barbadense in our laboratory.
Additionally, our recently published markers were also
included in this map [27-29], and a final map with 2316
loci map was constructed. This sequence-based,
high-density map allowed us to detect segregation dis-
tortion regions within the whole genome, to identify
gene distribution on chromosomes and homologs
between chromosomes.
Results
Marker development
A total of 1831 new EST-SSRs were developed from the
assembled cotton ESTs in the TIGR database http://www.
tigr.org based on the criteria of marker development (see
Materials and Methods): 346 from G. arboretum
(HAU231-HAU576), 293 from G. raimondii (HAU577-
HAU869), and 1192 from G. hirsutum (HAU870-
HAU2061).
The 131182 ESTs released by Yuxian Zhu were
clustered and assembled into 46296 unique sequences,
consisting of 10691 contigs and 35605 singletons.
A total of 1047 unique EST-SSRs (HAU2062-HAU3108)
were developed from these sequences.
The 10979 ESTs from developing fiber of G. barba-
dense acc. 3-79 generated in our laboratory were clus-
tered and assembled into 5852 unique sequences,
consisting of 1492 contigs and 4360 singletons. A total
of 299 novel EST-SSRs (HAU3109-HAU3407) were
developed from these sequences.
All the marker primers, sequence ID, sequences,
motifs, estimated product size, and BLASTX results are
listed in Additional file 1.
Maker polymorphism
Of the 700 Gh-prefixed gSSRs derived from G. hirsutum,
134 SSRs (19.1%) showed polymorphism and generated
172 polymorphic loci with an average of 1.28 loci/SSR.
Among the 1554 and 754 NAU-prefixed EST-SSRs
derived from G. raimondii and G. hirsutum, respectively,
and 578 gSSRs from BAC sequences of G. hirsutum,
439 (24.7%), 109 (14.5%), and 68 (11.8%) SSRs were
Yu et al. BMC Genomics 2011, 12:15 Page 3 of 14
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polymorphic, and they generated 537, 131, and 71 loci,

Chr01 Chr15
respectively, with an average of 1.22 loci/SSR, 1.20 loci/ 0.0 Gh565
8.4 NAU2936
SSR, and 1.0 loci/SSR, respectively. 11.5 MUSS563
MUSS537 NAU3922
For these EST-SSRs from the assembled ESTs in TIGR, 14.4 MUCS141 MUCS410
HAU0059
14.9 MUCS422 MUCS152
28 (8.1%), 33 (13.8%), and 233 (19.5%) SSRs were poly- 15.4 HAU0077
16.7 BNL2440
morphic for EST-SSRs from G. arboretum, G. raimondii, 0.0
15.2
NAU3384
HAU0309
18.5
19.4
NAU2437
HAU3132
HAU1351 20.6 HAU2936
and G. hirsutum, respectively, and they generated 29, 36, 16.7
19.6 NAU4891 21.7 HAU0331
22.3 TMB0142 29.9 NAU2814
and 236 loci, respectively. One hundred and sixty-eight 23.7 Gh350b 35.6 NAU2901b
NAU2823
27.0 BNL1350a 36.4
SSRs (16.0%) of the 1047 EST-SSRs (HAU2062- 28.0 NAU3365b 40.7
42.7
HAU2861a
DPL0318
28.4 DPL0513
HAU3108) were polymorphic and 199 loci were 29.3
29.7
CIR049
TMB0062
46.6
54.1
TMB1492
NAU3530
54.9 BNL2920
produced; 42 SSRs (14.0%) were polymorphic from the 29.8 BNL3090a JESPR205
57.1
30.6 DPL0094
57.8 CIR307
31.4 BNL2702
299 EST-SSRs (HAU3109-HAU3407) and 47 loci were 32.9 HAU0672b 59.9
60.5
NAU3736a
NAU3433
33.0 Gh649a
produced. 33.2 TMB0011
61.8
62.1
TMB1633
DPL0322
33.5 NAU2182
62.8 BNL2700 NAU3496
33.6 JESPR56a
63.0 MGHES59
34.8 CIR018
63.4 NAU3690
Map construction and overview 36.4 MUSS422a 63.6 BNL162
MGHES10 NAU3533b 63.9 JESPR180
JESPR298
A total of 1458 loci obtained in this study, adding to the 37.8 Gh216 BNL2564a
JESPR240b
64.4
64.9 HAU2353
65.2 NAU3680
1026 loci published by Zhang et al. [8] and other pub- 39.1
40.0
BNL2921
TMB1869
65.9 DPL0300
66.0 BNL1666
42.5 GLB2 DPL0490
lished loci [27-29], a total of 2521 loci were applied to 43.2 TMB2544
66.9
69.5
NAU3178
NAU6459
43.9 BNL3888
69.7 BNL2646b BNL4082
map construction. After calculation, 2316 loci including 45.5
46.4
HAU0611
Gh336
70.2 MUSS440
70.4 DPL0615
48.6 HAU1229
2311 SSR loci and 5 gene-derived loci were mapped on 52.2 BNL3580
70.6
70.8
NAU2985
NAU3067
52.4 NAU4074
26 cotton chromosomes; the total length of this map 56.8 JESPR63*****
72.7
73.4
MUSS012 BNL3902
MUCS084 JESPR240a
57.2 HAU0940c DPL0264
73.5
was 4418.9 cM with an average of 1.91 cM between 58.7 HAU0940d NAU4073b 73.8 NAU3533a
63.0 NAU5100a 74.0 NAU2165
adjacent markers (see Additional file 2 Figure 1, 2, 3, 4, 64.1 NAU2962°°°°°°
HAU3193
74.6 MUSS422b
66.8
75.3 BNL2564b
5, 6, 7). 70.0
70.4
NAU2741b
HAU2138 77.1 MUSS325
73.2 NAU3736b 77.8 BNL1350b
The chromosome with most loci was Chr19 (134 loci); 74.6 NAU3002°°°°°° 78.9 NAU3188
75.5 NAU4044 79.5 HAU3351a
Chr02 and Chr04 (53 loci) were the chromosomes with 75.9 HAU2056 81.7 Gh649b
78.3 NAU5411 86.9 NAU5235
the fewest loci. Eighty-nine loci were on each chromo- 78.5
79.3
HAU2102
NAU4045a
87.6
89.4
NAU3615
HAU2490
90.0 BNL4095
some on average, with 1043 and 1273 loci on At and Dt 80.7
81.2
NAU5163
BNL2599 93.6 HAU0737
83.2 Gh075 94.6 Gh466
subgenomes, respectively. More loci were distributed on 84.7 HAU076b 95.1 BNL3090b
86.4 NAU3983 95.8 Gh350a
the Dt subgenome mainly because the NAU-prefixed 86.7
88.3
HAU0282
NAU2095
96.4 HAU1427
NAU5172°°
101.8
EST-SSRs were from G. raimondii (D5), the progenitor 89.1 HAU2861b 103.2 CIR158
92.3 MGHES37 109.1 JESPR243
94.3 HAU076a 109.3 CM35 MUSS128
of the Dt subgenome of tetraploid cotton [7]. 94.7 HAU1619a 109.6 BNL1667
100.1 HAU1166* 109.9 HAU3297
The longest chromosome was Chr21 (265.9 cM) and 103.1 HAU3053 110.7
112.2
HAU0294
NAU3057 NAU3056
105.5 BNL846*
HAU2425c
the shortest was Chr14 (102.2 cM); the average chromo- 106.4 HAU1045a 114.4
118.0 NAU5107c
110.8 HAU2307b 120.8 NAU3714
some length was 169.96 cM. The total lengths of the At 115.3 CIR110b 121.0 HAU1354
123.8 NAU5100b
and Dt subgenomes were 2250.1 cM and 2168.8 cM, 129.0
130.7
HAU0940a°°°
HAU1740
respectively, which was the result of more loci on the 135.3
136.5
HAU1001
NAU3346b°°°°°°
137.0 NAU4073a***
Dt subgenome to increase recombinants. 142.1 NAU4045b
145.0 HAU2489
The biggest average distance between markers was on 147.8 HAU1619b°°°
148.9 NAU3102°°°°°°
Chr02 (2.78 cM) and the least was on Chr14 (1.12 cM). 151.2 NAU3346c
157.9 BNL1688
The average distances for At and Dt subgenomes were 163.4
167.5
NAU3574a
NAU3347
HAU1721 CIR110a
2.16 and 1.70 cM, respectively, which also benefited 167.9
169.3 HAU1058
172.1 HAU2307a
from the more loci on the Dt subgenome. The biggest 179.0 HAU1045b
gap between markers was 23.2 cM on Chr03; there were Figure 1 The genetic map of Chr01/Chr15 homoeologous
a total of 35 gaps >10 cM with 15 on At and 20 on Dt chromosome. The interspecific genetic map was constructed using
subgenome, respectively. the BC1 population [(Emian22 × 3-79) × Emian22]. Duplicated loci
SSRs were not evenly distributed on the cotton are in bold. Map distances are given in centimorgans (cM). Markers
showing segregation distortion are underlined and indicated by
chromosomes with more gSSRs and EST-SSRs on the
asterisks (*P < 0.05; ** P < 0.01; *** P < 0.005; **** P < 0.001; ***** P
Dt subgenome. More gSSRs were on Chr11, Chr19, < 0.0005; ****** P < 0.0001 for markers skewed toward the
and Chr21, and more EST-SSRs on Chr05, Chr11, ‘Emian22’ allele or degree symbols (°P < 0.05; °°P < 0.01; °°°P <
Chr15, Chr19, Chr21, Chr24, and Chr26. gSSRs and 0.005; °°°°P < 0.001; °°°°°P < 0.0005; °°°°°°P < 0.0001 for markers
EST-SSRs were also differently distributed on each skewed toward the heterozygous allele). Segregation distortion
regions (SDRs) are named as ‘Chromosome + No. SDR’, for example,
chromosome; they were similar on Chr02, Chr04,
SDR2.1 refers to the first SDR on Chr02.
Chr11, Chr19, and Chr20 (difference < 5%), but
Yu et al. BMC Genomics 2011, 12:15 Page 4 of 14
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Chr02 Chr14 Chr03 Chr17

0.0 HAU0167
2.9 NAU4022
6.1 HAU1192b
7.0 NAU3820a
9.3 STV097
9.7 HAU1951
11.0 HAU2127b
12.6 NAU5465
13.8 NAU3598
15.4 NAU3214
16.8 NAU5027
17.8 HAU2337
19.1 NAU6236
19.9 NAU3225
20.6 NAU2312
22.7 BNL3034*
BNL519°°°
SDR4.1
24.0
24.3 DPL0901a°°° 0.0 NAU3083
25.5 HAU1741 14.5 NAU2836°° 0.0 HAU0119
25.8 NAU3913 24.1 HAU0292 4.2 NAU3016°°°°°°
25.9 NAU3242 27.9 MUCS547 26.9 TMB1540
26.3 NAU2901a 29.5 NAU3172 27.5 NAU2691
0.0 NAU3535 28.2 BNL3033° 52.7 NAU3839b 33.6 NAU5260a
2.9 BNL2877 29.8 Gh471 52.8 NAU5233 34.9 BNL2496b
10.0 TMB1738 31.3 HAU1057 55.0 NAU3479 35.0 BNL2486 BNL2496a
29.7 CIR381***** 32.1 TMB0324 56.0 BNL3408b 43.5 BNL3408a
37.6 BNL1434 33.4 NAU6416 CIR263****** 52.7 BNL1606
60.1
45.5 BNL4060 34.3 BNL1607 CIR030 53.3 BNL3371°°°°°
63.8
51.5 TMB2386a 35.3 HAU1527b JESPR303 55.4 DPL0045
65.7
BNL3547 36.1 TMB0921 HAU0920 58.1 HAU0197 HAU0195
57.3 66.5
36.8 NAU4024 63.5 HAU0764
58.4 HAU0296
38.1 HAU1141 71.1 HAU2860b STV099**
59.4 BNL3512 67.4
38.3 TMB1174 72.7 HAU3176b 70.6 HAU1022
59.9 BNL1897
39.0 HAU1888 NAU3120 76.5 HAU1624 71.3 HAU1564
60.6 HAU1980a 39.3 TMB1687 79.3 NAU3309b Gh071b
71.9
65.6 NAU5134°°° 39.5 CIR295 BNL2882 80.1 NAU5443b 73.3 BNL2443
67.3 Gh669° 39.7 JESPR161
68.3 HAU2917a 81.9 NAU3671 73.9 NAU2761b
40.2 BNL3932 MUSS444 JESPR195
83.0 76.1
68.9 NAU3189a° 40.7 BNL1059
83.1 TMB2826 76.3 BNL3460
69.6 BNL2651° 41.0 HAU1219 NAU3884 BNL4073
83.3 NAU2928 NAU2929 76.5
70.6 NAU3485a° SDR2.1 41.3 NAU2845
83.4 BNL3441 77.6 HAU0625
72.0 DPL0674° 41.7 Gh462 NAU3394 NAU6542
83.5 78.2
72.6 JESPR93°°° NAU3119 CIR181 BNL3267
42.0 NAU2155
83.8 79.1 HAU3176a
73.1 CIR401b°°° 84.4 NAU3382a
73.5 BNL1410° 42.1 Gh067 79.7 NAU5443a NAU3309a
42.3 BNL3523 85.4 DPL0901b 80.1 TMB2081
74.1 HAU2923
42.4 BNL3443 85.9 BNL1379 80.2 TMB2939
75.0 HAU2643°°°
42.6 NAU3312 87.2 HAU0992 80.4 NAU2662
75.5 DPL0046
43.3 BNL3477 88.0 HAU0604 80.9 HAU1024
76.0 HAU2154°° JESPR101°°
43.8 HAU2537 89.5 TMB2069 81.0 BNL2742 TMB0349
76.8 BNL3590
44.3 TMB1393 93.0 Gh681a 81.1 NAU6234
78.3 BNL3971°
44.5 NAU3308 97.1 BNL3398 81.2 NAU2909
80.0 Gh198°°
97.5 MUSS172
80.1 NAU3875°° SDR2.2 44.9 NAU2712
97.8 Gh129
81.3
81.7
NAU3639
CIR038
80.2 TMB0514° 46.3 HAU0438
46.9 NAU3691 98.2 BNL140 82.0 BNL2471
80.7 MUSS073°°°
47.8 NAU6623 101.3 DPL0733 82.8 HAU1967
81.0 NAU3626°
48.1 JESPR165 104.2 BNL226 83.2 NAU2994
81.2 DPL0216°
48.7 Gh051 104.5 DPL0631 83.4 DPL0058
81.6 BNL3292
49.6 TMB1513 105.7 DPL0605 83.9 BNL2182
82.2 HAU0306°
50.8 HAU1049 106.3 NAU3541 85.4 NAU3700
84.1 MUSB0915
106.6 NAU3573 86.2 BNL4003
86.9 NAU2908b°° 52.1 NAU3485b 107.3 BNL244
52.5 HAU2046 86.7 HAU1486
88.4 NAU4035b° 110.6 BNL4017 MUSS162 87.3 HAU0449
90.4 HAU0880b°°° 53.6 HAU1980b 112.6 HAU2511 87.9 HAU2782
92.1 HAU2803° SDR2.3 55.5 HAU2917b 114.5 HAU2588 90.1 HAU2860a
94.0 HAU1155°°° 55.8 NAU5421 115.7 NAU5035
91.6 CIR375
56.4 DPL0871 121.7 BNL1080**
95.8 NAU2761a° Gh210 92.2 NAU2908a
56.9 HAU0133 128.5
99.9 HAU2690°°° 92.5 NAU4035a
57.4 JESPR293 129.1 HAU1322
107.1 NAU3684°
57.7 NAU6486a 133.9 HAU2127a 94.0 NAU3349
108.6 JESPR304° CIR376°
57.8 NAU2960b°°°°°° 134.6 HAU0875 98.3 NAU3805
116.1 BNL663
99.5 HAU1029******
124.6 NAU2858° 58.4 HAU0883b°°°°° 137.6 HAU1192a* BNL2706
MGHES66** 103.0
135.1 NAU3419c 59.0 NAU3885 139.5
142.3 NAU3775 60.1 NAU4009 143.2 JESPR231 109.6 HAU0880a
147.2 HAU2001 61.8 NAU2633 147.5 HAU2024 118.9 HAU1264
63.5 HAU1455° 151.9 JESPR107 127.4 BNL834
72.5 NAU6486b 153.1 CIR228 141.0 NAU5111
142.2 NAU2898
74.4 TMB0071°°°°°° 154.1 NAU2960a NAU5153
77.9 NAU3733 145.7
154.4 CIR202
80.4 HAU1485 155.5 HAU0883a
81.4 NAU4025 CIR133
157.1
84.7 HAU3236 NAU5289°
162.0
86.2 STV030
86.5 BNL1510
86.9 NAU5467
92.4 TMB2386c
95.4 NAU3585b
96.5 JESPR156
102.2 NAU5499°°°°°°

Figure 2 The genetic maps of Chr02/Chr14 and Chr03/Chr17 homoeologous chromosome. All legends are same as described for Figure 1.

dramatically different on Chr05, Chr15, Chr18, and Segregation distortion

Chr26 (difference > 50%).
For different genome-derived SSRs, the A genome-
derived SSRs mostly targeted Chr05 and Chr15, and of
course preferentially targeted the At subgenome; D gen-
ome-derived SSRs mostly targeted Chr05, Chr11, Chr19,
Chr21, and Chr26, and also preferentially targeted the
Dt subgenome; the AD genome-derived SSRs mostly
targeted Chr11, Chr19, and Chr21, but preferentially
targeted the Dt subgenome.
Among the 2521 polymorphic loci, 423 loci (16.8%)
including one gene-specific locus showed segregation
distortion (P < 0.05) with 139 loci segregating toward
the ‘Emian22’ allele and 284 loci toward the heterozy-
gous allele. For SSR loci, 15.0% of gSSRs and 18.2%
EST-SSRs were distorted, respectively.
A total of 323 distorted loci, accounting for 12.8% of
the mapped loci, were mapped on cotton chromosomes
with 74.9% segregating toward the heterozygous allele
Yu et al. BMC Genomics 2011, 12:15 Page 5 of 14
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Chr04 Chr22 Chr05 Chr19

0.0 GhGLP1-280°°°°°°
7.5 DPL0792
8.7 NAU3631
9.5 NAU3656
9.7 JESPR122
10.1 BNL3043
0.0 TMB0478 10.2 HAU0139
13.4 NAU3737 10.4 DPL0247
23.8 NAU4034 11.3 Gh182
27.8 CIR224 11.9 NAU3024
29.1 NAU3450 NAU1137 12.9 NAU3092
29.7 BNL2865 14.0 TMB0835
32.9 TMB1418 15.6 NAU5475
33.9 NAU3607 19.0 MUSB1056
34.5 BNL1042 20.2 NAU3405
35.5 HAU1797 21.9 HAU2846
36.8 MUSS106 22.5 HAU1094
37.6 NAU3828 23.3 HAU111
40.8 NAU3012a 24.7 HAU117
46.0 NAU3197b 27.7 HAU112
48.8 NAU5387 28.6 NAU3012b
66.0 BNL3020 29.6 BNL1075
68.5 HAU0633 31.3 GhGLP1-250
0.0 MUSS124 69.8 DPL0838b 32.6 DPL0140
16.9 HAU3161 76.9 DPL0225a 35.8 BNL3452
HAU0878a°°°°°° NAU2894
26.3 NAU3392 81.1
83.0 NAU3416°°°°°°
SDR5.1 40.2
48.2 HAU3069
28.9 TMB1648
29.3 NAU3777b 85.6 NAU5273°°°°°° 53.3 BNL2715
89.9 NAU1372b 54.9 NAU4884
29.7 BNL3873
58.8 HAU3214
30.1 NAU3791b 92.1 NAU1372c DPL0594
NAU5015 61.5
31.3 NAU2235 92.8 HAU2112
65.1
32.1 NAU3386 95.9 NAU5255a 66.5 Gh459
39.2 Gh152 97.7 BNL3029 68.1 HAU0216
40.1 NAU2932a 98.4 NAU3650a 69.3 BNL4071
0.0 HAU0751*** 41.3 HAU1071 99.6 BNL3492b 69.6 CIR212
8.6 HAU3302 42.0 MUSB1112a 100.9 NAU2630 69.8 NAU3372
16.2 CIR122 42.9 NAU5294 101.9 NAU3212 70.4 Gh071a
18.6 NAU5236 44.2 NAU3868b 103.6 NAU5160 72.8 DPL0169
22.2 HAU1895 73.3 BNL1690
50.7 HAU3012 104.6 NAU3935a JESPR53
32.1 MUSB1112b* HAU0558 HAU2223 75.9
52.2 105.1
77.5 BNL1611
38.9 NAU3868c 57.2 NAU2291 105.9 HAU2783a 78.1 Gh229
47.6 HAU0101 57.5 BNL4030b 106.8 CIR373°
51.4 HAU0036 60.0 HAU086a 79.5 NAU1372a
108.6 DPL0368
80.5 BNL285
53.8 HAU086b 61.8 HAU0747 109.9 HAU3372
55.6 DPL0451 64.1 STV112 111.0 NAU3097 82.5 BNL3492a
66.8 Gh330* 83.4 HAU3110
59.7 DPL0494 111.5 Gh109a
60.5 TMB2483b 69.1 HAU3083 85.6 NAU5447
112.6 HAU1034
61.8 HAU2016 71.0 BNL358 114.3 Gh381a
88.2 NAU3935b
62.8 NAU3791a****** NAU3093 72.3 CIR036 88.6 HAU2783b
116.8 BNL2988
63.2 JESPR223 73.2 HAU1790 91.5 MGHES21
116.9 NAU1339
75.0 HAU0938
64.1 NAU3777a****** BNL3324 118.0 NAU2736 92.0 NAU5255b
75.9
68.1 Gh117 118.9 NAU3325 92.3 NAU3217
NAU3514 BNL2771
69.7 NAU2363 76.3 119.9 HAU0535 HAU1952b 92.4 DPL0444
HAU2206
70.6 MUSB1050a 78.5 CIR048 120.3 DPL0156 92.8 NAU3650b
72.1 DPL0667 80.0 TMB1919*** 122.0 BNL218 93.2 BNL852
72.3 BNL530 81.2 NAU2783 122.8 HAU1197 97.6 TMB0189
73.9 NAU6672 NAU2654 82.0 MUSB1050b 125.0 NAU2800a 97.7 BNL3569
74.1 BNL3988 82.3 JESPR221 126.8 TMB0193 97.8 Gh109c CIR139
75.1 HAU3371 DPL0489 128.5 HAU0627 98.4 NAU3674
82.8
77.9 HAU1300 131.1 NAU3036°° 98.7 Gh381c
83.7 NAU3825a
81.8 NAU3825b 85.6 NAU3138 131.6 NAU2932b 99.4 NAU2126
83.5 Gh209 NAU3942* NAU2945* 133.6 NAU5299 102.4 NAU5330
86.1
84.8 BNL2939 TMB0120* 137.7 HAU0576 104.0 NAU3497
86.6
85.6 NAU3491
NAU2672a
86.8 NAU3103* SDR22.1 138.5 MUCS108 104.6 HAU2008
86.3 87.0 TMB0086** 139.0 NAU3014 105.2 BNL3903
86.8 DPL0273 BNL4015* 139.1 NAU861 105.5 DPL0898
87.4
87.2 BNL3994 DPL0196 87.5 BNL2609* 140.7 MUSS118 108.3 HAU3001
87.7 NAU5180b HAU1056a 87.7 BNL3881 BNL206 142.7 HAU1496 108.5 BNL3811
88.3 HAU3120 87.9 Gh052 146.6 NAU3620 MUSS219 108.7 HAU1952a
89.1 HAU1332 88.4 HAU2434 148.5 CIR401a 109.1 NAU2959
89.8 Gh124 88.7 NAU3633 148.7 NAU4057 111.1 NAU2800b
90.8 BNL4047 89.2 Gh166b* 150.7 NAU5088
111.4 MGHES300 BNL4096
91.3 DPL0299 152.0 JESPR197
89.8 NAU6237* 114.0 HAU0979
94.6 HAU2085 152.3 NAU5417
90.5 NAU5180a 115.8 NAU2980b
100.0 CIR222
NAU2302*
152.4 NAU3001b 120.5 NAU5005
104.2 Gh107 91.8
153.3 BNL3992 122.7 NAU3664
107.4 BNL2821b 92.8 NAU5046c* 154.6 Gh083 125.0 NAU6619
113.8 DPL0573 93.7 NAU3824 156.1 BNL2448 126.4 NAU6406
119.3 NAU3592°°°°°° 95.3 NAU5099c 156.9 HAU1500 127.3 NAU3253
127.8 NAU6626° 96.8 NAU4062 157.1 HAU0032 128.1 BNL3602
131.6 HAU1400 99.2 Gh012*** 159.7 HAU2313 128.8 NAU2741a
137.3 BNL3089 103.7 Gh200 161.9 HAU2691a 129.6 DPL0071a
140.8 CIR223 105.2 NAU6578* 162.0 HAU1168 132.2 HAU3238
106.2 NAU3591 165.1 HAU1385 132.5 HAU1185a°°°°°°
108.3 Gh591a 167.8 CIR253 135.8 BNL3875*
110.7 NAU3539 168.2 HAU1384 139.6 DPL0309
114.1 BNL3945 169.1 HAU0042a 141.1 JESPR134 BNL390
114.9 BNL4092 170.5 Gh206 142.5 HAU3366
116.0 HAU2691b 171.9 HAU0506 143.6 NAU3001a
120.6 HAU1527a 172.6 HAU1976a 144.6 HAU1446
124.9 BNL4030a 173.7 NAU2140 146.8 BNL2656
126.7 Gh641 175.7 BNL1038 147.1 TMB0131
137.1 DPL0722 176.8 CIR185 CM65 148.1 BNL1878
138.8 NAU2795 JESPR50
NAU4058
177.5 152.2 HAU1976b°°°°°
139.6 178.2 BNL2732 155.7 NAU5489
140.8 NAU2120 178.9 NAU3382b 156.9 NAU4042
152.6 HAU1115 179.2 NAU3402 158.9 BNL3401
167.4 HAU3261 180.3 NAU5400 160.2 NAU2918b
182.1 HAU0968 161.3 NAU4055
184.7 Gh211 164.9 NAU3096
186.0 Gh594 165.1 NAU2274
187.0 Gh422 167.0 JESPR204
187.8 MUSB0977b 167.2 TMB2527
189.6 NAU3569 168.6 HAU1097
189.8 CIR301 170.1 NAU4896
190.6 NAU5046a 174.0 Gh354
191.2 CIR294 176.7 BNL3798
178.0 JESPR1
191.8 NAU5099b
NAU3652 BNL3426
192.7 DPL0810 181.1 NAU6318
193.3 BNL3955
181.2 NAU6205
193.5 DPL0637
181.3 NAU2650
194.3 Gh166a 182.8 NAU5121
194.7 NAU4898 184.4 BNL3662
195.7 NAU5149 185.1 Gh447
197.8 NAU2562 186.5 BNL1671
199.5 DPL0837 189.8 MUSB0977a
201.5 Gh262
193.3 DPL0163
207.2 NAU2561
196.0 BNL3535
201.8 BNL3347
209.4 CM51*****
210.2 CM3******
214.0 BNL2821a
216.2 NAU3110a°
222.7 HAU1785
229.6 NAU3946
230.8 NAU2232
235.6 NAU3095
243.4 NAU4907

Figure 3 The genetic maps of Chr04/Chr22 and Chr05/Chr19 homoeologous chromosome. All legends are same as described for Figure 1.

(Figure 1, 2, 3, 4, 5, 6, 7). These segregation distorted
loci were unevenly distributed on the 26 cotton chromo-
somes with 3-51 loci on each chromosome (see Addi-
tional file 2). More distorted loci were located on the Dt
subgenome than on the At subgenome (195 versus 128).
The most distorted loci were on Chr02, Chr16, and
Chr18 (> 50% of loci were distorted), and the least on
Chr05, Chr08, Chr20, and Chr25 (< 5% of loci were dis-
torted). A total of 21 segregation distortion regions
(SDRs) were found on the 26 cotton chromosomes with
Yu et al. BMC Genomics 2011, 12:15 Page 6 of 14
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Chr06 Chr25 Chr07 Chr16

0.0 BNL3436******
6.9 NAU2714a
7.6 NAU2713a°
15.8 CIR298
0.0 NAU3003
17.6 CIR109
3.0 NAU3486
18.4 NAU3502 MUSS095
6.7
21.8 BNL827 10.0 TMB1706
25.8 HAU2022 10.1 CIR175
33.5 Gh449 11.0 NAU3550
0.0 STV106 35.3 BNL2569 11.6 NAU3459
7.5 NAU2714b 39.6 NAU2641 13.6 NAU2597
45.4 BNL1047 16.7 NAU3004
9.6 NAU2713b 45.8 BNL1061 24.3 HAU3082
9.8 JESPR119
13.3 DPL0328 47.7 NAU3243b 28.0 BNL1022
50.6 NAU3298 0.0 HAU1279 32.1 HAU3104
15.4 BNL1902
17.3 BNL584 51.5 NAU4969a 4.0 NAU5152a* 38.2 NAU5152b
8.0 HAU2371 39.0 HAU0120
21.6 HAU1481 53.7 NAU5270b 40.6 NAU3197a
27.6 Gh039 NAU2611 11.9 NAU5120a
54.5 43.0 STV023
30.5 DPL0588 13.7 HAU3319
54.7 TMB2377 44.3 DPL0501
31.6 DPL0035 15.1 DPL0186
55.7 NAU6269b 45.5 JESPR292
32.7 Gh032 16.1 MGHES58
58.0 HAU3340 NAU2685 48.2 NAU3939°
33.9 TMB0154 17.5 SDR16.1
58.6 NAU3578 20.2 NAU2657 50.0 NAU3053°°°
39.4 NAU5270a 61.8 HAU3095°° 24.2 JESPR38 53.1 HAU1129°°°
40.7 BNL1746 63.7 Gh100a 24.9 NAU2820a 55.6 BNL1706
43.2 Gh100b 65.3 BNL3655 26.3 NAU2863 57.9 BNL2986
66.7 BNL3806 26.7 DPL0136 61.0 Gh345b
45.6 NAU4969b
HAU0975 68.2 NAU2717 27.5 NAU3735 62.4 NAU4956b°°°°°
49.6
69.2 DPL0874 28.4 BNL1597 64.3 NAU2931
50.7 NAU3243a 70.1 BNL3190 29.4 HAU0775 65.6 BNL3793°
52.4 DPL0238 NAU6573 33.2 NAU4956a 66.7 HAU1836
70.5
52.7 BNL4004 HAU3157 36.3 MGHES75 67.3 MUCS616°
71.0
53.6 NAU5269 Gh537 41.5 CIR169 67.8 Gh056b°
72.2
54.7 CIR280 Gh591b 41.9 NAU2772 69.7 NAU2749°°
72.6
55.7 DPL0101 HAU3055 42.8 STV085 70.4 HAU1520°°°
73.5 HAU1195°°°
60.3 TMB1530 HAU0615 47.3 NAU2432**** 71.3
73.9 71.9 NAU2721°°°°°°
61.5 JESPR273 BNL272 49.7 Gh055e°
74.4 72.3 CIR107°°°
65.2 DPL0847 DPL0239 52.1 BNL3319
76.1 73.0 NAU3594°°°
67.6 DPL0080 BNL4100 58.9 HAU1754
77.0 73.2 DPL0511°°°
69.7 NAU2156****** TMB1583 61.4 TMB2844
77.8 73.3 NAU2620°°°°
70.2 Gh082b***** NAU6347 62.7 DPL0292
78.5 73.5 NAU5408°°°°°
72.1 HAU0376 Gh224 67.7 TMB1618
78.8 BNL3008°°° BNL2734a°°°
73.3 DPL0681**** DPL0323 69.0 Gh548b 74.4
78.9 JESPR102°°° SDR16.2
76.3 DPL0153 BNL1440 69.9 HAU1780
79.0 74.7 NAU2628°°°°
78.0 CS097 BNL1517 JESPR215 73.0 BNL3415
76.0 NAU2881°°°°
84.2 HAU2467a 75.1 CIR141
79.2 Gh220 JESPR227 77.3 NAU2627°°°
85.4 CIR233 JESPR229 76.9 HAU1399a 78.6 BNL580°°°°
87.3 BNL3295 79.4 BNL3538 77.3 CM60° 80.1 HAU1669°°°
89.0 JESPR247 79.5 NAU2119 78.2 CS057 82.5 Gh055d°°°°°
89.7 BNL861 BNL3405 BNL1153 78.3 BNL3871°
79.7 86.5 JESPR128°°°
90.5 BNL3812 79.5 NAU2975a°°
80.3 DPL0067 86.6 NAU2556a******
91.5 HAU2768 80.8 TMB0046
80.8 HAU2759 87.1 TMB1820°°°°°
BNL1064 81.1 CM66b CM66a
93.4 83.3 DPL0075 88.1 BNL3287°°°°
HAU0668 82.5 BNL1026
94.0 84.2 Gh515 89.9 Gh684°°°°°
84.4 HAU0033°
94.7 TMB2959 MUSB1164 84.3 DPL0519 92.7 DPL0342°°°°°
84.6 TMB2944° SDR7.1 94.8
HAU1488 NAU2679d 84.7 NAU6398 HAU1527c°
94.8 85.0 DPL0652°
95.6 NAU5061°°
HAU1537 MUSB1064 85.6 HAU2467b HAU0597° HAU1172°
97.3 NAU5325
94.9 HAU0091 85.1 DPL0403
85.9 HAU1783a
96.0 HAU1293 86.2 HAU1774 85.9 CIR262 98.5 Gh055b°°°
96.8 TMB2958 86.5 Gh506° 100.4 NAU3279
86.6 NAU2679a 100.7 HAU2162° SDR16.3
98.7 HAU0483 86.9 Gh527
86.9 CIR407 101.8 JESPR237°°°
98.8 NAU5433 NAU5434 88.4 HAU1882
87.9 NAU2388 BNL2733 103.1 HAU0137°°°°°
100.1 HAU2119 89.5
CIR150 BNL3103 103.8 HAU1764a
101.1 JESPR194 88.2 HAU3121 HAU1931 91.3 NAU3180a°°°
101.4 HAU0210 95.0 HAU1510°° 104.1 DPL0283
88.3 BNL3264 106.1 NAU3906
103.5 NAU3803 NAU2963 96.6 MUSB1081
88.7 Gh548a 106.3 BNL2441
103.7 NAU2968 Gh371
97.4
89.0 98.7 HAU1205 107.3 HAU1145
105.2 BNL3650 NAU3588
89.3 103.4 BNL3308 108.6 NAU6326°°°°°°
109.0 NAU4946 HAU2625
90.1 103.8 NAU5491 109.7 BNL2766°°°
112.7 NAU3365a NAU6379
90.7 104.5 NAU4082 111.1 TMB1114
113.2 BNL2884 DPL0377 BNL3500
92.4 109.5 HAU1764b** 111.5
117.6 DPL0665a HAU1936b 112.5 Gh002°°°°°
93.9 NAU5406
121.3 TMB1922 115.5 NAU3678
94.2 BNL150 112.6
123.1 GhCFE NAU2565°° 112.7 DPL0168°°°°
96.0
128.1 HAU1143°°°°°° HAU2064 113.0 Gh073°°°° DPL0385°°°°
97.5
129.8 Gh185 113.2 JESPR297°°°
NAU3206
98.1 NAU3171 SDR16.4
137.4 99.0 NAU2397 113.7 TMB0180°°°
149.4 NAU3677b° 100.1 Gh077 114.6 NAU6664°°°
150.9 HAU0504 HAU3258 115.2 NAU6375°°°
102.9
153.5 BNL2823 116.9 HAU1555°°°
105.8 NAU6441
154.9 CIR128 117.3 BNL2734b°°
107.0 BNL2691b
157.1 HAU1056b°° 117.8 HAU1918a
108.7 NAU3532 BNL1604°°°
117.9
160.3 NAU2773a°° 111.0 HAU2367
Gh513 114.1 TMB2898 120.8 NAU3180b°°°
168.5
DPL0365 125.0 HAU2481
172.1 NAU3427 122.3
130.8 NAU2733
133.6 HAU1919
132.0 NAU2974
135.2 BNL3594 HAU2662
136.3
135.9 NAU3677a 140.2 HAU1399b
138.7 HAU0591 152.9 HAU2688
143.6 NAU2773b
154.0 HAU1324

Figure 4 The genetic maps of Chr06/Chr25 and Chr07/Chr16 homoeologous chromosome. All legends are same as described for Figure 1.

8 SDRs on the At subgenome and 13 on the Dt subge-
nome. More SDRs were found on Chr02, Chr16, and
Chr18, the chromosomes with the most distorted loci.
The distorted loci showed a phenomenon in which loci
skewing toward the same allele appeared on the same
chromosomes or within the same SDRs (e.g., Chr02,
Chr13, Chr16, and Chr18; Figure 2, 4, 7). Interestingly,
adjacent markers in some SDRs showed the same degree
of segregation (SDR5.1, SDR7.1, SDR18.1, SDR18.2,
SDR24.1, and SDR24.2).
Yu et al. BMC Genomics 2011, 12:15 Page 7 of 14
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Chr08 Chr24 Chr09 Chr23

0.0 NAU5335
2.3 JESPR307
3.4 Gh146******
3.7 Gh237a******
7.7 CIR289
11.0 NAU2631
13.6 NAU5379° 0.0 NAU3868a
16.3 NAU3667 11.8 HAU2382
0.0 HAU1782 13.7 NAU2771
HAU2583b
17.4 NAU3771° SDR24.1
1.7 18.4 MGHES22° 15.0 CIR286
6.5 HAU2583a 19.0 STV025° 0.0 NAU5468 17.2 BNL686
10.7 HAU1390 19.5 NAU2230 3.4 DPL0222 18.3 NAU3100
13.2 JESPR230 20.1 BNL2582° 11.8 HAU2496a 18.7 NAU3972
15.3 BNL3627 BNL252 26.1 NAU5508
15.7 HAU1308
20.9 13.6 STV164a MUSB1040
22.4 Gh573a° 26.8
16.3 CIR343 13.8 NAU3888a 28.2 STV164b
23.8 NAU6616°
17.9 NAU2293 14.4 BNL1670a
24.4 HAU1533 28.6 HAU2496b
22.4 HAU1749 17.0 Gh486b
24.8 NAU6389
25.0 HAU1547 BNL3604 21.1 TMB0991 29.0 NAU3888b
26.0 Gh499b* TMB2354
27.2 NAU3769 NAU3954 25.4 32.2
26.9 Gh539 NAU3159
28.9 BNL2527 NAU2926 30.6 33.8
27.8 DPL0679 TMB0157
30.1 TMB1717 Gh465 32.3 35.4
28.2 DPL0618 NAU6700
30.6 NAU3324a JESPR127 34.9 35.9
28.4 DPL0659 TMB1769°°°
31.1 CM43 MUSS255 37.5 41.7
28.6 DPL0854 BNL2690
31.9 CS101 38.5 44.8
29.4 HAU1288b 38.8 Gh098 47.0 MGHES11b
33.7 TMB0029b° 30.0 NAU2619°
34.3 MUSS136 39.4 BNL1162 47.6 NAU3732
34.7 DPL0030 30.6 NAU3207b 41.1 NAU2575b 48.7 TMB109
35.2 HAU1632 30.8 HAU1905 43.5 MUSB0907 49.5 TMB1700
35.7 MUSB0662 31.2 NAU2731 44.2 Gh027 50.6 NAU6136
36.4 HAU0672a 31.4 BNL3084 44.5 DPL0550 53.0 Gh302
NAU3988 DPL0231 44.7 Gh111b 53.5 DPL0079°
37.3 NAU3207a 31.7 TMB1182 54.2 NAU6701
45.0 Gh112b
37.9 HAU2086b 31.9 NAU2240 45.8 Gh584 54.5 NAU2964
38.1 NAU2914b BNL1017 32.4 HAU2522 47.2 HAU2780* 54.6 NAU6130
38.3 BNL387 32.8 NAU2914a 54.8 NAU6138 TMB2862
48.5 NAU2739a CIR060 NAU6386
38.5 MUCS148 33.0 BNL2655
38.7 BNL3792 BNL2499
49.5 NAU3194a 54.9
NAU3194b NAU6323
33.4 HAU2083
39.4 CIR209 BNL2568 51.9
33.5
53.1 NAU5017 55.0 HAU2067b JESPR274
39.9 HAU3346b 33.7 Gh128
55.7 TMB2920 55.3 NAU2739b
41.1 BNL1664 34.0 HAU3346a 58.3 MUSS87 55.5 HAU1933
41.9 Gh532° 34.2 Gh171 60.5 NAU3439* 55.7 BNL3823
43.0 HAU1288a 35.3 NAU6213 64.0 HAU2067a 55.9 JESPR151
46.0 NAU3668b 36.3 HAU2086a 67.2 BNL3779 56.1 NAU2575a
47.6 MUSB0818b 38.5 HAU0722 70.5 BNL3031 57.1 Gh443a
50.3 HAU2756 40.4 DPL0534 TMB2901
71.8 BNL1672b 58.1
52.0 Gh634 43.2 TMB1639 58.7 NAU2753
73.8 HAU0361°°°°°°
53.8 Gh390 44.1 HAU2640a 78.5 MUSB0818a* 59.0 NAU6581
60.7 HAU0356 45.2 NAU3708 80.6 MUSS547 61.5 NAU4079
61.7 BNL2993 45.7 TMB0072 81.1 HAU1966 62.3 BNL3511
62.6 CIR278°° 45.9 DPL0191 83.8 HAU0253 65.7 BNL1672a
63.1 HAU3349 46.0 NAU3071 86.8 HAU1835 66.3 NAU3763
64.4 TMB2107 46.2 NAU2434 NAU2567
65.1 TMB2103 90.2 BNL3410b 67.6
46.4 HAU1846 67.9 HAU1918b
94.7 Gh118
66.2 HAU2640b 46.7 NAU3804 69.1 HAU2893
68.0 DPL0176 48.0 BNL2616 96.1 NAU3967b BNL2977
Gh495 72.2
68.9 TMB1675 49.1 NAU2169 HAU2015 97.6
100.0 NAU3358 76.8 BNL3410a
69.4 JESPR46 49.2 MUCS113
101.8 HAU2146a 77.3 TMB0913
69.7 HAU3211 NAU3605b 49.3 NAU3499
49.5 HAU3293 102.4 HAU3109 81.8 NAU3967a
70.1 TMB2279 103.0 HAU3027 82.8 DPL0378
71.2 BNL1044 49.6 JESPR78
50.1 HAU3247 103.3 Gh484 83.1 BNL1579
72.0 TMB0834b 104.0 DPL0850 83.9 Gh498c°
73.6 NAU3964 51.4 NAU3605a TMB2551 HAU2140
BNL3638 104.9 85.4
75.8 HAU0690 52.9 TMB2483a DPL012
NAU3562° 105.6 87.5
76.5 NAU3201a 53.7 JESPR248 TMB0170
JESPR305° 106.8 89.5
77.6 BNL3255 54.7 MUSS397 BNL1648
NAU3721 113.1 90.8
78.0 NAU2887 55.5 HAU2553
57.7 Gh597 114.5 Gh247b 93.1
78.4 HAU0333 116.9 BNL1317 94.7 TMB1758
79.4 HAU2585 60.2 BNL1521°
63.3 HAU2738 117.5 BNL219 96.0 Gh247a
79.6 HAU1639a 118.3 MGHES73 96.9 HAU2222
81.3 GA3-hydroxylase1 64.5 HAU1639b MGHES70 NAU2954
119.1 98.2
83.4 NAU4900 65.5 NAU3201b° SDR24.2 119.2 HAU3150 99.9 HAU0261
84.3 HAU1739b 66.9 NAU2439° 121.6 JESPR208 100.5 CM7
86.5 HAU0964° 67.0 MUSS250° 122.3 CM71 102.1 HAU1572
90.1 CIR237 68.9 NAU3324b 122.5 BNL1414 104.3 HAU2158
92.0 NAU1369 71.6 NAU3773 123.4 BNL1030 105.4 NAU5494
96.9 TMB2899 72.7 NAU3668a 123.8 JESPR290 106.6 DPL0262
98.1 NAU3558 72.8 NAU3424b 124.2 BNL1043 107.4 BNL2608
98.7 JESPR66 124.9 BNL4028 111.4 DPL0307
74.4 HAU1739a° NAU5454 DPL0218
100.5 NAU5357 NAU3904 126.0 116.1
75.2 NAU2827 NAU3966°°°°°°
102.2 TMB1702 NAU3424c** 126.7 118.7
78.2 BNL2590 HAU2517
104.3 NAU5129 TMB2386b* 130.9 119.9
79.9 HAU1683 HAU3241°°°
107.9 NAU2407 DPL0068 135.3 127.5
81.6 BNL274 NAU3655°°°°°
108.2 TMB2781 HAU1432 138.6 129.4
82.3 NAU3414 NAU2591
111.0 NAU2876 JESPR70 142.9 140.3
83.3 MUSS022 MUSS298
112.8 BNL2772 DPL0461 144.9 147.9
84.3 DPL0395 NAU2873
115.3 NAU5368 BNL1513 149.8 150.2
85.3 BNL4099 MUCS006
119.4 JESPR232 BNL2835 150.4 150.9
88.0 HAU0085 NAU2689
124.2 HAU1181 NAU3158a 156.7 152.5
89.3 HAU0583 BNL597
128.0 NAU3010b NAU2602° 161.8 154.2
91.1 BNL2750 NAU2722
131.9 MUSB0812 NAU5128 163.3 156.5
95.5 DPL0541 BNL4053
136.6 CIR244 MGHES29 165.6 157.2
99.7 HAU2852 BNL3985
142.0 NAU3482 HAU0761 168.8 157.7
103.1 Gh416 HAU1165
JESPR157 173.6 157.8
109.8 Gh662 BNL3173
JESPR308 187.0 158.3
111.6 JESPR95
JESPR302 158.9
111.9 MUSS151
NAU3287 174.5
113.2
120.6 NAU4091°°°°°°
122.9 HAU1567
132.9 CIR388
135.1 CIR026
137.7 Gh325
146.0 NAU3010a
162.4 Gh310

Figure 5 The genetic maps of Chr08/Chr24 and Chr09/Chr23 homoeologous chromosome. All legends are same as described for Figure 1.

Annotation and functional characteristics of sequences
containing SSRs
In addition to the 1261 EST-SSRs and 5 gene-derived mar-
kers, 367 gSSR loci had homologous sequences to cotton
ESTs by BLASTN with E ≤ 1 e-15 (see Additional file 3),
which indicated that they were transcribed sequences.
Thus, a total of 1633 loci of this map (70.6%) were
functional markers. The BLASTX results of these tran-
scribed loci showed that 809 loci sequences had no hits to
protein; 976, 302, and 54 loci sequences (total 57.5%) had
hits to known gene products, hypothetical proteins, and
unknown genes, respectively (see Additional file 4).
These sequences containing SSRs totally targeted 38
items of molecular function with 1236 sequences
Yu et al. BMC Genomics 2011, 12:15 Page 8 of 14
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Chr10 Chr20 Chr11 Chr21

0.0 HAU2559
HAU2681° HAU1283 7.0 NAU3415
0.0
11.2 BNL2650
8.6 HAU1809a
14.6 MUSB1076
13.5 HAU1809b
17.9 BNL3402
18.7 Gh561b 21.1 NAU4002
21.5 NAU3480 27.4 HAU1592°
23.0 NAU2016b 29.2 DPL0475
24.1 MUCS088 32.6 NAU6525
26.7 NAU3770a 34.0 NAU6431
27.6 CM140a 36.4 NAU3740
BNL1231 36.5 NAU3806
30.5
HAU1222****** 37.7 HAU3342
0.0 32.1 NAU5428b
16.6 Gh277 34.2 NAU3390
39.3 NAU5428c
21.7 MUSB1048 37.1 Gh288a 40.3 NAU2016a
23.6 BNLlea 38.7 NAU2152 41.3 CM140b
25.5 BNL2553 40.2 MUSS404 41.8 Gh561a
42.2 DPL0209
27.7 HAU1267 42.1 NAU3770b
43.5 BNL4011
28.1 Gh110 46.6 BNL1066 42.4 MGhES16
43.7 NAU6562 NAU5505 42.7 NAU6697
48.2
45.5 Gh428 BNL836 44.4 STV067
54.5
46.1 NAU6520
46.8 NAU6179 57.3 NAU3806
NAU5480 48.0 Gh0288b
47.0 NAU6512 60.8
0.0 NAU5323° NAU4962 51.6 BNL3279
47.8 NAU6305 63.4
9.0 HAU2824 58.0 TMB1871
52.6 TMB0272 64.9 NAU3493b 61.2 Gh133
10.7 HAU2147 66.0 Gh300
53.9 HAU1840 62.9 Gh132
19.8 Gh058° 67.1 JESPR296 64.5 BNL1154
55.2 HAU0685
26.9 BNL2691a 68.0 DPL0270 64.7 MUSB0953b
57.3 HAU1459b 69.7 NAU3115
30.3 Gh283 70.2 HAU2592
59.0 MUSS096 70.2 NAU4086
41.1 HAU0949 75.4 HAU3394
61.2 HAU0590 71.4 NAU2809 77.4 DPL0228
43.6 CIR166°°°
64.9 NAU2971 76.5 DPL0325 78.0 NAU3158b
43.8 NAU3262° 80.4 MUSB0827
47.4 DPL026b 67.1 DPL026a 80.9 BNL1595
78.9 HAU2116
68.6 DPL0442* 81.3 TMB1667
81.6 NAU3493a
49.8 NAU2991a 82.9 NAU4026°°°°°°
69.0 NAU6495 81.6 DPL0338
52.4 HAU2500 84.8 TMB1276
70.0 CM45* 84.1 BNL1408
53.1 NAU4008 88.2 HAU1794a
72.0 Gh048 84.4 BNL3592
54.3 NAU2082 85.1 NAU2877 89.3 HAU1901
73.5 NAU3368 95.2 BNL2895°°°°°°
54.4 MUSS068 85.4 JESPR244
74.6 CIR043 101.3 NAU4004
54.7 NAU2911 87.0 BNL261
75.9 JESPR235 103.0 HAU0684
55.8 HAU1936a°°°°°° 88.1 NAU2661
76.3 BNL4035 89.0 HAU1756 104.0 NAU6289
56.3 HAU2009°°°°°°
77.1 BNL169 89.5 TMB0628a 105.0 TMB0628b
56.8 BNL511
Gh199 78.2 HAU0230a 89.7 NAU2599 106.4 Gh498b
60.8 DPL0215
Gh498a 107.2
64.6 NAU2869 79.1 NAU3665a 89.8
TMB2931 CIR068
68.4 NAU6515° 79.5 NAU6667 90.1 MGHES74 107.9 NAU6146
69.0 NAU6215°°° SDR10.1 79.8 NAU3122 90.2 HAU0639
108.5 NAU6224
90.5 TMB1786
69.3 BNL3790°° 80.1 BNL119 90.7 Gh316 109.1 TMB0985
70.5 HAU0230b°° 80.9 NAU3404 HAU3174 109.2 NAU3792 TMB1061
91.4
81.5 TMB0987 NAU2852 110.6 MUSB0823
70.9 NAU3665b°° 92.4
HAU1532 114.0 MUSB0849
82.0 94.5 HAU0217
74.1 HAU1968b 82.6 DPL0225b 98.3 BNL2805 BNL625 114.7 NAU2758
115.5 TMB1222
75.6 NAU4928a° 83.4 HAU2508 98.5 TMB2453
116.7 HAU1311
NAU3813 105.7 TMB1210
77.6 NAU3873a 84.0
107.7 BNL1689 117.4 TMB1262
78.0 NAU6153 84.8 NAU4881 109.2 BNL2632 118.2 NAU2904
HAU1344 85.4 HAU1968a 118.8 NAU3094°
78.7 111.1 JESPR245
MUSB0953a°
119.1
80.1 HAU2874 86.5 HAU3156 112.5 NAU5212a 120.2 HAU1295
80.6 NAU5438 87.0 NAU6269a 113.3 NAU3478 120.3 NAU6594°
81.8 HAU1796b°°°°°° 87.5 HAU3385 115.1 BNL4094 120.7 NAU2110
87.6 TMB0317 116.7 DPL0199 121.9 NAU6178°
84.2 STV100a 117.5 HAU2837 123.6 NAU6444°°
84.6 BNL1161 87.8 NAU3873b 119.3 NAU3367 HAU3303
124.3
84.8 TMB0307 TMB0325 88.8 NAU4928b 119.8 NAU6334a 125.2 NAU3354°
85.0 BNL2705 89.5 CIR063 120.4 Gh369 126.1 NAU5212b
93.7 BNL2872 90.2 NAU6365 121.9 NAU6598 126.3 NAU5217
94.9 CM27 90.7 BNL3670 129.4 HAU1397b****** SDR11.1 126.9 NAU2950
98.7 HAU1314 90.8 TMB1838 130.4 TMB2281a****** 128.1 HAU1805
100.6 TMB0858 MUSS319 BNL3993 130.5 NAU3657a****** 129.4 HAU3047a
90.9 HAU2178 MUSB0831 131.5 HAU1397a****** 129.8 NAU5091°°°°°°
101.6 BNL3895 BNL1580
135.8 NAU2651 131.2
103.6 NAU6393 91.0 Gh119 132.2 NAU4039
138.7 TMB2281b******
104.0 DPL0431 91.2 NAU3574c 133.6 NAU6334b
139.8 NAU3657b
105.7 Gh236b 91.6 JESPR171 145.6 Gh329 135.9 HAU2515
108.1 Gh573b 92.8 HAU1796a 149.2 MUSS155 137.8 HAU2044
111.0 CIR171 151.5 CIR399 138.6 JESPR251
93.5 NAU2579 HAU2026
112.5 BNL1665 155.1 NAU3784 140.6
93.7 BNL946 NAU3234 143.2 HAU3074°°
113.7 CIR400 156.9
94.2 BNL3660 158.0 DPL0675 145.7 NAU5418°
114.3 BNL4016 94.8 Gh424 BNL1151 148.5 NAU3284
159.9
114.6 NAU3574b 95.3 DPL0135 160.0 BNL3431 152.2 NAU3657c*
115.3 NAU5362 96.2 Gh236a 160.5 NAU2933 153.3 CM23
115.9 NAU3013 160.7 TMB1915 154.4 NAU4014
96.6 TMB0281 JESPR135
160.9 159.1 HAU2004
116.5 HAU3201a 97.6 HAU3201b 161.2 BNL1404 159.8 MUSB0810
116.9 BNL2641 98.5 Gh511 161.9 Gh246 161.6 NAU6627
117.6 TMB1806 99.6 BNL2689 162.8 TMB2803 163.2 NAU6222
119.3 HAU1423 99.8 BNL3948 163.4 Gh074 164.5 NAU3585a
119.9 JESPR56b 100.9 CIR121 165.4 NAU3265a 165.1 BNL2812
121.5 BNL3499 167.3 DPL0585 166.9 NAU2826
101.6 BNL3838 NAU3531 170.7 HAU2442
122.6 NAU4880a 101.7 JESPR261 171.1 BNL3147a
BNL2589 172.4 NAU2141
122.9 HAU0635 102.1 HAU2200 172.3
DPL0701 173.0 JESPR158
174.1
124.1 BNL256 102.6 NAU2698b 180.7 DPL0472 176.2 NAU3265b
125.3 HAU2507 103.3 NAU6693 183.7 NAU3074a 178.0 BNL1492 CIR385
126.6 NAU2698a 103.6 NAU3464 184.6 BNL1034 178.7 TMB0043
MUSS143 179.1 DPL0181
127.6 MUSS135 103.8 184.9 MUSS332
HAU1430 179.9 Gh523
128.8 MGHES27 103.9 NAU3434 185.6
187.5 NAU3731a 180.4 TMB2281c
130.2 Gh645 104.4 STV100b 182.1 NAU3481
131.9 HAU2873 188.5 HAU2624
106.0 NAU5013 STV069 182.9 BNL3171
133.9 HAU1491 190.1
107.2 HAU2825 193.1 NAU3317 183.1 BNL3449
137.5 HAU0894 110.7 BNL2570 184.4 TMB1642
147.1 NAU3917 195.8 NAU3653a****** 185.5 BNL3935
112.6 HAU1969*** 201.0 TMB0434
154.5 NAU5166 115.6 NAU3407 204.4 NAU1148
185.6 BNL3147b
175.2 Gh379 117.6 NAU4880b 205.6 BNL3442 186.4 HAU0720
179.6 DPL0317° BNL1078 187.8 NAU3381
120.3 HAU0773b 206.5
NAU3474 191.8 DPL0062
185.7 BNL1145 208.0 HAU0618
122.3 209.8 CIR254 194.1 NAU3653b
125.7 NAU3682 216.2 STV176 194.7 NAU3074b
128.9 HAU3101 216.8 MUCS557 197.0 HAU1016
131.8 NAU4071 218.0 NAU3621 198.9 NAU3156
133.1 NAU5307 220.5 HAU3356 200.6 NAU3731b
149.3 MUSS467 221.1 MUSS123 210.6 CIR013
160.9 STV117 221.4 NAU5461 211.5 Gh470
224.8 NAU3008 214.3 MUSB1197
225.2 TMB1980 222.0 NAU3341
226.9 HAU3249 224.8 NAU5389
228.5 MUSS281 230.8 TMB1493
229.7 DPL0715a 232.3 BNL197
233.1 NAU3377c° 233.8 MUSS532
235.6 DPL0570 236.7 NAU4865°
239.2 NAU3373b 243.9 NAU2653
245.2 HAU1484
246.5 NAU3373c
251.6 NAU3377d°
265.9 BNL1655

Figure 6 The genetic maps of Chr10/Chr20 and Chr11/Chr21 homoeologous chromosome. All legends are same as described for Figure 1.

involved in, 85 items of biology process with 2123
sequences involved in and 23 items of cell component
with 2273 sequences involved in. However, sequences
on different chromosomes targeted different Gene
Ontology (GO) catalogs: Chr05, Chr11, Chr21, and
Chr26 targeted more molecular functions; Chr03,
Chr05, Chr11, Chr16, Chr19, and Chr21 targeted more
biology processes; and Chr05, Chr11, and Chr26 tar-
geted more cell components. Most chromosomes tar-
geted more molecular functions and biology processes
Yu et al. BMC Genomics 2011, 12:15 Page 9 of 14
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Chr12 Chr26 Chr13 Chr18

0.0 HAU1081°°°°°°
0.5 NAU2902°°°°°°
3.5 HAU3344
9.6 DPL0183b
12.3 Gh568b
13.2 DPL0866
14.6 NAU4090
0.0 HAU1086
15.7 HAU2599b
6.0 MUSB1135a
17.4 Gh055g
CIR167
8.8 NAU3991b
19.8 NAU2980a
9.6
21.4 NAU6636 JESPR246
16.0
0.0 DPL0469 22.8 HAU1783b 18.2 HAU2276
11.9 HAU2486 23.9 NAU3865 20.4 HAU0209
NAU3862°°° 24.6 NAU3163 0.0 BNL3281
15.4 23.7 NAU3447
NAU6659 9.2 HAU2304
19.8 NAU3561° 26.6 24.9 HAU1922
11.8 MGHES48
32.6 BNL2578 27.8 CIR039 25.7 NAU3223
16.3 NAU2285
36.6 HAU2835 28.2 BNL1669 26.1 NAU3843
NAU3897 28.4 NAU2195
18.1 MUSB1135b 26.7 NAU3827
39.9
28.6 PGCT116 21.7 NAU3991a 30.5 HAU0899
44.7 Gh568a 26.7 HAU2977 NAU3080
NAU5425 MUSS303 30.9
46.9 MUSB1242** 28.8 48.3 NAU5345 NAU3161b
NAU2356 32.6
48.4 BNL2657 52.2 HAU2792 35.4 NAU4861
51.8 BNL2621 29.1 NAU3189b
61.3 HAU3035 37.2 TMB2295
55.2 BNL2768 29.3 BNL116 BNL4061
66.1 39.7 NAU3130
56.2 JESPR270 HAU2587 BNL3510 70.9 NAU3540a*** HAU1355
41.8
56.7 CM50 29.4 NAU3920 JESPR92 72.6 HAU1997 49.4 JESPR178°
56.8 MUSS026 NAU3006 BNL3435 74.5 MUCS145 52.4 HAU2332
57.8 BNL3599 29.7 DPL0838a 78.8 CIR040 54.0 HAU3406
60.8 BNL3867 29.8 DPL0665b 83.1 NAU3468 55.7 HAU1212
61.5 BNL2967 TMB2557 30.0 BNL840 85.3 HAU2857* 57.3 Gh055a
HAU1313 30.4 NAU3007 86.6 TMB2904
62.1
87.9 HAU0539
58.5 NAU3017b
63.4 BNL3835 31.4 HAU0677 58.8 DPL0229
64.3 DPL0601 31.9 BNL1227 89.4 HAU2856a** 59.2 HAU2856b
32.5 NAU2857 89.9 NAU3017a*
65.5 HAU2663b NAU3005
59.8 NAU3861°°°°°
33.4 92.6 BNL569a 62.4 HAU1182
68.1 HAU2599a 34.2 HAU2663a Gh501b
94.3 64.8 NAU3589a°
74.1 HAU0545
35.5 HAU1452 96.1 NAU5392b 65.6 NAU3452°
79.4 DPL0280 HAU1909° SDR18.1
36.4 NAU3961 97.5 NAU3183 67.2
80.6 NAU2176 68.8 HAU1381°
37.6 NAU3647 98.6 TMB0820
83.6 Gh055f 39.4 MGhES44 99.5 TMB1767a 69.7 MUSS603°
86.2 NAU2096 42.0 HAU1292 HAU1389 70.4 TMB0834a
100.0
88.6 NAU2202 42.1 HAU2243 BNL4064 70.9 NAU5364
100.5
94.7 HAU1434 44.8 NAU5043 100.9 Gh592 72.9 BNL569b°
100.6 HAU1666 47.8 DPL0770 101.8 Gh034 75.4 HAU1036
102.3 Gh312****** 103.9 DPL0635 76.6 TMB0029a
51.4 Gh243b*
103.2 Gh188******
BNL341 105.1 BNL1555 77.9 TMB1767b
54.0 HAU1513
107.5 BNL391 105.4 78.4 NAU5392a
56.8 MUCS064 106.0 BNL4029
110.2 Gh243a 56.9 NAU4912 79.4 BNL1040°
106.6 NAU3307 81.6 NAU3211°
114.6 HAU2168a 58.4 NAU2913
116.4 BNL1673 107.4 NAU3079a 82.0 BNL3479° SDR18.2
59.4 NAU3236 109.8 HAU3220
118.1 HAU3165b 60.0 HAU2027 82.7 NAU3079b°
113.1 STV080 83.3 BNL3280°
119.1 NAU5419 60.6 NAU4081** HAU1091b
113.3 83.6 DPL0049°
119.4 BNL2717 63.5 HAU0723* 114.0 NAU2975b
123.3 BNL2709 83.7 BNL3445
66.6 BNL2495 115.0 NAU3570 83.9 JESPR153°
125.1 NAU3294 68.0 NAU4925 115.4 MUSB0972** 84.9 HAU3061
126.3 BNL2894 68.5 NAU2715b 116.8 Gh215b BNL1079°°
85.7
128.0 DPL0139 117.5 NAU2381* NAU3534°
70.5 NAU3032°°°°°° SDR13.1 86.1
129.4 NAU2715a 71.2 Gh463 118.3 MUSS572* 86.5 BNL1721°
132.2 TMB2789 118.7 STV120* 87.4 CM63°°
71.9 NAU2696 BNL2449***
136.2 NAU5047 119.5 87.8 CS059°
74.4 Gh629 120.5 JESPR201
138.6 HAU0107 Gh660 88.5 BNL4079°°°
75.8 120.8 BNL1394
141.8 HAU1828° 91.4 BNL2652°
76.9 JESPR136 120.9 MUSS550
145.2 BNL3865 91.9 HAU2675°°
78.0 NAU3850 121.1 BNL1438 NAU6682°°°
145.6 JESPR121 92.9 SDR18.3
80.3 NAU3713a 121.2 JESPR186 93.2 Gh443b°
147.3 NAU3713b 80.5 BNL2725 122.3 JESPR175
93.5 CIR020a°°°
148.3 HAU0153° 80.7 DPL0890 122.6 MUCS535
BNL4007 95.5 NAU3816°°°°°°
149.5 HAU0154 81.3 NAU3186 123.0
96.7 NAU3232°°°°°°
151.3 CIR081 123.6 CIR406 CM118
83.4 NAU5321 NAU3989* 98.6 HAU2850b°°°°°°
153.0 CIR293 123.9
84.7 TMB0083 124.9 Gh092 98.7 HAU2992°°°°°°
154.9 CM85 87.7 HAU0908 99.4 HAU1908°°°°°°
125.5 Gh678
155.7 CM68b 88.4 NAU4905 TMB2108 100.0 MUSS140°°°°°°
127.6
157.4 HAU1454 89.1 NAU3896 130.1 HAU2224 100.9 NAU3398°°°°°°
162.1 NAU2671 91.0 NAU4914 101.6 BNL3558°°
131.0 HAU2558b
170.2 NAU2672b 91.6 NAU5462 133.9 CIR020b* 102.3 NAU3948a°
172.1 NAU2640 92.0 NAU3876 135.4 TMB0635** 103.0 Gh525
172.5 HAU0717b NAU2868b 92.4 NAU3084 104.0 HAU083
138.5 NAU3948b 105.2 HAU0693
172.6 MGHES31 94.2 NAU3905 140.6 NAU2094a****** 105.9 NAU3203
172.9 BNL3414 95.7 STV122 141.7 Gh055c** 110.3 MUSB0685a°°°°°°
173.8 BNL598 96.0 HAU1477 147.6 BNL1652 110.7 BNL2544°
176.8 STV130 97.0 BNL1402a 151.5 HAU1779 111.0 NAU2697°° SDR18.4
177.3 NAU2251a 98.8 BNL1600 154.8 Gh681b 111.2 HAU0100°°
100.0 CIR272 157.3 Gh697 112.1 HAU2497°
180.1 NAU3860a
180.9 HAU1137 103.7 NAU2868a 162.6 NAU2094b 114.8 NAU3011a°
105.2 HAU0103 166.1 BNL137 115.2 BNL193°
184.6 HAU0567 171.6 CIR054 NAU3943°
115.8
188.4 HAU1568 108.5 HAU0717a
CIR362 BNL2557
176.3 HAU2631b 118.2 NAU4103
193.9 111.2 126.0 HAU2631a°
180.1 NAU6699
195.1 NAU3778 112.5 NAU2251b HAU2414 NAU6582°°°
181.4 129.1
196.0 HAU2229 113.8 HAU2137 SDR18.5
HAU2748
185.7 HAU0250b 132.5 HAU0250a°°
196.7 113.9 STV033 BNL1660
194.0 135.3 NAU3785°°
198.0 HAU1321 115.2 NAU3860b BNL409
194.7 136.9 TMB2762°°
204.2 DPL0443 HAU1577
117.0 BNL3368 195.6
205.1 NAU1301 197.6 BNL2906
118.3 NAU3795
206.0 BNL1441 205.6 STV038*
119.4 NAU3774
206.9 BNL4059 213.8 HAU2901
120.3 HAU1830
210.0 JESPR300
122.1 NAU3305
212.1 HAU0211
123.7 NAU5306
213.9 HAU0780
222.3 HAU0295

Figure 7 The genetic maps of Chr12/Chr26 and Chr13/Chr18 homoeologous chromosome. All legends are same as described for Figure 1.

than cell components, and some chromosomes tar-
geted more special catalogs: Chr03 and Chr21 predo-
minately targeted biology processes and Chr05, Chr11,
and Chr26 predominately targeted cell components
(Figure 8).
A correlation analysis between gSSRs, EST-SSRs, total
loci and GO catalogs showed that GO catalogs were
highly correlated to EST-SSR and total loci; gSSR was
highly correlated only to the ‘biology process’. The
results agreed with the concept that functional SSR
sequences were mainly derived from EST-SSRs (Table 1).
On level 2 of the GO classification, ‘binding’ (48.95%)
and ‘catalytic activity’ (30.87) dominated the molecular
function; ‘metabolic process’ (27.82%) and ‘cellular
Yu et al. BMC Genomics 2011, 12:15 Page 10 of 14
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Molecular function
Biology process
180 Cell component
160
140
Number of SSR-ESTs

120
100
80
60
40
20
0
1

6
r0

r0

r0

r0

r0

r0

r0

r0

r0

r1

r1

r1

r1

r1

r1

r1

r1

r1

r1

r2

r2

r2

r2

r2

r2

r2
Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch
Chromosomes

Figure 8 Chromosome distribution of GO catalogs.

process’ (27.69%) dominated 50% of the biology process;
and ‘cell part’ (32.86%), ‘cell’ (32.86%), and ‘organelle’
(25.27%) predominated the cellular component (see
Additional file 5).
On level 3 of the GO classification, ‘nucleic acid bind-
ing’, ‘ion binding’, ‘transferase activity’, ‘protein binding’,
‘nucleotide binding’, and ‘hydrolase activity’ predomi-
nated in nearly 70% of the molecular function; ‘cellular
metabolic process’, ‘primary metabolic process’, ‘macro-
molecule metabolic process’, and ‘biosynthetic process’
took more than 50% of the biology process; and ‘intra-
cellular’, ‘intracellular part’, ‘intracellular organelle’, and
‘membrane-bounded organelle’ were major items of cell
component (see Additional file 6).
When taking individual chromosomes into account,
we found that some GO items were found only in some
chromosomes, for example, Chr08 occupied many
special GO items of biology process. Also, some chro-
mosomes dominated some GO items, for example,
Chr05 and Chr26 dominated the four major items of
cell component (see Additional file 7).
Discussion
High-density genetic maps are becoming increasingly
important in theoretical and applied genetic research
[30]. The construction of genetic maps in cotton with
molecular markers has been hampered by the limited
polymorphism which is 18.2%-47.9% between G.
Table 1 Correlation between GO catalogs and gSSRs,
EST-SSRs and total loci
GO catalog gSSR EST-SSR Total loci
Molecular function 0.48* 0.77** 0.73**
Biology process 0.60** 0.56** 0.66**
Cell component 0.46* 0.81** 0.74**
*, **: significant at the 0.05 and 0.01 probability levels, respectively.
hirsutum and G. barbadense [5,7,31-33] and even less
(4.13%-7.9%) among G. hirsutum germplasms
[12,13,34,35]. Due to the low polymorphism and the
large genome size in cotton, the only way to construct a
high-density genetic linkage map is to apply more mar-
kers. In light of this, we developed new SSRs from ESTs
annotated to proteins and newly released ESTs including
novel ESTs from G. barbadense acc. 3-79 developed in
our laboratory. As a result, 3177 new EST-SSRs were
developed.
These EST-SSRs showed a lower polymorphism ratio
(8.1%-19.5%) when compared with other researches
[7,31-33]. Among the NAU-prefixed EST-SSRs and
gSSRs, only half of the polymorphism was detected
compared to the results of Guo et al. [7,25]. Although
our population and the population described by Guo
et al. [7] are both interspecific populations, a different
polymorphism was found between the two populations,
which might result from different materials or different
genotyping methods (denatured polyacrylamide gel vs.
non-denatured polyacrylamide gel).
The 6185 SSR primers developed in this study gener-
ated 1458 loci, and with our previous data [8], a total of
2521 loci were applied to map construction. The result-
ing map included 2316 loci on the 26 cotton chromo-
somes, 4418.9 cM long with an average distance of 1.91
cM between adjacent markers. This map is one of the
three maps composed of more than 2000 markers.
Compared to the map published by Rong et al. (2584
loci, 4447.9 cM in length with an average distance of
1.72 cM) [3] and the map published by Guo et al. (2247
loci, 3440.4 cM in length with an average distance of
1.58 cM) [25], the total map length and the average
marker distance of our map were more similar to the
map of Rong et al. [3], but longer than that of Guo
et al. [25]. The marker distribution on chromosomes
was similar to the map of Guo et al. [7] with the most
Yu et al. BMC Genomics 2011, 12:15
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loci on Chr19 and the fewest on Chr02 and Chr04.
More loci were found on the Dt subgenome than on the
At subgenome in our map and the map of Guo et al.
[7], but more loci were present on the At subgenome in
the map of Rong et al. [3]. The At subgenome was
longer than the Dt subgenome in our map and the map
of Rong et al. [3], but shorter in the map of Guo et al.
[7]. The average marker distance of the At subgenome
is longer than that of the Dt subgenome in all the three
maps. The number of gaps (> 10 cM) in our map was
similar to the map of Guo et al. [7], but fewer than
shown in the map of Rong et al. [3]; there were more
gaps on the Dt subgenome than on the At subgenome
in our map, but fewer in the other maps.
By comparing the distribution of SSRs, we found that
both gSSRs and EST-SSRs were prone to be mapped on
the Dt subgenome, with more gSSRs and EST-SSRs on
Chr11, Chr19, and Chr21. The distributions of gSSRs
and EST-SSRs on each chromosome were also different
with four chromosomes having 50% more EST-SSRs.
The uneven distribution of SSRs on subgenomes and
chromosomes could help us to determine the distribu-
tion of SSR motifs; and the function of SSR sequences
could be conducive to further target genes in the cotton
genome. The distribution of different genome-derived
SSRs can provide us with some evidence for the evolu-
tion of tetraploid cotton; for example, Chr05, Chr11,
and Chr15 may undergo concerted evolution because of
the distributions of other genome-derived SSRs on
them.
Segregation distortion is widespread in plant popula-
tions. In this study, 16.8% of the total loci showed segre-
gation distortion (P < 0.05), which is similar to other
reports on cotton (12.3%-19.9%) [6,7,23]. Twice as many
loci segregated toward the heterozygous allele than the
‘Emian22’ allele, and EST-SSRs showed more segrega-
tion distortion than gSSRs did. For the mapped loci,
12.8% of them were mapped on cotton chromosomes
with 74.9% segregating toward the heterozygous allele.
The loci segregated toward the heterozygous allele with
a high frequency because the heterozygous allele could
not be distinguished from the ‘3-79’ allele in the BC 1
population. Three chromosomes (Chr02, Chr16, and
Chr18) showed extreme segregation distortion in that
>50% of loci were distorted, among which 99.9% of the
distorted loci segregated toward the heterozygous allele
(Figures 2, 4, 7). Other maps have also proved that
these chromosomes show more segregation distortion
[3,6,7]. The extremely distorted chromosomes indicated
to us that segregation distortion loci exist on these chro-
mosomes. Faris et al. [36] and Kumar et al. [37] used
reciprocal backcross populations to identify segregation
distortion loci in Aegilops tauschii and tetraploid wheat,
respectively, which provided us with an example for
Page 11 of 14
identifying segregation distortion loci in cotton. The loci
skewing toward the same allele clustered on the same
chromosomes or within the same SDRs indicated that
genetic hitchhiking effects occur in cotton.
More than 8000 EST-SSRs were used in our mapping
population; however, only 1261 EST-SSRs were mapped.
Although gSSRs derived from genomic sequences, their
mother sequences can also be transcribed or translated.
By blasting the gSSR sequences to cotton ESTs, 367
gSSR sequences were matched to cotton ESTs. As a
result, 1633 loci of this map (70.6%) including five gene-
derived markers were functional markers, which was
fewer than those reported by Guo et al. [7]. By blasting
to the protein database, 1332 loci were derived from
translated sequences. Functional annotation of these loci
sequences revealed that some chromosomes preferen-
tially targeted certain GO catalogs, specifically, Chr03
and Chr21 mostly targeted the biology process; some
GO items were found only on some chromosomes, that
is, many special GO items of the biology process were
detected only on Chr08. These results indicated that
some chromosomes in cotton perform special functions.
What’s more, because these ESTs were mainly devel-
oped from developing fibers, this map can also be used
to identify fiber-related genes and to detect expressed
QTLs (eQTLs) for fiber quality.
Conclusions
A total of 3177 new EST-SSRs were developed to
enrich our interspecific BC1 genetic linkage map. The
final map included 2316 loci on the 26 cotton chromo-
somes, 4418.9 cM in total length and 1.91 cM in aver-
age distance between adjacent markers. Segregation
distorted chromosomes were identified, which is a
guide to identify segregation distortion loci in cotton
and to understand the mechanism of segregation dis-
tortion in interspecific cross between G. hirsutum and
G. barbadense in cotton. SSR sequences were function-
ally annotated, which is helpful to identify functions of
cotton chromosomes and to detect eQTLs for fiber
quality. This map can be compared and integrated
with other cotton maps to construct a consensus map
in cotton.
Methods
Plant materials
The mapping population used in this study is the BC1
population [(Emian22 × 3-79) × Emian22] including 141
individuals which had been used to construct a 917-
locus map [8]. ‘Emian22’ is an upland cotton cultivar
with high yield and moderate fiber quality but not resis-
tant to verticillium wilt in Hubei Province. It was once
widely cultivated and is still used as a parent for hybrid
production. Sea-island cotton accession ‘3-79’ is the
Yu et al. BMC Genomics 2011, 12:15
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genetic and cytogenetic standard line for G. barbadense
with super fiber quality and high resistance to verticil-
lium wilt. The cross between these two materials is per-
formed to improve the performance of ‘Emian22’ by
backcrossing and molecular-assisted selection.
EST-SSR marker development
To effectively identify SSRs in ESTs, a Windows-
based tool named Serafer was developed in our
laboratory, available at ftp://ensembl.genomics.org.cn/
other/Serafer_1.9.5.zip. Serafer combines CAP3 [38],
Sputnik (Abajian, Washington University; http://
espressosoftware.com/sputnik), and Primer3.0 [39]
into a package; it can assemble the sequences, search
SSRs, and design primers at the same time, so it is a
powerful pipeline for SSR identification. Serafer takes
a FASTA formatted sequence file as an input and can
produce an Excel file with number of SSRs, sequence
ID, SSR type, SSR motif, SSR position, repeat length,
repeat number, repeat score, and the length of the
sequence.
The assembled cotton EST sequences (G. arboretum
release 2, G. raimondii release 2, and G. hirsutum
release 3) were downloaded in FASTA format from the
Institute for Genome Research (TIGR) database http://
www.tigr.org. The default criteria for SSR detection
were a minimum of seven repeats for dinucleotide
motifs, five repeats for trinucleotide motifs, and four
repeats for tetra-, penta-, and hexanucleotide motifs.
The contig or singleton sequences were used to design
primers flanking the putative SSRs. The input criteria
for primer design were primer length 18-24 bp with 20
bp as the optimum, GC content 35%-60% with 50% as
the optimum, optimum annealing temperature 57°C,
and PCR product size 100-300 bp. After the SSR identi-
fication and primer design for the three sets of data
were completed, three steps were conducted to generate
the final unique SSR markers. First, EST-SSRs (ESTs
containing SSR) with no BLAST hits to known genes
were excluded; second, unique SSRs for each dataset
were generated by comparing them to all public cotton
microsatellites deposited in CMD http://www.cotton-
marker.org according to sequence ID, target SSR, and
primer sequences; and third, internal companions
among the three datasets were conducted to reduce
redundancies. This work was finished as of January
2008.
The ESTs from fast-elongating fiber of G. hirsutum cv.
Xu-142 released by Yuxian Zhu were the second
sequence source for EST-SSRs development, which was
not included in the assembled ESTs of G. hirsutum
release 3 in TIGR. These sequences were analyzed in
the Serafer pipeline from sequence assembly to primer
Page 12 of 14
design. More strict criteria were set for SSR detection
with a minimum length of 18 bp for di- to hexanucleo-
tide motifs, and the parameters for primer design were
the same as before except that the PCR product size
was 100-400 bp. These SSR markers were also com-
pared to all existing markers by primer sequences to
ensure that they were not redundant. This process was
finished as of July 2008.
The third sequence data for the development of EST-
SSRs were the new ESTs from developing fiber of
G. barbadense acc. 3-79 generated in our laboratory
(unpublished data). Aiming at understanding the
mechanism of fiber development in G. barbadense, we
have constructed a normalized fiber cDNA library (from
-2 to 25 dpa) of G. barbadense acc. 3-79 [40]. A preli-
minary sequencing of the cDNA library produced 887
high-quality ESTs that were used to construct the tran-
script map of developing fiber [40] and also to isolate
EST-SSRs [41]. After that, an additional 10090 high
quality ESTs were obtained. These new sequences com-
bined with the previous sequences were explored in the
Serafer pipeline to develop SSR markers. The SSR mar-
kers that were the same as all the previously developed
SSRs were excluded from the results, and this was fin-
ished as of August 2008.
All the SSR primers were named with a prefix HAU
and synthesized by Sunbiotech Co. Ltd. (Beijing).
Marker analysis
PCR, electrophoresis and silver staining were performed
as previously described [23].
Map construction
The mapping data for each parent were scored as the
BC 1 data according to the definition of JoinMap 3.0
[42], and the linkage map was constructed using a loga-
rithm of odds (LOD) threshold of 5.0 and a maximum
recombination fraction of 0.4. Map distances in centi-
Morgans (cM) were calculated using the Kosambi map-
ping function [43]. The resulting linkage map was
drawn using MapChart 2.2 software [44]. Linkage
groups were assigned to corresponding chromosomes by
mapped SSRs http://www.cottonmarker.org. Homoeolo-
gous chromosomes were identified by duplicated loci as
described in previous reports [2,3,7].
Segregation distortion
For each segregating marker, a c 2 analysis was per-
formed to test for deviation from the 1:1 expected seg-
regation ratio. A region with at least three adjacent
loci showing significant segregation distortion (P <
0.05) was defined as the segregation distorted region
(SDR) [45].
Yu et al. BMC Genomics 2011, 12:15
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Annotation and functional classification of sequences
containing SSRs
Sequences corresponding to gSSRs were indentified to
be transcribed sequences by BLASTN to cotton ESTs
with E ≤ 1 e -15 and were annotated using BLASTX
(NCBI, Bethesda, MD, USA). The BLASTX results were
classified into three groups: known gene products,
hypothetical proteins, and unknown genes.
Functional annotation of ESTs was based on GO anno-
tation [46], and performed with BLAST2GO [47,48].
When running BLAST2GO, BLASTX DB was set to NCBI
non-redundant DB and expectation value threshold was
set at 1.0E-3, whereas high-scoring segment pairs (HSPs)
length cutoff was set at 15. The top 20 BLAST hits were
retained, then go-mapping was run, and an annotation
step with default parameters was performed. Furthermore,
InterPro Scan was performed and InteProScan GOs was
merged to annotation. Finally, the ‘goslim_plant.obo’
ontology subset was used to achieve specific GO terms.
Additional material
Additional file 1: EST-SSRs developed from cotton ESTs (The details
of marker name, sequence ID, sequence, motif, primer sequences,
product size, Tm and putative function are listed).
Additional file 2: Chromosome assignment, marker distribution,
length of chromosomes, marker density, gaps and segregation
distortion in genetic linkage map constructed with the [(Emian22 ×
3-79) × Emian22] BC1 population.
Additional file 3: gSSRs derived from transcribed sequences.
Additional file 4: Description: BLASTX results of SSR sequences.
Additional file 5: GO classification of mapped loci sequences (level
2): (a) molecular function; (b) cell component; and (c) biology
process.
Additional file 6: GO items of mapped loci sequences (level 3): (a)
molecular function; (b) cell component; and (c) biology process.
Additional file 7: Details of GO results.
Acknowledgements
This work was financially supported by the National Basic Research Program
(No. 2010CB126001) and the National High Tech Project (No.
2006AA10Z153).
Author details
1
National Key Laboratory of Crop Genetic Improvement & National Centre of
Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan
430070, Hubei, PR China. 2Cotton Institute, Xinjiang Academy of Agriculture
and Reclamation Science, Shihezi 832000, Xinjiang, PR China.
Authors’ contributions
YY carried out most of the genotyping of the BC1 population. DJY carried
out the bioinformatics analysis of the functional annotation of these SSR
sequences. SGL developed the SSR analysis pipeline. XML participated in
part of the genotyping of the BC1 population. XQW also participated in part
of the genotyping of the BC1 population. ZXL designed the study,
conducted the data analysis and drafted the manuscript. XLZ participated in
the design of the study and proofread the manuscript. All authors
contributed to the interpretation of the results, read and approved the final
manuscript.
Page 13 of 14
Received: 11 July 2010 Accepted: 9 January 2011
Published: 9 January 2011
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