Please wait a minute...
Frontiers of Agriculture in China

ISSN 1673-7334

ISSN 1673-744X(Online)

CN 11-5729/S

Front. Agric. China    2010, Vol. 4 Issue (3) : 257-264    https://doi.org/10.1007/s11703-010-0012-3
Research articles
Mapped SSR markers unevenly distributed on the cotton chromosomes
Zhongxu LIN,Daojun YUAN,Xianlong ZHANG,
Department of Plant Science & Technology, National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China;
 Download: PDF(269 KB)  
 Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks
Abstract In the past 15 years, more than 9000 SSR markers have been developed, which are a valuable resource for cotton genetics and breeding. Many of them have been mapped in cotton, and several high-density genetic maps have been constructed. In this paper, we jointly analyzed the mapped SSRs to characterize their motifs on cotton chromosomes. The results showed that SSR loci were distributed unevenly on cotton chromosomes with more on C11 and C19 and less on C02 and C04. Different sources of SSRs contributed different predominant SSR types, which were also distributed unequally on cotton chromosomes. Compared to SSRs derived from enriched libraries and BAC end sequences, EST-SSRs could generate novel SSR motifs especially for AT/TA of di-, tetra-, penta- and hexanucleotide. SSR motifs showed a biased distribution on cotton chromosomes with more on C05, C11, and C19, and less on C02 and C04. The uneven distribution of SSRs on cotton chromosomes would help us to enrich the cotton genetic map by motif-specific SSRs. This analysis gave us new knowledge on the architecture of the cotton genome.
Keywords cotton      SSR      motif      genetic linkage map      
Issue Date: 05 September 2010
 Cite this article:   
Zhongxu LIN,Daojun YUAN,Xianlong ZHANG. Mapped SSR markers unevenly distributed on the cotton chromosomes[J]. Front. Agric. China, 2010, 4(3): 257-264.
 URL:  
https://academic.hep.com.cn/fag/EN/10.1007/s11703-010-0012-3
https://academic.hep.com.cn/fag/EN/Y2010/V4/I3/257
Brown S M, Hopkins M S, Mitchell S E, Senior M L, Wang T Y, Duncan R R, Gonzalez-Candelas F, Kresovich S (1996). Multiple methods for the identification of polymorphic simple sequence repeats(SSRs) in sorghum [Sorghum bicolor (L.) Moench.]. Theor Appl Genet, 93: 190–198

doi: 10.1007/BF00225745
Connell J P, Pammi S, Iqbal M J, Huizinga T, Reddy A S (1998). A high throughput procedure for capturing microsatellites from complex plantgenomes. Plant Mol Biol Rep, 16: 341–349

doi: 10.1023/A:1007536421700
Field D, Wills C (1996). Long, polymorphic microsatellites in simple organisms. Proc Biol Sci, 263: 209–215

doi: 10.1098/rspb.1996.0033
Frelichowski Jr J E, Palmer M B, Main D, Tomkins J P, Cantrell R G, Stelly D M, Yu J, Kohel R J, Ulloa M (2006). Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends. Mol Gen Genomics, 275: 479–491

doi: 10.1007/s00438-006-0106-z
Fryxell P A (1992). A revised taxonomic interpretationof Gossypium L. (Malvaceae). Rheedea, 2: 108–165
Guo W Z, Cai C P, Wang C B, Han Z G, Song X L, Wang K, Niu X W, Wang C, Lu K Y, Shi B, Zhang T Z (2007). A microsatellite-based, gene-richlinkage map reveals genome structure, function and evolution in Gossypium. Genetics, 176: 527–541

doi: 10.1534/genetics.107.070375
Guo Y, Saha S, Yu J Z, Jenkins J N, Kohel R J, Scheffler B E, Stelly D M (2008). BAC-derived SSR markers chromosome locations in cotton. Euphytica, 161: 361–370

doi: 10.1007/s10681-007-9585-1
Han Z G, Guo W Z, Song X L, Zhang T Z (2004). Genetic mapping of EST-derived microsatellites fromthe diploid Gossypium arboreum in allotetraploid cotton. Mol Gen Genomics, 272: 308–327

doi: 10.1007/s00438-004-1059-8
Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T (2006). Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet, 112: 430–439

doi: 10.1007/s00122-005-0142-9
He D H, Lin Z X, Zhang X L, Nie Y C, Guo X P, Zhang Y X, Li W (2007). QTL mapping for economic traits based on a dense genetic map of cottonwith PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica, 153:181–197

doi: 10.1007/s10681-006-9254-9
Kantety R V, Rota M L, Matthews D E, Sorrells M E (2002). Data mining for simple sequence repeatsin expressed sequence tags from barley, maize, sorghum and wheat. Plant Mol Biol, 48: 501–510

doi: 10.1023/A:1014875206165
Lacape J M, Nguyen T B, Thibivilliers S, Bojinov B, Courtois B, Cantrell R G, Burr B, Hau B (2003). A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum × Gossypium barbadense backcross population. Genome, 46: 612–626

doi: 10.1139/g03-050
Li Y C, Korol A B, Fahima T, Nevo E (2004). Microsatellites within genes: structure, function andevolution. Mol Biol Evol, 21: 991–1007

doi: 10.1093/molbev/msh073
Nguyen T B, Giband M, Brottier P, Risterucci A M, Lacape J M (2004). Wide coverage of the tetraploid cotton genome usingnewly developed microsatellite markers. Theor Appl Genet, 109: 167–175

doi: 10.1007/s00122-004-1612-1
Park Y H, Alabady M S, Ulloa M, Sickler B, Wilkins T A, Yu J, Stelly D M, Kohel R J, El-Shihy O M, Cantrell R G (2005). Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinantinbred line cotton population. Mol Gen Genomics, 274: 428–441

doi: 10.1007/s00438-005-0037-0
Qureshi S N, Saha S, Kantety R V, Jenkins J N (2004). EST-SSR: A new class of genetic markers in cotton. J Cotton Sci, 8: 112–123
Reddy O K, Pepper A E, Abdurakhmonov I, Saha S, Jenkins J N, Brooks T, Bolek Y, El-Zik K M (2001). New dinucleotide and trinucleotide microsatellite markerresources for cotton genome research. J Cotton Sci, 5: 103–113
Reinisch A J, Dong J M, Brubaker C L, Stelly D M, Wendel J F, Paterson A H (1994). A detailed RFLP map of cotton Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics, 138: 829–847
Scott K D (2001). Microsatellites derived from ESTs,and their comparison with those derived by other methods. In plantgenotyping: the DNA fingerprinting of plants. CAB International, Wellingford, 255–237
Taliercio E, Allen R D, Essenberg M, Klueva N, Nguyen H, Patil M A, Payton P, Millena A C M, Phillips A L, Pierce M L, Scheffler B, Turley R, Wang J, Zhang D, Scheffler J (2006). Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs. Genome, 49: 306–319

doi: 10.1139/G05-115
Tian A G, Wang J, Cui P, Han Y J, Xu H, Cong L J, Huang X G, Wang X L, Jiao Y Z, Wang B J, Wang Y J, Zhang J S, Chen S Y (2004). Characterization of soybean genomic features by analysis of its expressed sequencetags. Theor Appl Genet, 108: 903–913

doi: 10.1007/s00122-003-1499-2
Wang C, Guo W, Cai C, Zhang T (2006). Characterization, development and exploitation of EST-derivedmicrosatellites in Gossypium raimondii Ulbrich. Chin Sci Bull, 51: 557–561

doi: 10.1007/s11434-006-0557-y
Yi G, Lee J M, Lee S, Choi D, Kim B D (2006). Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor Appl Genet, 114: 113–130

doi: 10.1007/s00122-006-0415-y
Yu J W, Yu S X, Lu C R, Wang W, Fan S L, Song M Z, Lin Z X, Zhang X L, Zhang J F (2007). High-density linkage map of cultivated allotetraploidcotton based on SSR, TRAP, SRAP and AFLP markers. J Integr Plant Biol, 49: 716–724

doi: 10.1111/j.1744-7909.2007.00459.x
Zhang H B, Li Y N, Wang B H, Chee P W (2008a). Recent Advances in Cotton Genomics. Int J Plant Genomics, Volume 2008: Article ID 742304, 20 pages, doi:

doi: 10.1155/2008/742304
Zhang Y X, Lin Z X, Li W, Tu L L, Nie Y C, Zhang X L (2007). Studies of new EST-SSRs derived from Gossypium barbadense. Chin Sci Bull, 52: 2522–2531

doi: 10.1007/s11434-007-0399-2
Zhang Y X, Lin Z X, Xia Q Z, Zhang M J, Zhang X L (2008b). Characteristics and analysis of simple sequence repeats in the cotton genome basedon a linkage map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. Genome, 51: 534–546

doi: 10.1139/G08-033
[1] Daling FENG, Shuxin XUAN, Aixia GU, Airu MA, Jiuhuan LI, Shuxing SHEN. PCR-based screening of BAC clones of different chromosomes in Chinese cabbage[J]. Front Agric Chin, 2011, 5(4): 524-528.
[2] Ghulam ABBAS, Tariq MANZOOR KHAN, Jehanzeb FAROOQ, Abid MAHMOOD, Rana Nadeem ABBAS, Wajad NAZEER, Amjad FAROOQ, Zuhair HASNAIN, Muhammad Naeem AKHTAR. Exploring influential plant traits for enhancing upland cotton yield under salt stress[J]. Front Agric Chin, 2011, 5(4): 443-449.
[3] Xinyan WEI, Lifeng LIU, Shunli CUI, Huanying CHEN, Jingjing ZHANG. Development of EST-SSR markers in peanut (Arachis hypogaea L.)[J]. Front Agric Chin, 2011, 5(3): 268-273.
[4] Muhammad IQBAL, Mueen Alam KHAN. Response of cotton genotypes to planting date and plant spacing[J]. Front Agric Chin, 2011, 5(3): 262-267.
[5] Muhammad Shahzad AHMED, Ihsan KHALIQ, Jehanzeb FAROOQ, Shahid Iqbal AWAN, Nisar AHMED, Faisal Saeed AWAN. Assessment of the combining ability and authentication of F1 hybrids using SSR markers in wheat (Triticum aestivum L.)[J]. Front Agric Chin, 2011, 5(2): 135-140.
[6] Xiuli ZHANG, Jinjin CAI, Joseph M. ANDERSON, Maolin ZHAO, Herbert W. OHM, Lingrang KONG. Identification of disease resistances in wheat-Leymus multicaulis derivatives and characterization of L. multicaulis chromatin using microsatellite DNA markers[J]. Front Agric Chin, 2010, 4(4): 394-405.
[7] Chengjin GUO, Jinfeng ZHAO, Cundong LI, Kai XIAO, Haina ZHANG, Chuanfan SUN, Juntao GU, . Identification of senescence-related genes by cDNA-AFLP in cotton ( Gossypium hirsutum L.)[J]. Front. Agric. China, 2010, 4(3): 308-316.
[8] Jiaqing WANG, Lin HOU, . Unigene derived SSR analysis for the Fugu rubripes and insights into the characteristics of EST-SSR distribution in tissues/organs[J]. Front. Agric. China, 2010, 4(1): 121-127.
[9] Dongxiao LI, Cundong LI, Hongchun SUN, Wenxin WANG, Liantao LIU, Yongjiang ZHANG, . Effects of drought on soluble protein content and protective enzyme system in cotton leaves[J]. Front. Agric. China, 2010, 4(1): 56-62.
[10] Kai WEI, Hao ZHANG, Xianfeng XU, Zuxin ZHANG, Hewei DU, Yiqin HUANG, . Evaluation of phenotype and genetic diversity of maize landraces from Hubei Province, Southwest China[J]. Front. Agric. China, 2009, 3(4): 374-382.
[11] Haina ZHANG, Fanghua ZHAO, Yuxin ZHAO, Chengjin GUO, Cundong LI, Kai XIAO. Establishment of transgenic cotton lines with high efficiency via pollen-tube pathway[J]. Front. Agric. China, 2009, 3(4): 359-365.
[12] Jingyan SUN, Weiming LI, Hanshuang ZHANG, Junli ZHAO, Xiaolin YIN, Li’an WANG. Somatic embryogenesis and plant regeneration in glandless upland cotton (Gossypium hirsutum L.)[J]. Front Agric Chin, 2009, 3(3): 279-283.
[13] Ying ZHU, Shuna LI, Hongshui YUAN, Xiaojun GUO, Baocheng ZHU. Isolation and identification of the antagonistic strain DM-54 of Bacillus amyloliquefacien against Verticillium dahliae, and optimization of antifungal protein producing conditions[J]. Front Agric Chin, 2009, 3(1): 16-23.
[14] WU Yuxiang, CHEN Chongqian, GAO Yanhui, ZHU Shuijin, JI Daofan. Effect of plant preservation on the fertility and chromosome configuration of a quadri-specific hybrid derived from 4 cultivated cotton species[J]. Front. Agric. China, 2008, 2(4): 380-385.
[15] PAN Zhifen, LONG Hai, YU Maoqun, DENG Guangbing, ZHAI Xuguang, TANG Yawei, QIANG Xiaolin. Molecular analysis of cultivated naked barley ( L.) from Qinghai-Tibet Plateau in China using SSR markers[J]. Front. Agric. China, 2008, 2(4): 372-379.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed