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Acta Agron Sin ›› 2012, Vol. 38 ›› Issue (08): 1443-1451.doi: 10.3724/SP.J.1006.2012.01443


Development and Evaluation of New Non-Redundant EST-SSR Markers from Gossypium

WANG Wei1,2,**,WANG Chang-Biao3,**,LIU Fang1,CHEN Hao-Dong1,4,WANG Lin1,WANG Chun-Ying1,ZHANG Xiang-Di1,WANG Yu-Hong1,WANG Kun-Bo1,*   

  1. 1 Cotton Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratoy of Cotton Biology, Anyang 455000, China; 2 Agricultural Sciences Institute of Coastal Area of Jiangsu, Observation and Experimental Station of Saline Land of Coastal Area, Ministry of Agriculture, Yancheng 224002, China;3 Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng 044000; 4 Hunan Cotton Research Institute, NationaL Hybrid Cotton Research Promotion Center, Changde 415101 China
  • Received:2011-12-30 Revised:2012-04-20 Online:2012-08-12 Published:2012-06-04
  • Contact: 王坤波, E-mail: wkbcri@163.com, wkbcri@cricaas.com.cn

Abstract: A software Clustal X was used to analyse the redundancy of 393 753 ESTs of Gossypium available in public database. By mining 349 815 non-redundant ESTs, a total of 11 372 SSR loci derived from 10 507 ESTs using a software SSRmine developed by ourselves were observed. The frequency of ESTs containing SSRs was 3%, with an average of one SSR in every 21 kb of EST sequence. Besides, trinucleotide and hexanucleotide repeats were found to be the most abundant among 2–6-nucleotide repeat types, accounting for 34.1% and 40.6% respectively. In dinucleotide repeats, trinucleotide repeats, tetranucleotide repeats, pentanucleotide repeats and hexanucleotide repeats, AG/CT, AAG/CTT, AAAT/ATTT, AAAAG/CTTTT, AAAAAG/CTTTTT motifs accounted for the highest proportion respectively. Two hundred pairs of new non-redundant EST-SSR primers were developed based on 410 EST sequences removed the redundancy which have not been developed so far in Gossypium arboreum L.,G. hirsutum,and G. barbadense. Andwe used a software SSRmine developed by ourselvesto obtain non-similarity primers, designated CRI (Cotton Research Institute) XXX through six steps, including SSR primer sequences download, pretreatment, Blastn, extraction of primer numbers of similarity score more than 81%, extraction of redundant primers pairs and making redundant primers in a line, to remove homologous sequences from themselves and similar primers released in CMD from different cotton species. Among them, 100 primers were evaluated in polymorphism information content (PIC) and transferability using twelve cotton species including seven representative diploids species and five tetraploid species. The results showed that a total of 56 from the 100 pairs of SSR primers could be amplified the stable and clear polymorphic bands in the 12 accessions mentioned above, moreover, 35 out of 56 pairs of primers were polymorphic, with the primer polymorphism ratio of 35%. PIC of these primers ranged from 0.097 to 0.888, with the average of 0.482. Totally, the transferability among twelve cotton species was 100% for a pair of EST-SSR primers from Gossypium barbadense L., 81% for 25 primers from G. arboreum and 80.1% for 74 primers from G. hirsutum, respectively.

Key words: Gossypium, EST-SSR marker, Redundancy, Polymorphism, Transferability

[1]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. A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics, 2007, 176: 527-541

[2]Yu Y, Yuan D J, Liang S G, Li X M, Wang X Q, Lin Z X, Zhang X L. Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genomics, 2011, 12: 15

[3]Shen X L, Guo W Z, Zhu X F, Yuan Y L Kohel R J, Zhang T Z. Molecular mapping of QTLs for qualities in three diverse lines in Upland cotton using SSR markers. Mol Breed, 2005, 15: 169-181

[4]Liu R Z, Wang B H, Guo W Z, Qin Y S, Wang L G, Zhang Y M, Zhang T Z. Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Mol Breed, 2011, DOI: 10.1007/s11032-011-9547-0

[5]Song X L, Zhang T Z. Identification of quantitative trait loci controlling seed physical and nutrient traits in cotton. Seed Sci Res, 2007, 17: 243-251

[5]Yang C, GuoW Z, Li G Y, Gao F, Lin S S, Zhang T Z. QTLs mapping for verticillium wilt resistance at seedling and maturity stages in Gossypium barbadense L. Plant Sci, 2008, 174: 290-298

[6]Dong C G, Ding Y Z, Guo W Z, Zhang T Z. Fine mapping of the dominant glandless gene G l 2e in Sea island cotton (Gossypium barbadense L.). Chin Sci Bull, 2007, 52: 3105-3109

[7]Qian N, Zhang X W, Guo W Z, Zhan T Z. Fine mapping of open bud duplicate genes in homoelogous chromosomes of tetraploid cotton. Euphytica, 2009, 165: 325-331

[8]Zhao L, Cai C P, Zhang T Z, Guo W Z. Fine mapping of the red plant gene R1 in upland cotton (Gossypium hirsutum). Chin Sci Bull, 2009, 54(9): 1529-1533

[9]Gao W(高伟), Liu F(刘方), Li S-H(黎绍惠), Wang C-Y(王春英), Zhang X-D(张香娣), Wang Y-H(王玉红), Wang K-B(王坤波). Genetic diversity of allotetraploid cotton based on SSR markers. Acta Agron Sin (作物学报), 2010, 36(11): 1902-1909 (in Chinese with English abstract)

[10]Scott K D, Eggler P, Seaton G, Rossetto M, Ablett E M,. Lee S L, Henry R J. Analysis of SSRs derived from grape ESTs. Theor Appl Genet, 2000, 100: 723-726

[11]Cordeiro G M, Casu R, McIntyre C L, Manners J M, Henry R J. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci, 2001, 160: 1115-1123

[12]Eujayl I, Sorrells M E, Baum M. Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet, 2002, 104: 399-407

[13]Hackauf B, Wehling P. Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed, 2002, 121: 17-25

[14]Thiel T, Michalek W, Varshney R K. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L). Theor Appl Genet, 2003, 106: 411-422

[15]Peng J H, Nore L, Lapitan V. Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct Integr Genom, 2005, 5: 80-96

[16]Feingold S, Lloyd J, Norero N. Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor Appl Genet, 2005, 111: 456-466

[17]Chen X-Y(陈相艳), Li W(李伟), Dai H-Y(戴海英), Zhang L-F(张礼凤). Analysis of SSR Information in EST Resource of Soybean (Glycine max). Soybean Sci (大豆科学), 2009, 28(3): 394-399 (in Chinese with English abstract)

[18]An Z-W(安泽伟), Zhao Y-H(赵彦宏), Cheng H(程汉), Li W-G(李维国), Huang H-S(黄华孙). Development and application of EST-SSR markers in Hevea brasiliensis Muell. Arg. Hereditas (遗传), 2009, 31(3): 311-319 (in Chinese with English abstract)

[19]Wei L-B(魏利斌), Zhang H-Y(张海洋), Zheng Y-Z(郑永战), Guo W-Z(郭旺珍), Zhang T-Z(张天真). Development and utilization of EST-derived microsatellites in sesame (Sesamum indicum L.). Acta Agron Sin (作物学报), 2008, 34(12): 2077-2084 (in Chinese with English abstract)

[20]Xu Z-L(徐照龙), Yi J-X(易金鑫), Yu G-H(余桂红), Zhang D-Y(张大勇), He X-L(何晓兰), Wang X-E(王秀娥), Ma H-X(马鸿翔). EST-SSR based genetic diversity analysis on salt tolerant plants from six species in Chenopodiaceae. J Plant Genet Resour (植物遗传资源学报), 2011, 12(1): 113-120 (in Chinese with English abstract)

[21]Han Z G, Guo W Z, Song X L, Zhang T Z. Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Mol Genet Genom, 2004, 272: 308-327

[22]Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet, 2006, 112: 430-439

[23]Wang C B, Guo W Z, Cai C P, Zhang T Z. Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich. Chin Sci Bull, 2006, 21(3): 316-320

[24]Yu Y(余渝), Wang Z-W(王志伟), Feng C-H(冯常辉), Zhang Y-X(张艳欣), Lin Z-X(林忠旭), Zhang X-L(张献龙). Genetic Evaluation of EST-SSRs Derived from Gossypium herbaceum. Acta Agron Sin (作物学报), 2008, 34(12): 2085-2091 (in Chinese with English abstract)

[25]Zhang P-P(张培培), Wang X-Q(王夏青), Yu Y(余杨), Yu Y(余渝), Lin Z-X(林忠旭), Zhang X-L(张献龙). Isolation, characterization, and mapping of genomic microsatellite markers for the first time in sea-island cotton (Gossypium barbadense). Acta Agron Sin (作物学报), 2009, 35(6): 1013-1020 (in Chinese with English abstract)

[26]Lü Y D, Cai C P, Wang L, Lin S Y, Zhao L, Tian L L, Lü J H, Zhang T Z, Guo W Z. Mining, characterization and exploitation of EST-derived microsatellites in Gossypium barbadense. Chin Sci Bull, 2010, 55, DOI: 10.1360/s11434-010-3230-4

[27]Song G-L(宋国立), Cui R-X(崔荣霞), Wang K-B(王坤波), Guo L-P(郭立平), Li S-H(黎绍惠), Wang C-Y(王春英), Zhang X-D(张香娣). A rapid improved CTAB method for extraction of cotton genomic. Acta Gossypii Sin (棉花学报), 1998, 10(5) 273-275 (in Chinese with English abstract)

[28]Zhang J(张军), Wu Y-T(武耀廷), Guo W-Z(郭旺珍), Zhang T-Z(张天真). Fast screening of microsatellite markers in cotton with PAGE/silver staining. Acta Gossypii Sin (棉花学报), 2000, 12(5): 267-269 (in Chinese with English abstract)

[29]Bassamb J, Caetano-Anoles G, Gresshoff P M. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem, 1991, 196: 80-83

[30]GuoW Z, Wang W, Zhou B L, Zhang T Z. Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium. Theor Appl Genet, 2006, 112: 1573-1581

[31]Zhang W(张伟), Liu F(刘方), Li S-H(黎绍惠), Wang W(王为), Wang C-Y(王春英), Zhang X-D(张香娣), Wang Y-H(王玉红), Song G-L(宋国立), Wang K-B(王坤波). QTL analysis on yield and its components in upland cotton RIL. Acta Agron Sin (作物学报), 2011, 37(3): 433-442 (in Chinese with English abstract)

[32]Qin H D, Guo W Z, Zhang Y M, Zhang T Z. QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L. Theor Appl Genet, 2008, 117: 883-894

[33]Zhu H Y, Han X Y, Lü J H, Zhao L, Xu X Y, Zhang T Z, Guo W Z. Structure, expression differentiation and evolution of duplicated fiber developmental genes in Gossypium barbadense and G. hirsutum. BMC Plant Biol, 2011, 11: 40

[34]Cardle L, Ratnsay L, Milbourne D. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 2000, 156: 847-854

[35]Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res, 2000, 10: 72-80

[36]Botstein D, White R L, Skolnick M. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Human Genet, 1980, 32: 314-331

[37]Adams K L, Cronn R, Percifield R. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA, 2003, 100: 4649-4654

[38]Wendel J F. New World cottons contain Old World cytoplasm. Proc Natl Acad Sci USA, 1989, 86: 4132-4136
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