花生栽培种EST-SSRs分布特征及应用研究

doi:10.3724/SP.J.1006.2009.00246

摘要/Abstract

摘要：

利用自行开发的20 160条花生栽培种荚果EST, 通过序列拼接, 获得8 289条无冗余EST。经搜索, 共检测出740个SSR位点, 分布于651条EST中, 发生频率为7.8%, 平均每6.8 kb EST序列含一个SSR位点。功能注释结果表明具生物过程、分子功能和细胞组分的EST分别为73、111和56条。在花生荚果EST-SSR中, 三核苷酸重复类型出现频率最高, 占总SSR的62.8%, 其次是二核苷酸重复类型, 占总SSR的33.6%。在出现的26类重复基序中, AG/TC重复基序出现频率最高, AAG/TTC次之。利用Primer premier 5从651条含有SSR的EST中共设计引物233对, 从中随机选取100对引物检测EST-SSR在花生栽培种中的多态性及在野生种中的可转移性。结果表明, 有86对引物在供试的22个花生栽培品种中得到有效扩增, 其中10对在栽培种中具有多态性, 每对引物检测出的等位基因数2~3个, 平均2.2个。可扩增引物在野生种中的可转移率为12.5%~100%，平均96%。在野生种间检测出多态性的引物76对，每对引物检测出等位基因2~9个, 平均4.06个。

关键词: 花生栽培种, EST, SSR, 开发

Abstract:

Peanut (Arachis hypogaea L.) is one of the most important oilseed crops in China. Although there is a great difference in growth habit, growth stage, and agronomic traits for peanuts, there is little polymorphism on the molecular level of RFLP, RAPD and AFLP. With development of peanut EST, a vast amount of available EST sequence has been documented. The objective of this study was to investigate distribution characteristics of EST-SSRs. Developed with a total of 20 160 EST from cDNA library of two peanut cultivars, There were 651 SSR-containing EST identified, on average, one SSR had 6.8 kb of EST sequence with tri-nucleotide motif (62.8%) as the most abundant motif types followed by di- (33.6%), tetra- (1.9%), hexa- (0.8%) and penta-nucleotide (0.8%). The top six motif types with high frequency included AG/TC (25.8%), AAG/TTC (19.1%), AAT/TTA (10.1%), ACC/TGG (7.4%), ACT/TGA (7.0%) and AT/TA (6.1%). Based on the 651 SSR-EST, a total of 233 primer pairs were successfully designed and a subset (100 pairs) were synthesized to test the amplification and polymorphism in 22 peanut cultivars, and to assess the transferability among 16 different wild species. The results showed that 86 primer pairs were amplified effectively in peanut cultivars, 10 primer pairs of which exhibited polymorphism with 2–3 alleles, with an average of 2.2 alleles, were detected. The cross-transferability of cultivated peanut EST-SSR markers to peanut wild species was very high, ranging from 12.5 to 100% with an average of 96%. Seventy-six markers exhibited polymorphism in wild species with 2–9 alleles, and an average of 4.06 alleles. The results indicated that peanut EST could be a resource for developing SSR. The high level of transferability to wild species also implied that EST-SSR is a potentially useful marker for genetic studies in wild species.

Key words: Peanut(Arachis hypogaea :.), EST, mining, SSR

梁炫强;洪彦彬;陈小平;刘海燕;周桂元;李少雄;温世杰. 花生栽培种EST-SSRs分布特征及应用研究[J]. 作物学报, 2009, 35(2): 246-254.

LIANG Xuan-Qiang,HONG Yan-Bin,CHEN Xiao-Ping,LIU Hai-Yan,ZHOU Gui-Yuan,LI Shao-Xiong,WEN Shi-Jie. Characterization and Application of EST-SSRs in Peanut(Arachis hypogaea L.)[J]. Acta Agron Sin, 2009, 35(2): 246-254.

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链接本文: https://zwxb.chinacrops.org/CN/10.3724/SP.J.1006.2009.00246

https://zwxb.chinacrops.org/CN/Y2009/V35/I2/246

参考文献

[1]Krapovickas A, Gregory W C. Taxonomia del genero Arachis (Leguminosae). Bonplandia, 1994, 8: 1-186
[2]Kochert G, Halward T, Branch W D, Simpson C E. RFLP vari-ability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet, 1991, 81: 565-570
[3]Subramanian V, Gurtu S, Rao R C N, Nigam S N. Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (PAPD) assay. Genome, 2000, 43: 656-660
[4]Milla S R, Isleib T G, Stalker H T. Taxonomic relationships among Arachis sect: Arachis species as revealed by AFLP mark-ers. Genome, 2005, 8: 1-11
[5]Ferguson M E, Burow M D, Schulze S R, Bramel P J, Paterson A H, Kresovich S, Mitchell S. Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet, 2004, 108: 1064-1070
[6]Kantety R V, La Rota M, Matthews D E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol, 2002, 48: 501-510
[7]Bozhko M, Riegel R, Schubert R, Muller-Starck G. A cyclophilin gene marker confirming geographical differentiation of Norway spruce populations and indicating viability response on excess soil-born salinity. Mol Ecol, 2003, 12: 3147-3155
[8]Schubert R, Starck G M, Riegel R. Development of EST-PCR markers and monitoring their intrapopulational genetic variation in Picea abies L. Karst. Theor Appl Genet, 2001, 103: 1223-1231
[9]Brown G R, Kadel E E, Bassoni D L, Kiehne K L, Temesgen B, van Buijtenen J P, Sewell M M, Marshall K A, Neale D B. An-chored reference loci in loblolly pine (Pinus taeda L.) for inte-grating pine genomics. Genetics, 2001, 159: 799-809
[10]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
[11]Varshney P K, Sigmund R, Borner A, Korzun V, Stein N, Sorrells M E, Langridge P, Grane A. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci, 2005, 168: 195-202
[12]Gadaleta A, Mangini G, Mulè G, Blanco A. Characterization of dinucleotide and trinucleotide EST-derived microsatellites in the wheat genome. Euphytica, 2007, 153: 73-85
[13]Kantety R V, La Rota M, Matthews D E, Sorrells M E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol, 2002, 48: 501-510
[14]Scott K D, Eggler P, Seaton G, Rossetto M, Ablett E M, Lee L S, Henny R J. Analysis of SSRs derived from grape ESTs. Theor Appl Genet, 2000, 100: 723-726
[15]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
[16]Gupta P K, Rustgi S, Sharma S, Singh R, Kumar N, Balyan H S. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genom, 2003, 270: 315-323
[17]Graham J, Smith K, MacKenzie K, Jorgenson L, Hackett C, Powell W. The construction of a genetic linkage map of red rasp-berry (Rubus idaeus subsp. idaeus) based on AFLPs, ge-nomic-SSR and EST-SSR markers. Theor Appl Genet, 2004, 109: 740-749
[18]Lu S-D(卢圣栋). Current Protocols for Molecular Biology (现代分子生物学实验技术). Beijing: Chinese Academy of Medical Sciences & Peking Union Medical College Press, 1999. pp 101-136 (in Chinese)
[19]Proite K, Leal-Bertioli S C, Bertioli D J. ESTs from a wild Ara-chis species for gene discovery and marker development. BMC Plant Biol, 2007, 7: 7
[20]Kantety R V, La Rota M, Matthews D E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol, 2002, 48: 501-510
[21]Varshney R K, Graner A, Sorrells M E. Genomic microsatellite markers in plants: Features and applications. Trends Biotechnol, 2005, 23: 48-55
[22]Eujayl I, Sledge M K, Wang L. Medicago truncatula EST-SSRs reveals cross-species genetic markers for Medicago spp. Theor Appl Genet, 2004, 108: 414-422
[23]Gao L, Tang J, Li H, Jia J. Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed, 2003, 12: 245-261
[24]Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 2000, 156: 847-854
[25]Li X-B((李小白), Cui H-R(崔海瑞), Zhang M-L(张明龙). De-tecting the genetic diversity of Brassica napus by EST-SSRs. J Agric Biotechnol (农业生物技术学报), 2007, 15(4): 661-667(in Chinese with English abstract)
[26]Aggarwal R K, Hendre P S, Varshney R K. Identification, char-acterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet, 2007, 114: 359-372
[27]Guo W, Wang W, Zhou B. Cross-species transferability of Gar-boreum-derived EST-SSRs in the diploid species of Gossypium. Theor Appl Genet, 2006, 112: 1573-1581
[28]Ferguson M E, Burow M D, Schulze S R, Bramel P J, Paterson A H, Kresovich S, Mitchell S. Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet, 2004, 108: 1064-1070
[29]Cho Y G, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch S R, Park W D, Ayres N, Cartinhour S. Diversity of microsatellites de-rived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet, 2000, 100: 713-722
[30]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
[31]Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P. Study of simple sequence repeat (SSR) markers from wheat expressed sequences tags (ESTs). Theor Appl Genet, 2004, 109: 800-805
[32]Areshchenkova T, Ganal M W. Comparative analysis of poly-morphism and chromosomal location of tomato microsatellite markers isolated from different sources. Theor Appl Genet, 2002, 104: 229-235
[33]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
[34]Ramsay L, Macaulay M, Ivanissivich S, MacLean K, Cardle L, Fuller J, Edwards K, Tuvesson S, Morgante M, Massari A, Maes-tri E, Marniorlin N, Sjakste T, Ganal M, Powell W, Powell W, Waugh R. A simple sequence repeat-based linkage map of barley. Genetics, 2000, 156: 1997-2005

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