Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (05): 924-933.doi: 10.3724/SP.J.1006.2014.00924

• RESEARCH NOTES • Previous Articles     Next Articles

Development of Genomic SSR Markers in Common Bean and Their Transferability in Cowpea and Adzuki Bean

CHEN Ming-Li1,WANG Lan-Fen1,WU Jing1,ZHANG Xiao-Yan2,YANG Guang-Dong3,WANG Shu-Min1,*   

  1. 1 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 2 Institute of Vegetables, Qingdao Academy of Agricultural Sciences, Qingdao 266100, China; 3 Keshan Branch, Heilongjiang Academy of Agricultural Sciences, Keshan 161606, China
  • Received:2013-12-10 Revised:2014-03-04 Online:2014-05-12 Published:2014-03-25
  • About author:王述民, E-mail: wangshumin@caas.cn, Tel: 010-62175628

Abstract:

Transferability analysis of molecular markers has significantly improved their development efficiency and reduced their development cost. A total of 560 novel SSR markers were successfully developed based on common bean genomic sequences, and 421 (75.2%) of those markers generated effective amplification bands from two accessions of the cultivated common bean. Two Vigna species, cowpea and adzuki bean were used to test the transferability and polymorphism of new genomic markers. The results indicated that the transferability rate of common bean genomic-SSR in cowpea and adzuki bean was 43.9% and 38.2%, and the ratio of polymorphism SSR markers in the crops was 34.0% and 24.8%, respectively. A total of 138 common bean genomic-SSR primers were detected to be highly transferable between two species of Vigna. In addition, the diversity of transferability gene-SSR markers was higher for cowpea and adzuki bean than that of intergenic regions-SSR. These transferable markers are useful for further genetic diversity analysis, genetic linkage map construction, quantitative trait loci annotation, genetic evolution and marker-assisted selection in Vigna species because of their multi-allelic nature, reproducibility, co-dominant inheritance, high abundance in genome.

Key words: Common bean, Genus Vigna, SSR markers, Transferability

[1]Schoonhoven A V, Voysest O. Common Beans: Research for Crop Improvement. Wallingford, UK: CAB. International, 1991



[2]董玉琛, 郑殿升. 中国作物及其野生近缘植物. 北京: 中国农业出版社, 2006. pp 412–425



Dong Y C, Zheng D S. Crops and Their Wild Relatives in China. Beijing: China Agriculture Press, 2006. pp 412–425 (in Chinese)



[3]郑卓杰, 王述民, 宗绪晓. 中国食用豆类学. 北京: 中国农业出版社, 1997. pp 3–6



Zheng Z J, Wang S M, Zong X X. Chinese legumes. Beijing: Chinese Agriculture Press, 1997. pp 3–6 (in Chinese)



[4]郑殿升, 刘旭, 黎裕. 起源于中国的栽培植物. 植物遗传资源学报, 2012, 13: 1–10



Zheng D S, Liu X, Li Y. Cultivated Plants Originated in China. J Plant Genet Res, 2012, 13: 1–10 (in Chinese with English abstract)



[5]瓦维洛夫, 董玉琛. 主要栽培植物的世界起源中心. 北京: 农业出版社, 1982



Vavilov N I, Dong Y C. The Center of Origin of Cultivated Plants. Beijing: Agriculture Press, 1982 (in Chinese)



[6]Richard F. New opportunities in Vigna. In: Janick J, Whipkey A, eds. Trends in New Crops and New Uses. Alexandria, VA, USA: ASHA Press, 2002. pp 424–428



[7]Andargie M, Pasquet R S, Gowda B S, Muluvi G M, Timko M P. Construction of a SSR-based genetic map and identification of QTL for domestication traits using recombinant inbred lines from a cross between wild and cultivated cowpea (V. unguiculata (L.) Walp.). Mol Breed, 2011, 28: 413–420



[8]Han O K, Kaga A, Isemura T, Wang X W, Tomooka N, Vaughan D A. A genetic linkage map for adzuki bean [Vigna angularis (Willd.) Ohwi & Ohashi]. Theor Appl Genet, 2005, 111: 1278–1287



[9]Chen M L, Wu J, Wang L F, Zhang X Y, Blair M W, Jia J Z, Wang S M. Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation. Mol Breed, 2014, 33: 489–496



[10]Singha R K, Jenab S N, Khana S, Yadava S, Banarjeea N. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene, 2013, 524(2): 309–329



[11]张扬勇, 方智远, 王庆彪, 刘玉梅, 杨丽梅, 庄木, 孙培田. 拟南芥叶绿体SSR引物在甘蓝上的应用. 园艺学报, 2011, 38: 549–555



Zhang Y Y, Fang Z Y, Wang Q B, Liu Y M, Yang L M, Zhuang M, Sun P T. Utility of Arabidopsis chloroplast simple sequence repeat (cpSSR) primers in cabbage (Brassica oleracea L. var. capitata L.). Acta Hortic Sin, 2011, 38: 549–555 (in Chinese with English abstract)



[12]Wang M L, Chen Z B, Bakley N A, Newman M L, Kim W, Raymer P, Pederson G A. Characterization of seashore paspalum (Paspalumm vaginatum Swartz) germplasm by transferred SSRs from wheat, maize and sorghum. Genetic Resour Crop Evol, 2006, 53: 779–791



[13]Hu J B, Zhou X Y, Li J W. Development of novel EST-SSR markers for cucumber (Cucumis sativus) and their transferability to related species. Sci Hortic, 2010, 125: 534–538



[14]王丽侠, 程须珍, 王素华, 刘长友, 梁辉. 小豆SSR引物在绿豆基因组中的通用性分析. 作物学报, 2009, 35: 816–820



Wang L X, Cheng X Z, Wang S H, Liu C Y, Liang H. Transferability of SSR from adzuki bean to mungbean. Acta Agron Sin, 2009, 35: 816–820 (in Chinese with English abstract)



[15]钟敏, 程须珍, 王丽侠, 王素华, 王小宝. 绿豆基因组SSR 引物在豇豆属作物中的通用性. 作物学报, 2012, 38: 223–230



Zhong M, Cheng X Z, Wang L X, Wang S H, Wang X B. Transferability of mungbean genomic-SSR markers in other Vigna species. Acta Agron Sin, 2012, 38: 223–230 (in Chinese with English abstract)



[16]da Maia L C, Palmieri D A, de Souza V Q, Kopp M M, de Carvalho F I, Costa de Oliveira A. SSR locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics, 2008, DOI: 10.1155/2008/412696



[17]高东, 杜飞, 朱有勇. 低背景、高分辨率PAGE简易银染法. 遗传, 2009, 31: 668–672



Gao D, Du F, Zhu Y Y. Low-background and high-resolution contracted silver-stained method in polyacrylamide gels electrophoresis. Hereditas (Beijing), 2009, 31: 668–673 (in Chinese with English abstract)



[18]Yeh F C, Yang R C, Boyle B J T, Ye Z H, Mao X J. POPGENE 32 version 1.32, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada, 1999 Available at http://www.ualberta.ca/~fyeh/popgene_download.html [Verified December 2000] [Visited time 2013-10-15]



[19]Davey J W, Hohenlohe P A, Etter P D, Boone J Q, Catchen J M, Blaxter M L. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet, 2011, 12: 499–510



[20]Trebbi D, Maccaferri M, De Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti M, Massi A, Van der-Vossen E, Tuberosa R. High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet, 2011, 123: 555–569



[21]McCouch S R, Teytelman L, Xu Y, Lobos K B, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 2002, 9: 199–207



[22]Wang Z Y, Fang B P, Chen J Y, Zhang X J, Luo Z X, Huang L F, Chen X L, Li Y C. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genom, 2010, 11: 726–739



[23]Cavagnaro P F, Senalik D A, Yang L M, Simon P W, Harkin T T, Kodira C D, Huang S W, Weng Y Q. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics, 2010, 11: 569–586



[24]Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B. Transcriptome characterization and high throughput SSRs and SNPs discovery in cucurbita pepo (Cucurbitaceae). BMC Genom, 2011, 12: 104–118



[25]Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol, 2009, 9: 137



[26]Kaur S, Cogan N O, Pembleton L W, Shinozuka M, Savin K W, Materne M, Forster J W. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics, 2011, 12: 265



[27]Garg R, Patel R K, Tyagi A K, Jain M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res, 2011, 18: 53–63



[28]Dutta S, Kumawat G, Singh B P, Gupta D K, Singh S, Dogra V, Gaikwad K, Sharma T R, Raje R S, Bandhopadhya T K, Datta S, Singh M N, Bashasab F, Kulwal P, Wanjari K B, Varshney R K, Cook D R, Singh N K. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol, 2011, 11: 17



[29]Kalia R K, Rai M K, Kalia S, Singh R, Dhawan A K. Microsatellite markers: an overview of the recent progress in plants. Euphytica, 2011, 177: 309–334



[30]Gupta S, Prasad M. Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome, 2009, 52: 761–771



[31]文明富, 陈新, 王海燕, 卢诚, 王文泉. 木薯基因组SSR和EST-SSR在麻疯树和橡胶树中的通用性分析. 作物学报, 2011, 37: 74–78



Wen M F, Chen X, Wang H Y, Lu C, Wang W Q. Transferability analysis of cassava EST-SSR and genomic-SSR markers in jatropha and rubber tree. Acta Agron Sin, 2011, 37: 74–78 (in Chinese with English abstract)



[32]Varshney R K, Sigmund R, Borner A, Korzun V, Stein N, Sorrells M E, Langridge P, Graner A. Interspeci?c transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci, 2005, 168: 195–202



[33]Pejic I, Ajmone-Marsan P, Morgante M, Vozumplick K, Castiglioni P, Taramino G, Motto M. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet, 1998, 97: 1248–1255



[34]Frankham R, Ballou J D, Briscoe D A. Introduction to Conservation Genetics. New York: Cambridge University Press, 2002. pp 29–62



[35]王丽, 赵桂仿. 植物不同种属间共用微卫星引物的研究. 西北植物学报, 2005, 25: 1540–1546



Wang L, Zhao G F. Mico-satellite primers shared by different plant species and genera. Acta Bot Boreal-Occid Sin, 2005, 25: 1540–1546 (in Chinese with English abstract)



[36]Sumanasinghe V A, Tomooka N, Fukuoka S. Phylogenetic relationships of the subgenus Ceratotropis based on random ampli?ed polymorphic DNA. J Natn Sci Coun Sri Lanka, 1997, 25: 73–82

[1] CHEN Fang,QIAO Lin-Yi,LI Rui,LIU Cheng,LI Xin,GUO Hui-Juan,ZHANG Shu-Wei,CHANG Li-Fang,LI Dong-Fang,YAN Xiao-Tao,REN Yong-Kang,ZHANG Xiao-Jun,CHANG Zhi-Jian. Genetic analysis and chromosomal localization of powdery mildew resistance gene in wheat germplasm CH1357 [J]. Acta Agronomica Sinica, 2019, 45(10): 1503-1510.
[2] Ren-Feng XUE, Li WANG, Ming FENG, Wei-De GE. Identification and Expression Analysis of Likely Orthologs of Tobacco Salicylic Acid Binding Protein 2 in Common Beans [J]. Acta Agronomica Sinica, 2018, 44(05): 642-649.
[3] Lan-Fen WANG, Jing WU, Zhao-Li WANG, Ji-Bao CHEN, Li YU, Qiang WANG, Shu-Min WANG. Adaptability and Phenotypic Variations of Agronomic Traits in Common Bean Germplasm Resources in Different Environments [J]. Acta Agronomica Sinica, 2018, 44(03): 357-368.
[4] GENG Qing-He,WANG Lan-Fen,WU Jing,WANG Shu-Min. QTL Mapping for Seed Size and Shape in Common Bean [J]. Acta Agron Sin, 2017, 43(08): 1149-1160.
[5] WANG Jian-Hua,ZHANG Yao-Wen,CHENG Xu-Zhen,WANG Li-Xia. Construction of New Genetic Map and Identification of QTLs Related to Agronomic Traits in Mung Bean [J]. Acta Agron Sin, 2017, 43(07): 1096-1102.
[6] QIAO Lin-Yi,CHANG Jian-Zhong,GUO Hui-Juan,GAO Jian-Gang,ZHENG Jun,CHANG Zhi-Jian. Genome-Wide Analysis of TaNBS Resistance Genes and Development of Chromosome 2AL-specific NBS-SSR Markers in Wheat [J]. Acta Agron Sin, 2016, 42(06): 795-802.
[7] ZHANG Ti-Fu,QI Wi-Cong,GU Min-Feng,ZHANG Xiao-Lin,LI Tan,ZHAO Han. Exploration and Transferability Evaluation of EST-SSRs in Quinoa [J]. Acta Agron Sin, 2016, 42(04): 492-500.
[8] LI Long,WANG Lan-Fen,WU Jing,JING Rui-Lian,WANG Shu-Min*. Identification of Drought Resistence at Seedlings Stage in Common Bean (Phaseolus vulgaris L.) Varieties [J]. Acta Agron Sin, 2015, 41(06): 963-971.
[9] QIN Jin-Yan,LI Zai-Feng,YAN Xiao-Cui,SU Ji-Hua,YAO Zhan-Jun,LIU Da-Qun. Molecular Identification of Leaf Rust Resistance Gene in Wheat Line 5R625 [J]. Acta Agron Sin, 2015, 41(04): 651-657.
[10] LI Jian-Bo,QIAO Lin-Yi,LI Xin,ZHANG Xiao-Jun,ZHAN Hai-Xian,GUO Hui-Juan,REN Yong-Kang,CHANG Zhi-Jian. Molecular Mapping of Powdery Mildew Resistance Gene PmCH7124 in a Putative Wheat–Thinopyrum intermedium Introgression Line [J]. Acta Agron Sin, 2015, 41(01): 49-56.
[11] BAI Peng,CHENG Xu-Zhen*,WANG Li-Xia,WANG Su-HuaCHEN Hong-Lin. Genetic Diversity, Population Structure and Linkage Disequilibrium in Adzuki Bean by Using SSR Markers [J]. Acta Agron Sin, 2014, 40(05): 788-797.
[12] LU Xu-Zhong,NI Jin-Long,LI Li,WANG Xiu-Feng,MA Hui,ZHANG Xiao-Juan,YANG Jian-Bo. Construction of Rice Variety Based on ID Used SSR Fingerprint and Commodity Information [J]. Acta Agron Sin, 2014, 40(05): 823-829.
[13] LI Long,WANG Lan-Fen,WU Jing,JING Rui-Lian,WANG Shu-Min. Physiological Characteristics of Drought Resistance in Common Bean (Phaseolus vulgaris L.) [J]. Acta Agron Sin, 2014, 40(04): 702-710.
[14] WANG Cai-Jie,SUN Shi,JIN Su-Juan,LI Wei,WU Cun-Xiang,HOU Wen-Sheng,HAN Tian-Fu. Genetic Diversity Analysis of Widely-planted Soybean Varieties from Different Decades and Major Production Regions in China [J]. Acta Agron Sin, 2013, 39(11): 1917-1926.
[15] WANG Wei,WANG Chang-Biao,LIU Fang,CHEN Hao-Dong,WANG Lin,WANG Chun-Ying,ZHANG Xiang-Di,WANG Yu-Hong,WANG Kun-Bo. Development and Evaluation of New Non-Redundant EST-SSR Markers from Gossypium [J]. Acta Agron Sin, 2012, 38(08): 1443-1451.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!