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Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (05): 788-797.doi: 10.3724/SP.J.1006.2014.00788


Genetic Diversity, Population Structure and Linkage Disequilibrium in Adzuki Bean by Using SSR Markers

BAI Peng,CHENG Xu-Zhen*,WANG Li-Xia,WANG Su-HuaCHEN Hong-Lin   

  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2013-11-18 Revised:2014-01-12 Online:2014-05-12 Published:2014-03-24
  • About author:程须珍, E-mail: chengxz@caas.net.cn, Tel: 010-62189159


A total of 249 Chinese adzuki bean accessions were analyzed with 57 adzuki bean SSR markers and 31 mungbean SSR markers to ascertain genetic diversity, population structure and linkage disequilibrium (LD) with five Japanese materials as the contrast. The results indicated that 630 alleles were detected with 2–17 alleles per locus and a mean genetic diversity index of 0.574, ranging from 0.024 to 0.898. There were significant differences among 15 populations of adzuki bean resources in genetic diversity from diversed geographic origins, with the highest in Yunnan and the lowest in Hebei and Tianjin. The 254 adzuki bean accessions could be divided into three subgroups based on STRUCTURE and NJ cluster. The population structure derived from them was positively correlated to some extent with the geographic eco-type. LD analysis revealed that there was a shorter LD decay distance in adzuki bean than that in other crops. The maximum LD decay distance, estimated by curvilinear regression, was 5.8 cM (R2>0.1), with a whole genome LD decay distance less than1 cM (R2>0.1, P<0.001). The results of this study should provide valuable information for future association mapping using this Chinese adzuki bean collection.

Key words: Adzuki beanSSR markers, Genetic diversity, Population structure, Linkage disequilibrium

[1]Yoon M S, Lee J, Kim C Y, Baek H J. Genetic relationships among cultivated and wild Vigna angularis (Willd.) Ohwi & Ohashi and relatives from Korea based on AFLP markers. Genet Resour Crop Evol, 2007, 54: 875–883

[2]金文林. 中国小豆生态气候资源分区初探. 北京农业科学, 1995, 13(6): 1–4

Jin W L. The Primary study on ecological regions of Chinese adzuki bean. Beijing Agric Sci, 1995, 13(6): 1–4 (in Chinese with English abstract)

[3]Erlich H A, Gelfand D, Sminsky J J. Recent advances in polymerase chain reaction. Science, 1991, 252: 1643–1651

[4]Mullis K B. The Unusual origin of the polymerase chain reaction. Sci Am, 1990, 262: 56–61

[5]Wang L X, Guan R X, Liu Z X, Chang R Z, Qiu L J. Genetic diversity of Chinese cultivated soybean revealed by SSR markers. Crop Sci, 2006, 46: 1032–1038

[6]Chen X J, Min D H, Tauqeer Ahmad Yasir, Hu Y G. Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS One, 2012, 7: e44510

[7]Flint-Garcia S A, Thornsberry J M, Buckler E S. Structure of linkage disequilibrium in plants. Annu Rev Plant Biol, 2003, 54: 357–374

[8]Rafalski A, Morgante M. Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet, 2004, 20: 103–111

[9]Zhang X Y, Tong Y P, You G X, Hao C Y, Ge H M, Wang L F, Li B, Dong Y C, Li Z S. Hitchhiking effect mapping: a new approach for discovering agronomic important genes. Sci Agric Sin, 2006, 39: 1526–1535

[10]Pritchard J K, Rosenberg N A. Use of unlinked genetic markers to detect population stratification in association studies. Am J Human Genet, 1999, 65: 220–228

[11]Buckler E S, Thornsberry J M. Plant molecular diversity and applications to genomics. Plant Biol, 2002, 5: 107–111

[12]Pritchard J K, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics, 2000, 155: 945–959

[13]Remington D L, Thornsberry J M, Matsuoka Y, Wilson L M, Whitt S R, Doebley J, Kresovich S, Goodman M M, Buckler E S. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA, 2001, 98: 11479–11484

[14]Kraakman A T W, Niks R E, Van den Berg P M M M, Stam P, Van Eeuwijk F A. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics, 2004, 168: 435–446

[15]Yu J, Pressoir G, Briggs W H, Vroh Bi I, Yamasaki M, Doebley J F, McMullen M D, Gaut B S, Nielsen D M, Holland J B, Kresovich S, Buckler E S. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet, 2006, 38: 203–208

[16]Doyle J J, Doyle J E. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull, 1987, 19: 11–15

[17]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

[18]Wang X X, Kaga A, Tomooka N, Vaughan D A. The development of SSR markers by a new method in plants and their application to gene flow studies in adzuki bean [Vigna angularis (Willd.) Ohwi & Ohashi]. Theor Appl Genet, 2004, 109: 352–360

[19]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)

[20]Goudet J. FSTAT (Ver. 1.2): A computer program to calculate F-statistics. J Hered, 1995, 86: 485–486

[21]Rohlf F. NTSYSpc: Numerical Taxonomy System (Ver. 2.2). Setauket, New York: Exeter Publishing, Ltd. 2006

[22]Yeh F C, Yang R C, Boyle T. Popgene Version 1.31 Quick User Guide. University of Alberta, and Centre for International Forestry Research, Canada, 1999

[23]Liu K, Muse S V. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21: 2128–2129

[24]Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol, 2005, 14: 2611–2620

[25]Rambaut A. FigTree.Ver. 1.3.1 [computer program]. ?Issued on 2012-12-05??Visited on 2013-10-15? http://tree.bio.ed.ac.uk/

[26]Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. TASSEL: software for association mapping of complex traits in diverse samples. Bioinform, 2007, 23: 2633–2635

[27]濮绍京, 金文林, 赵波, 王占丽. 中国北方小豆地方品种资源研究. 北京农学院学报, 2003, 18: 174–177

Pu S J, Jin W L, Zhao B, Wang Z L. Study on adzuki bean variety sources of North China. J Beijing Agric Coll, 2003, 18: 174–177 (in Chinese with English abstract)

[28]金文林. 中国北方小豆地方品种资源的研究: I. 小豆农艺性状在南京生态条件下表现的相关性研究. 北京农学院学报, 1989, 4(3): 34–41

Jin W L. A research on local variety resources of adzuki bean of northern China: I. Study on correlation of quantitative traits of adzuki bean in Nanjing. J Beijing Agric Coll, 1989, (4): 34–41 (in Chinese with English abstract)

[29]Sharma J D, Rathore P K. Genetic divergence in adzuki bean. Crop Improv, 1994, 21: 49–53

[30]Zong X X, Kaga A, Tomooka N, Wang X W, Han O K, Vaughan D. The genetic diversity of the Vigna angularis complex in Asia. Genome, 2003, 46: 647–658

[31]金文林, 文自翔, 濮绍京, 赵波. 应用RAPD分析小豆种质资源遗传多样性及遗传演化趋势. 中国农业科学, 2005, 38: 241–249

Jin W L, Wen Z X, Pu SJ, Zhao B. Genetic diversity and evolution of adzuki bean germplasm resources based on RAPD markers. Sci Agric Sin, 2005, 38: 241–249 (in Chinese with English abstract)

[32]叶剑, 赵波, 佟星, 濮绍京, 万平. 栽培小豆种质资源遗传多样性SSR标记分析. 北京农学院学报, 2008, 23: 8–13

Ye J, Zhao B, Tong X, Pu S J, Wan P. Genetic diversity of cultivated adzuki bean germplasm resources based on SSR markers. J Beijing Univ Agric, 2008, 23: 8–13 (in Chinese with English abstract)

[33]王丽侠, 程须珍, 王素华. 利用SSR标记分析小豆种质资源的遗传多样性. 生物多样性, 2011, 19: 17–23

Wang L X, Cheng X Z, Wang S H. Genetic diversity in adzuki bean and its relatives based on SSR markers. Biodivers Sci, 2011, 19: 17–23 (in Chinese with English abstract)

[34]Knowler W C, Williams R C, Pettitt D J, Steinberg G A. Gin3;5,13,14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. Am J Hum Genet, 1988, 43: 520–526

[35]Nordborg M, Borevitz J O, Bergelson J, Berry C C, ChoryJ, Hagenblad J, Kreitman M, Maloof J N, Noyes T, Oefner P J, Stahl E A, Weigel D. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet, 2002, 30: 190–193

[36]Nordborg M, Hu T T, Ishino Y, Jhaveri J, Toomajian C, Zheng H G, Calabrese P, Goyal R, Kim S, Padhukasahasram B, Plagnol V, Rosenberg N A, Shah C, Wall J D, Zhao K. The pattern of polymorphism in Arabidopsis thaliana. PloS Biol, 2005, 3: e196

[37]Hyten D L, Choi I Y, Song Q, Shoemaker R C, Nelson R L, Costa J M, Specht J E, Cregan P B. Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics, 2007, 175:1937–1944

[38]Parida A, Raina S N, Narayan R K J. Quantitative DNA variation between and within chromosome complements of Vigna species (Fabaceae). Genetica, 1990, 82:125–133

[39]徐宁, 程须珍, 王素华, 王丽侠, 赵丹. 以地理来源分组、利用表型数据构建中国小豆核心种质. 作物学报, 2008, 34: 1366–1373

Xu N, Cheng X Z, Wang S H, Wang L X, Zhao D. The establishment of Chinese adzuki bean core collection based on the geographical distribution and phenotypes. Acta Agron Sin, 2008, 34: 1366–1373 (in Chinese with English abstract)

[40]王丽侠, 程须珍, 王素华, 徐宁, 梁辉, 赵丹. 利用SSR标记分析小豆种质资源的遗传多样性. 中国农业科学, 2009, 42: 2661–2666

Wang L X, Cheng X Z, Wang S H, Xu N, Liang H, Zhao D. Genetic diversity among adzuki bean germplasm revealed by SSR markers. Sci Agric Sin, 2009, 42: 2661–2666 (in Chinese with English abstract)

[41]Yee E, Kidwell K K, Sills G R, Lumpkin T A. Diversity among selected Vigna angularis (Azuki) accessions on the basis of RAPD and AFLP markers. Crop Sci, 1999, 39: 268–275

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