中国野生大豆群体特征和地理分化的遗传分析

doi:10.3864/j.issn.0578-1752.2012.03.002

摘要/Abstract

摘要： 【目的】从分子标记等位变异水平上探讨中国野生大豆群体的遗传特征、连锁不平衡特点和地理生态分化的遗传机制，并以重要生态性状全生育期为代表解析性状地理分化的遗传基础。【方法】从全国24个省区不同地理生态型的野生大豆材料中抽选174份组成代表性样本，选用204个SSR标记，利用TASSEL及STRUCTURE 2.2软件进行群体连锁不平衡（linkage disequilibrium，LD）和群体遗传结构分析。在此基础上对群体的地理分化、亚群体特异性及全生育期位点等位变异的地理分化进行遗传分析。【结果】中国野生大豆群体蕴含丰富的遗传变异，20条连锁群中，I和C2连锁群有相对较多的位点平均等位变异和遗传分化。不论是共线性组合，还是非共线性组合，都有一定程度的LD存在，说明历史上发生过连锁群间的大量重组；野生群体D ′平均值为0.34，高值多，比栽培大豆高，说明野生群体发生过更多的重组，保留下较高的LD。采用H-W平衡模型将野生群体聚成4类，模型聚类亚群划分与地理生态分类相关、有交叉，推测各地理亚群体发生过材料的迁移。各地理亚群经长期自然选择，各位点等位基因的频率发生变化，还有新生的与绝灭的，因此，各地理亚群间产生明显的等位基因分化。与地理生态性状全生育期关联的有15个位点160个等位变异，其中，亚群特有等位变异共58个，来自14个位点，同一位点可以在多个亚群体产生不同的特有等位变异，其效应从南至北逐渐下降，这说明生态区间不仅有强烈的遗传分化，而且是有规律的遗传分化。【结论】中国野生大豆群体遗传多样性高，共线、非共线位点间连锁不平衡程度高，4个生态亚群体间位点高度遗传分化，产生大量地区特有等位变异，全生育期还表现由南向北降效的规律性遗传分化。

关键词: 野生大豆(Glycine soja Sieb. et Zucc.), SSR, 连锁不平衡（LD）, 群体结构, 地理分化, 全生育期遗传分化

Abstract: 【Objective】 The objective of the present study was to explore the genetic characteristics, linkage disequilibrium (LD) and genetic mechanism of geographic differentiation of the Chinese wild soybean population, and based on it, the geographic differentiation mechanism of days to maturity, the key geographic-ecological trait, is to be revealed. 【Method】 A sample composed of 174 accessions of wild soybean (Glycine soja Sieb. et Zucc.) from all growing areas (24 provinces) in China was established as the representative population of the Chinese wild soybean. The genotyping data of 204 simple-sequence repeat (SSR) markers on 174 accessions were obtained and analyzed for LD among marker pairs and the genetic structure of the population by using the TASSEL and STRUCTURE 2.2 program. Based on it, the genetic mechanism of the geographic differentiation of the population, the characteristics of the geographic subpopulations, and geographic differentiation of alleles of loci related to days to maturity were studied. 【Result】 There showed a plenty of genetic diversity in the Chinese wild soybean population and showed relatively larger average number of alleles and genetic differentiation on Linkage group (LG) I and C2 than others among the 20 LGs. Different LD degrees were detected not only among syntenic marker pairs but also among nonsyntenic pairs, suggesting there had been historical recombination among linkage groups. The average D′ was 0.34 for the population, larger than the previously reported value for cultivated soybean (G. max (L.) Merr.), implying more recombination occurred in the history and therefore higher LD values remained at present. The population was classified into four subpopulations according to H-W model-clustering analysis which was not completely but somewhat consistent with the geographic classification, indicating multiple migrations among eco-regions happened in the long history. There showed a great deal of allelic differentiation among the geographic subpopulations, including changes of allelic frequencies, new outcome of alleles and extinct of old alleles due to the long term natural selection. For the key geographic-ecological trait of the wild population, days to maturity, 160 alleles on 15 loci were detected, among them, 58 alleles from 14 loci were subpopulation-specific. Even multiple subpopulation-specific alleles of a same locus happened on each of the four subpopulations. The allelic genetic effects varied in a systematic decrease from the south to the north, which indicates not only strong but also systematic genetic differentiation among ecological subpopulations happened in the history for the trait. 【Conclusion】 The Chinese wild soybean population is characterized by higher genetic diversity and higher syntenic and nonsytenic LD. Among the four geographic subpopulations, there happened great genetic differentiation, which caused outcomes of subpopulation-specific alleles. The genetic differentiation of the key geographic-ecological trait, days to maturity, is characterized by not only strong but also systematic decrease of allelic effect from the south to the north.

Key words: wild soybean (Glycine soja Sieb. et Zucc.), simple-sequence repeat (SSR), linkage disequilibrium (LD), population structure, geographic differentiation, genetic differentiation of days to maturity

范虎, 赵团结, 丁艳来, 邢光南, 盖钧镒. 中国野生大豆群体特征和地理分化的遗传分析[J]. 中国农业科学, 2012, 45(3): 414-425.

FAN Hu, ZHAO Tuan-Jie, DING Yan-Lai, XING Guang-南, GAI Jun-Yi. Genetic Analysis of the Characteristics and Geographic Differentiation of Chinese Wild Soybean Population[J]. Scientia Agricultura Sinica, 2012, 45(3): 414-425.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2012.03.002

https://www.chinaagrisci.com/CN/Y2012/V45/I3/414

参考文献

[1]徐豹, 徐航, 庄炳昌, 路琴华, 王玉民, 李福山. 中国野生大豆(G.soja)籽粒性状的遗传多样性及其地理分布. 作物学报, 1995, 21(6): 733-739.

Xu B, Xu H, Zhuang B C, Lu Q H, Wang Y M, Li F S. Polymorphism and geographical distribution of seed characters of wild soybean (G. soja) in China. Acta Agronomica Sinica, 1995, 21(6): 733-739. (in Chinese)

[2]庄炳昌, 徐航, 王玉民, 路琴华, 徐豹, 李福山. 中国野生大豆(G. soja)茎叶性状的多态性及其地理分布. 作物学报, 1996, 22(5): 583-586.

Zhuang B C, Xu H, Wang Y M, Lu Q H, Xu B, Li F S. Polymorphism and geographical distribution of the stem and leaf characters of wild soybean (G. soja) in China. Acta Agronomica Sinica, 1996, 22(5): 583-586. (in Chinese)

[3]Dong Y S, Zhuang B C, Zhao L M, Sun H, He M Y. The genetic diversity of annual wild soybean grown in China. Theoretical and Applied Genetics, 2001, 103: 98-103.

[4]Chen Y W, Nelson R L. Genetic variation and relationships among cultivated, wild, and semiwild soybean. Crop Science, 2004, 44: 316-325.

[5]Nichols D M, Wang L Z, Pei Y L, Glover K D, Diers B W. Variability among Chinese Glycine soja and Chinese and North American soybean genotypes. Crop Science, 2007, 47: 1289-1298.

[6]田清震, 盖钧镒, 喻德跃, 吕慧能, 贾继增. 我国野生大豆与栽培大豆AFLP指纹图谱研究. 中国农业科学, 2001, 34(5): 465-468.

Tian Q Z, Gai J Y, Yu D Y, Lü H N, Jia J Z. Fingerprint analysis of G.soja and G.max in China. Scientia Agricultura Sinica, 2001, 34(5): 465-468. (in Chinese)

[7]Powell W, Morgante M, Doyle J J, McNicol J W, Tingey S V, Rafalski A J. Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics, 1996, 144: 793-803.

[8]Abe J, Xu D H, Suzuki Y, Kanazawa A, Shimamoto Y. Soybean germplasm pools in Asia revealed by nuclear SSR. Theoretical and Applied Genetics, 2003, 106: 445-453.

[9]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 Science, 2006, 46: 1032-1038.

[10]赵丽梅, 董英山, 刘宝, 郝水, 王克晶, 李向华. 中国一年生野生大豆(Glycine soja)核心资源构建. 科学通报, 2005, 50(10): 992-999.

Zhao L M, Dong Y S, Liu B, Hao S, Wang K J, Li X H. Establishment of a core collection for the Chinese annual wild soybean (Glycine soja). Chinese Science Bulletin, 2005, 50(10): 992-999. (in Chinese)

[11]赵茹, 程舟, 陆伟峰, 卢宝荣. 基于分子标记的野生大豆居群遗传多样性估算. 科学通报, 2006, 51(9): 1042-1048.

Zhao R, Cheng Z, Lu W F, Lu B R. Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers. Chinese Science Bulletin, 2006, 51(9): 1042-1048. (in Chinese)

[12]Choi I Y, Kang J H, Song H S, Kim N S. Genetic diversity measured by simple sequence repeat variations among the wild soybean, Glycine soja, collected along the riverside of five major rivers in Korea. Genes and Genetic Systems, 1999, 74: 169-177.

[13]Kuroda Y, Kaga A, Tomooka N, Vaughan D A. Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation. Molecular Ecology, 2006, 15: 959-974.

[14]赵洪锟, 王玉民, 李启云, 张明, 庄炳昌. 中国不同纬度野生大豆和栽培大豆SSR分析. 大豆科学, 2001, 20(3): 172-176.

Zhao H K, Wang Y M, Li Q Y, Zhang M, Zhuang B C. SSR analysis of wild soybean (G. soja) and cultivated soybean from different latitude in China. Soybean Science, 2001, 20(3): 172-176. (in Chinese)

[15]丁艳来, 赵团结, 盖钧镒. 中国野生大豆的遗传多样性和生态特异性分析. 生物多样性, 2008, 16(2): 133-142.

Ding Y L, Zhao T J, Gai J Y. Genetic diversity and ecological differentiation of Chinese annual wild soybean (Glycine soja). Biodiversity Science, 2008, 16(2): 133-142. (in Chinese)

[16]文自翔, 赵团结, 丁艳来, 盖钧镒. 中国栽培及野生大豆的遗传多样性、地理分化和演化关系研究. 科学通报, 2009, 54(21): 3301-3310.

Wen Z X, Zhao T J, Ding Y L, Gai J Y. Genetic diversity, geographic differentiation and evolutionary relationship among ecotypes of Glycine max and G. soja in China. Chinese Science Bulletin, 2009, 54(21): 3301-3310. (in Chinese)

[17]文自翔, 赵团结, 郑永战, 刘顺湖, 王春娥, 王芳, 盖钧镒. 中国栽培和野生大豆农艺品质性状与SSR标记的关联分析Ⅰ群体结构及关联标记. 作物学报, 2008, 34(7): 1169-1178.

Wen Z X, Zhao T J, Zheng Y Z, Liu S H, Wang C E, Wang F, Gai J Y. Association analysis of agronomic and quality traits with SSR markers in Glycine max and Glycine soja in China: Ⅰ. Population structure and associated markers. Acta Agronomica Sinica, 2008, 34(7): 1169-1178. (in Chinese)

[18]邱丽娟, 常汝镇. 大豆种质资源描述规范和数据标准. 北京: 中国农业出版社, 2006.

Qiu L J, Chang R Z. Descriptors and Data Standard for Soybean (Glycine spp.). Beijing: Chinese Agriculture Press, 2006. (in Chinese)

[19]Doyle J J, Doyle J I. Isolation of plant DNA from fresh tissue. Focus, 1990, 12: 13-15.

[20]Song Q J, Marek L F, Shoemaker R C, Lark K G, Concibido V C, Delannay X, Specht J E, Cregan P B. A new integrated genetic linkage map of the soybean. Theoretical and Applied Genetics, 2004, 109: 122-128.

[21]Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S. Characterization of the soybean genome using EST-derived microsatellite markers. DNA Research, 2007, 14: 271-281.

[22]Liu K J, Muse S V. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21(9): 2128-2129.

[23]Farnir F, Coppieters W, Arranz J J, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mni M, Nezer C, Simon P, Vanmanshoven P, Wagenaar D, Georges M. Extensive genome-wide linkage disequilibrium in cattle. Genome Research, 2000, 10: 220-227.

[24]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. Bioinformatics, 2007, 23: 2633-2635.

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

[26]张军, 赵团结, 盖钧镒. 大豆育成品种农艺性状QTL与SSR标记的关联分析. 作物学报, 2008, 34(12): 2059-2069.

Zhang J, Zhao T J, Gai J Y. Association analysis of agronomic trait QTLs with SSR markers in released soybean cultivars. Acta Agronomica Sinica, 2008, 34(12): 2059-2069. (in Chinese)

[27]张军, 赵团结, 盖钧镒. 亚洲大豆栽培品种遗传多样性、特异性和群体分化研究. 中国农业科学, 2008, 41(11): 3511-3520.

Zhang J, Zhao T J, Gai J Y. Genetic diversity, specificity and population differentiation of soybean cultivars in Asia. Scientia Agricultura Sinica, 2008, 41(11): 3511-3520. (in Chinese)

[28]Wen Z X, Ding Y L, Zhao T J, Gai J Y. Genetic diversity and peculiarity of annual wild soybean (G. soja Sieb. et Zucc.) from various eco-regions in China. Theoretical and Applied Genetics, 2009, 119(2): 371-381.

[29]Gupta P K, Rustgi S, Kulwal P L. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology, 2005, 57(4): 461-485.

[30]Cregan P B, Bhagwat A A, Akkay M S, Rongwen J. Microsatallite fingerprinting and mapping of soybean. Methods in Molecular and Cellular Biology, 1994, 5: 49-61.

[31]Hyten D L, Choi I Y, Song Q J, 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.

[32]Zhu Y L, Song Q J, Hyten D L, Van Tassell C P, Matukumalli L K, Grimm D R, Hyatt S M, Fickus E W, Young N D, Cregan P B. Single nucleotide polymorphisms in soybean. Genetics, 2003, 163: 1123-1134.

[33]Palmer R G, Pfeiffer T W, Buss, G R, Kilen T C. Qualitative genetics//Boerma H R, Specht J E. Soybeans: Improvement, Production and Uses: 3rd ed. ASA, CSSA, SSSA Publishers, Madison, WI, USA, 2004: 137-233.

[34]Watanabe S, Harada K, Abe J. Genetic and molecular bases of photoperiod responses of flowering in soybean. Breeding Science, 2012, 61: 531-543.