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

Association Analysis of Agronomic and Quality Traits with SSR Markers in Glycine max and Glycine soja in China: I. Population Structure and Associated Markers

关联作图是一种利用连锁不平衡(linkage disequilibrium,LD)检测自然群体中基因位点及其等位变异的方法。利用60个SSR标记,对全国大豆地方品种群体(393份代表性材料)和野生大豆群体(196份代表性材料)的基因组变异进行扫描,分析两类群体的连锁不平衡位点、群体结构,并采用TASSEL软件的GLM(general linear model)方法对16个农艺、品质性状观测值进行标记与性状的关联分析。结果表明:(1)在公共图谱上不论共线性的或是非共线性的SSR位点组合都有一定程度的LD,说明历史上发生过连锁群间的重组;栽培群体的连锁不平衡成对位点数较野生群体多,但野生群体位点间连锁不平衡程度高,随距离的衰减慢。(2)群体SSR数据遗传结构分析发现,栽培群体和野生群体分别由9和4个亚群体组成,亚群的划分与群体地理生态类型相关联,证实地理生态类型划分有其遗传基础。(3)栽培群体中累计有27个位点与性状相关;野生大豆种质中累计有34个位点与性状相关。部分标记在两类群体中都表现与同一性状关联,检出的位点有一致性,也有互补性;一些标记同时与2个或多个性状相关联,可能是性状相关乃至一因多效的遗传基础;关联位点中累计有24位点(次)与遗传群体连锁分析定位的QTL一致。

Association mapping is a procedure for detecting QTLs as well as their alleles based on linkage disequilibrium （LD）. The genotyping data of 60 simple-sequence repeat （SSR） markers on representative samples of 393 landraces of Glycine max （L.） Merr. and 196 wild accessions of Glycine soja Sieb. et Zucc. were used in the present study. Linkage disequilibrium of pairwise loci and population structure were firstly analyzed for the two populations, then the association analysis between SSR loci and 16 agronomic and quality traits was performed by using TASSEL GLM （general linear model） program. The different degrees of LD were detected not only among syntenic markers but also among nonsyntenic ones, suggesting that there had been historical recombination among linkage groups. The cultivated soybean population had more LD loci pairs than wild soybean population, while the later had higher degree and slower attenuation of LD than the former. Genetic structure analysis showed that both of the cultivated and wild populations were composed of nine and four subpopulations, respectively, which associated with their geographic eco-types, indicating the classification of geographic eco-types was of sound genetic bases. Twenty seven and thirty four SSR loci associated with the traits were screened out from cultivated and wild populations, respectively. Some loci were found toassociate with a same trait in both populations, and there existed both consistent and inconsistent association between the cultivated and wild populations. There were a few loci associated with two or more traits simultaneously, which might be the genetic reason of correlation among traits or pleiotropic phenomena. In addition, twenty-four associated markers were in agreement with mapped QTLs from family-based linkage mapping procedure.