Association Analysis of Rice Grain Traits with SSR Markers

doi:10.3969/j.issn.1001-7216.2014.03.004

Abstract

Abstract: The genetic diversity, population structure and linkage disequilibrium of 540 rice varieties from different ecological regions were assessed with 262 pairs of simple sequence repeat (SSR) markers. The general linear model method in software of TASSEL was used to analyze the association between SSR markers and four grain traits. The main results were as follows: 1)the population was classified into seven subpopulations,with linkage disequilibrium at certain extent between SSR marker loci either intrachromosome or interchromosome within each subpopulation. 2)Among 45 grain lengthassociated SSR marker loci detected in all three years, RM5849 had the highest contribution rate (5286%), RM3766140 had the highest positive phenotypic effect, their carrier variety was Nongxiang 25. Among 7 grain widthassociated SSR marker loci, RM17 had the highest contribution rate (63.61%), RM17145 and RM573235 had the highest positive phenotypic effect, the carrier varieties were Ningjinghui 338 and Zaoshirihuangdao, respectively. Among 11 grain thicknessassociated SSR marker loci, RM276 had the highest contribution rate (25.44%), RM508215 and RM7288205 had the highest positive phenotypic effect, carrier varieties were both Hongmangshajing. Among six 1000grain weightassociated SSR marker loci, RM17 had the highest contribution rate (32.17%), RM17145 had the highest positive phenotypic effect, the carrier variety was Ningjinghui 338. Potential parental combinations for hybridization were predicted for improving grain traits by using the carrier varieties screened.

Key words: rice, grain traits, SSR molecular marker, association analysis, elite allele

摘要： 用262个SSR标记对来自不同生态区的540份水稻品种的基因组变异进行扫描，分析该自然群体的遗传多样性、群体结构和连锁不平衡位点，并采用TASSEL软件的一般线性模型（GLM）方法进行标记与性状的关联分析。结果表明：1）该自然群体由7个亚群体组成；每个亚群内，无论是共线SSR标记位点之间还是非共线SSR标记位点之间均存在一定程度的连锁不平衡。2）三年均检测到的与粒长显著相关的标记位点有45个，贡献率最高的是RM5849（52.86%），M3766140是增加表型效应最大的等位变异，载体品种是农香25。与粒宽显著相关的位点有7个，贡献率最高的是RM17（63.61%），增加表型效应最大的等位变异是RM17145和RM573235，载体品种分别是宁粳恢338和早十日黄稻。与粒厚显著相关的位点有11个，贡献率最高的是RM276（25.44%），增加表型效应最大的等位变异是RM508215和RM7288205，载体品种都是红芒沙粳。与千粒重显著相关的位点有6个，贡献率最高的是RM17（32.17%），增加表型效应最大的等位变异是RM17145，载体品种是宁粳恢338。预测了利用这些载体材料改良籽粒性状的潜在杂交亲本组合。

关键词: 水稻, 籽粒性状, SSR分子标记, 关联分析, 有利等位变异

CLC Number:

TRAN Thi Thu Giang1,2, DANG Xiaojing1, LIU Qiangming1, ZHAO Kaiming1,3, WANG Hui1, HONG Delin1 ,*. Association Analysis of Rice Grain Traits with SSR Markers[J]. Chinese Journal of Rice Science, 2014, 28(3): 243-257.

陈氏秋江1，2,党小景1 ,刘强明1,赵凯铭1,3 ,王卉1,洪德林1,*. 水稻籽粒性状的SSR关联分析[J]. 中国水稻科学, 2014, 28(3): 243-257.

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