Journal of Nuclear Agricultural Sciences ›› 2015, Vol. 29 ›› Issue (4): 674-684.DOI: 10.11869/j.issn.100-8551.2015.04.0674

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Association Analysis on Source Sink-related Traits in Rice Based on Linkage Disequilibrium

ZHAO Hongliang1, CHEN Kai2, ZHANG Qiang3, XU Zhengjin1, XU Jianlong2,3, LI Zhikang3   

  1. 1. Rice Research Institute/Key Laboratory for Northeast Rice Biology and Breeding of Ministry of Agriculture, Shenyang Agricultural University, Shenyang Liaoning 110866;
    2. Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen, Guangdong 518120;
    3. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081
  • Received:2015-02-05 Revised:2015-03-16 Online:2015-04-13 Published:2015-04-16

基于连锁不平衡水稻源库相关性状的关联分析

赵宏亮1, 陈凯2, 张强3, 徐正进1, 徐建龙2,3, 黎志康3   

  1. 1. 沈阳农业大学 水稻研究所/北方超级粳稻育种教育部重点实验室, 辽宁 沈阳 110161;
    2. 中国农业科学院深圳农业基因组研究所, 广东 深圳 518120;
    3. 中国农业科学院作物科学研究所, 北京 100081
  • 通讯作者: 徐建龙, 男, 研究员, 主要从事水稻遗传育种研究.E-mail:xujlcaas@126.com
  • 作者简介:赵宏亮, 男, 助理研究员, 主要从事水稻遗传育种研究.E-mail:hongliang_1979@126.com
  • 基金资助:

    引进国际先进农业科学技术计划(“948”计划)项目(2010-G2B),全球水稻科学伙伴协作计划“水稻适应性与产量表型组学”项目(DRPC2012)

Abstract:

To mine excellent alleles of source sink-related traits, association mapping analysis was conducted using 6 704 SNP markers across whole genome for 9 source sink-related traits including flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), top second leaf length (TSLL), top second leaf width (TSLW), top second leaf area (TSLA), spikelet number per panicle (SNPP), thousand grain weight (TGW) and grain yield per plant (GYP) of 261 indica rice germplasms collected from 31 countries based on its analysis of population structure and linkage disequilibrium. The results showed that variation coefficients of those 9 traits for 261 core rice germplasms were from 12.46% to 26.21%, indicating there was rich diversity involved in the natural population. Population structure analysis indicated that the optimum number of subpopulation was three. LD analysis showed that there was certain extent linkage disequilibrium between SNP loci. At the significant level of logP >3(P <10-3), total of 68 QTLs were detected as associations with 9 source sink-related traits, of which 55 QTLs associated with source traits, 13 with sink traits. Four overlapping loci affecting source sink-related traits were simultaneously detected on chromosomes 2, 5 and 11, which could be important reference value for marker-assisted improvement of source-sink traits of rice variety.

Key words: SNP marker, linkage disequilibrium, association analysis

摘要:

为挖掘水稻源库相关性状优异等位基因, 利用分布于12条染色体的6 704个SNP标记与来自31个国家和地区的261份籼稻核心种质资源的剑叶长、剑叶宽、剑叶叶面积、倒2叶长、倒2叶宽、倒2叶叶面积、每穗粒数、千粒重、单株产量共9个源库相关性状进行群体结构、连锁不平衡状况和全基因组关联分析.结果表明, 261份籼稻核心种质资源的9个源库相关性状的变异系数介于12.46%~26.21%, 表型变异丰富.群体结构显示261份籼稻核心种质资源的最适亚群数为3.LD分析表明, SNP位点之间存在着一定程度的连锁不平衡, 在显著水平-logP>3(P<10-3)下, 共检测到68个与9个水稻源库相关性状显著相关的QTL位点, 其中与源性状相关的QTL位点55个, 与库性状相关的QTL位点13个.在第2、第5和第11染色体上检测到同时影响源库性状的关联位点4个, 可能对通过分子标记辅助育种改良品种的源库性状具有重要参考价值.

关键词: 水稻, SNP标记, 连锁不平衡, 关联分析