作物学报Issue(7)：1007-1016,10.DOI:10.3724/SP.J.1006.2015.01007
用全基因组关联分析解析籼稻垩白的遗传基础
Genetic Dissection of Grain Chalkiness in Indica Mini-core Germplasm Using Genome-wide Association Method
摘要
Abstract
In order to dissect the genetic bases and mine novel alleles of grain chalkiness in indica, we conducted an experiment with genome-wide association analysis using phenotypic data collected from multiple locations (Sanya of Hainan, Shenzhen of Guangdong, Hangzhou of Zhejiang, and Jingzhou of Hubei) and 6704 re-sequenced SNP markers distributed in whole genome for 272 indica mini-core germplasm collected worldwide. All accessions were classified into three subpopulations based on SNP data. Total of 42 and 44 loci were detected as significant associations with percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), respectively, which distributed all over the 12 chromosomes. Twenty one and nineteen loci were stably expressed for PGWC and DEC in multiple locations, respectively, and 12 simultaneously affected the two traits. Eleven of the said loci were co-located in the same or near regions harboring the quality genes cloned previously. Of them, the region of 3.3–5.3 Mb on chromosome 5 was significantly associated with PGWC at all four locations, having the largest phenotypic contri-bution detected in Hangzhou location, and the carrier variety with the best favorable allele was IRGC121689;another region of 17.5–22.7 Mb on chromosome 12 was significantly associated with DEC at Sanya and Hangzhou, having the largest phenotypic contribution detected in Sanya, and the carrier variety with the best favorable allele was IRGC122285. These loci and germplasms are important potential genes and variety resources that can be used in molecular breeding for rice appearance quality.关键词
水稻/垩白/关联分析/SNP标记/连锁不平衡Key words
Rice/Chalkiness/Association mapping analysis/SNP marker/Linkage disequilibrium引用本文复制引用
邱先进,袁志华,陈凯,杜斌,何文静,杨隆维,徐建龙,邢丹英,吕文恺..用全基因组关联分析解析籼稻垩白的遗传基础[J].作物学报,2015,(7):1007-1016,10.基金项目
本研究由湖北省科技支持计划项目(2013BBB23),长江大学作物学省级重点学科项目(2015),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),粮食作物种质创新与遗传改良重点实验室开放课题(2014lzjj04),主要粮食作物产业化湖北省协同创新中心开放基金(2015MS008)和深圳市海外高层次人才资金资助。 （2013BBB23）
