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Acta Agron Sin ›› 2015, Vol. 41 ›› Issue (07): 1007-1016.doi: 10.3724/SP.J.1006.2015.01007

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic Dissection of Grain Chalkiness in Indica Mini-core Germplasm Using Genome-wide Association Method

QIU Xian-Jin1,2,YUAN Zhi-Hua1,CHEN Kai4,DU Bin1,HE Wen-Jing1,YANG Long-Wei1,2,XU Jian-Long3,4,*,XING Dan-Ying1,2,*,LÜ Wen-Kai1   

  1. 1 College of Agriculture, Yangtze University, Jingzhou434025, China; 2 Hubei Collaborative Innovation Center for Grain Industry / Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, China; 3 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 4 Institute of Agricultural Genomics at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
  • Received:2015-01-14 Revised:2015-04-02 Online:2015-07-12 Published:2015-05-04

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 contribution detected in Hangzhou location, and the carrier variety with the best favorable allele was IRGC121689; the 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.

Key words: Rice, Chalkiness, Association mapping analysis, SNP marker, Linkage disequilibrium

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