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Acta Agron Sin ›› 2018, Vol. 44 ›› Issue (01): 32-42.doi: 10.3724/SP.J.1006.2018.00032


Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

FANG Ya-Jie1,2,ZHU Ya-Jun2,3,WU Zhi-Chao2,CHEN Kai2,3,SHEN Cong-Cong3,SHI Ying-Yao1,*,XU Jian-Long2,3,4,*   

  1. 1 Anhui Agricultural University, Hefei 230036, China; 2 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 3 Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518210, China; 4 Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
  • Received:2017-04-05 Revised:2017-09-10 Online:2018-01-12 Published:2017-09-28
  • Supported by:

    This study was supported by National High-Tech Research & Development Plan (863) (2014AA10A601), Introduction of International Advanced Agricultural Science and Technology of Ministry of Agriculture (948) (2016-X16), ShenZhen Peacock Plan (20130415095710361), and Scientific and Technological Innovation Project of Chinese Academy of Agricultural Sciences.


Appearance and milling quality are two crucial properties of rice affecting their market acceptability. Understanding the genetic basis of rice grain quality could improve the efficiency of breeding for high quality. Here we carried out genome-wide association analysis using the 404K SNP genotype and data of grain appearance and milling quality for a diverse panel of 400 indica accessions selected from 3K Rice Genome Project collected in two environments. These were closely correlation between grain shape and quality (appearance and milling) of indica rice. The chalk trait reduced milled rice rate and high milled rice rate. In addition to grain shape, the phenotype value of appearance and milling quality traits was obviously affected by environments. Total of 39 QTL were detected which was significantly associated with grain appearance and milling quality in two environments and 17 of them were new QTL. Six new QTL (qMRR9, qGL2, qGL10, qGW1, qGLWR1, and qGLWR2.1) with minor or small effect were considered as stably expressed QTL because they were simultaneously identified in two environments. In addition, we found 21 QTL probably having multiple-effect in appearance and milling quality of indica rice. Combined with the results of previous studies, we concluded that qSW5, GSE5 and GS3 play important role in affecting appearance and milling quality. This research provides valuable information for cloning QTL controlling appearance and milling quality and breeding rice with high yield and good quality by molecular techniques.

Key words: Indica germplasms, Appearance and milling quality, GWAS, Quantitative trait loci/locus (QTL)

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