title: New Candidate Genes Affecting Rice Grain Appearance and Milling Quality Detected by Genome-Wide and Gene-Based Association Analyses.
abstract: Appearance and milling quality are two crucial properties of rice grains affecting its market acceptability. Understanding the genetic base of rice grain quality could considerably improve the high quality breeding. Here, we carried out an association analysis to identify QTL affecting nine rice grain appearance and milling quality traits using a diverse panel of 258 accessions selected from 3K Rice Genome Project and evaluated in two environments Sanya and Shenzhen. Genome-wide association analyses using 22,488 high quality SNPs identified 72 QTL affecting the nine traits. Combined gene-based association and haplotype analyses plus functional annotation allowed us to shortlist 19 candidate genes for seven important QTL regions affecting the grain quality traits, including two cloned genes (GS3andTUD), two fine mapped QTL (qGRL7.1andqPGWC7) and three newly identified QTL (qGL3.4, qGW1.1, andqGW10.2). The most likely candidate gene(s) for each important QTL were also discussed. This research demonstrated the superior power to shortlist candidate genes affecting complex phenotypes by the strategy of combined GWAS, gene-based association and haplotype analyses. The identified candidate genes provided valuable sources for future functional characterization and genetic improvement of rice appearance and milling quality.
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Pang
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Chunchao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences Shenzhen, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Chen
authors.affiliation: Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences Shenzhen, China.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Congcong
authors.initials: C
authors.lastname: Shen
authors.affiliation: International Rice Research Institute Metro Manila, Philippines.
authors.forename: Jauhar
authors.initials: J
authors.lastname: Ali
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China; Agricultural Genomics Institute, Chinese Academy of Agricultural SciencesShenzhen, China; Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural SciencesShenzhen, China.
authors.forename: Jianlong
authors.initials: J
authors.lastname: Xu
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China; Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural SciencesShenzhen, China.
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
keywords: GWAS; chalkiness; gene-based association analysis; grain shape; milling; rice