Genomic selection is an e cient tool for breeding selection, especially for quantitative traits controlled by multiples genes with low heritability. To validate the application of genomic selection in hybrid rice breeding, the yield, grain quality and agronomic traits of 404 hybrid rice breeding lines were investigated, and the same accessions were genotyped by using a 56K SNP chip. There were wide variances among the tested accessions for all the measured traits, and most of the traits were correlated. A total of 67 signi cant loci were identi ed for the yield and agronomic traits, and 123 signi cant loci were identi ed for the grain quality traits by GWAS. Two of these loci associated with increasing grain yield but decreasing grain quality. The GEBVs of all the yield, quality and agronomic traits were calculated by using 15 different prediction algorithms. The plant height, panicle length, thousand grain weight, grain length and width ratio, amylose content and alkali value have higher predictability than other traits. However, the predictability of different GS models is different for different traits. This study provided useful information for genomic selection of speci c trait using proper markers and prediction models.
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