Genome-wide Association Analysis and Screening of Candidate Genes for Grain Length in Oryza sativa subsp.japonica Germplasm Resources
In order to explore the candidate genes related to rice grain length,139 core germplasm resources of Northwest early Oryza sativa subsp.japonica were used as materials,combined with 255 501 high-quality SNPs obtained by resequencing,and genome-wide association analysis of rice grain length was conducted using FarmCPU model.Significant SNPs extending 50 kb upstream and downstream were used as candidate intervals,and then functional annotation and haplotype analysis were performed for genes with differences in CDS region within the candidate intervals.The results showed that the coefficient of variation of 139 rice germplasm length was 9.18％,and the distribution was approximately normal.Under the condition of threshold-log10(p)≥6.41,seven significant and representative SNPs were detected on chromosomes 3,5,7 and 10,respectively,in the FarmCPU model.Two rice grain length candidate genes were screened within the candidate interval.LOC_Os05g10420 and LOC_Os05g10560 both encoded and expressed proteins.LOC_Os05g10420 was divided into two haplotypes by typing,and the grain length of varieties containing Hap1 was signifi-cantly lower than that of varieties containing Hap2.LOCOs05g10560 was divided into three haplo-types,and the length of the germplasm containing Hap1 was significantly lower than that containing Hap2 and Hap3.
Oryza sativa subsp.japonica germplasmgrain lengthgenome-wide association analysis
万方数据
维普
