Genome-wide Association Studies Of Tiller Angle And Grain Shape In Rice

Rice tiller angle is an important trait for constructing ideal plant type,and grain type is an important trait affecting yield and rice appearance quality.The excavation and study of genes regulating tiller angle and grain size traits in rice can help breed superior varieties.Using 463 germplasm resources,we used genome-wide association study to explore the genes regulating rice tiller angle and grain shape,which can help improve rice varieties and have important significance for high and stable yield.In this study,463 rice varieties were resequenced and phenotypically characterized for tiller angle and grain shape for two consecutive years(2020 and 2021).Genome-wide association analysis was performed in the population using a linear mixed model,with the following main findings.1.A total of 740,582 high-quality SNPs,were screened through whole-genome resequencing.All SNPs were evenly distributed on 12 rice chromosomes with an average of 2.06SNPs/kb.Using these high-density SNP markers,we were able to effectively associate to functional variants.2.A total of six and four significant loci associated with rice tiller angle in 2020 and2021 were associated by genome-wide association analysis,four of which were detected in both years.A cloned gene TAC1 associated with rice tiller angle was included in the q MTA9 range.Haplotype analysis of the tiller angle gene TAC1 and comparison of the maximum tiller angle between haplotypes revealed that the maximum tiller angle in rice was significantly different between Hap1,Hap2 and Hap3,and there was no significant difference between Hap4 and Hap2,Hap3 and Hap1,and Hap4.Meanwhile,two possible functional SNPs of the TAC1 gene were used to develop KASP markers suitable for molecular marker-assisted breeding.3.A total of nine and two loci associated with rice grain length were identified by genome-wide association studies in 2020 and 2021,of which two loci were detected in both years.There cloned genes GS3 and GL7 controlling rice grain length,were located in q GL3 and q GL7;a total of twenty and three loci associated with rice grain width were identified,of which 3 loci were detected in both years.The cloned genes GL7 and GW5 controlling rice grain width were present within q GW5.2(q GW5)and q GW7.3(q GW7);a total of eleven and eleven loci were associated with the rice aspect ratio trait,of which nine loci were detected in both years.The cloned genes GS3 and GL7,controlling rice grain width,were present within q GWL3 and q GWL7.Haplotype analysis was performed on the GL7 gene in 463 rice resources,and 182 rice resources could be classified into six haplotypes after filtering the low-frequency haplotypes.