Genome-wide Association Analysis Of Rice Grain Thickness Main Potent QTL

Rice grain type is an important yield trait and quality trait,and the evaluation indicators mainly include grain length,grain width and grain thickness.The use of genome-wide association study(GWAS)can quickly mine the genes that control rice grain type genes,which is of great significance for cultivating high-yield and high-quality rice.In this study,a natural population of 162 strains was constructed using the main varieties in production to genetically map QTLs that control the thick traits of rice grains based on the genotype data obtained from high-density SNP chips.1.A 5K chip was used to scan the whole genome of 162 materials,and a total of 911 highquality SNP sites were screened,distributed in 12 chromosomes of rice.For the analysis of population structure and genetic distance,162 materials can be divided into two categories according to genetic distance;The population differentiation used in this study is not obvious,and the background is relatively close.False positives are low,and population structure has little effect on positive sites.Suitable for GWAS analysis.2.The data after quality control were analyzed in association with the grain type traits(including grain length,grain width and grain thickness),and the P value was greater than4.27 as the threshold.Two thick QTLs: q GT5.1 and q GT5.2 were colocated,both located on chromosome 5,and the contribution rates were 9.86% and 9.66%,respectively.A total of 57 genes were detected in these two QTL intervals.The q GT5.2 interval contained rice grain width regulatory genes GW5 and Der1,and five rice grain thickness candidate genes LOC＿Os05g01610,LOC＿Os05g01675,LOC＿Os05g01970,LOC＿Os05g01820 and LOC＿Os05g01810 were screened in the q GT5.1 interval,and four rice grain thickness candidate genes LOC＿Os05g09600 and LOC＿OS05G01960,LOC＿Os05g01230,and LOC＿Os05g09480 were screened in the q GT5.2 interval.3.For 11 candidate genes,the grain type-related genes GW5 and Der1 in the extreme population were verified,indicating that the Der1 gene is the most likely gene that controls the grain thickness trait.Rice XPro whole growth stage expression profile and mature embryo and endosperm gene expression profile analysis were used to predict that LOC＿Os05g01230and LOC＿Os05g01960 of uncloned genes were the genes most likely to control grain thickness traits.