Genome-Wide Association Analysis And Gene Mining Of Grain Shape Related Traits In Rice

Grain shape is an important yield and quality character of rice.Its evaluation indicators mainly include grain length,grain width,grain weight,and aspect ratio.Using the Genome-wide Association Study（GWAS）method to discover genes related to rice grain shape traits and perform functional research will help to better understand the molecular mechanisms that regulate rice grain shape and further use excellent rice resources.In this study,a natural population of 161 indica rice varieties from 11 provinces in China was used as experimental materials.The phenotypic statistics and correlation analysis of the four grain shape traits such as grain length,grain width,grain weight and aspect ratio show that there are abundant genetic variations in this group.Grain shape traits are typical quantitative traits controlled by multiple genes,and GWAS method can be used to conduct genetic mapping analysis on the natural rice population.A total of 16,352 high-quality SNP sites were screened in the whole genome in combination with the sequencing results.The distribution numbers of all SNP sites on the 12 chromosomes of rice were different.Polymorphic information content（PIC）values indicate that the selected SNP markers are relatively polymorphic and can be used for GWAS analysis covering the entire genome of rice.Utilize software to calculate the genetic distance from the SNP data of 161 materials and analyze the population structure and genetic relationship.According to the genetic distance,161 materials can be divided into two categories,A and B,and B materials can be divided into I and II sub-categories;the results of kinship value and frequency of kinship show that the material kinship between groups is far,suitable for performing GWAS analysis.The TASSEL software was used to analyze the correlation of the four grain traits,and-log10（p）> 4 was used as the screening threshold to determine 38 significant correlation sites.Using the 100 kb ranges upstream and downstream of these significant sites as candidate intervals,a number of candidate genes/QTLs related to particle shape were found.Some marker show different correlations to different grain traits,which may be caused by the tight linkage of genes or a pleiotropic effect.There are 92 known genes / QTLs related to the candidate interval of the significant site,of which 6 are related to the regulation of granular shape: including qKw5,qGL9,GS3,GL3.1,TGW6 and GW6 a.LOC_Os01g22920 was identified in the candidate region of chromosome 1 at the position of chr01₁2869918,which is considered to be related to the regulation of gibberellin.At the same time,genome-wide nucleotide diversity analysis was performed on SNP loci of 161 indica rice varieties.LOC_Os03g30420 in chromosome 3 window was domesticated.This gene is involved in the synthesis of cytochrome P450,which may be related to the regulation of rice grain length.Subsequent experiments can focus on the two genes and carry out further functional mining.According to the results of association analysis and previous research reports,combined with the 3K resource library and Halpoview software to perform haplotype analysis on the highly correlated GS3 and TGW6 among the candidate genes,and screen the dominant haplotype GH4 and TH1.The above results conclude that the rice natural population material in this experiment is suitable for GWAS analysis.The GWAS method can quickly mine candidate genes related to grain shape traits.The results of association analysis are conducive to further mining and identification of excellent rice grain shape resources.