Preliminary Genome-wide Association Mpping Of Some Agronomic And Ouslity Traits In Rice(Oryza Sativa L.)

Agronomic and quality traits such as grain shape,1000grain weight, and physicochemical properties are quantitative traits that are controlled by mutli-genes and affected by genotype by environment interaction. Dissection of the genetic basis of these complex traits is difficult. Deep dissection and utilization of the important genetic variations is very important for rice breeding. With the technical development of mining the single nucleotide polymorphisms (SNP) in target genome, genome-wide association studies (GWAS) based on linkage disequilibrium (LD) offers a new method to analyze the genetic basis of the complex traits. In the present study, preliminary GWAS was used to study the genetic basis of14agronomic traits, five nutritional traits and eight starch quality traits with the genome-wide1288SNPs. The main results are summarized as follows:1. The population structure analysis showed that20rice varieties could be divided into indica and japonica subgroups. The obvious clusters could also be revealed by the principal component analysis with54.1%of the genetic variation explained by the top four principal components. The optimum model was chosen among the six models, i.e. Anova, K, P, P+K, Q, Q+K for GWAS.2. Ten SNP were identified by GWAS of14agronomic traits in two years, which were distributed in all the chromosomes expect the chromosome6and8. The loci detected for rice grain length and brown rice grain length is near the gene GS3in two years.3. GWAS for the phenol content, flavonoid content, proanthocyanidin content and antioxidant capacity showed that the identified SNPs were located in the chromosome1,4and8. The locus in the chromosome4might be Ra gene.4. GWAS for the starch RVA pasting viscosities and apparent amylose content (AAC) showed that a total13SNPs were associated with the starch quality traits. Four SNPs were detected for AAC in both years. An SNP for AAC, breakdown viscosity, cool paste viscosity and pasting temperature was located around the region of Wx gene in the chromosome6.