Abstract

Background and Objective: Grain chalkiness is an important indicator of rice appearance quality. It is a multi-gene complex trait and understanding its genetic bases in medium rice provides the basis for improving grain quality. This study was conducted to identify new SNPs and genes controlling chalkiness in medium-grain rice. 

Materials and Methods: In this study, a rice diversity panel of 114 genotypes was applied to evaluate the percentage of chalkiness (PC) and identify its genetic characteristics. Genome-Wide Association Study (GWAS) and other bioinformatic tools (IRRI SNP-Seek, RiceFREND and ePlant databases) were utilized to identify significant SNPs and candidate genes related to the trait of grain chalkiness. 

Results: A total of 17 SNPs were identified on ten chromosomes and these SNPs explained 0.94-60.38% of the variations in the chalkiness among medium-grain rice varieties. Of these, three of them were updated in the IRRI SNP-seek database. Two predicted genes, LOC_Os02g12580 on chromosome 2 and LOC_Os11g07840 on chromosome 11, were associated with chalkiness in medium-grain rice varieties. Conclusion: The candidate genes play crucial roles during starch synthesis in the endosperm and are important in developing rice varieties of high-grain quality.