Association analysis of rice grain traits with single nucleotide polymorphisms in a Brassinosteroid-insensitive 1 (BRI1)-associated receptor kinase 1-like gene

Abstract

The Brassinosteroid insensitive 1-associated kinase 1-like gene (LOC_Os03g32580) was previously found to be highly expressed after heading in rice panicles, suggesting its involvement in grain development. In this study, single nucleotide polymorphisms (SNPs) in this structural gene and its promoter from Nipponbare were analysed, and compared with those in the homologous regions from 3024 rice varieties available in the Rice SNP-Seek Database (http://www.snp-seek.irri.org/) and nine Malaysian rice varieties. A total of 12 SNPs were detected in LOC_Os03g32580, with two of them located at the exons whereby SNP-G5 causes a non-synonymous mutation at exon 4 while SNP-G1 causes a synonymous mutation at exon 1. Of the 40 SNPs identified in the promoter sequence of LOC_Os03g32580, ten SNPs were found to be significantly associated with 100-grain weight while nine SNPs were significantly associated with grain width. The changes of G to A at SNP-8, 17 and 31 in the promoter sequence have resulted in three additional cis-acting regulating elements (CAREs) i.e. Skn-1 (SNP-8), MBSI (SNP-17) and CAAT-box (SNP-31). The frequency of allele A at these SNP positions was higher (71–73%) among the indica subpopulation in the Rice SNP-Seek Database (http://www.snp-seek.irri.org/) and Malaysian rice varieties that have a low grain weight compared with the rice varieties with a higher grain weight (48 to 50%). Although different allele frequencies were observed at six SNPs in japonica rice varieties with high and low grain width, nucleotide variation was not observed among the indica subpopulation and Malaysian rice varieties at respective positions suggesting that these SNPs could be subpopulation-dependent.