HAPLOTYPE-BASED IDENTIFICATION OF SUPERIOR OSPYL9 ALLELES ASSOCIATED WITH GRAIN YIELD IN DIVERSE RICE GERMPLASM

Abstract

Rice (Oryza sativa L.) is one of the most important staple crops, and enhancing yield and ensuring its resilience to environmental stresses is vital to ensure food security in the future. Use of favourable natural alleles is a potential tool to improve complex traits like grain yield. The gene OsPYL9 encodes ABA receptor that is associated with drought and grain yield responses in rice. But the role of naturally-occurring OsPYL9 allelic variation in grain yield has not been adequately studied. In this study, 203 rice accessions from the 3K Rice Genome panel were tested for plant yield. Haplotype analysis was performed using single nucleotide polymorphisms (SNPs) in the coding region of OsPYL9 (LOC_Os06g33670) in the Rice SNP-Seek database. Eight SNPs resulted in two major haplotypes, H1 (60.0%) and H2 (37.3%). The allelic combinations were GGGGAATG for H1 and AGGGTATG for H2. Haplo-pheno analysis showed significant difference between the two haplotypes. The mean single plant yield of the accessions carrying H1 allele was about 17.3 g while for H2 it was higher at about 19.5 g. The difference between the two haplotypes was 2.26 g and significant when tested by one-way analysis of variance (P = 0.031) and Hsu's simultaneous multiple-comparison test (adjusted P = 0.015). Thus, H2 was identified as a superior OsPYL9 haplotype associated with higher plant yield in the evaluated germplasm. The identified haplotype H2 could be a potential genetic target for further validation and use in haplotype-assisted rice breeding.