Exploring the genetic basis of pre-harvest sprouting in rice through genome-wide association study-based haplotype analysis

Abstract

Pre-harvest sprouting (PHS) poses a significant global challenge to cereal production, impacting yield and quality. In this study, we employed genome-wide association studies (GWAS) on diverse rice accessions to identify novel PHS-associated haplotypes. Assessment of 127 cultivated accessions for panicle germination (PHS) and detached grain (D14) germination revealed considerable phenotypic variation among rice ecotypes. GWAS analysis identified 91 significant signals, including 15 SNPs for PHS and 76 SNPs for D14, at -log10P>5. Subsequent LD block-based GWAS analysis detected 227 significant SNPs for both traits, consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes. Further haplotype analysis identified 32 haplotypes, with 10 exclusive to cultivated accessions, 19 specific to the wild type, and 3 shared between them. Phenotypic assessment of major haplotypes revealed significant differences between resistant (Hap1 and Hap2) and susceptible haplotypes (Hap5, Hap27, and hap28), distinguished by a G/A SNP within a novel gene, Os04g0545200. The identified haplotypes offer promising prospects for haplotype-based breeding aimed at enhancing PHS resistance in rice.