Genome-wide association study for yield-related traits in a diverse panel of indica rice

Abstract:

An observation that keeps recurring in rice breeding programmes is that yield gains from conventional selection have slowed to less than 1% per year in many indica gene pools ^[1]. Genome-wide association studies (GWAS) offer a way to identify the loci underlying this plateau and guide marker-assisted improvement. This research genotyped 287 diverse indica accessions with a 50K SNP array and phenotyped them for grain yield, panicle length, grains per panicle, 1000-grain weight, and days to heading across three seasons (2020–2022) at Hermosillo, Sonora, Mexico. A mixed linear model (MLM) with kinship and population structure correction detected 14 significant marker-trait associations (MTAs) at −log₁₀P ≥ 5.0. Four MTAs on chromosomes 3, 5, 8, and 11 collectively explained 23.7% of phenotypic variance for grain yield. The chromosome 3 locus co-localised with the known yield gene GW3.1. Three novel loci on chromosomes 5 and 11 represent candidates for fine-mapping and marker-assisted selection in tropical indica breeding.