Genome-wide association studies for identifying SNPs and candidate genes associated with grain quality traits in rice (Oryza sativa L.).

Abstract

Ensuring superior quality is of paramount objective in modern rice (Oryza sativa L.) breeding program and investigating quality traits is crucial for developing superior rice varieties. The current study aimed for identifying single nucleotide polymorphisms (SNPs) and potential candidate genes for eleven quality traits, namely, hulling %, milling %, kernel length, kernel breadth, kernel length to breadth ratio, grain type, head rice recovery, chalkiness, amylose content, alkali spreading value, and gel consistency, using genome-wide association studies (GWASs) on diverse germplasm sourced from various rice-growing regions around the world. Phenotypic evaluation revealed significant genetic diversity among germplasm, with substantial natural variation observed across 10 quality-related traits. GWAS using 7K SNP chip identified 31 SNPs significantly linked to grain quality traits, of which 20 were novel and 11 had been previously reported, including two co-localized SNPs (GS3 and SNP-6.6652023) associated with multiple traits. In addition, 121 candidate genes related with these traits were identified and categorized into seven molecular functions, four cellular components, and nine biological processes. Notably, 17 putative grain quality-related genes were identified, viz., GS3 (Grain size regulator), Wx (granule-bound starch synthase), OsZIP7 (ZIP family protein), OsRING4 (RING-type E3 ubiquitin ligase), OsMKK3 (Mitogen-activated protein kinase), OsSSIV-2, OsSSIIa/SSII-3 (ALK; soluble starch synthase), and OsbZIP58 (bZIP transcription factor). The identified SNPs and potential candidate genes represent a valuable genomic resource for accelerating rice breeding programs focused on the enhancement of key quality traits.