ArticleFood chemistry. Molecular sciences2025
Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (
Article in Food chemistry. Molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Grain quality is the key concern for rice breeders and is paramount to consumer acceptability. We characterized a diverse subset of 198 rice accessions of 3 K Rice Genome Project (RGP) for grain quality attributes, specifically glycemic index %, total dietary fibre, oil %, protein, amylose, moisture %, phytate, phenol, and starch content. A set of 5,53,229 single nucleotide polymorphism (SNP) markers obtained from the 3 K RG 1 M filtered SNP dataset used for genome wide association studies (GWAS). Consequently, we discovered 200 Quantitative trait nucleotides (QTNs) associated with the traits mentioned above distributed across the genome. These QTNs were grouped into 26 Quantitative Trait Loci (QTL) clusters, of which 20 clusters validated with at least three GWAS methods were considered reliable. Furthermore, 869 putative candidate genes were identified, many of which overlapped between quality traits. Integrating the GWAS, RNA-seq and qRT-PCR results, we finally identified two important genes (
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