Sachdeva, S and Singh, R K and Singh, H and Bhardwaj, R and Jain, A and Singh, V K and Singh, U M and Kumar, A and Singh, G P (2025) Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.). Food Chemistry: Molecular Sciences, 11. pp. 1-13. ISSN 2666-5662
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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 (LOC_Os11g303700 and LOC_Os11g30500) associated with rice quality, and they may affect the grain quality by regulating the textural properties, appearance and eating quality. The findings of our study highlighted the role of molecular machinery in future rice breeding.
| Item Type: | Article |
|---|---|
| Divisions: | Others |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Rice, GWAS, Grain quality, QTN, GO enrichment, Candidate gene |
| Subjects: | Others > Rice Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 04 Mar 2026 05:33 |
| Last Modified: | 04 Mar 2026 05:33 |
| URI: | http://oar.icrisat.org/id/eprint/13516 |
| Official URL: | https://www.sciencedirect.com/science/article/pii/... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | We would like to thank the International Rice Research Institute South Asia Regional Centre (IRRI-SARC), Varanasi, India, for providing the rice accessions for the GWAS study. The facility provided by the Director, ICAR-NBPGR, is also duly acknowledged. |
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