Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.)
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...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier Ltd.
2025
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| Acceso en línea: | https://hdl.handle.net/10568/179455 |
| _version_ | 1855536639453954048 |
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| author | Sachdeva, Supriya Singh, Rakesh Bharadwaj, Rakesh Jain, Antil Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap |
| author_browse | Bharadwaj, Rakesh Jain, Antil Kumar, Arvind Sachdeva, Supriya Singh, Gyanendra Pratap Singh, Rakesh Singh, Uma Maheshwar Singh, Vikas K. |
| author_facet | Sachdeva, Supriya Singh, Rakesh Bharadwaj, Rakesh Jain, Antil Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap |
| author_sort | Sachdeva, Supriya |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace179455 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Elsevier Ltd. |
| publisherStr | Elsevier Ltd. |
| record_format | dspace |
| spelling | CGSpace1794552026-01-08T02:15:07Z Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) Sachdeva, Supriya Singh, Rakesh Bharadwaj, Rakesh Jain, Antil Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap rice genome-wide association studies grain quality candidate genes molecular genetics 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. 2025-10-08 2026-01-07T08:39:03Z 2026-01-07T08:39:03Z Journal Article https://hdl.handle.net/10568/179455 en Open Access application/pdf Elsevier Ltd. Sachdeva, Supriya, Rakesh Singh, Harshita Singh, Rakesh Bharadwaj, Antil Jain, Vikas K. Singh, Uma Maheshwar Singh, Arvind Kumar, and Gyanendra Pratap Singh. "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 (2025): 100313. |
| spellingShingle | rice genome-wide association studies grain quality candidate genes molecular genetics Sachdeva, Supriya Singh, Rakesh Bharadwaj, Rakesh Jain, Antil Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) |
| title | Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) |
| title_full | Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) |
| title_fullStr | Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) |
| title_full_unstemmed | Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) |
| title_short | Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) |
| title_sort | genome wide association studies for identification of qtls and key candidate genes to improve grain quality in rice oryza sativa l |
| topic | rice genome-wide association studies grain quality candidate genes molecular genetics |
| url | https://hdl.handle.net/10568/179455 |
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