Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.)
Abstract Finger millet (Eleusine coracana (L.) Gaertn.) is a calcium-rich, nutritious and resilient crop that thrives even in harsh environmental conditions. In such ecologies, seed longevity and seedling vigor are crucial for sustainable crop production amid climate change. The current study explor...
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Nature Portfolio
2025-02-01
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| Online Access: | https://doi.org/10.1038/s41598-025-89315-3 |
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| author | Netyam Kannababu Sandeep Nanjundappa Neha Narayanan Mani Vetriventhan Ronda Venkateswarlu Indra Kanta Das Arutla Srikanth Aswini Viswanath Swati Singh Renuka Malipatil Tara C Satyavathi Nepolean Thirunavukkarasu |
| author_facet | Netyam Kannababu Sandeep Nanjundappa Neha Narayanan Mani Vetriventhan Ronda Venkateswarlu Indra Kanta Das Arutla Srikanth Aswini Viswanath Swati Singh Renuka Malipatil Tara C Satyavathi Nepolean Thirunavukkarasu |
| author_sort | Netyam Kannababu |
| collection | DOAJ |
| description | Abstract Finger millet (Eleusine coracana (L.) Gaertn.) is a calcium-rich, nutritious and resilient crop that thrives even in harsh environmental conditions. In such ecologies, seed longevity and seedling vigor are crucial for sustainable crop production amid climate change. The current study explores the genetics of accelerated aging on seed longevity traits across 221 diverse accessions of finger millet through genome-wide association approach (GWAS). A significant variation was identified in germination percentage, germination rate indices, mean germination time, seedling vigor indices and dry weight upon aging treatment. GWAS model from 11,832 high-quality SNPs identified through Genotyping-by-Sequencing (GBS) approach produced 491 marker-trait associations (MTAs) for 27 traits, of which 54 were FDR-corrected. A pleiotropic SNP, FM_SNP_9478 identified on chromosome 7B was associated with the traits viz., germination after aging, germination index after aging and their relative measures. Functional annotation revealed DET1 and expansin-A2 influenced seed coat integrity, critical for germination and aging resilience. Probable protein phosphatase 2C3 and piezo-type ion channels contributed to mechanical sensing and stress adaptation in seeds. Beta-amylase and acetyl-CoA carboxylase 2 were identified for seed metabolism and stress response. These insights lay the framework for targeted breeding efforts to improve seed quality and resilience under diverse production conditions. |
| format | Article |
| id | doaj-art-5c0f2e2a68da4cbf93382c0c8846928d |
| institution | OA Journals |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-5c0f2e2a68da4cbf93382c0c8846928d2025-08-20T02:29:45ZengNature PortfolioScientific Reports2045-23222025-02-0115111910.1038/s41598-025-89315-3Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.)Netyam Kannababu0Sandeep Nanjundappa1Neha Narayanan2Mani Vetriventhan3Ronda Venkateswarlu4Indra Kanta Das5Arutla Srikanth6Aswini Viswanath7Swati Singh8Renuka Malipatil9Tara C Satyavathi10Nepolean Thirunavukkarasu11Seed Science and Technology Lab, ICAR-Indian Institute of Millets ResearchGenomics and Molecular Breeding Lab, Global Centre of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets ResearchGenomics and Molecular Breeding Lab, Global Centre of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets ResearchInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Biochemistry Lab, ICAR-Indian Institute of Millets ResearchPlant Pathology Lab, ICAR-Indian Institute of Millets ResearchSeed Science and Technology Lab, ICAR-Indian Institute of Millets ResearchGenomics and Molecular Breeding Lab, Global Centre of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets ResearchGenomics and Molecular Breeding Lab, Global Centre of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets ResearchGenomics and Molecular Breeding Lab, Global Centre of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets ResearchGenomics and Molecular Breeding Lab, Global Centre of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets ResearchGenomics and Molecular Breeding Lab, Global Centre of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets ResearchAbstract Finger millet (Eleusine coracana (L.) Gaertn.) is a calcium-rich, nutritious and resilient crop that thrives even in harsh environmental conditions. In such ecologies, seed longevity and seedling vigor are crucial for sustainable crop production amid climate change. The current study explores the genetics of accelerated aging on seed longevity traits across 221 diverse accessions of finger millet through genome-wide association approach (GWAS). A significant variation was identified in germination percentage, germination rate indices, mean germination time, seedling vigor indices and dry weight upon aging treatment. GWAS model from 11,832 high-quality SNPs identified through Genotyping-by-Sequencing (GBS) approach produced 491 marker-trait associations (MTAs) for 27 traits, of which 54 were FDR-corrected. A pleiotropic SNP, FM_SNP_9478 identified on chromosome 7B was associated with the traits viz., germination after aging, germination index after aging and their relative measures. Functional annotation revealed DET1 and expansin-A2 influenced seed coat integrity, critical for germination and aging resilience. Probable protein phosphatase 2C3 and piezo-type ion channels contributed to mechanical sensing and stress adaptation in seeds. Beta-amylase and acetyl-CoA carboxylase 2 were identified for seed metabolism and stress response. These insights lay the framework for targeted breeding efforts to improve seed quality and resilience under diverse production conditions.https://doi.org/10.1038/s41598-025-89315-3Accelerated agingAssociation mappingFinger milletFunctional genesSeed longevitySeedling vigor |
| spellingShingle | Netyam Kannababu Sandeep Nanjundappa Neha Narayanan Mani Vetriventhan Ronda Venkateswarlu Indra Kanta Das Arutla Srikanth Aswini Viswanath Swati Singh Renuka Malipatil Tara C Satyavathi Nepolean Thirunavukkarasu Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.) Scientific Reports Accelerated aging Association mapping Finger millet Functional genes Seed longevity Seedling vigor |
| title | Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.) |
| title_full | Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.) |
| title_fullStr | Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.) |
| title_full_unstemmed | Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.) |
| title_short | Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.) |
| title_sort | role of functional genes for seed vigor related traits through genome wide association mapping in finger millet eleusine coracana l gaertn |
| topic | Accelerated aging Association mapping Finger millet Functional genes Seed longevity Seedling vigor |
| url | https://doi.org/10.1038/s41598-025-89315-3 |
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