Bomireddy, D and Sharma, V and Gangurde, S S and Mohinuddin, D K and Kumar, Rakesh and Senthil, R and Singh, K and Reddisekhar, M and Bera, S K and Pandey, M K (2024) Multi-locus genome wide association study uncovers genetics of fresh seed dormancy in groundnut. BMC Plant Biology (TSI), 24. pp. 1-14. ISSN 1471-2229
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Abstract
Pre-harvest sprouting (PHS) in groundnut leads to substantial yield losses and reduced seed quality, resulting in reduced market value of groundnuts. Breeding cultivars with 14–21 days of fresh seed dormancy (FSD) holds promise for precisely mitigating the yield and quality deterioration. In view of this, six multi-locus genome-wide association study (ML-GWAS) models alongside a single-locus GWAS (SL-GWAS) model were employed on a groundnut mini-core collection using multi season phenotyping and 58 K “Axiom_Arachis” array genotyping data. A total of 9 significant SNP-trait associations (STAs) for FSD were detected on A01, A04, A08, A09, B02, B04, B05, B07 and B09 chromosomes using six ML-GWAS models. Additionally, the SL-GWAS model identified 38 STAs across 14 chromosomes of groundnut. A single STA on chromosome B02 (qFSD-B02-1) was consistently identified in both ML-GWAS and SL-GWAS models. Furthermore, candidate gene mining identified nine high confidence genes viz., Cytochrome P450 705 A, Dormancy/auxin associated family protein, WRKY family transcription factor, Protein kinase superfamily protein, serine/threonine protein phosphatase, myb transcription factor, transcriptional regulator STERILE APETALA-like, ethylene-responsive transcription factor 7-like and F-box protein interaction domain protein as prime regulators involved in Abscisic acid/Gibberellic acid signaling pathways regulating dormancy/germination. In addition, three of the allele-specific markers developed from the identified STAs were validated across a diverse panel. These markers hold potential for increasing dormancy in groundnut through marker-assisted selection (MAS). Thus, this research offers insights into genetic and molecular mechanisms underlying groundnut seed dormancy in addition to providing markers and donors for breeding future varieties with 2–3 weeks of FSD.
| Item Type: | Article |
|---|---|
| Divisions: | Center of Excellence in Genomics and Systems Biology Genebank Global Research Program - Accelerated Crop Improvement |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Seed dormancy, Seed in-situ germination, Association mapping, Candidate genes, Molecular mechanism, Diagnostic markers |
| Subjects: | Others > Molecular Biology Mandate crops > Groundnut Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 28 Jul 2025 03:43 |
| Last Modified: | 28 Jul 2025 03:43 |
| URI: | http://oar.icrisat.org/id/eprint/13241 |
| Official URL: | https://link.springer.com/article/10.1186/s12870-0... |
| Projects: | ICAR-ICRISAT Collaborative Project, Indo-UK (Newton-Bhabha) Project, Tropical Legumes III |
| Funders: | Indian Council of Agricultural Research, Government of India - Department of Biotechnology, Bill & Melinda Gates Foundation |
| Acknowledgement: | The authors are thankful to ICRISAT Gene-Bank for providing seed material. DB acknowledges Acharya N.G. Ranga Agricultural University for collaborating with ICRISAT and opportunity given as a PhD student to pursue this investigation at ICRISAT. VS acknowledges the Council of Scientific and Industrial Research (CSIR), Govt. of India for the award of SRF-Direct fellowship (File No: 09/0800(18433)/2024-EMR-I) for PhD. |
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