Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut
Groundnut is an important oilseed crop; however, its productivity and seed quality are frequently reduced due to lack of fresh seed dormancy (FSD). To address this challenge, a mini-core collection of 184 accessions was phenotyped to identify potential donors in each agronomic type. In addition, who...
| Autores principales: | , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2025
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/180347 |
| _version_ | 1855520026837123072 |
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| author | Mohinuddin, Khaja D. Gangurde, Sunil S. Khan, Hasan Bomireddy, Deekshitha Sharma, Vinay Shah, Priya Sagar, Nikhil U. Dube, Namita Senthil, Ramachandran Tembhurne, B.V. Nayak, V. Hanumanth Peerzada, Ovais Hamid Amaregouda, A. Babu, Kisan Singh, Kuldeep Janila, Pasupuleti Guo, Baozhu Liao, Boshou Varshney, Rajeev K. Pandey, Manish K. |
| author_browse | Amaregouda, A. Babu, Kisan Bomireddy, Deekshitha Dube, Namita Gangurde, Sunil S. Guo, Baozhu Janila, Pasupuleti Khan, Hasan Liao, Boshou Mohinuddin, Khaja D. Nayak, V. Hanumanth Pandey, Manish K. Peerzada, Ovais Hamid Sagar, Nikhil U. Senthil, Ramachandran Shah, Priya Sharma, Vinay Singh, Kuldeep Tembhurne, B.V. Varshney, Rajeev K. |
| author_facet | Mohinuddin, Khaja D. Gangurde, Sunil S. Khan, Hasan Bomireddy, Deekshitha Sharma, Vinay Shah, Priya Sagar, Nikhil U. Dube, Namita Senthil, Ramachandran Tembhurne, B.V. Nayak, V. Hanumanth Peerzada, Ovais Hamid Amaregouda, A. Babu, Kisan Singh, Kuldeep Janila, Pasupuleti Guo, Baozhu Liao, Boshou Varshney, Rajeev K. Pandey, Manish K. |
| author_sort | Mohinuddin, Khaja D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Groundnut is an important oilseed crop; however, its productivity and seed quality are frequently reduced due to lack of fresh seed dormancy (FSD). To address this challenge, a mini-core collection of 184 accessions was phenotyped to identify potential donors in each agronomic type. In addition, whole genome re-sequencing and multi-season phenotypic evaluations were analyzed to identify stable marker-trait associations (MTAs) linked to FSD. Phenotypic analysis revealed substantial variability in dormancy durations, with days to 50 % germination (DFG) ranging from 1 to 30 days. Multi-locus genome-wide association study (ML-GWAS) identified 27 MTAs in individual seasons and 12 MTAs in pooled seasons data, respectively. Key candidate genes identified included Cytochrome P450 superfamily proteins, protein kinase superfamily proteins, and MYB transcription factors involved in the Abscisic acid (ABA) pathway, as well as F-box interaction domain proteins, ATP-binding ABC transporters, associated with the Gibberellic acid (GA) pathway. SNP-based KASP (Kompetitive Allele-Specific Polymerase chain reaction) markers were developed for 12 SNPs, of which four markers (snpAH00577, snpAH00580, snpAH00586 and snpAH00588) were found useful for the selection of FSD. The combination of favourable allele from four genes namely Ahfsd1 (Arahy.8B3CAL), Ahfsd2 (Arahy.NRZN5K), Ahfsd3 (Arahy.JJ8FJQ), and Ahfsd4 (Arahy.PI0JM6) provides stable 24–30 days of dormancy. Incorporating favourable dormant alleles into breeding programs could enable the development of high-yielding cultivars with a dormancy period of more than two weeks. |
| format | Journal Article |
| id | CGSpace180347 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1803472026-01-22T02:04:19Z Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut Mohinuddin, Khaja D. Gangurde, Sunil S. Khan, Hasan Bomireddy, Deekshitha Sharma, Vinay Shah, Priya Sagar, Nikhil U. Dube, Namita Senthil, Ramachandran Tembhurne, B.V. Nayak, V. Hanumanth Peerzada, Ovais Hamid Amaregouda, A. Babu, Kisan Singh, Kuldeep Janila, Pasupuleti Guo, Baozhu Liao, Boshou Varshney, Rajeev K. Pandey, Manish K. candidate genes genome-wide association studies genetic markers breeding methods groundnuts Groundnut is an important oilseed crop; however, its productivity and seed quality are frequently reduced due to lack of fresh seed dormancy (FSD). To address this challenge, a mini-core collection of 184 accessions was phenotyped to identify potential donors in each agronomic type. In addition, whole genome re-sequencing and multi-season phenotypic evaluations were analyzed to identify stable marker-trait associations (MTAs) linked to FSD. Phenotypic analysis revealed substantial variability in dormancy durations, with days to 50 % germination (DFG) ranging from 1 to 30 days. Multi-locus genome-wide association study (ML-GWAS) identified 27 MTAs in individual seasons and 12 MTAs in pooled seasons data, respectively. Key candidate genes identified included Cytochrome P450 superfamily proteins, protein kinase superfamily proteins, and MYB transcription factors involved in the Abscisic acid (ABA) pathway, as well as F-box interaction domain proteins, ATP-binding ABC transporters, associated with the Gibberellic acid (GA) pathway. SNP-based KASP (Kompetitive Allele-Specific Polymerase chain reaction) markers were developed for 12 SNPs, of which four markers (snpAH00577, snpAH00580, snpAH00586 and snpAH00588) were found useful for the selection of FSD. The combination of favourable allele from four genes namely Ahfsd1 (Arahy.8B3CAL), Ahfsd2 (Arahy.NRZN5K), Ahfsd3 (Arahy.JJ8FJQ), and Ahfsd4 (Arahy.PI0JM6) provides stable 24–30 days of dormancy. Incorporating favourable dormant alleles into breeding programs could enable the development of high-yielding cultivars with a dormancy period of more than two weeks. 2025-12 2026-01-21T21:55:28Z 2026-01-21T21:55:28Z Journal Article https://hdl.handle.net/10568/180347 en Open Access application/pdf Elsevier Mohinuddin, Khaja D.; Gangurde, Sunil S.; Khan, Hasan; Bomireddy, Deekshitha; Sharma, Vinay; Shah, Priya; Sagar, Nikhil U.; Dube, Namita; Senthil, Ramachandran; Tembhurne, B.V.; Nayak, V. Hanumanth; Peerzada, Ovais Hamid; Amaregouda, A.; Babu, Kisan; Singh, Kuldeep; Janila, Pasupuleti; Guo, Baozhu; Liao, Boshou; Varshney, Rajeev K.; & Pandey, Manish K. 2025. Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut, Plant Physiology and Biochemistry, Volume 229, Part C, https://doi.org/10.1016/j.plaphy.2025.110539. |
| spellingShingle | candidate genes genome-wide association studies genetic markers breeding methods groundnuts Mohinuddin, Khaja D. Gangurde, Sunil S. Khan, Hasan Bomireddy, Deekshitha Sharma, Vinay Shah, Priya Sagar, Nikhil U. Dube, Namita Senthil, Ramachandran Tembhurne, B.V. Nayak, V. Hanumanth Peerzada, Ovais Hamid Amaregouda, A. Babu, Kisan Singh, Kuldeep Janila, Pasupuleti Guo, Baozhu Liao, Boshou Varshney, Rajeev K. Pandey, Manish K. Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut |
| title | Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut |
| title_full | Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut |
| title_fullStr | Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut |
| title_full_unstemmed | Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut |
| title_short | Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut |
| title_sort | genomic analysis reveals the interplay between aba ga in determining fresh seed dormancy in groundnut |
| topic | candidate genes genome-wide association studies genetic markers breeding methods groundnuts |
| url | https://hdl.handle.net/10568/180347 |
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