Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance
Abstract Background Groundnut is mainly grown in the semi-arid tropic (SAT) regions worldwide, where abiotic stress like drought is persistent. However, a major research gap exists regarding exploring the genetic and genomic underpinnings of tolerance to drought. In this study, a multi-parent advanc...
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2024-11-01
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| Online Access: | https://doi.org/10.1186/s12870-024-05749-3 |
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| author | Vinay Sharma Supriya S. Mahadevaiah Putta Latha S. Anjan Gowda Surendra S. Manohar Kanchan Jadhav Prasad Bajaj Pushpesh Joshi T. Anitha Mangesh P. Jadhav Shailendra Sharma Pasupuleti Janila Ramesh S. Bhat Rajeev K. Varshney Manish K. Pandey |
| author_facet | Vinay Sharma Supriya S. Mahadevaiah Putta Latha S. Anjan Gowda Surendra S. Manohar Kanchan Jadhav Prasad Bajaj Pushpesh Joshi T. Anitha Mangesh P. Jadhav Shailendra Sharma Pasupuleti Janila Ramesh S. Bhat Rajeev K. Varshney Manish K. Pandey |
| author_sort | Vinay Sharma |
| collection | DOAJ |
| description | Abstract Background Groundnut is mainly grown in the semi-arid tropic (SAT) regions worldwide, where abiotic stress like drought is persistent. However, a major research gap exists regarding exploring the genetic and genomic underpinnings of tolerance to drought. In this study, a multi-parent advanced generation inter-cross (MAGIC) population was developed and evaluated for five seasons at two locations for three consecutive years (2018–19, 2019–20 and 2020–21) under drought stress and normal environments. Results Phenotyping data of drought tolerance related traits, combined with the high-quality 10,556 polymorphic SNPs, were used to perform multi-locus model genome-wide association study (GWAS) analysis. We identified 37 significant marker-trait associations (MTAs) (Bonferroni-corrected) accounting, 0.91- 9.82% of the phenotypic variance. Intriguingly, 26 significant MTAs overlap on four chromosomes (Ah03, Ah07, Ah10 and Ah18) (harboring 70% of MTAs), indicating genomic hotspot regions governing drought tolerance traits. Furthermore, important candidate genes associated with leaf senescence (NAC transcription factor), flowering (B3 domain-containing transcription factor, Ulp1 protease family, and Ankyrin repeat-containing protein), involved in chlorophyll biosynthesis (FAR1 DNA-binding domain protein), stomatal regulation (Rop guanine nucleotide exchange factor; Galacturonosyltransferases), and associated with yield traits (Fasciclin-like arabinogalactan protein 11 and Fasciclin-like arabinogalactan protein 21) were found in the vicinity of significant MTAs genomic regions. Conclusion The findings of our investigation have the potential to provide a basis for significant MTAs validation, gene discovery and development of functional markers, which could be employed in genomics-assisted breeding to develop climate-resilient groundnut varieties. |
| format | Article |
| id | doaj-art-6803cfbc4fc74e4ab3eb58e5a88995a1 |
| institution | DOAJ |
| issn | 1471-2229 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-6803cfbc4fc74e4ab3eb58e5a88995a12025-08-20T02:49:56ZengBMCBMC Plant Biology1471-22292024-11-0124112110.1186/s12870-024-05749-3Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought toleranceVinay Sharma0Supriya S. Mahadevaiah1Putta Latha2S. Anjan Gowda3Surendra S. Manohar4Kanchan Jadhav5Prasad Bajaj6Pushpesh Joshi7T. Anitha8Mangesh P. Jadhav9Shailendra Sharma10Pasupuleti Janila11Ramesh S. Bhat12Rajeev K. Varshney13Manish K. Pandey14Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Department of Biotechnology, University of Agricultural SciencesRegional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU)Department of Biotechnology, University of Agricultural SciencesCenter of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Department of Biotechnology, University of Agricultural SciencesCenter of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU)Department of Biotechnology, University of Agricultural SciencesDepartment of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU) Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Department of Biotechnology, University of Agricultural SciencesCentre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Murdoch UniversityCenter of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Abstract Background Groundnut is mainly grown in the semi-arid tropic (SAT) regions worldwide, where abiotic stress like drought is persistent. However, a major research gap exists regarding exploring the genetic and genomic underpinnings of tolerance to drought. In this study, a multi-parent advanced generation inter-cross (MAGIC) population was developed and evaluated for five seasons at two locations for three consecutive years (2018–19, 2019–20 and 2020–21) under drought stress and normal environments. Results Phenotyping data of drought tolerance related traits, combined with the high-quality 10,556 polymorphic SNPs, were used to perform multi-locus model genome-wide association study (GWAS) analysis. We identified 37 significant marker-trait associations (MTAs) (Bonferroni-corrected) accounting, 0.91- 9.82% of the phenotypic variance. Intriguingly, 26 significant MTAs overlap on four chromosomes (Ah03, Ah07, Ah10 and Ah18) (harboring 70% of MTAs), indicating genomic hotspot regions governing drought tolerance traits. Furthermore, important candidate genes associated with leaf senescence (NAC transcription factor), flowering (B3 domain-containing transcription factor, Ulp1 protease family, and Ankyrin repeat-containing protein), involved in chlorophyll biosynthesis (FAR1 DNA-binding domain protein), stomatal regulation (Rop guanine nucleotide exchange factor; Galacturonosyltransferases), and associated with yield traits (Fasciclin-like arabinogalactan protein 11 and Fasciclin-like arabinogalactan protein 21) were found in the vicinity of significant MTAs genomic regions. Conclusion The findings of our investigation have the potential to provide a basis for significant MTAs validation, gene discovery and development of functional markers, which could be employed in genomics-assisted breeding to develop climate-resilient groundnut varieties.https://doi.org/10.1186/s12870-024-05749-3Climate resilientDroughtGroundnutGeneMarkerMAGIC population |
| spellingShingle | Vinay Sharma Supriya S. Mahadevaiah Putta Latha S. Anjan Gowda Surendra S. Manohar Kanchan Jadhav Prasad Bajaj Pushpesh Joshi T. Anitha Mangesh P. Jadhav Shailendra Sharma Pasupuleti Janila Ramesh S. Bhat Rajeev K. Varshney Manish K. Pandey Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance BMC Plant Biology Climate resilient Drought Groundnut Gene Marker MAGIC population |
| title | Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance |
| title_full | Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance |
| title_fullStr | Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance |
| title_full_unstemmed | Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance |
| title_short | Dissecting genomic regions and underlying candidate genes in groundnut MAGIC population for drought tolerance |
| title_sort | dissecting genomic regions and underlying candidate genes in groundnut magic population for drought tolerance |
| topic | Climate resilient Drought Groundnut Gene Marker MAGIC population |
| url | https://doi.org/10.1186/s12870-024-05749-3 |
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