Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties
Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (la...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/163853 |
| _version_ | 1855524947231768576 |
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| author | Singh, Preeti Sundaram, Krishna T. Vinukonda, Vishnu Prasanth Venkateshwarlu, Challa Paul, Pronob J. Pahi, Bandana Gurjar, Anoop Singh, Uma Maheshwar Kalia, Sanjay Kumar, Arvind Singh, Vikas K. Sinha, Pallavi |
| author_browse | Gurjar, Anoop Kalia, Sanjay Kumar, Arvind Pahi, Bandana Paul, Pronob J. Singh, Preeti Singh, Uma Maheshwar Singh, Vikas K. Sinha, Pallavi Sundaram, Krishna T. Venkateshwarlu, Challa Vinukonda, Vishnu Prasanth |
| author_facet | Singh, Preeti Sundaram, Krishna T. Vinukonda, Vishnu Prasanth Venkateshwarlu, Challa Paul, Pronob J. Pahi, Bandana Gurjar, Anoop Singh, Uma Maheshwar Kalia, Sanjay Kumar, Arvind Singh, Vikas K. Sinha, Pallavi |
| author_sort | Singh, Preeti |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties. |
| format | Journal Article |
| id | CGSpace163853 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1638532025-02-18T10:03:23Z Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties Singh, Preeti Sundaram, Krishna T. Vinukonda, Vishnu Prasanth Venkateshwarlu, Challa Paul, Pronob J. Pahi, Bandana Gurjar, Anoop Singh, Uma Maheshwar Kalia, Sanjay Kumar, Arvind Singh, Vikas K. Sinha, Pallavi climate resilience haplotypes high-yielding varieties genetic improvement drought tolerance genetic markers Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties. 2024-01-12 2024-12-19T12:53:05Z 2024-12-19T12:53:05Z Journal Article https://hdl.handle.net/10568/163853 en Open Access Springer Singh, Preeti; Sundaram, Krishna T.; Vinukonda, Vishnu Prasanth; Venkateshwarlu, Challa; Paul, Pronob J.; Pahi, Bandana; Gurjar, Anoop; Singh, Uma Maheshwar; Kalia, Sanjay; Kumar, Arvind; Singh, Vikas K. and Sinha, Pallavi. 2024. Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties. Commun Biol, Volume 7, no. 1 |
| spellingShingle | climate resilience haplotypes high-yielding varieties genetic improvement drought tolerance genetic markers Singh, Preeti Sundaram, Krishna T. Vinukonda, Vishnu Prasanth Venkateshwarlu, Challa Paul, Pronob J. Pahi, Bandana Gurjar, Anoop Singh, Uma Maheshwar Kalia, Sanjay Kumar, Arvind Singh, Vikas K. Sinha, Pallavi Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties |
| title | Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties |
| title_full | Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties |
| title_fullStr | Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties |
| title_full_unstemmed | Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties |
| title_short | Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties |
| title_sort | superior haplotypes of key drought responsive genes reveal opportunities for the development of climate resilient rice varieties |
| topic | climate resilience haplotypes high-yielding varieties genetic improvement drought tolerance genetic markers |
| url | https://hdl.handle.net/10568/163853 |
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