Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties

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dc.creatorSingh, Preeti
dc.creatorSundaram, Krishna T.
dc.creatorVinukonda, Vishnu Prasanth
dc.creatorVenkateshwarlu, Challa
dc.creatorPaul, Pronob J.
dc.creatorPahi, Bandana
dc.creatorGurjar, Anoop
dc.creatorSingh, Uma Maheshwar
dc.creatorKalia, Sanjay
dc.creatorKumar, Arvind
dc.creatorSingh, Vikas K.
dc.creatorSinha, Pallavi
dc.date2024-01-12
dc.date2024-12-19T12:53:05Z
dc.date2024-12-19T12:53:05Z
dc.date.accessioned2026-06-27T04:10:45Z
dc.descriptionHaplotype-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.
dc.identifierhttps://hdl.handle.net/10568/163853
dc.identifier.urihttp://hdl.handle.net/123456789/24118
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceSingh, 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
dc.subjectclimate resilience
dc.subjecthaplotypes
dc.subjecthigh-yielding varieties
dc.subjectgenetic improvement
dc.subjectdrought tolerance
dc.subjectgenetic markers
dc.titleSuperior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)