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

Singh, Preeti and Sundaram, K T and Vinukonda, V P and Venkateshwarlu, Ch and Paul, P J and Pahi, B and Gurjar, A and Singh, U M and Kalia, S and Kumar, A and Singh, V K and Sinha, P (2024) Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties. Communications Biology, 7. pp. 1-11. ISSN 2399-3642

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Abstract

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.

Item Type:	Article
Divisions:	Others
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Plant breeding, Plant physiology
Subjects:	Others > Plant Breeding Others > Rice Others > Plant Physiology
Depositing User:	Mr Nagaraju T
Date Deposited:	14 Nov 2024 05:08
Last Modified:	14 Nov 2024 05:08
URI:	http://oar.icrisat.org/id/eprint/12859
Official URL:	https://www.nature.com/articles/s42003-024-05769-7
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	The authors express sincere thanks to the Department of Biotechnology (DBT), Government of India for financial support under the project ‘Development of superior haplotype-based near-isogenic lines (Haplo-NILs) for enhanced genetic gain in rice’ grant (BT/PR32853/AGill/103/1159/2019) and DBT-RA program in Biotechnology and Life Sciences for financial support to V.P.V. This work has been undertaken as part of the ICAR-IRRI collaborative research project. IRRI is a member of the CGIAR Consortium.
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