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

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 PallaviORCID

Abstract

AbstractHaplotype-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.

Funder

Department of Biotechnology, Ministry of Science and Technology

Publisher

Springer Science and Business Media LLC

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Medicine (miscellaneous)

Reference74 articles.

1. Hanafiah, N. M., Mispan, M. S., Lim, P. E., Baisakh, N. & Cheng, A. The 21st century agriculture: when rice research draws attention to climate variability and how weedy rice and underutilized grains come in handy. Plants Basel Switz. 9, E365 (2020).

2. Adhikari, M. et al. Evaluation of drought tolerant rice cultivars using drought tolerant indices under water stress and irrigated condition. Am. J. Clim. Change 8, 228–236 (2019).

3. Li, M. et al. Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system. Front. Plant Sci. 7, 377 (2016).

4. Vikram, P. et al. qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genet. 12, 89 (2011).

5. Ghimire, K. H. et al. Identification and mapping of a QTL (qDTY1.1) with a consistent effect on grain yield under drought. Field Crops Res. 131, 88–96 (2012).

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