A genome sequencing approach to identify candidate genes for drought tolerance in rice, using a drought-tolerant mutant

Document Type : Research Paper

Authors

1 Department of Biotechnology and Plant Breeding Faculty of Agriculture, Ferdowsi University of Mashhad

2 Professor, Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of ‎Mashhad, Mashhad, Iran.

3 Associate Professor, ‎ Rice Research Institute of Iran (RRII), Agricultural Research Education and Extension ‎Organization (AREEO), Rasht, Iran.

4 Associate Professor, Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, ‎Mashhad, Iran.

10.30473/cb.2025.73217.1996

Abstract

Rice is a globally important food crop, and drought is a major constraint on its production, highlighting the need for drought-tolerant varieties. Next-generation sequencing (NGS) enables the identification of DNA variations, even within closely related rice lines, offering a powerful approach to unravel the genetic basis of traits like drought tolerance. Identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) is a crucial application of NGS. This study aimed to identify candidate genes for drought tolerance by re-sequencing the genome of a drought-tolerant rice mutant and comparing it to its drought-sensitive parent, Hashemi. We identified 73,077 polymorphisms (SNPs and InDels) between the two lines. We then analyzed the segregation of large-effect variants in a segregating F2 population derived from a cross between the two lines, comparing drought-sensitive and drought-tolerant progeny. The identified SNPs were validated against previously reported SNPs, and their functional relevance was assessed based on their location within known quantitative trait loci (QTLs) and conserved protein domains. This research pinpoints a potentially valuable target gene for enhancing drought tolerance in rice breeding programs. It is hoped that by inducing targeted mutations or using genome editing techniques to produce this protein in drought-sensitive rice varieties, cultivars can be developed that, in addition to having the desired traits, will also be tolerant to drought stress.

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References

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