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. 2025 Mar;31(3):435-452.
doi: 10.1007/s12298-025-01573-7. Epub 2025 Mar 23.

Genome-wide association analysis in identification of superior haplotypes for vegetative stage drought stress tolerance in rice

Gyanisha Nayak  1   2 , C Parameswaran  1 , Nairita Vaidya  1 , Madhuchhanda Parida  1 , S Sabarinathan  1 , Prabharani Chaudhari  2 , Pallavi Sinha  3 , Vikas Kumar Singh  3 , Sanghamitra Samantaray  1 , Jawahar Lal Katara  1
Affiliations

Genome-wide association analysis in identification of superior haplotypes for vegetative stage drought stress tolerance in rice

Gyanisha Nayak et al. Physiol Mol Biol Plants. 2025 Mar.

Abstract

Water availability is the most critical factor limiting rice yield in rainfed agro-ecosystems. Drought stress during the vegetative stage inhibits key growth processes, such as leaf formation and tillering, significantly impacting yield. This study aimed to investigate the genetic basis of vegetative stage drought tolerance and identify QTLs and genes associated with it through GWAS. A total of 19 major QTLs were identified for six traits: leaf rolling, relative water content, plant height, leaf area, tiller number, and leaf number, with phenotypic variances ranging from 10.55 to 80.05%. Additionally, haplotypes for six candidate genes were identified: OsCYP72A32 for leaf rolling, OsNCX5.2 for relative water content, OsSPX2 for plant height, OsSTA104 for tiller number, OsRING313 for leaf number and Os3BGlu6 for leaf area. Besides, genotypes such as NCS 901 A, H 15-23-DA, LOHAMBITRO and MEJANES 2 were found to be superior donors. These tolerant genotypes and superior haplotypes can be used in haplotype-based breeding programs to enhance drought tolerance in rice at vegetative stage.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-025-01573-7.

Keywords: Candidate gene; GWAS; Haplotype breeding; Rice; Vegetative stage drought stress.

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Conflict of interest statement

Conflict of interestThe authors declare that they have no conflict of interest.

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References

    1. Bae H, Kim SK, Cho SK, Kang BG, Kim WT (2011) Overexpression of OsRDCP1, a rice RING domain-containing E3 ubiquitin ligase, increased tolerance to drought stress in rice (Oryza sativa L.). Plant Sci 180(6):775–782. 10.1016/j.plantsci.2011.02.008 - PubMed
    1. Beena R, Kirubakaran S, Nithya N, Manickavelu A, Sah RP, Abida PS, Sreekumar J, Jaslam PM, Rejeth R, Jayalekshmy VG, Roy S (2021) Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces. BMC Plant Biol 21(1):1–21. 10.21203/rs.3.rs-127517/v1 - PMC - PubMed
    1. Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A (2020) Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel. Rice 13:1–22. 10.1186/s12284-020-00406-3 - PMC - PubMed
    1. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635. 10.1093/bioinformatics/btm308 - PubMed
    1. Bunnag S, Pongthai P (2013) Selection of rice (Oryza sativa L.) cultivars tolerant to drought stress at the vegetative stage under field conditions. Am J Plant Sci 4(9):1701. 10.4236/ajps.2013.49207