Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, et al. Snp-seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res. 2015;43(DI):D1023–7. https://doi.org/10.1093/nar/gku1039.

Article  CAS  PubMed  Google Scholar 

Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23:2633–5. https://doi.org/10.1093/bioinformatics/btm308.

Article  CAS  PubMed  Google Scholar 

Aslam MM, Waseem M, Jakada BH, Okal EJ, Lei Z, Saqib HSA, et al. Mechanisms of abscisic acid-mediated drought stress responses in plants. Int J Mol Sci. 2022;23(3):1084. https://doi.org/10.3390/ijms23031084.

Article  CAS  Google Scholar 

Bahbahani H. Long-range linkage disequilibrium events on the genome of dromedary camels as a signal of epistatic and directional positive selection. Heliyon. 2024;10(14):e34343. https://doi.org/10.1016/j.heliyon.2024.e34343.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chung MY, Merila J, Li J, Mao K, López-Pujol J, Tsumura Y, et al. Neutral and adaptive genetic diversity in plants: an overview. Front Ecol Evol. 2023;11:1116814. https://doi.org/10.3389/fevo.2023.1116814.

Article  Google Scholar 

Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, et al. Phylogeny. fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008;36:W465–9. https://doi.org/10.1093/nar/gkn180.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dixit S, Swamy BP, Vikram P, Ahmed HU, Sta Cruz MT, Amante M, et al. Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities. Theor Appl Genet. 2012;125(1):155–69. https://doi.org/10.1007/s00122-012-1823-9.

Article  PubMed  Google Scholar 

Dixit S, Kumar Biswal A, Min A, Henry A, Oane RH, Raorane ML, et al. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL. Sci Rep. 2015;5(1):1–16. https://doi.org/10.1038/srep15183.

Article  CAS  Google Scholar 

Geng A, Lian W, Wang Y, Liu M, Zhang Y, Wang X, et al. Molecular mechanisms and regulatory pathways underlying drought stress response in rice. Int J Mol Sci. 2024;25(2):1185. https://doi.org/10.3390/ijms25021185.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang L, Bao Y, Qin S, Ning M, Li Q, Li Q, et al. The ABA synthesis enzyme allele OsNCED2T promotes dryland adaptation in upland rice. The Crop J. 2024;12(1):68–78. https://doi.org/10.1016/j.cj.2023.12.001.

Article  CAS  Google Scholar 

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010;42(11):961–7.

Article  CAS  PubMed  Google Scholar 

IRRI-International Rice Research Institute. Standard evaluation system for rice. 5th ed. Philippines. 2013;29.

Kassambara A. Ggpubr: ‘ggplot2’ Based Publication Ready Plots. 2023. https://rpkgs.datanovia.com/ggpubr/

Kiran K, Selvaraj S, Parameswaran C, Balasubramaniasai C, Katara JL, Devanna BN, et al. Genome-wide association analysis and candidate genes identification for pericarp color in rice (Oryza sativa L.). Trop Plant Biol. 2025;18:8. https://doi.org/10.1007/s12042-024-09371-3.

Article  CAS  Google Scholar 

Kumar A, Dixit S, Ram T, Yadaw RB, Mishra KK, Mandal NP. Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches. J Exp Bot. 2014;65(21):6265–78. https://doi.org/10.1093/jxb/eru363.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Latif A, Ying S, Cuixia P, Ali N. Rice curled its leaves either adaxially or abaxially to combat drought stress. Rice Sci. 2023;30(5):405–16. https://doi.org/10.1016/j.rsci.2023.04.002.

Article  Google Scholar 

Lyu J, Zhang S, Dong Y, He W, Zhang J, Deng X, et al. Analysis of elite variety tag SNPs reveals an important allele in upland rice. Nat Commun. 2013;4:2138. https://doi.org/10.1038/ncomms3138.

Article  CAS  PubMed  Google Scholar 

Mishra KK, Vikram P, Yadaw RB, Swamy BP, Dixit S, Cruz MT, et al. qDTY12.1: a locus with a consistent effect on grain yield under drought in rice. BMC Genet. 2013. https://doi.org/10.1186/1471-2156-12-89.

Article  PubMed  PubMed Central  Google Scholar 

Narisetti N, Henke M, Seiler C, Junker A, Ostermann J, Altmann T, et al. Fully-automated root image analysis (faRIA). Sci Rep. 2021;11(1):16047.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nayak G, Parameswaran C, Vaidya N, Parida M, Sabarinathan S, Chaudhari P, et al. Genome-wide association analysis in identification of superior haplotypes for vegetative stage drought stress tolerance in rice. Physiol Mol Biol Plants. 2025;31:435–52. https://doi.org/10.1007/s12298-025-01573-7.

Article  CAS  PubMed  Google Scholar 

Nayak G, Parameswaran C, Vaidya N, Parida M, Verma RL, Chaudhari P, et al. Marker-trait association of the major pyruvate pathway genes regulating yield related traits in rice (Oryza sativa L.). Indian J Genet Pl Breed. 2024;84(3):329–35.

Article  CAS  Google Scholar 

Negm S, Veller C. The effect of long-range linkage disequilibrium on allele-frequency dynamics under stabilizing selection. bioRxiv. 2024;2024–06. https://doi.org/10.1101/2024.06.27.601075

Sahoo SK, Dash GK, Kumar A, Lal MK, Guhey A, Baig MJ, et al. Phenological and yield responses for the identification of both vegetative and reproductive stages drought-tolerant rice genotypes for future breeding. Cereal Res Commun. 2024;52(2):655–69. https://doi.org/10.1007/s42976-023-00434-x.

Article  CAS  Google Scholar 

Sanchez J, Kaur PP, Pabuayon ICM, Karampudi NBR, Kitazumi A, Sandhu N, et al. DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds. Plant Genome. 2022;15(1):e20168. https://doi.org/10.1002/tpg2.20168.

Article  CAS  PubMed  Google Scholar 

Selvaraj S, Chidambaranathan P, Dash GK, Sanghamitra P, Jeughale KP, Balasubramaniasai C, et al. Long-range admixture linkage disequilibrium and allelic responses of Sub1 and TPP7 under consecutive stresses in rice validated through Mendelian randomization. Rice Sci. 2025. https://doi.org/10.1016/j.rsci.2025.06.009.

Article  Google Scholar 

Sharma E, Bhatnagar A, Bhaskar A, Majee SM, Kieffer M, Kepinski S, et al. Stress-induced F-box protein-coding gene OsFBX257 modulates drought stress adaptations and ABA responses in rice. Plant Cell Environ. 2023;46(4):1207–31. https://doi.org/10.1111/pce.14496.

Article  CAS  PubMed  Google Scholar 

Singh P, Sundaram KT, Vinukonda VP, Venkateshwarlu C, Paul PJ, Pahi B, et al. Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties. Commun Biol. 2024;7(1):89. https://doi.org/10.1038/s42003-024-05769-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sruthi P, Surendran U, Siddiqui MH, Alamri S. Understanding the leaf rolling of paddy and exploring its management options under aerobic rice. Sci Rep. 2024;14(1):19335. https://doi.org/10.1038/s41598-024-68244-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Su J, Xu K, Li Z, Hu Y, Hu Z, Zheng X, et al. Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential. Sci Rep. 2021;11(1):6894. https://doi.org/10.1038/s41598-021-86389-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Swain N, Sahoo RK, Jeughale KP, Sarkar S, Selvaraj S, Parameswaran C, et al. Rice homolog of Arabidopsis Xylem NAC domain 1 (OsXND1), a NAC transcription factor regulates drought stress responsive root system architecture in indica rice. Mol Genet Genomics. 2024;299(1):94. https://doi.org/10.1007/s00438-024-02178-7.

Article