Integrated GWAS and Transcriptome Analysis Identifies Candidate Genes for Seedling-Stage Drought Tolerance in Indica Rice

Integrated GWAS and Transcriptome Analysis Identifies Candidate Genes for Seedling-Stage Drought Tolerance in Indica Rice | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Integrated GWAS and Transcriptome Analysis Identifies Candidate Genes for Seedling-Stage Drought Tolerance in Indica Rice Kaixuan He, Yongxin Li, Zijie Liu, Hexing Yin, Hongyan Zhang, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9077877/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 10 You are reading this latest preprint version Abstract Drought stress is a major constraint on rice productivity, especially at the seedling stage. In this study, we evaluated 283 indica rice accessions adapted to the middle and lower Yangtze River region for seedling-stage drought tolerance using four morphological traits: leaf senescence resistance index, leaf wilting score, plant height, and root length. A comprehensive drought tolerance metric (CDTM) was developed to integrate these traits, leading to the identification of ten superior drought-tolerant accessions. Genome-wide association study (GWAS) revealed 128 significantly associated SNPs, mapping to 133 candidate genes for drought-related traits. Transcriptome analysis of drought-tolerant and drought-sensitive cultivars under PEG-induced stress showed distinct expression profiles, with differential expression enriched in pathways related to fatty acid degradation, amino acid metabolism, and hormone signaling. By integrating GWAS and transcriptome analysis, we prioritized 12 core candidate genes repeatedly associated with multiple drought-related traits, six of which were further validated using an independent drought-stress transcriptome dataset from the water-saving and drought-resistant variety Hanyou 73 under drought stress. Alternative splicing analysis revealed a significant skipped exon event in Os03g0700700 under drought stress. Our findings provide valuable genetic resources and candidate genes for molecular breeding amied at enhancing seedling-stage drought tolerance in rice breeding programs. Rice seedling Drought tolerance Genome-wide association studies Transcriptome analysis Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryMaterial1.xlsx SupplementaryMaterial2.docx FigS1.tif FigS2.png FigS3.png FigS4.png FigS5.png FigS6.png FigS7.png Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 10 May, 2026 Reviewers agreed at journal 07 May, 2026 Reviews received at journal 04 May, 2026 Reviewers agreed at journal 02 Apr, 2026 Reviewers agreed at journal 01 Apr, 2026 Reviewers agreed at journal 28 Mar, 2026 Reviewers invited by journal 27 Mar, 2026 Editor assigned by journal 18 Mar, 2026 Submission checks completed at journal 10 Mar, 2026 First submitted to journal 09 Mar, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9077877","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":613626061,"identity":"6c5ba4d7-8dcd-4a8d-ae35-0bfbca4d4041","order_by":0,"name":"Kaixuan 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