Genetic interactions among flowering loci shape phenology, vigour, and yield trade-offs in chickpea

Genetic interactions among flowering loci shape phenology, vigour, and yield trade-offs in chickpea | 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 Genetic interactions among flowering loci shape phenology, vigour, and yield trade-offs in chickpea Raul Ortega Martinez, L. Lake, J.E. Hayes, J.L. Weller, R. French, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9193912/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 8 You are reading this latest preprint version Abstract Flowering time and vegetative vigour are central adaptive traits in chickpea, shaping the balance between stress escape, biomass accumulation, and yield. Major phenology loci have been identified in this species, including ELF3a , CaLG3b and a cluster of FT homologues on chromosome 3 ( CaLG3a ), but their individual and interactive contributions to field adaptation remain unclear. Here, we developed near-isogenic lines (NILs) to dissect these loci under controlled conditions and across eight field environments in Southern and Western Australia. In a phytotron, NILs revealed strong photoperiod dependence: ELF3a suppressed flowering under short days, while early alleles at CaLG3b and the FT cluster promoted flowering under long days, with additive effects across loci. In the field, allelic substitutions consistently shifted phenology by a few days or nodes but rarely conferred direct yield benefits. Yield responses were variable and environment-dependent, with one NIL pair exhibiting a consistent penalty in environments with yield above 255 g m − 2 . In contrast, canopy traits showed clearer divergence between NIL pairs, aligning with pleiotropic effects of the FT cluster. These results highlight the utility of NILs for attributing modest but adaptive phenological shifts to defined genomic regions, and suggest that the primary breeding value of these loci lies in fine-tuning crop development to local stress patterns rather than delivering robust yield gains. Stacking early and late alleles may offer breeders a genetic tool to broaden adaptive flexibility, while yield improvement will likely require integration with physiological traits related to resource capture, efficiency and higher reproductive allocation. breeding canopy genotype environment phenotype phenology Full Text Additional Declarations No competing interests reported. Supplementary Files ESM1.pdf Cite Share Download PDF Status: Under Review Version 1 posted Reviewers agreed at journal 07 May, 2026 Reviewers agreed at journal 07 May, 2026 Reviewers agreed at journal 07 May, 2026 Reviewers agreed at journal 07 May, 2026 Reviewers invited by journal 07 May, 2026 Editor assigned by journal 25 Mar, 2026 Submission checks completed at journal 24 Mar, 2026 First submitted to journal 22 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. We do this by developing innovative software and high quality services for the global research community. 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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-9193912","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":637406491,"identity":"37b6beb6-5c06-4439-847b-558e6176b6d9","order_by":0,"name":"Raul Ortega Martinez","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA1klEQVRIiWNgGAWjYBADOSjNTJRqxgYgYczARqqWxAaitZi39z5/8OGXXfqG+82PPzBUWCc2sJ8xwKtF5sxxw8aZfcm5G46xmUkwnElPbODJwa9FQiKNsZm3hxmohcGMgbHtcGIDAzFa/vbUpxscY//8gfEfUAv/GyK0MPw4nGBwjMdAgrEBqEWCkC08xxhn9jYcN5x5LKdMIuFYunGbxLMC/FrY2xg+/PhTLc93+PjmDx9qrGX7+ZM34NUCBoxtUEYCELMRVg8Cf4hTNgpGwSgYBSMUAAAONUW8gSj72wAAAABJRU5ErkJggg==","orcid":"","institution":"University of Tasmania","correspondingAuthor":true,"prefix":"","firstName":"Raul","middleName":"Ortega","lastName":"Martinez","suffix":""},{"id":637406499,"identity":"756b043e-f49e-49aa-8f47-eb5bf602cec2","order_by":1,"name":"L. 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