{"paper_id":"37f40dd6-e4cd-4195-b37d-75708ba13c20","body_text":"Genetic Admixture Analysis of Fecundity-associated Genes in Captive Deer Populations and Its Implications for Reproductive Management | 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 Admixture Analysis of Fecundity-associated Genes in Captive Deer Populations and Its Implications for Reproductive Management MUHAMMAD SANUSI YAHAYA, MOHD SHAHROM SALISI, Nur Mahiza MD Isa, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6966336/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract The decline in the fertility of captive deer populations presents significant challenges for wildlife farming and conservation breeding programs. This study investigated whether genetic admixture in fecundity-associated genes contributes to reduced reproductive performance in a captive population comprising three deer breeds (Axis axis, Rusa timorensis, and Rusa unicolor). We analyzed sequence variation in five key fertility genes (BMP15, FOXL2, GDF9, MTNR1A, and MHCDQA1) across 26 individuals via ADMIXTURE analysis. Cross-validation identified K=4 as the optimal number of ancestral populations, exceeding the three recognized breeds and revealing complex admixture patterns, particularly between R. timorensis and R. unicolor. Gene-specific analyses revealed differential evolutionary dynamics, with MTNR1A exhibiting the greatest breed differentiation (Fst=0.31) and MHCDQA1 the lowest (Fst=0.09). Notably, we found a significant negative correlation between admixture complexity (Shannon entropy) and conception rate (r=-0.58, p=0.012) in females with reproductive records (n=18), which remained significant after controlling for age and parity. Specific ancestral components showed contrasting associations with fertility: Ancestry 2 correlated positively with the conception rate (r=0.61, p=0.007), whereas Ancestry 1 correlated negatively (r=-0.47, p=0.049). These findings provide strong evidence that hybridization disrupts coadapted gene complexes governing reproduction, which may result in outbreeding depression. Our results highlight the importance of genetic management in multibreed captive settings and offer a foundation for developing targeted breeding strategies to mitigate fertility decline in managed cervid populations, with broader implications for wildlife conservation and animal breeding programs worldwide. Admixture animal breeding animal reproduction deer fecundity Full Text Additional Declarations No competing interests reported. Supplementary Table 1 is not available with this version. Cite Share Download PDF Status: Posted Version 1 posted 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-6966336\",\"acceptedTermsAndConditions\":true,\"allowDirectSubmit\":true,\"archivedVersions\":[],\"articleType\":\"Research Article\",\"associatedPublications\":[],\"authors\":[{\"id\":492191728,\"identity\":\"bccc4750-d8f6-4126-ba8d-bd940230500f\",\"order_by\":0,\"name\":\"MUHAMMAD SANUSI YAHAYA\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Usmanu Danfodiyo University\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"MUHAMMAD\",\"middleName\":\"SANUSI\",\"lastName\":\"YAHAYA\",\"suffix\":\"\"},{\"id\":492191729,\"identity\":\"ac90205e-e9ce-44d7-b5a1-a042a18b18a6\",\"order_by\":1,\"name\":\"MOHD SHAHROM 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This study investigated whether genetic admixture in fecundity-associated genes contributes to reduced reproductive performance in a captive population comprising three deer breeds (Axis axis, Rusa timorensis, and Rusa unicolor). We analyzed sequence variation in five key fertility genes (BMP15, FOXL2, GDF9, MTNR1A, and MHCDQA1) across 26 individuals via ADMIXTURE analysis. Cross-validation identified K=4 as the optimal number of ancestral populations, exceeding the three recognized breeds and revealing complex admixture patterns, particularly between R. timorensis and R. unicolor. Gene-specific analyses revealed differential evolutionary dynamics, with MTNR1A exhibiting the greatest breed differentiation (Fst=0.31) and MHCDQA1 the lowest (Fst=0.09). Notably, we found a significant negative correlation between admixture complexity (Shannon entropy) and conception rate (r=-0.58, p=0.012) in females with reproductive records (n=18), which remained significant after controlling for age and parity. Specific ancestral components showed contrasting associations with fertility: Ancestry 2 correlated positively with the conception rate (r=0.61, p=0.007), whereas Ancestry 1 correlated negatively (r=-0.47, p=0.049). These findings provide strong evidence that hybridization disrupts coadapted gene complexes governing reproduction, which may result in outbreeding depression. 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