Genome-wide association studies on the Autosomes and Chromosome X uncover genetic basis of reproductive traits in Yorkshire pigs

Genome-wide association studies on the Autosomes and Chromosome X uncover genetic basis of reproductive traits in Yorkshire pigs | 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 Genome-wide association studies on the Autosomes and Chromosome X uncover genetic basis of reproductive traits in Yorkshire pigs Teddy Tinashe Chitotombe, Qing Lin, Wondossen Ayalew, Zhe Zhang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8093455/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 Background Reproductive efficiency is a fundamental determinant of productivity in pig breeding programs. However, the role of the X chromosome in shaping the genetic basis of reproductive traits remains underexplored. Results To address this problem, 2,659 Yorkshire genotyped sows with 39,048 autosomal and 1,947 X-chromosomal SNPs were analyzed for four reproductive traits: total number born (TNB), number weaned (NWEAN), total litter weight at birth (TLWT_BA), and total litter weight at 21 days (TLWT_D21). After stringent quality control, heritability estimates ( \(\:{h}^{2}\) ) ranged from 0.037 (TLWT_BA_P1) to 0.215 (TNB_P3). While autosomes accounted for most genetic variation, the X chromosome contributed substantially, explaining nearly half of the total heritability for TNB_P3 and about one-quarter for NWEAN_P2. Genome-wide association analysis identified 23 independent SNPs significantly associated with the traits, pinpointing candidate genes including ARHGEF2, TENM2, ACACA , and RBM10 . Functional enrichment analysis revealed that ARHGEF2, DEFB1, DNAI2 , and SPACA5 were involved in sperm flagellum assembly, cilium organization, and developmental processes. KEGG pathway analysis highlighted the insulin and ErbB signaling pathways, involving ACACA, ARAF, ELK1 , and SHC1 genes. Several candidate genes, including SPACA5, ELK1 , and ARAF , were located on the X chromosome, suggesting potential X-linked regulatory effects on reproductive performance. Conclusions These findings demonstrate the substantial contribution of the X chromosome to the genetic regulation of sow reproductive traits and emphasize the importance of incorporating X-linked information into genomic selection strategies for improving reproductive efficiency in pigs. Yorkshire pigs Autosomes X chromosome Reproductive trait GWAS Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryTableS1.csv SupplementaryFigureS1.pdf 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-8093455","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":552072919,"identity":"068db8f7-756a-47bd-9a6d-ed88b5e45053","order_by":0,"name":"Teddy Tinashe Chitotombe","email":"","orcid":"","institution":"South China Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Teddy","middleName":"Tinashe","lastName":"Chitotombe","suffix":""},{"id":552072920,"identity":"fea43b86-e738-4950-a67d-22746b36b1ad","order_by":1,"name":"Qing Lin","email":"","orcid":"","institution":"South China Agricultural 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pigs","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Yorkshire pigs, Autosomes, X chromosome, Reproductive trait, GWAS","lastPublishedDoi":"10.21203/rs.3.rs-8093455/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8093455/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eReproductive efficiency is a fundamental determinant of productivity in pig breeding programs. However, the role of the X chromosome in shaping the genetic basis of reproductive traits remains underexplored.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eTo address this problem, 2,659 Yorkshire genotyped sows with 39,048 autosomal and 1,947 X-chromosomal SNPs were analyzed for four reproductive traits: total number born (TNB), number weaned (NWEAN), total litter weight at birth (TLWT_BA), and total litter weight at 21 days (TLWT_D21). After stringent quality control, heritability estimates (\u003cspan class=\"InlineEquation\"\u003e\u003cspan class=\"mathinline\"\u003e\\(\\:{h}^{2}\\)\u003c/span\u003e\u003c/span\u003e) ranged from 0.037 (TLWT_BA_P1) to 0.215 (TNB_P3). While autosomes accounted for most genetic variation, the X chromosome contributed substantially, explaining nearly half of the total heritability for TNB_P3 and about one-quarter for NWEAN_P2. Genome-wide association analysis identified 23 independent SNPs significantly associated with the traits, pinpointing candidate genes including \u003cem\u003eARHGEF2, TENM2, ACACA\u003c/em\u003e, and \u003cem\u003eRBM10\u003c/em\u003e. Functional enrichment analysis revealed that \u003cem\u003eARHGEF2, DEFB1, DNAI2\u003c/em\u003e, and \u003cem\u003eSPACA5\u003c/em\u003e were involved in sperm flagellum assembly, cilium organization, and developmental processes. KEGG pathway analysis highlighted the insulin and ErbB signaling pathways, involving \u003cem\u003eACACA, ARAF, ELK1\u003c/em\u003e, and \u003cem\u003eSHC1\u003c/em\u003e genes. Several candidate genes, including \u003cem\u003eSPACA5, ELK1\u003c/em\u003e, and \u003cem\u003eARAF\u003c/em\u003e, were located on the X chromosome, suggesting potential X-linked regulatory effects on reproductive performance.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eThese findings demonstrate the substantial contribution of the X chromosome to the genetic regulation of sow reproductive traits and emphasize the importance of incorporating X-linked information into genomic selection strategies for improving reproductive efficiency in pigs.\u003c/p\u003e","manuscriptTitle":"Genome-wide association studies on the Autosomes and Chromosome X uncover genetic basis of reproductive traits in Yorkshire pigs","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-03 11:00:16","doi":"10.21203/rs.3.rs-8093455/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"aa6940a1-a54e-4878-9f65-beac68d6b03a","owner":[],"postedDate":"December 3rd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-01-02T04:53:56+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-03 11:00:16","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8093455","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8093455","identity":"rs-8093455","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}