Genomic inbreeding and runs of homozygosity analyses identify shared genomic regions associated with adaptation and production traits in Gudali and Simgud crossbred cattle from Cameroon

Genomic inbreeding and runs of homozygosity analyses identify shared genomic regions associated with adaptation and production traits in Gudali and Simgud crossbred cattle from Cameroon | 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 Genomic inbreeding and runs of homozygosity analyses identify shared genomic regions associated with adaptation and production traits in Gudali and Simgud crossbred cattle from Cameroon Youchahou Poutougnigni Matenchi, Bernt Guldbrandtsen, Kazi Tanzina Rahman, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7357748/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: Domesticated animal breeds frequently possess large homozygous (or nearly homozygous) regions across their genomes. These homozygous stretches - known as runs of homozygosity (ROH) - can be caused by inbreeding as well as be signatures of positive selection. They moreover provide a highly accurate estimate of inbreeding and inbreeding depression. We analysed ROH in Cameroon’s Gudali and Simgud cattle and identified genomic regions with high ROH frequencies (so-called ROH islands). Further, we investigated their association with body traits (Body length, height at wither, sacrum height and ear length), based on a two-step imputation to whole genome sequence data. Results: We detected a total of 45,312 and 6,646 homozygous segments in local Gudali and crossbred Simgud cattle respectively. The average number of ROH per individual was 83.24 in Gudali and 45.75 in Simgud. Overlapping ROH were evident across the genomes, notably, we detected 133 and 19 ROH islands exceeding 20% frequency within the population. These regions harbour 128 and 20 genes in Gudali and Simgud, respectively. In Gudali, the regions identified are mostly on BTA5 (17.6%) within 46.9-112.7 Mbp, on BTA7 within 49.7-61.1 Mbp (20.4%), and on BTA12 (23.2%) between 26.6-38.5 Mbp. For the Simgud population, 47% of the ROH islands were located on BTA7 between 10.28-51.15 Mbp. The shared region between Gudali and Simgud on BTA7 overlaps with quantitative trait loci reported to be associated with key cattle traits such as heat tolerance (DNAJC18, SLC23A1, RXFP2), immunity (SIL1, TMEM173), growth, reproduction, etc. As expected, genomic inbreeding estimates from ROH (FROH) were higher in Gudali (2.97%) than in Simgud (1.6%). Recent inbreeding, as reflected by medium and long ROH, was negatively associated with body traits, indicating inbreeding depression. Conclusions: Our study investigated the patterns of ROH and their potential associations with production traits in beef cattle. Our findings offer important insights into these patterns in Gudali and Simgud, their association with production and survival traits, and the impact of inbreeding in these populations. These insights contribute to the sustainable management of genetic resources in Cameroon’s indigenous Gudali and provide a valuable baseline for the design of effective breeding programs. Animal Science Evolutionary Biology Bioinformatics ROH inbreeding body traits Gudali Simgud Full Text Additional Declarations The authors declare no competing interests. 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-7357748","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":499519770,"identity":"06684287-59b7-45b6-ac06-ba573eccba1c","order_by":0,"name":"Youchahou Poutougnigni 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interests.","formattedTitle":"\u003cp\u003eGenomic inbreeding and runs of homozygosity analyses identify shared genomic regions associated with adaptation and production traits in Gudali and Simgud crossbred cattle from Cameroon\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Swedish University of Agricultural Sciences","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":"ROH, inbreeding, body traits, Gudali, Simgud","lastPublishedDoi":"10.21203/rs.3.rs-7357748/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7357748/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e Domesticated animal breeds frequently possess large homozygous (or nearly homozygous) regions across their genomes. These homozygous stretches - known as runs of homozygosity (ROH) - can be caused by inbreeding as well as be signatures of positive selection. They moreover provide a highly accurate estimate of inbreeding and inbreeding depression. We analysed ROH in Cameroon’s Gudali and Simgud cattle and identified genomic regions with high ROH frequencies (so-called ROH islands). Further, we investigated their association with body traits (Body length, height at wither, sacrum height and ear length), based on a two-step imputation to whole genome sequence data.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults: \u003c/strong\u003eWe detected a total of 45,312 and 6,646 homozygous segments in local Gudali and crossbred Simgud cattle respectively. The average number of ROH per individual was 83.24 in Gudali and 45.75 in Simgud. Overlapping ROH were evident across the genomes, notably, we detected 133 and 19 ROH islands exceeding 20% frequency within the population. These regions harbour 128 and 20 genes in Gudali and Simgud, respectively. In Gudali, the regions identified are mostly on BTA5 (17.6%) within 46.9-112.7 Mbp, on BTA7 within 49.7-61.1 Mbp (20.4%), and on BTA12 (23.2%) between 26.6-38.5 Mbp. For the Simgud population, 47% of the ROH islands were located on BTA7 between 10.28-51.15 Mbp. The shared region between Gudali and Simgud on BTA7 overlaps with quantitative trait loci reported to be associated with key cattle traits such as heat tolerance (DNAJC18, SLC23A1, RXFP2), immunity (SIL1, TMEM173), growth, reproduction, etc. As expected, genomic inbreeding estimates from ROH (FROH) were higher in Gudali (2.97%) than in Simgud (1.6%). Recent inbreeding, as reflected by medium and long ROH, was negatively associated with body traits, indicating inbreeding depression.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions:\u003c/strong\u003e Our study investigated the patterns of ROH and their potential associations with production traits in beef cattle. Our findings offer important insights into these patterns in Gudali and Simgud, their association with production and survival traits, and the impact of inbreeding in these populations. These insights contribute to the sustainable management of genetic resources in Cameroon’s indigenous Gudali and provide a valuable baseline for the design of effective breeding programs.\u003c/p\u003e","manuscriptTitle":"Genomic inbreeding and runs of homozygosity analyses identify shared genomic regions associated with adaptation and production traits in Gudali and Simgud crossbred cattle from Cameroon","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-13 09:10:31","doi":"10.21203/rs.3.rs-7357748/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":"83b42570-a816-4837-b214-1505b99d1c3d","owner":[],"postedDate":"August 13th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":53092499,"name":"Animal Science"},{"id":53092500,"name":"Evolutionary Biology"},{"id":53092501,"name":"Bioinformatics"}],"tags":[],"updatedAt":"2025-08-13T09:10:31+00:00","versionOfRecord":[],"versionCreatedAt":"2025-08-13 09:10:31","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7357748","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7357748","identity":"rs-7357748","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}