Analysis of genetic diversity and inbreeding levels in the Korean native black goat population using whole-genome sequencing

Analysis of genetic diversity and inbreeding levels in the Korean native black goat population using whole-genome sequencing | 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 Analysis of genetic diversity and inbreeding levels in the Korean native black goat population using whole-genome sequencing Ho-Chan Kang, Cheol-Hyun Myung, Ji-Yeong Kim, Seung-Chang Kim, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8825232/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 The Korean native black goat (KNG) is the sole indigenous goat genetic resource of the Korean Peninsula, adapted to local environmental conditions. However, because it has been managed as a closed population over a long period, a sustainability assessment of the population is necessary. Results Consistent with the results of previous MS marker-utilizing studies, KNG and Korean crossbred goat (KCB) were clearly distinguished by population, with similar clustering trends. Although nucleotide diversity (pi) peaks existed at specific sites per contig in the KNG population, in most contigs, pi demonstrated a uniformly low aspect. The general observed heterozygosity (Ho) value of the KNG population was lower than that of the KCB population; however, the variation width between contigs was relatively larger than the average Ho. Therefore, among the four populations, the Jangsu (JS) and Tongyeong (TY) lineages are the most genetically similar, whereas KCB is the most diverse. Runs of homozygosity (ROH) analysis was used to assess the inbreeding levels and genomic fixation patterns of the KNG and KCB populations, determining that the KNG population had a high ROH total per individual, with a predominance of short-range ROH. In contrast, the total number of ROH in the KCB population was relatively small, and the proportions of medium-range and long-range ROH were higher than that of short-range ROH in the KNG population. Conclusions Compared to the KCB, the KNG showed overall lower pi and Ho, the patterns of homozygosity confirmed through ROH length distribution and inbreeding coefficient based on runs of homozygosity (F ROH ) analysis reflect the demographic history of a closed population maintained for a long period rather than that of recent rapid inbreeding. In particular, the pattern where short ROHs are distributed in large numbers across the entire genome shows that the KNG population has been maintained as an independent population for a long time. This is not a simple inbreeding risk signal but a genomic structure unique to native breeds. Korean native black goat runs of homozygosity nucleotide diversity inbreeding observed heterozygosity Full Text Additional Declarations No competing interests reported. Supplementary Files Additionalfile1.docx Additional File 1.docx Supplementary Fig. 1.Results of LD decay analysis. Supplementary Fig. 2.Optimization of principal component selection for PCA. Supplementary Table 1. Summary of annotations number and region counts 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. 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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-8825232","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":597816256,"identity":"2a223e8d-6972-4287-b036-2076da446b02","order_by":0,"name":"Ho-Chan Kang","email":"","orcid":"","institution":"Gyeongsang National University","correspondingAuthor":false,"prefix":"","firstName":"Ho-Chan","middleName":"","lastName":"Kang","suffix":""},{"id":597816257,"identity":"c5052850-dbde-469b-9aba-95d39c33ed57","order_by":1,"name":"Cheol-Hyun Myung","email":"","orcid":"","institution":"Gyeongsang National 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1.\u003c/strong\u003e Summary of annotations number and region counts\u003c/p\u003e","description":"","filename":"Additionalfile1.docx","url":"https://assets-eu.researchsquare.com/files/rs-8825232/v1/37049b1654e53334d0396750.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Analysis of genetic diversity and inbreeding levels in the Korean native black goat population using whole-genome sequencing","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":"Korean native black goat, runs of homozygosity, nucleotide diversity, inbreeding, observed heterozygosity","lastPublishedDoi":"10.21203/rs.3.rs-8825232/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8825232/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eThe Korean native black goat (KNG) is the sole indigenous goat genetic resource of the Korean Peninsula, adapted to local environmental conditions. However, because it has been managed as a closed population over a long period, a sustainability assessment of the population is necessary.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eConsistent with the results of previous MS marker-utilizing studies, KNG and Korean crossbred goat (KCB) were clearly distinguished by population, with similar clustering trends. Although nucleotide diversity (pi) peaks existed at specific sites per contig in the KNG population, in most contigs, pi demonstrated a uniformly low aspect. The general observed heterozygosity (Ho) value of the KNG population was lower than that of the KCB population; however, the variation width between contigs was relatively larger than the average Ho. Therefore, among the four populations, the Jangsu (JS) and Tongyeong (TY) lineages are the most genetically similar, whereas KCB is the most diverse. Runs of homozygosity (ROH) analysis was used to assess the inbreeding levels and genomic fixation patterns of the KNG and KCB populations, determining that the KNG population had a high ROH total per individual, with a predominance of short-range ROH. In contrast, the total number of ROH in the KCB population was relatively small, and the proportions of medium-range and long-range ROH were higher than that of short-range ROH in the KNG population.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003eCompared to the KCB, the KNG showed overall lower pi and Ho, the patterns of homozygosity confirmed through ROH length distribution and inbreeding coefficient based on runs of homozygosity (F\u003csub\u003eROH\u003c/sub\u003e) analysis reflect the demographic history of a closed population maintained for a long period rather than that of recent rapid inbreeding. In particular, the pattern where short ROHs are distributed in large numbers across the entire genome shows that the KNG population has been maintained as an independent population for a long time. This is not a simple inbreeding risk signal but a genomic structure unique to native breeds.\u003c/p\u003e","manuscriptTitle":"Analysis of genetic diversity and inbreeding levels in the Korean native black goat population using whole-genome sequencing","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-02 19:03:21","doi":"10.21203/rs.3.rs-8825232/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":"d7a4426d-b957-4a01-a3a8-2a561efe5169","owner":[],"postedDate":"March 2nd, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-04-01T08:28:15+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-02 19:03:21","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8825232","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8825232","identity":"rs-8825232","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}