Identification of Selection Signatures and Genetic Diversity in the Sheep

Identification of Selection Signatures and Genetic Diversity in the Sheep | 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 Identification of Selection Signatures and Genetic Diversity in the Sheep Mustafa KARABAŞ, Onur YILMAZ This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3836943/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 study utilized genome-wide data from the Illumina OvineSNP50K platform and specifically targeted the Eşme sheep population. The integrated haplotype score (iHS) and runs of homozygosity (ROH) statistical approaches were used to identify selection signatures. Using the iHS analysis, it was discovered that there are 10 genomic regions and 51 genes on chromosomes 1, 9, 11, and 12 that are under selection. Three genomic regions and 97 genes on chromosomes 6 and 11 were found to be under selection using the ROH analysis. Candidate genes associated with economic and ecological traits were detected using both approaches. Among the genetic diversity parameters considered in the study, the minor allele frequency (MAF), genetic distance between individuals (D), observed heterozygosity (Ho), and expected heterozygosity (He) values were found to be 0.300, 0.309, 0.388, and 0.390, respectively. The ratio of polymorphic SNPs (PN) was 0.947, and the average values of F ROH and F HOM were 0.030 and 0.029, respectively. The study demonstrates that selection signature approaches can define the economic and ecological characteristics of farm animals using phenotypic information. The information obtained through these approaches can be utilized in breeding and conservation programs for the genetic resources of farm animals. Integrated haplotype score runs of homozygosity genetic diversity selective sweep Full Text Additional Declarations No competing interests reported. Table 1 to 4 are available in the Supplementary Files section. Supplementary Files Tables.docx SupplementaryTables.docx 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-3836943","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":265545060,"identity":"70436f14-262c-4832-835c-27333f5dde17","order_by":0,"name":"Mustafa KARABAŞ","email":"","orcid":"","institution":"Aydın Adnan Menderes University","correspondingAuthor":false,"prefix":"","firstName":"Mustafa","middleName":"","lastName":"KARABAŞ","suffix":""},{"id":265545061,"identity":"97abf716-0d1e-4d3e-8351-731698243810","order_by":1,"name":"Onur YILMAZ","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAyklEQVRIiWNgGAWjYFACxsYDQFKOgSEBSLERp6UBpMUYroWHGE0gLYkNRGvhl0huOHSjpi69vz3HgOFD2WEGe+kD+LVIzkhsOJxzjC13xpk3Bowzzh1m4OFLwK/F4AZICxtPbsONHANm3jagFkIug2j5J5EuD9Lyl2gtuW0GCQYgLYzEaJHseQjU0pdguPHMs4KDPefSeXjOENDCz57+8HHOtzp5uePJGx/8KLOWY+8hoIVBIAHBPsBAVEzyHyCsZhSMglEwCkY4AAATYkSh+KRU9AAAAABJRU5ErkJggg==","orcid":"","institution":"Aydın Adnan Menderes University","correspondingAuthor":true,"prefix":"","firstName":"Onur","middleName":"","lastName":"YILMAZ","suffix":""}],"badges":[],"createdAt":"2024-01-05 10:15:46","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3836943/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3836943/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":56273313,"identity":"48589299-3bac-493c-a0c2-e9940fe55540","added_by":"auto","created_at":"2024-05-10 18:56:51","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":362506,"visible":true,"origin":"","legend":"","description":"","filename":"IdentificationofSelectionSignaturesandGeneticDiversityintheSheep.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3836943/v1_covered_4dbdbdb5-4d66-46c7-b790-1dc3b8158d2d.pdf"},{"id":49333944,"identity":"c482fa5c-f184-46cc-8f5c-a8fc4323d1cc","added_by":"auto","created_at":"2024-01-08 20:14:43","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":18841,"visible":true,"origin":"","legend":"","description":"","filename":"Tables.docx","url":"https://assets-eu.researchsquare.com/files/rs-3836943/v1/db7e537d97d3aeb6b50711cf.docx"},{"id":49333945,"identity":"7255d7fa-087f-4f3e-a990-2eaae39a04e1","added_by":"auto","created_at":"2024-01-08 20:14:43","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":1054333,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryTables.docx","url":"https://assets-eu.researchsquare.com/files/rs-3836943/v1/f94366fa3e65db93c6b49ae5.docx"}],"financialInterests":"\u003cp\u003eNo competing interests reported.\u003c/p\u003e\n\u003cp\u003eTable 1 to 4 are available in the Supplementary Files section.\u003c/p\u003e","formattedTitle":"Identification of Selection Signatures and Genetic Diversity in the Sheep","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":"Integrated haplotype score, runs of homozygosity, genetic diversity, selective sweep ","lastPublishedDoi":"10.21203/rs.3.rs-3836943/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3836943/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe study utilized genome-wide data from the Illumina OvineSNP50K platform and specifically targeted the Eşme sheep population. The integrated haplotype score (iHS) and runs of homozygosity (ROH) statistical approaches were used to identify selection signatures. Using the iHS analysis, it was discovered that there are 10 genomic regions and 51 genes on chromosomes 1, 9, 11, and 12 that are under selection. Three genomic regions and 97 genes on chromosomes 6 and 11 were found to be under selection using the ROH analysis. Candidate genes associated with economic and ecological traits were detected using both approaches. Among the genetic diversity parameters considered in the study, the minor allele frequency (MAF), genetic distance between individuals (D), observed heterozygosity (Ho), and expected heterozygosity (He) values were found to be 0.300, 0.309, 0.388, and 0.390, respectively. The ratio of polymorphic SNPs (PN) was 0.947, and the average values of F\u003csub\u003eROH\u003c/sub\u003e and F\u003csub\u003eHOM\u003c/sub\u003e were 0.030 and 0.029, respectively. 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