Association of RAPGEF6 Gene Polymorphism with Some Traits and Egg Production Covariance Structure in Marandi Chickens

Association of RAPGEF6 Gene Polymorphism with Some Traits and Egg Production Covariance Structure in Marandi Chickens | 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 Association of RAPGEF6 Gene Polymorphism with Some Traits and Egg Production Covariance Structure in Marandi Chickens Mohammad Taghi Zarrinnia, Karim Hasanpur, Sadegh Alijani, Arash Javanmard, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7888664/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 11 You are reading this latest preprint version Abstract Sustaining egg production is crucial for the economic viability of layer farms. The Marandi chicken, a well-known native breed from Iran’s Azerbaijan region, has the inherent capacity for high egg production, reaching up to 250 eggs annually. However, its genetic potential remains largely untapped. This research explores the relationship between the RAPGEF6 gene and key performance indicators in 153 Marandi hens, using molecular markers to analyze complex economic traits. Production, reproduction, and performance data were examined through repeated-measure and single-record models. The RAPGEF6 genotype at the 13:16120088–16120089 locus was identified via PCR-RFLP, and its connection to phenotypic variation was evaluated. Results showed that the RAPGEF6 genotype had little effect on most traits; however, hens with the TT genotype displayed significantly lower maturity weight compared to the TC and CC genotypes. Additionally, a mixed-effects model, which for the first time included an analysis of the covariance structure (ARMA (1,1)) to account for repeated egg weight records from individual hens, revealed no significant link between RAPGEF6 genotype and egg weight. These findings suggest that selecting for the T allele could be a viable strategy to reduce maturity weight in Marandi layer chickens, potentially improving overall production efficiency. Further studies are needed to better understand the genetic factors influencing egg production traits in this breed and to verify these results in larger populations. Marandi Polymorphism RAPGEF6 Gene Covariance Structure Chicken Traits Full Text Additional Declarations No competing interests reported. Supplementary Files PCRRFLPLOGeRAPGEF6MNII.jpg Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 22 Feb, 2026 Reviews received at journal 27 Jan, 2026 Reviewers agreed at journal 22 Jan, 2026 Reviews received at journal 21 Jan, 2026 Reviewers agreed at journal 19 Jan, 2026 Reviewers agreed at journal 13 Jan, 2026 Reviewers invited by journal 13 Jan, 2026 Editor assigned by journal 25 Dec, 2025 Editor invited by journal 17 Dec, 2025 Submission checks completed at journal 16 Dec, 2025 First submitted to journal 09 Dec, 2025 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-7888664","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":575082457,"identity":"7ed21bf7-9747-4715-adb0-486f1fbf8ece","order_by":0,"name":"Mohammad Taghi Zarrinnia","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABB0lEQVRIie3RsUrDQBzH8d/xh+ty1PUgQV8hk21A01e5EKiLdMmoYCQQl+DcwUdxuBJIXiGTIkInh4ogFaV4pulkWsXJ4b7LHRwf/gd/wGb7h3kavYU5BcASmJsCtU98C/FLwzaETdUvyKglTSS+yE8d3idQb7d37sBJL1+Ol8FkcNWbS5wH6Du6m5gps3weC/9mljqnKordAmOJMgLvd080hCVCK+HVYWIIhVNCKcE1uOj+mFeC2MeapO9DdWEIyyRWOwmndkrmQBWGEJcs20XCjNyW+Pm4iiVxGobXkdhKiqJ6ftJq5NUnj/Xy6Gwi96qHevEa7B/k3aRZ+vdUs1ybzWaz/bVPCZZVCj6PAaoAAAAASUVORK5CYII=","orcid":"","institution":"University of Tabriz","correspondingAuthor":true,"prefix":"","firstName":"Mohammad","middleName":"Taghi","lastName":"Zarrinnia","suffix":""},{"id":575082458,"identity":"baaf1fc4-16cb-4948-b249-2a21210c3b06","order_by":1,"name":"Karim Hasanpur","email":"","orcid":"","institution":"University of Tabriz","correspondingAuthor":false,"prefix":"","firstName":"Karim","middleName":"","lastName":"Hasanpur","suffix":""},{"id":575082459,"identity":"3257cc40-940e-4026-b73f-be3c0d4d323f","order_by":2,"name":"Sadegh Alijani","email":"","orcid":"","institution":"University of Tabriz","correspondingAuthor":false,"prefix":"","firstName":"Sadegh","middleName":"","lastName":"Alijani","suffix":""},{"id":575082463,"identity":"f09acfb9-b210-48dd-a9d5-7b15739238ff","order_by":3,"name":"Arash Javanmard","email":"","orcid":"","institution":"University of Tabriz","correspondingAuthor":false,"prefix":"","firstName":"Arash","middleName":"","lastName":"Javanmard","suffix":""},{"id":575082466,"identity":"119070ba-013b-46ea-9ec3-5b399e85452b","order_by":4,"name":"Majid Olyayee","email":"","orcid":"","institution":"University of Tabriz","correspondingAuthor":false,"prefix":"","firstName":"Majid","middleName":"","lastName":"Olyayee","suffix":""}],"badges":[],"createdAt":"2025-10-17 16:53:29","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7888664/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7888664/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":100448005,"identity":"30b6f882-3608-46e8-8b67-1f6f5bf4c5b5","added_by":"auto","created_at":"2026-01-16 19:08:54","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":192383,"visible":true,"origin":"","legend":"","description":"","filename":"BMCGenomicsPAPERRAPGEF6Zarrinniaetal..docx","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/1dc046f46a19535e8381687a.docx"},{"id":100547107,"identity":"1470e9b9-060c-490c-a862-4e0be36e34ac","added_by":"auto","created_at":"2026-01-19 08:14:28","extension":"json","order_by":1,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":7087,"visible":true,"origin":"","legend":"","description":"","filename":"5bdbfabe793f44ff91936c3c5a306eed.json","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/3287394b0da944055e858d55.json"},{"id":100547121,"identity":"d57647a0-300f-4fd0-b311-ad7a2c626875","added_by":"auto","created_at":"2026-01-19 08:14:32","extension":"jpg","order_by":2,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":217450,"visible":true,"origin":"","legend":"","description":"","filename":"PCRRFLPLOGeRAPGEF6MNII.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/24beb1e9a4c7e931e7a2f43d.jpg"},{"id":100547535,"identity":"acea06d4-48c2-4dd1-8746-b01b6991ba1f","added_by":"auto","created_at":"2026-01-19 08:15:57","extension":"xml","order_by":3,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":154648,"visible":true,"origin":"","legend":"","description":"","filename":"5bdbfabe793f44ff91936c3c5a306eed1enriched.xml","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/3a2cbafb8287b720bbeb93f1.xml"},{"id":100547157,"identity":"0429fbd6-4979-431d-9a6d-7385d29f65f2","added_by":"auto","created_at":"2026-01-19 08:14:42","extension":"jpeg","order_by":4,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":53199,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage1.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/0527c549e7bbbd96cc280f5c.jpeg"},{"id":100547592,"identity":"709d8fba-0e41-4f79-ad91-70f72781eef4","added_by":"auto","created_at":"2026-01-19 08:16:05","extension":"jpeg","order_by":5,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":304892,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage2.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/cf7284f29e7760a91190ea2b.jpeg"},{"id":100448007,"identity":"9057932f-0bf2-418c-8436-e9f3be58738a","added_by":"auto","created_at":"2026-01-16 19:08:54","extension":"png","order_by":6,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":103911,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/3a4c4244fe38711978c1106b.png"},{"id":100448001,"identity":"f1b922aa-404b-43c7-8570-4619fa2d8d57","added_by":"auto","created_at":"2026-01-16 19:08:54","extension":"png","order_by":7,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":53547,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/829217737c7663c629ab874d.png"},{"id":100448011,"identity":"f584fda1-ed5a-44fe-be35-e60658278275","added_by":"auto","created_at":"2026-01-16 19:08:55","extension":"xml","order_by":8,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":153913,"visible":true,"origin":"","legend":"","description":"","filename":"5bdbfabe793f44ff91936c3c5a306eed1structuring.xml","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/824125831d9b954af4c3a439.xml"},{"id":100547289,"identity":"c9bc31c6-a820-497a-9611-875b2a6ca14e","added_by":"auto","created_at":"2026-01-19 08:15:09","extension":"html","order_by":9,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":169675,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/6ba7a9ab5ef2d822894422f5.html"},{"id":100554279,"identity":"3017014e-e122-408f-b72e-ed90587712c2","added_by":"auto","created_at":"2026-01-19 08:38:43","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":621204,"visible":true,"origin":"","legend":"","description":"","filename":"BMCGenomicsPAPERRAPGEF6Zarrinniaetal..pdf","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1_covered_04e68a74-cbad-496b-b9d8-fe71d6c5995a.pdf"},{"id":100547122,"identity":"6c1eadbd-c421-4565-a830-f1c18c74cfb4","added_by":"auto","created_at":"2026-01-19 08:14:32","extension":"jpg","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":217450,"visible":true,"origin":"","legend":"","description":"","filename":"PCRRFLPLOGeRAPGEF6MNII.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7888664/v1/b8c8d07d7df6c5f941bc66dd.jpg"}],"financialInterests":"No competing interests reported.","formattedTitle":"Association of RAPGEF6 Gene Polymorphism with Some Traits and Egg Production Covariance Structure in Marandi Chickens","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"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":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Marandi, Polymorphism, RAPGEF6 Gene, Covariance Structure, Chicken Traits","lastPublishedDoi":"10.21203/rs.3.rs-7888664/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7888664/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eSustaining egg production is crucial for the economic viability of layer farms. The Marandi chicken, a well-known native breed from Iran\u0026rsquo;s Azerbaijan region, has the inherent capacity for high egg production, reaching up to 250 eggs annually. However, its genetic potential remains largely untapped. This research explores the relationship between the RAPGEF6 gene and key performance indicators in 153 Marandi hens, using molecular markers to analyze complex economic traits. Production, reproduction, and performance data were examined through repeated-measure and single-record models. The RAPGEF6 genotype at the 13:16120088\u0026ndash;16120089 locus was identified via PCR-RFLP, and its connection to phenotypic variation was evaluated. Results showed that the RAPGEF6 genotype had little effect on most traits; however, hens with the TT genotype displayed significantly lower maturity weight compared to the TC and CC genotypes. Additionally, a mixed-effects model, which for the first time included an analysis of the covariance structure (ARMA (1,1)) to account for repeated egg weight records from individual hens, revealed no significant link between RAPGEF6 genotype and egg weight. These findings suggest that selecting for the T allele could be a viable strategy to reduce maturity weight in Marandi layer chickens, potentially improving overall production efficiency. Further studies are needed to better understand the genetic factors influencing egg production traits in this breed and to verify these results in larger populations.\u003c/p\u003e","manuscriptTitle":"Association of RAPGEF6 Gene Polymorphism with Some Traits and Egg Production Covariance Structure in Marandi Chickens","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-16 19:08:50","doi":"10.21203/rs.3.rs-7888664/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-02-23T04:59:43+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-01-27T22:05:00+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"339270956467922598206624550373360453891","date":"2026-01-22T11:06:07+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-01-21T18:35:15+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"36805182283143586322910994892675946263","date":"2026-01-19T16:51:36+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"146897062387170456608167111091295671116","date":"2026-01-13T11:56:25+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-01-13T10:21:49+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-12-26T01:15:06+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-12-17T06:31:44+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-12-17T00:44:13+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-12-09T11:31:22+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"91f0502a-fdf3-4862-939f-14033a2331a1","owner":[],"postedDate":"January 16th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-05-03T14:08:32+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-16 19:08:50","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7888664","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7888664","identity":"rs-7888664","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}