Remarquable heterogeneity in the genetic architecture of resistance to a key bacterial pathogen in commercial populations of rainbow trout

Remarquable heterogeneity in the genetic architecture of resistance to a key bacterial pathogen in commercial populations of rainbow trout | 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 Remarquable heterogeneity in the genetic architecture of resistance to a key bacterial pathogen in commercial populations of rainbow trout Simon Pouil, Dimitri Rigaudeau, Bo-Hyung Lee, Emilien Segret, and 7 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6591460/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 28 Nov, 2025 Read the published version in BMC Genomics → Version 1 posted 10 You are reading this latest preprint version Abstract Background Bacterial cold-water disease (BCWD), caused by Flavobacterium psychrophilum , remains a major challenge for rainbow trout ( Oncorhynchus mykiss ) aquaculture, due to the absence of effective vaccines and increasing concerns over antibiotic use. Genetic selection for disease resistance offers a sustainable alternative. In this study, we investigated the genetic architecture of BCWD resistance in two French commercial rainbow trout populations using a standardized waterborne infection model and high-density SNP genotyping. Results Survival following experimental infection varied significantly between populations, with population B showing higher resistance (71.3% vs 50.7% of survival at 29 days post-infection). Genome-wide association studies (GWAS) were performed using a Bayesian sparse linear mixed model (BSLMM), separately in each population and in a combined dataset. Eleven quantitative trait loci (QTLs) were identified across the analyses, with limited overlap between populations, highlighting the complexity and partial divergence of resistance architectures. Several candidate genes located within QTL regions were involved in immune signalling, inflammation, macrophages/neutrophils biology, and soluble factors important for antibacterial defences. Notably, two QTLs contained genes from the complement system (e.g., C3, Cfb), highlighting their central role in resistance to F. psychrophilum . Conclusions Our findings underscore the polygenic nature of BCWD resistance, the influence of host genetic background, and provide valuable targets for selection for BCWD resistance in rainbow trout breeding programs. QTL Flavobacterium psychrophilum BCWD resistance to pathogens antibacterial response aquaculture Oncorhynchus mykiss bath infection Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryMaterial1.docx SupplementaryMaterial2.xlsx SupplementaryMaterial3.xlsx SupplementaryMaterial4.xlsx Cite Share Download PDF Status: Published Journal Publication published 28 Nov, 2025 Read the published version in BMC Genomics → Version 1 posted Editorial decision: Revision requested 08 Aug, 2025 Reviews received at journal 07 Aug, 2025 Reviews received at journal 30 Jul, 2025 Reviewers agreed at journal 14 Jul, 2025 Reviewers agreed at journal 11 Jul, 2025 Reviewers invited by journal 11 Jul, 2025 Editor assigned by journal 11 Jul, 2025 Editor invited by journal 09 Jul, 2025 Submission checks completed at journal 09 Jul, 2025 First submitted to journal 09 Jul, 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. 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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-6591460","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":485270424,"identity":"6efd7e42-3cb0-46ac-8535-40755dd31b88","order_by":0,"name":"Simon 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Flavobacterium psychrophilum, BCWD, resistance to pathogens, antibacterial response, aquaculture, Oncorhynchus mykiss, bath infection","lastPublishedDoi":"10.21203/rs.3.rs-6591460/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6591460/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eBacterial cold-water disease (BCWD), caused by \u003cem\u003eFlavobacterium psychrophilum\u003c/em\u003e, remains a major challenge for rainbow trout (\u003cem\u003eOncorhynchus mykiss\u003c/em\u003e) aquaculture, due to the absence of effective vaccines and increasing concerns over antibiotic use. Genetic selection for disease resistance offers a sustainable alternative. In this study, we investigated the genetic architecture of BCWD resistance in two French commercial rainbow trout populations using a standardized waterborne infection model and high-density SNP genotyping.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eSurvival following experimental infection varied significantly between populations, with population B showing higher resistance (71.3% vs 50.7% of survival at 29 days post-infection). Genome-wide association studies (GWAS) were performed using a Bayesian sparse linear mixed model (BSLMM), separately in each population and in a combined dataset. Eleven quantitative trait loci (QTLs) were identified across the analyses, with limited overlap between populations, highlighting the complexity and partial divergence of resistance architectures. Several candidate genes located within QTL regions were involved in immune signalling, inflammation, macrophages/neutrophils biology, and soluble factors important for antibacterial defences. Notably, two QTLs contained genes from the complement system (e.g., C3, Cfb), highlighting their central role in resistance to \u003cem\u003eF. psychrophilum\u003c/em\u003e.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eOur findings underscore the polygenic nature of BCWD resistance, the influence of host genetic background, and provide valuable targets for selection for BCWD resistance in rainbow trout breeding programs.\u003c/p\u003e","manuscriptTitle":"Remarquable heterogeneity in the genetic architecture of resistance to a key bacterial pathogen in commercial populations of rainbow trout","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-07-15 12:54:34","doi":"10.21203/rs.3.rs-6591460/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-08-08T19:42:23+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-08T00:41:27+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-30T18:45:07+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"225274531652773212422684357620131753172","date":"2025-07-14T15:25:33+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"225876250301846738817387031517389352771","date":"2025-07-11T19:32:28+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-07-11T18:46:18+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-07-11T15:45:20+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-07-09T15:10:49+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-07-09T12:48:34+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-07-09T12:43:58+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":"870cc5ac-c2ef-49d5-8d64-bc52990cd541","owner":[],"postedDate":"July 15th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-12-01T16:11:29+00:00","versionOfRecord":{"articleIdentity":"rs-6591460","link":"https://doi.org/10.1186/s12864-025-12231-3","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2025-11-28 15:57:26","publishedOnDateReadable":"November 28th, 2025"},"versionCreatedAt":"2025-07-15 12:54:34","video":"","vorDoi":"10.1186/s12864-025-12231-3","vorDoiUrl":"https://doi.org/10.1186/s12864-025-12231-3","workflowStages":[]},"version":"v1","identity":"rs-6591460","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6591460","identity":"rs-6591460","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}