GWAS-informed genomic selection for cold tolerance in pepper (Capsicum annuum L.)

GWAS-informed genomic selection for cold tolerance in pepper (Capsicum annuum L.) | 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 GWAS-informed genomic selection for cold tolerance in pepper (Capsicum annuum L.) Kyeongseok Lee, Geon Woo Kim, Hee-Jin Jeong, Hyeon-Seok Jeong, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9143989/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 13 You are reading this latest preprint version Abstract Background Breeding for cold tolerance in pepper ( Capsicum annuum L.) is critical to mitigate yield losses caused by unpredictable temperature fluctuations associated with climate change. However, genetic improvement of this trait is hindered by challenges in accurate phenotyping, particularly at the adult stage, and by its complex genetic architecture involving numerous minor-effect loci. While genomic selection (GS) offers a promising solution to accelerate genetic gain, its predictive ability is often limited by statistical noise from uninformative markers within whole-genome marker sets. This study aimed to overcome this limitation by developing a robust phenotypic index and implementing a genome-wide association study (GWAS)-informed GS strategy. Results We phenotyped 192 pepper accessions from a core collection for cold tolerance using a visual survival score (Surv) and a newly developed composite cold-tolerance index (CTI). Both CTI ( h 2 = 0.55) and Surv ( h 2 = 0.53) showed moderate heritability, suggesting a substantial contribution from additive genetic variance to the phenotypic variation of cold tolerance in adult plants. GWAS identified 13 candidate genomic regions associated with cold tolerance; these regions included TRM9 , CAP1 , and PP2A-2 , genes previously implicated in abiotic stress responses. A GWAS-informed GS model using a selected subset of 1,024 markers achieved a prediction accuracy of 0.78, representing a substantial improvement over that obtained with the standard model using the full marker set of 73,502 markers (0.203). Notably, a control model using a random marker set of identical size (1,024 markers) yielded an accuracy of only 0.122, confirming that the greater predictive power of the GWAS-informed GS model was driven by the genetic relevance of the selected markers rather than by lower marker density. Conclusions Our study demonstrates that assessing cold tolerance via the CTI is pivotal for overcoming the limitations of small-scale sample collection. By turning ordinal data into a continuous spectrum, the CTI can effectively unmask hidden genetic variation. Integrating this refined phenotype with GWAS-informed marker selection into prediction models significantly enhanced the accuracy of genomic prediction for cold tolerance in adult pepper plants. This integrated framework offers a practical and efficient roadmap for accelerating breeding cycles and improving selection precision for complex abiotic stress traits in pepper breeding. Pepper Cold tolerance Cold-tolerance index (CTI) Genome-wide association study (GWAS) Genomic selection (GS) Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 13 Apr, 2026 Reviews received at journal 11 Apr, 2026 Reviews received at journal 08 Apr, 2026 Reviews received at journal 02 Apr, 2026 Reviewers agreed at journal 23 Mar, 2026 Reviewers agreed at journal 23 Mar, 2026 Reviewers agreed at journal 22 Mar, 2026 Reviewers agreed at journal 20 Mar, 2026 Reviewers invited by journal 20 Mar, 2026 Editor invited by journal 19 Mar, 2026 Editor assigned by journal 18 Mar, 2026 Submission checks completed at journal 18 Mar, 2026 First submitted to journal 17 Mar, 2026 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-9143989","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":610904707,"identity":"7424d018-a20b-4ceb-a1ba-c5faa40d03db","order_by":0,"name":"Kyeongseok Lee","email":"","orcid":"","institution":"Seoul National University","correspondingAuthor":false,"prefix":"","firstName":"Kyeongseok","middleName":"","lastName":"Lee","suffix":""},{"id":610904709,"identity":"89d4f0e7-982a-48d3-a1b4-531e827aaa69","order_by":1,"name":"Geon Woo Kim","email":"","orcid":"","institution":"Seoul National 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Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Pepper, Cold tolerance, Cold-tolerance index (CTI), Genome-wide association study (GWAS), Genomic selection (GS)","lastPublishedDoi":"10.21203/rs.3.rs-9143989/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9143989/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eBreeding for cold tolerance in pepper (\u003cem\u003eCapsicum annuum\u003c/em\u003e L.) is critical to mitigate yield losses caused by unpredictable temperature fluctuations associated with climate change. However, genetic improvement of this trait is hindered by challenges in accurate phenotyping, particularly at the adult stage, and by its complex genetic architecture involving numerous minor-effect loci. While genomic selection (GS) offers a promising solution to accelerate genetic gain, its predictive ability is often limited by statistical noise from uninformative markers within whole-genome marker sets. This study aimed to overcome this limitation by developing a robust phenotypic index and implementing a genome-wide association study (GWAS)-informed GS strategy.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eWe phenotyped 192 pepper accessions from a core collection for cold tolerance using a visual survival score (Surv) and a newly developed composite cold-tolerance index (CTI). Both CTI (\u003cem\u003eh\u003c/em\u003e\u003csup\u003e2\u003c/sup\u003e\u0026thinsp;=\u0026thinsp;0.55) and Surv (\u003cem\u003eh\u003c/em\u003e\u003csup\u003e2\u003c/sup\u003e\u0026thinsp;=\u0026thinsp;0.53) showed moderate heritability, suggesting a substantial contribution from additive genetic variance to the phenotypic variation of cold tolerance in adult plants. GWAS identified 13 candidate genomic regions associated with cold tolerance; these regions included \u003cem\u003eTRM9\u003c/em\u003e, \u003cem\u003eCAP1\u003c/em\u003e, and \u003cem\u003ePP2A-2\u003c/em\u003e, genes previously implicated in abiotic stress responses. A GWAS-informed GS model using a selected subset of 1,024 markers achieved a prediction accuracy of 0.78, representing a substantial improvement over that obtained with the standard model using the full marker set of 73,502 markers (0.203). Notably, a control model using a random marker set of identical size (1,024 markers) yielded an accuracy of only 0.122, confirming that the greater predictive power of the GWAS-informed GS model was driven by the genetic relevance of the selected markers rather than by lower marker density.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003eOur study demonstrates that assessing cold tolerance via the CTI is pivotal for overcoming the limitations of small-scale sample collection. By turning ordinal data into a continuous spectrum, the CTI can effectively unmask hidden genetic variation. Integrating this refined phenotype with GWAS-informed marker selection into prediction models significantly enhanced the accuracy of genomic prediction for cold tolerance in adult pepper plants. This integrated framework offers a practical and efficient roadmap for accelerating breeding cycles and improving selection precision for complex abiotic stress traits in pepper breeding.\u003c/p\u003e","manuscriptTitle":"GWAS-informed genomic selection for cold tolerance in pepper (Capsicum annuum L.)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-24 17:40:17","doi":"10.21203/rs.3.rs-9143989/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-04-13T17:59:36+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-11T15:15:46+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-08T11:13:37+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-02T10:34:54+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"144261970725579574920472937241139165672","date":"2026-03-23T18:23:05+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"4469264239228408392610339478651492974","date":"2026-03-23T09:04:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"108659019555197504665746894873664718394","date":"2026-03-22T05:24:41+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"37942274679499576133582858564142337939","date":"2026-03-20T04:51:06+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-03-20T04:45:27+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-03-19T16:53:45+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-03-18T11:34:47+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-03-18T11:34:07+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2026-03-17T04:30:09+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"96776c3e-5fe0-4a4a-a83a-bd42c723922c","owner":[],"postedDate":"March 24th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[],"tags":[],"updatedAt":"2026-05-08T11:24:43+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-24 17:40:17","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9143989","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9143989","identity":"rs-9143989","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}