Genetic diversity of NIP genes in Rynchosporium commune in France and genome wide association study of sensitivity to leaf scald in a French winter barley collection grown in the field and in controlled conditions.

Genetic diversity of NIP genes in Rynchosporium commune in France and genome wide association study of sensitivity to leaf scald in a French winter barley collection grown in the field and in controlled conditions. | 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 Genetic diversity of NIP genes in Rynchosporium commune in France and genome wide association study of sensitivity to leaf scald in a French winter barley collection grown in the field and in controlled conditions. MATTHIEU BOGARD, Faharidine Mohamadi, Isabelle Chaillet, Clément Debiton, and 16 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7865876/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 Leaf scald in barley ( Hordeum vulgare ) is a foliar disease caused by Rhynchosporium commune . This disease causes leaf necrosis and decreased grain yield and quality. Disease control consists in adapting management practices, using fungicides and resistant varieties. Knowledge of avirulence and resistance genes is crucial to develop resistant varieties and reduce the use of fungicides. This study aimed at characterizing the genetic diversity of NIP genes in R. commune isolates present in France and identifying genomic regions associated to leaf scald resistance. 103 isolates of R. commune from different locations and varieties were sampled. Characterization of NIP diversity for 81 isolates showed 15 haplotypes for NIP1 but only three for NIP2 and two for NIP3 . A panel of 289 winter barley varieties genotyped using the iSelect 50K SNP array was tested in 14 field trials under natural inoculation and against three isolates in controlled conditions. Single environment and GWAS meta-analysis across trials showed 19 QTLs associated to leaf scald resistance. Some regions corresponded to known resistance genes ( Rrs1, Rrs2, Rrs12, Rrs14, Rrs17 ), others colocalized with previously identified QTLs while a few could be new sources of resistance. Most of the regions were largely present in this germplasm although three remained underrepresented. There was a high correlation between the average resistance level and the number of favourable alleles present in the varieties and a genomic prediction model showed good predictive ability for leaf scald resistance. Barley Rhynchosporium commune leaf scald genome wide association study QTL Full Text Supplementary Files ESM1.xlsx ESM2.pdf ESM3.xlsx ESM4.xlsx 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. 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-7865876","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":538789186,"identity":"f2c8ae4c-f3fc-4467-a538-c850a166c536","order_by":0,"name":"MATTHIEU BOGARD","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA3ElEQVRIiWNgGAWjYFACHjDJ2A+mCiQYGJgPEKllZgOIMgBqYUsgUssGsNkGDIS16DbwHnz4peae7ObjZ59J/DCwsGdg432AV4vZAb5kY5ljxcbbzqSbSfYYSCQ2sLEbENDCYyYtwZaQuO1AGrMBj4FEAoN8G36HQbT8S0jc3P+M2fCPgQTQYWyEtUh+bEtI3CCRxvgYaAtjA0Eth4F+YexLMJ5x4xnjYxmgX9oIajnee/Dhj28Jsv39aQwH31TU2fMT0sLADEQ8yAKENIAB4w9iVI2CUTAKRsHIBQA2wj1dPcjzGgAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-1349-8330","institution":"Arvalis Institut du Vegetal","correspondingAuthor":true,"prefix":"","firstName":"MATTHIEU","middleName":"","lastName":"BOGARD","suffix":""},{"id":538789187,"identity":"284655ca-9693-4d05-8dda-aeb2384ca997","order_by":1,"name":"Faharidine Mohamadi","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Faharidine","middleName":"","lastName":"Mohamadi","suffix":""},{"id":538789188,"identity":"e2738dd0-a8be-473a-bf3a-6c499fdb168c","order_by":2,"name":"Isabelle Chaillet","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Isabelle","middleName":"","lastName":"Chaillet","suffix":""},{"id":538789189,"identity":"512cb814-438f-4255-8980-b2f56ca86d54","order_by":3,"name":"Clément Debiton","email":"","orcid":"","institution":"UCA INRAE GDEC","correspondingAuthor":false,"prefix":"","firstName":"Clément","middleName":"","lastName":"Debiton","suffix":""},{"id":538789190,"identity":"bf1d5f86-6d00-4ae8-981f-913e9e40d413","order_by":4,"name":"Johan Toussaint","email":"","orcid":"","institution":"Florimond-Deprez","correspondingAuthor":false,"prefix":"","firstName":"Johan","middleName":"","lastName":"Toussaint","suffix":""},{"id":538789191,"identity":"cc707f1d-9f6c-4644-a63e-d5382603a7bf","order_by":5,"name":"Eric Gillard","email":"","orcid":"","institution":"Lemaire-Deffontaines","correspondingAuthor":false,"prefix":"","firstName":"Eric","middleName":"","lastName":"Gillard","suffix":""},{"id":538789192,"identity":"8b4a9bab-122e-4bdc-9175-046a79122cb5","order_by":6,"name":"Jean-Marc Decherf","email":"","orcid":"","institution":"Unisigma","correspondingAuthor":false,"prefix":"","firstName":"Jean-Marc","middleName":"","lastName":"Decherf","suffix":""},{"id":538789193,"identity":"aae26d2d-45ae-4942-8235-58b20ea72073","order_by":7,"name":"Mathieu Tison","email":"","orcid":"","institution":"RAGT Seeds Ltd","correspondingAuthor":false,"prefix":"","firstName":"Mathieu","middleName":"","lastName":"Tison","suffix":""},{"id":538789194,"identity":"d3a5c471-afa5-47c5-80f7-8e30c224088a","order_by":8,"name":"Jean-François Herbommez","email":"","orcid":"","institution":"KWS-Momont","correspondingAuthor":false,"prefix":"","firstName":"Jean-François","middleName":"","lastName":"Herbommez","suffix":""},{"id":538789195,"identity":"c40ca292-b0a2-4186-8b9d-5de56cd90ea0","order_by":9,"name":"Emmanuelle Dyrszka","email":"","orcid":"","institution":"Syngenta","correspondingAuthor":false,"prefix":"","firstName":"Emmanuelle","middleName":"","lastName":"Dyrszka","suffix":""},{"id":538789196,"identity":"4f4ea750-9903-4426-bed2-7d89f6454ebf","order_by":10,"name":"Thierry Bouthillier","email":"","orcid":"","institution":"ASUR plant breeding","correspondingAuthor":false,"prefix":"","firstName":"Thierry","middleName":"","lastName":"Bouthillier","suffix":""},{"id":538789197,"identity":"94ac7e78-0b2a-4e60-a1f0-1dc6a02cd5e4","order_by":11,"name":"Jordan Peltier","email":"","orcid":"","institution":"Groupe Limagrain","correspondingAuthor":false,"prefix":"","firstName":"Jordan","middleName":"","lastName":"Peltier","suffix":""},{"id":538789198,"identity":"bc825b54-926a-4d4c-8cd7-110f8485dbc9","order_by":12,"name":"Claire Venel","email":"","orcid":"","institution":"SECOBRA","correspondingAuthor":false,"prefix":"","firstName":"Claire","middleName":"","lastName":"Venel","suffix":""},{"id":538789199,"identity":"3bff820b-8b79-45eb-a67a-2124d023227e","order_by":13,"name":"Amélie Genty","email":"","orcid":"","institution":"SECOBRA","correspondingAuthor":false,"prefix":"","firstName":"Amélie","middleName":"","lastName":"Genty","suffix":""},{"id":538789200,"identity":"0083f2a0-8372-4046-a0c9-65a871279df2","order_by":14,"name":"Cindy Vitry","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Cindy","middleName":"","lastName":"Vitry","suffix":""},{"id":538789201,"identity":"ff950d95-ae04-49f6-84c3-f1c5de33eac5","order_by":15,"name":"Madison Van't Klooster","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Madison","middleName":"Van't","lastName":"Klooster","suffix":""},{"id":538789202,"identity":"cb0546e3-1da6-4a28-9526-0083ae169c80","order_by":16,"name":"Agathe Jung","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Agathe","middleName":"","lastName":"Jung","suffix":""},{"id":538789203,"identity":"e308cde7-58a0-4554-9cd7-bf094eaf08d5","order_by":17,"name":"Ghislain Delestre","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Ghislain","middleName":"","lastName":"Delestre","suffix":""},{"id":538789204,"identity":"a8e40e82-e36a-4c19-8ef8-ceec97ba6f78","order_by":18,"name":"Florent Duyme","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Florent","middleName":"","lastName":"Duyme","suffix":""},{"id":538789205,"identity":"1901f742-98d7-4e67-a1f2-224dec767026","order_by":19,"name":"Romain Valade","email":"","orcid":"","institution":"Arvalis Institut du Vegetal","correspondingAuthor":false,"prefix":"","firstName":"Romain","middleName":"","lastName":"Valade","suffix":""}],"badges":[],"createdAt":"2025-10-15 08:45:28","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7865876/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7865876/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":95757642,"identity":"d4064834-13a6-4541-98d6-bfcc3cd60283","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"xml","order_by":2,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":17382,"visible":true,"origin":"","legend":"","description":"","filename":"taagTAAGD2500943.xml","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/102e127dfcb577489a75cfc9.xml"},{"id":95802523,"identity":"79704682-5696-4258-871e-dcc70a46cf57","added_by":"auto","created_at":"2025-11-13 08:27:46","extension":"xml","order_by":3,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":1092,"visible":true,"origin":"","legend":"","description":"","filename":"TAAGD250094319581.go.xml","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/385cb962280e80f72e933a78.xml"},{"id":95757644,"identity":"768a4784-5782-4b69-815e-1ec6c37dc19a","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"xml","order_by":4,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":920,"visible":true,"origin":"","legend":"","description":"","filename":"TAAGD2500943Import.xml","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/3d4ee11aed676afe1dad96a0.xml"},{"id":95802031,"identity":"ab558398-c5e6-40dc-be61-51a3d38f19fe","added_by":"auto","created_at":"2025-11-13 08:26:40","extension":"xml","order_by":9,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":206455,"visible":true,"origin":"","legend":"","description":"","filename":"TAAGD25009430enriched.xml","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/a4f342750081fb9a390b4d03.xml"},{"id":95757649,"identity":"eac0d1b4-6802-4bf3-bf33-b16ed2100b4d","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":10,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":38130,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/e0bc37a8371f7050390a020f.png"},{"id":95757648,"identity":"8165c15d-a9bd-4aca-b72c-8dc5258bf0b6","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":11,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":18528,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/f9a1ebb552346c90519e7879.png"},{"id":95757654,"identity":"beea5e24-db90-43cd-8d1f-3ebae5e1c4aa","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":12,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":141352,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/4a7a7fd0b32caae7ef2cf880.png"},{"id":95757653,"identity":"774382d3-9e76-4e0a-a13e-189f3d95305d","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":13,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":552885,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/89c88d36b1685232ef672d5a.png"},{"id":95757655,"identity":"0ef264bd-5b97-40c4-a725-e10bd7d6b2cb","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":14,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":27340,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/91bd53d796c45dc5892aa8bb.png"},{"id":95757660,"identity":"380c438d-dfbd-4bc1-b9d0-9e5f69918ece","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"jpeg","order_by":15,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":335709,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage6.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/7d4bcaef4e96ede510e8525e.jpeg"},{"id":95802509,"identity":"2dfd6dad-3010-43f7-9505-6312a2245a8a","added_by":"auto","created_at":"2025-11-13 08:27:44","extension":"png","order_by":16,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":18723,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/662d120ef3e804c444dddd9f.png"},{"id":95801713,"identity":"ed8babaf-3c41-42ce-bae2-d91b6de1424c","added_by":"auto","created_at":"2025-11-13 08:26:00","extension":"png","order_by":17,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":7775,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/f8389f059acb15002d5a6f66.png"},{"id":95757656,"identity":"9d50bcf3-8c26-4202-8b55-fab3a5106c1b","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":18,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":64082,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/277d404d478f4680bb208b38.png"},{"id":95757658,"identity":"8ffc16b0-ebe7-4db2-80ff-55a53160f3de","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":19,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":109751,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/687ca3bc201f4d03e17baca5.png"},{"id":95802094,"identity":"89cec330-9194-4957-bfaa-1ba79cd78746","added_by":"auto","created_at":"2025-11-13 08:26:51","extension":"png","order_by":20,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":11941,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/e7f15ba885dd3891d80dccdb.png"},{"id":95757662,"identity":"30f67b65-8924-426b-b980-00afefb7d7fa","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"png","order_by":21,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":79478,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage6.png","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/1d11befaeaaf66282f7efc27.png"},{"id":95757661,"identity":"6ff82ef1-341e-47d2-9b86-37d7049ae078","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"xml","order_by":22,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":204553,"visible":true,"origin":"","legend":"","description":"","filename":"TAAGD25009430structuring.xml","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/4c860a308a5d5ee0d6ab3998.xml"},{"id":95757663,"identity":"5e57e7ab-a8d7-4595-b9e9-ae2d259368fa","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"html","order_by":23,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":221969,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/6d3da935e39ba33c1541d484.html"},{"id":100549351,"identity":"ce9bbeb5-007c-41ef-a6c0-1203869cda34","added_by":"auto","created_at":"2026-01-19 08:23:06","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1061982,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1_covered_a2ea84f4-65a7-4fc2-8bde-dadbe1fa9206.pdf"},{"id":95757643,"identity":"1e256146-5fc9-433f-98a1-87bb60378e56","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":22913,"visible":true,"origin":"","legend":"","description":"","filename":"ESM1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/bd32109627b8b1aa9eada86f.xlsx"},{"id":95757650,"identity":"a1974a64-7793-44a7-ad24-c02526a02913","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"pdf","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":686128,"visible":true,"origin":"","legend":"","description":"","filename":"ESM2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/7f01038824cc1438f1e7b8f3.pdf"},{"id":95801897,"identity":"5717a3c6-6686-4558-b518-d40c76059f0b","added_by":"auto","created_at":"2025-11-13 08:26:25","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":26757,"visible":true,"origin":"","legend":"","description":"","filename":"ESM3.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/136cd46060f503c977cd07d2.xlsx"},{"id":95757646,"identity":"70a69fa7-b930-4027-9df1-5b24570ab153","added_by":"auto","created_at":"2025-11-12 17:02:34","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":14467,"visible":true,"origin":"","legend":"","description":"","filename":"ESM4.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7865876/v1/8cfdcd793f3fc080e447ba78.xlsx"}],"financialInterests":"","formattedTitle":"Genetic diversity of NIP genes in Rynchosporium commune in France and genome wide association study of sensitivity to leaf scald in a French winter barley collection grown in the field and in controlled conditions.","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":"Barley, Rhynchosporium commune, leaf scald, genome wide association study, QTL","lastPublishedDoi":"10.21203/rs.3.rs-7865876/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7865876/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eLeaf scald in barley (\u003cem\u003eHordeum vulgare\u003c/em\u003e) is a foliar disease caused by \u003cem\u003eRhynchosporium commune\u003c/em\u003e. This disease causes leaf necrosis and decreased grain yield and quality. Disease control consists in adapting management practices, using fungicides and resistant varieties. Knowledge of avirulence and resistance genes is crucial to develop resistant varieties and reduce the use of fungicides. This study aimed at characterizing the genetic diversity of \u003cem\u003eNIP\u003c/em\u003e genes in \u003cem\u003eR. commune\u003c/em\u003e isolates present in France and identifying genomic regions associated to leaf scald resistance. 103 isolates of \u003cem\u003eR. commune\u003c/em\u003e from different locations and varieties were sampled. Characterization of \u003cem\u003eNIP\u003c/em\u003e diversity for 81 isolates showed 15 haplotypes for \u003cem\u003eNIP1\u003c/em\u003e but only three for \u003cem\u003eNIP2\u003c/em\u003e and two for \u003cem\u003eNIP3\u003c/em\u003e. A panel of 289 winter barley varieties genotyped using the iSelect 50K SNP array was tested in 14 field trials under natural inoculation and against three isolates in controlled conditions. Single environment and GWAS meta-analysis across trials showed 19 QTLs associated to leaf scald resistance. Some regions corresponded to known resistance genes\u003cem\u003e \u003c/em\u003e(\u003cem\u003eRrs1, Rrs2, Rrs12, Rrs14, Rrs17\u003c/em\u003e),\u003cem\u003e \u003c/em\u003eothers colocalized with previously identified QTLs while a few could be new sources of resistance. Most of the regions were largely present in this germplasm although three remained underrepresented. There was a high correlation between the average resistance level and the number of favourable alleles present in the varieties and a genomic prediction model showed good predictive ability for leaf scald resistance.\u003c/p\u003e","manuscriptTitle":"Genetic diversity of NIP genes in Rynchosporium commune in France and genome wide association study of sensitivity to leaf scald in a French winter barley collection grown in the field and in controlled conditions.","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-12 17:02:29","doi":"10.21203/rs.3.rs-7865876/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":"77e7e193-68b8-4b0a-8c02-4b8bdfd69b08","owner":[],"postedDate":"November 12th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-01-19T03:42:41+00:00","versionOfRecord":[],"versionCreatedAt":"2025-11-12 17:02:29","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7865876","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7865876","identity":"rs-7865876","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}