Isolation of the major wheat domestication gene Tenacious glume1 reveals its multiple phenotypic effects and sheds light on evolution of wheat

Isolation of the major wheat domestication gene Tenacious glume1 reveals its multiple phenotypic effects and sheds light on evolution of wheat | 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 Article Isolation of the major wheat domestication gene Tenacious glume1 reveals its multiple phenotypic effects and sheds light on evolution of wheat Jan Dvorak, Mengyuan Xiao, Le Wang, Juan Debernardi, Karin Deal, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9315249/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Mutations at the Tenacious glume1 (Tg1) loci on chromosome 2A, 2B, and 2D were pivotal for evolution of free-threshing wheat. Here, we identified and validated a Tg1 candidate gene. The wheat 2A- and 2B-loci each contained a single copy of the gene but the 2D-locus was multigenic with at least one of the genes having a frameshift mutation. We found no fixed mutation in CDSs of the 2A- and 2B-genes and suggest that cis-regulatory mutations have led to evolution of free-threshing tetraploid wheat. Tg1 is equivalent to barley ELI-A gene controlling the development of leaf ligule and to the bread wheat reduced-height locus Rht8. In addition, mutations of Tg1 affected spike length, density, shape, and fertility, leaf rigidity, and lodging. Fluorescence in situ hybridization revealed association of Tg1 expression with vascular bundles and tissue boundaries. Durum wheat near isogenic lines harboring non-free-threshing and free-threshing 2B-alleles differed in the abundance of glume sclerenchyma. Our search for differentially expressed genes in the comparison of CRISPR/Cas9 free-threshing mutants vs the non-free-threshing parental line yielded genes for biogenesis of cell wall and cell wall functions. Past selection was centered on the 2A- and 2B-loci in durum wheat, but selection was primarily centered on the 2D-locus in bread wheat. This is consistent with the tetraploid parent of hexaploid wheat being free-threshing. Our haplotype analyses pinpointed the origin of hexaploid wheat in Iran, showed that European and Asian spelt originated separately and confirmed that European spelt and most Asian spelt were derived from free-threshing hexaploid wheat. Biological sciences/Genetics Biological sciences/Genetics/Plant genetics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryData1.xlsx Dataset 1 SupplementaryData2123022.xlsx Dataset 2 SupplementaryData3032326.xlsx Dataset 3 SupplementaryData4032426.xlsx Dataset 4 Supplementarydata5032026.xlsx Dataset 5 Supplementarydata6032126.xlsx Dataset 6 SupplementaryData7033026taushwheat.xlsx Dataset 7 SupplementaryData8033026nonfree.xlsx Dataset 8 SupplementaryData9033026.xlsx Dataset 9 SupplementaryData100330262B.xlsx Dataset 10 SupplementaryInformationplaintext.docx Supplementary Information Cite Share Download PDF Status: Under Review 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-9315249","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":618752786,"identity":"fa3fe229-40c4-4b21-9701-b9651931948e","order_by":0,"name":"Jan Dvorak","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA20lEQVRIiWNgGAWjYBACxoYEEJUgByQMwAjIIU6LMfFaoAoSEhug6glrYW7PMXxcUZOWvuH44Y2feQrqGPjZcwzwamHseWNseOZYTu6GM2nF0jwGhxkke94Q0DIjLU2yga0id8MNHgPJGQYHGAxuELIFrOVfRbrBDR7jnzMM6hjsCWtJPibZ2JaTANRiJvHBgJnBQIKgXx4fNmzsSzOceSatzOKDwWEeiTPPCvBqMWxPbHzY8C1Znu/44c03Ev7UyfG3J2/Ar6UBTYAHr3IQkCeoYhSMglEwCkYBANmRSC70Xv9jAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-0427-6528","institution":"University of California, Davis","correspondingAuthor":true,"prefix":"","firstName":"Jan","middleName":"","lastName":"Dvorak","suffix":""},{"id":618752787,"identity":"74157c26-e137-4ea3-ab46-9b89a862eaa5","order_by":1,"name":"Mengyuan Xiao","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Mengyuan","middleName":"","lastName":"Xiao","suffix":""},{"id":618752788,"identity":"19b332bb-4b43-4fe4-9d82-433cca2d140c","order_by":2,"name":"Le Wang","email":"","orcid":"","institution":"Jilin University","correspondingAuthor":false,"prefix":"","firstName":"Le","middleName":"","lastName":"Wang","suffix":""},{"id":618752789,"identity":"ae933b5e-9a4b-4733-bd6e-52b52b8cb2a7","order_by":3,"name":"Juan Debernardi","email":"","orcid":"https://orcid.org/0000-0002-4591-7061","institution":"UCDavis","correspondingAuthor":false,"prefix":"","firstName":"Juan","middleName":"","lastName":"Debernardi","suffix":""},{"id":618752790,"identity":"e9ac8fd8-495b-4d04-9e60-728c88d75494","order_by":4,"name":"Karin Deal","email":"","orcid":"","institution":"Department of Plant Sciences, University of California, Davis CA 95616","correspondingAuthor":false,"prefix":"","firstName":"Karin","middleName":"","lastName":"Deal","suffix":""},{"id":618752791,"identity":"6795f465-0a26-42a9-bf2e-e6bc57b361a6","order_by":5,"name":"Tingting Zhu","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Tingting","middleName":"","lastName":"Zhu","suffix":""},{"id":618752792,"identity":"baf29834-9deb-476e-9e32-7efaf42a51a1","order_by":6,"name":"Ming-Cheng Luo","email":"","orcid":"https://orcid.org/0000-0002-9744-5887","institution":"University of California Davis","correspondingAuthor":false,"prefix":"","firstName":"Ming-Cheng","middleName":"","lastName":"Luo","suffix":""},{"id":618752793,"identity":"6e4c3ea6-612e-4799-b1b2-1dcd3b0ca51e","order_by":7,"name":"Patrick McGuire","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Patrick","middleName":"","lastName":"McGuire","suffix":""},{"id":618752794,"identity":"6185e404-0a5b-43bf-ae48-4a7f84024e02","order_by":8,"name":"Jacob Yousif","email":"","orcid":"https://orcid.org/0009-0009-5087-9395","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Jacob","middleName":"","lastName":"Yousif","suffix":""},{"id":618752795,"identity":"fad54d61-49a6-438f-978f-750b03386f9d","order_by":9,"name":"Eduard Akhunov","email":"","orcid":"https://orcid.org/0000-0002-0416-5211","institution":"Kansas State University","correspondingAuthor":false,"prefix":"","firstName":"Eduard","middleName":"","lastName":"Akhunov","suffix":""},{"id":618752796,"identity":"a0418c67-74d7-4307-8d8f-c782c1ff681f","order_by":10,"name":"Fei He","email":"","orcid":"","institution":"Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing","correspondingAuthor":false,"prefix":"","firstName":"Fei","middleName":"","lastName":"He","suffix":""},{"id":618752797,"identity":"c574ce32-fc51-4332-83bf-19f376ad54cd","order_by":11,"name":"Yael Lev-Mirom","email":"","orcid":"https://orcid.org/0009-0008-8139-3286","institution":"University of Haifa","correspondingAuthor":false,"prefix":"","firstName":"Yael","middleName":"","lastName":"Lev-Mirom","suffix":""},{"id":618752798,"identity":"cc2964fc-4a1f-43dc-a591-cf94ea35ee22","order_by":12,"name":"Tamar Eilam","email":"","orcid":"","institution":"Institute for Cereal Crops Improvement and School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801 Israel","correspondingAuthor":false,"prefix":"","firstName":"Tamar","middleName":"","lastName":"Eilam","suffix":""},{"id":618752799,"identity":"74261547-00ea-4f6e-b9c0-c2167f4d4a11","order_by":13,"name":"Assaf Distelfeld","email":"","orcid":"","institution":"University of Haifa","correspondingAuthor":false,"prefix":"","firstName":"Assaf","middleName":"","lastName":"Distelfeld","suffix":""},{"id":618752800,"identity":"03ffb72a-bd53-4605-86ba-993d5297b1b2","order_by":14,"name":"Yidong Zhou","email":"","orcid":"https://orcid.org/0000-0003-1423-1857","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Yidong","middleName":"","lastName":"Zhou","suffix":""},{"id":618752801,"identity":"caf99a38-9c12-4c8c-be06-5e56e5970799","order_by":15,"name":"Hans-Georg Müller","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Hans-Georg","middleName":"","lastName":"Müller","suffix":""},{"id":618752802,"identity":"0edcb561-a235-4ec0-a2a9-ef3d7e51241c","order_by":16,"name":"Jorge Dubcovsky","email":"","orcid":"https://orcid.org/0000-0002-7571-4345","institution":"University of California, Davis and Howard Hughes Medical Institute","correspondingAuthor":false,"prefix":"","firstName":"Jorge","middleName":"","lastName":"Dubcovsky","suffix":""}],"badges":[],"createdAt":"2026-04-03 17:35:15","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9315249/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9315249/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":106963485,"identity":"4c3d89dc-7abb-4720-b460-c756c4811ac5","added_by":"auto","created_at":"2026-04-15 09:44:49","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1630435,"visible":true,"origin":"","legend":"","description":"","filename":"Main.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1_covered_ccda422e-6bf3-4846-a3ff-0a24baec4f3a.pdf"},{"id":106874340,"identity":"4e84c9a8-65ef-4020-9766-7da404e90854","added_by":"auto","created_at":"2026-04-14 10:17:18","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":21845,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 1\u003c/p\u003e","description":"","filename":"SupplementaryData1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/69fa021cd92b6f73cf4daca6.xlsx"},{"id":106961633,"identity":"c5e88ee8-76b6-4c47-84cc-a3e4ecfc5319","added_by":"auto","created_at":"2026-04-15 09:26:23","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":19565,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 2\u003c/p\u003e","description":"","filename":"SupplementaryData2123022.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/d8f15b88bed3686f9ed8cfde.xlsx"},{"id":106960456,"identity":"ca012ee6-5330-4744-8672-80288c7da965","added_by":"auto","created_at":"2026-04-15 09:21:14","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":9878,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 3\u003c/p\u003e","description":"","filename":"SupplementaryData3032326.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/1f81f8d523b36e3928039bef.xlsx"},{"id":106960390,"identity":"648075c8-fea8-4b8c-8331-3cafb4eea552","added_by":"auto","created_at":"2026-04-15 09:20:48","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":13076,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 4\u003c/p\u003e","description":"","filename":"SupplementaryData4032426.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/af637293720f9d19070b3ac9.xlsx"},{"id":106874343,"identity":"3e4b1d29-2bd4-4a87-85cc-1c88bec09d39","added_by":"auto","created_at":"2026-04-14 10:17:18","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":29638,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 5\u003c/p\u003e","description":"","filename":"Supplementarydata5032026.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/6c6ee62c92108f147aa7a0cc.xlsx"},{"id":106874344,"identity":"7c046980-949b-416e-b53d-61e8a2fe765b","added_by":"auto","created_at":"2026-04-14 10:17:18","extension":"xlsx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":61932,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 6\u003c/p\u003e","description":"","filename":"Supplementarydata6032126.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/6cd6656d998b9fe4f37be31c.xlsx"},{"id":106960787,"identity":"71eac204-ec9f-4eb7-9b28-8a03249a1c8e","added_by":"auto","created_at":"2026-04-15 09:23:07","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":50007,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 7\u003c/p\u003e","description":"","filename":"SupplementaryData7033026taushwheat.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/91b3ad36d2eb3dc36299d8d4.xlsx"},{"id":106961639,"identity":"7bc7e20c-5e8e-43d6-a3f6-ff91d8075682","added_by":"auto","created_at":"2026-04-15 09:26:24","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":17334,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 8\u003c/p\u003e","description":"","filename":"SupplementaryData8033026nonfree.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/cb7806eb11dd12a9a96523b0.xlsx"},{"id":106960463,"identity":"d8ccae02-3258-4cac-897a-08d94bfdb9eb","added_by":"auto","created_at":"2026-04-15 09:21:15","extension":"xlsx","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":50148,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 9\u003c/p\u003e","description":"","filename":"SupplementaryData9033026.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/26028fc4b61d51029351a8c6.xlsx"},{"id":106961104,"identity":"fdd5c48f-7ff5-4491-a1d0-cd881e983b21","added_by":"auto","created_at":"2026-04-15 09:24:18","extension":"xlsx","order_by":10,"title":"","display":"","copyAsset":false,"role":"supplement","size":63836,"visible":true,"origin":"","legend":"Dataset 10","description":"","filename":"SupplementaryData100330262B.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/36511eb881934c190c299a46.xlsx"},{"id":106874346,"identity":"88071278-da8e-4e77-ba71-3e3ae404087b","added_by":"auto","created_at":"2026-04-14 10:17:18","extension":"docx","order_by":11,"title":"","display":"","copyAsset":false,"role":"supplement","size":8762692,"visible":true,"origin":"","legend":"Supplementary Information","description":"","filename":"SupplementaryInformationplaintext.docx","url":"https://assets-eu.researchsquare.com/files/rs-9315249/v1/4da43dc98a39a439a090f4dc.docx"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Isolation of the major wheat domestication gene Tenacious glume1 reveals its multiple phenotypic effects and sheds light on evolution of wheat","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-9315249/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9315249/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Mutations at the Tenacious glume1 (Tg1) loci on chromosome 2A, 2B, and 2D were pivotal for evolution of free-threshing wheat. Here, we identified and validated a Tg1 candidate gene. The wheat 2A- and 2B-loci each contained a single copy of the gene but the 2D-locus was multigenic with at least one of the genes having a frameshift mutation. We found no fixed mutation in CDSs of the 2A- and 2B-genes and suggest that cis-regulatory mutations have led to evolution of free-threshing tetraploid wheat. Tg1 is equivalent to barley ELI-A gene controlling the development of leaf ligule and to the bread wheat reduced-height locus Rht8. In addition, mutations of Tg1 affected spike length, density, shape, and fertility, leaf rigidity, and lodging. Fluorescence in situ hybridization revealed association of Tg1 expression with vascular bundles and tissue boundaries. Durum wheat near isogenic lines harboring non-free-threshing and free-threshing 2B-alleles differed in the abundance of glume sclerenchyma. Our search for differentially expressed genes in the comparison of CRISPR/Cas9 free-threshing mutants vs the non-free-threshing parental line yielded genes for biogenesis of cell wall and cell wall functions. Past selection was centered on the 2A- and 2B-loci in durum wheat, but selection was primarily centered on the 2D-locus in bread wheat. This is consistent with the tetraploid parent of hexaploid wheat being free-threshing. Our haplotype analyses pinpointed the origin of hexaploid wheat in Iran, showed that European and Asian spelt originated separately and confirmed that European spelt and most Asian spelt were derived from free-threshing hexaploid wheat.","manuscriptTitle":"Isolation of the major wheat domestication gene Tenacious glume1 reveals its multiple phenotypic effects and sheds light on evolution of wheat","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-04-14 10:17:05","doi":"10.21203/rs.3.rs-9315249/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"f98d9e54-9c2d-4f5f-8663-699b6a5d79b1","owner":[],"postedDate":"April 14th, 2026","published":true,"recentEditorialEvents":[{"type":"editorInvitedReview","content":"This content is not available.","date":"2026-05-06T22:25:12+00:00","index":1,"fulltext":"This content is not available."}],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":65836689,"name":"Biological sciences/Genetics"},{"id":65836690,"name":"Biological sciences/Genetics/Plant genetics"}],"tags":[],"updatedAt":"2026-04-14T10:17:06+00:00","versionOfRecord":[],"versionCreatedAt":"2026-04-14 10:17:05","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9315249","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9315249","identity":"rs-9315249","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}