The TaBBM-TaWRKY41-TacAGPS1a module affects starch synthesis and grain quality by regulating embryo and endosperm development in wheat

The TaBBM-TaWRKY41-TacAGPS1a module affects starch synthesis and grain quality by regulating embryo and endosperm development in 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 The TaBBM-TaWRKY41-TacAGPS1a module affects starch synthesis and grain quality by regulating embryo and endosperm development in wheat Yuan Chen, Kunming Chen, Xiaohui Li, Yiman Wan, zhaoheng Zhang, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8619315/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 The BABY BOOM (BBM) AP2/ERF transcription factor is a key regulator of plant cell totipotency and embryogenesis, yet its function during zygotic development in monocots remains poorly defined. Here, using single-cell and spatial transcriptomic analyses in wheat, we show that BBM is specifically expressed in the embryo and in adjacent endosperm domains, where it coordinately regulates embryo and endosperm development. Upstream, the AT-hook transcription factor TaAHL10-B1 controls TaBBM-B1 expression, whereas downstream TaBBM-B1 directly associates with TaWRKY41-B1 to regulate TacAGPS1a-A1, which encodes a core enzyme in starch biosynthesis, thereby influencing grain nutrient accumulation and size. Natural polymorphisms in both promoter and coding regions fine-tune these regulatory interactions. Introgression of the large-grain TaBBM-B1 haplotype into small-grain wheat varieties significantly increased grain size. Together, our findings define a TaBBM-B1–TaWRKY41-B1–TacAGPS1a-A1 regulatory module that integrates embryonic growth with endosperm nutrient allocation to determine grain size, revealing an unexpected role for BBM in monocots and providing a molecular framework for improving wheat yield. Biological sciences/Plant sciences/Plant development/Plant embryogenesis Biological sciences/Plant sciences/Plant reproduction/Seed development Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryData9.ListofextremevarietiesandgrainphenotypesforthetwoBBMhaplotypes.xlsx Dataset 9 SupplementaryData10.Primersusedinthisstudy.xlsx Dataset 10 SupplementaryData6.DAPseqidentifiedmotif.xlsx Dataset 6 SupplementaryData5.ThelistDAPseqpeakanno.xlsx Dataset 5 SupplementaryFig.pdf Supplementary Figure SupplementaryData3.Listofdifferentiallyexpressedgenes.xlsx Dataset 3 SupplementaryData8.DNApulldownidentifiedTFs.xlsx Dataset 8 SupplementaryData1.ListofTFinthespatialtranscriptomicandsinglecelltranscriptomic.xlsx Dataset 1 SupplementaryData7.EmbryotranscriptomederivedDEGswithTaBBMB1DAPseqdatasets.xlsx Dataset 7 SupplementaryData2.Listofstarchsynthesisgenesinthe12DAPgrainRNAseq.xlsx Dataset 2 SupplementaryData4.ListofdifferentiallyexpressedGObetweenamiRBBMsandFielder.xlsx Dataset 4 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-8619315","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":575744193,"identity":"21399235-7025-4e82-80be-b6b0ff7a4b57","order_by":0,"name":"Yuan Chen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABCUlEQVRIiWNgGAWjYPCCAwwM7A3MQIYEhM9DlBaeAyRrkUhgRvDxaTG4kfzsAUPNHTlzybeHjXkYLOT5+w8wPnjbxiBvjlNLmrkBw7Fnxpaz85KTeRgkDGfcSGA2nNvGYLizAZeWBDMJxobDiRtu5xgf5v0HZN9gYJPmbWNIMDiAS0v6N5CW+g03zxgfBtpiP//8Afbf+LXkgG1JMLjBYwxyWOKGAwlszPi0SJ55UyaRcOyw4YYzecmGcxgkkjfeSGyWnHNOwnADDi18x9O3SXyoOSxvcPzsYYk3DHW2884fPvjhTZmNPC5bFEDiCWAmPC4YGxjgcYoFyDfAmUTE+CgYBaNgFIxMAADrDFrdlVC5sgAAAABJRU5ErkJggg==","orcid":"","institution":"Peking University Institute of Advanced Agricultural Sciences","correspondingAuthor":true,"prefix":"","firstName":"Yuan","middleName":"","lastName":"Chen","suffix":""},{"id":575744194,"identity":"8a41459f-5edd-4825-b207-3f223c0c7592","order_by":1,"name":"Kunming Chen","email":"","orcid":"https://orcid.org/0000-0002-0016-9995","institution":"Northwest A\u0026F University","correspondingAuthor":false,"prefix":"","firstName":"Kunming","middleName":"","lastName":"Chen","suffix":""},{"id":575744195,"identity":"6f0214b6-8172-480d-9ecc-33a6d4e9d83e","order_by":2,"name":"Xiaohui Li","email":"","orcid":"","institution":"Peking University Institute of Advanced Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Xiaohui","middleName":"","lastName":"Li","suffix":""},{"id":575744196,"identity":"f594f334-d2c3-47c5-962b-135a161f5a45","order_by":3,"name":"Yiman Wan","email":"","orcid":"","institution":"Peking University Institute of Advanced Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Yiman","middleName":"","lastName":"Wan","suffix":""},{"id":575744197,"identity":"6cacb156-540f-4399-9482-7a7dc21e50b6","order_by":4,"name":"zhaoheng Zhang","email":"","orcid":"","institution":"China Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"zhaoheng","middleName":"","lastName":"Zhang","suffix":""},{"id":575744198,"identity":"fd6a7973-c1ba-46d8-b9c4-014b81060a41","order_by":5,"name":"Dongzhi Wang","email":"","orcid":"","institution":"Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences","correspondingAuthor":false,"prefix":"","firstName":"Dongzhi","middleName":"","lastName":"Wang","suffix":""},{"id":575744199,"identity":"0bce34ee-5f93-436d-a40f-80317b59e8d8","order_by":6,"name":"Meng Yuan","email":"","orcid":"","institution":"Northwest A\u0026F University","correspondingAuthor":false,"prefix":"","firstName":"Meng","middleName":"","lastName":"Yuan","suffix":""},{"id":575744200,"identity":"97ddf3c2-e372-498b-9aab-1c020e624b1c","order_by":7,"name":"Fuqiang Zhu","email":"","orcid":"","institution":"Peking University Institute of Advanced Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Fuqiang","middleName":"","lastName":"Zhu","suffix":""},{"id":575744201,"identity":"5cd09e9e-c8bc-4077-9d3d-d1d76597ec79","order_by":8,"name":"Chunxue Xie","email":"","orcid":"","institution":"Peking University Institute of Advanced Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Chunxue","middleName":"","lastName":"Xie","suffix":""},{"id":575744202,"identity":"981c7bc1-1625-4dab-9ffe-4d59137daa9b","order_by":9,"name":"Qiangqiang Zhang","email":"","orcid":"","institution":"Peking University Institute of Advanced Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Qiangqiang","middleName":"","lastName":"Zhang","suffix":""},{"id":575744203,"identity":"c4228560-dc7b-47f2-a0a3-0cead912e71e","order_by":10,"name":"Xing Guo Li","email":"","orcid":"","institution":"Shandong Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Xing","middleName":"Guo","lastName":"Li","suffix":""},{"id":575744204,"identity":"755a0185-7e82-4b5b-aa68-2a26a87703a7","order_by":11,"name":"Jiajie Wu","email":"","orcid":"https://orcid.org/0000-0002-1536-2421","institution":"Shandong Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Jiajie","middleName":"","lastName":"Wu","suffix":""},{"id":575744205,"identity":"16f0bca3-cac3-4f19-b283-2765725c77f1","order_by":12,"name":"Jianhui Wu","email":"","orcid":"https://orcid.org/0000-0001-8154-1199","institution":"Northwest A\u0026F University","correspondingAuthor":false,"prefix":"","firstName":"Jianhui","middleName":"","lastName":"Wu","suffix":""},{"id":575744206,"identity":"577b92fe-217a-4a4b-badb-d7f4fbaa5960","order_by":13,"name":"Jun Xiao","email":"","orcid":"https://orcid.org/0000-0002-6077-2155","institution":"Institute of Genetics and Developmental Biology, Chinese Academy of Sciences","correspondingAuthor":false,"prefix":"","firstName":"Jun","middleName":"","lastName":"Xiao","suffix":""}],"badges":[],"createdAt":"2026-01-16 13:18:49","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8619315/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8619315/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":102295847,"identity":"c19fb202-1680-4b33-84e8-b62284f1b9fd","added_by":"auto","created_at":"2026-02-10 10:15:30","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1657782,"visible":true,"origin":"","legend":"Article File","description":"","filename":"Article.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1_covered_d36242ea-fb05-4ad7-8cb7-84fdaab41f36.pdf"},{"id":101249201,"identity":"871bd7b7-6132-45c3-95e9-df12da9584b8","added_by":"auto","created_at":"2026-01-27 17:15:04","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":11005,"visible":true,"origin":"","legend":"Dataset 9","description":"","filename":"SupplementaryData9.ListofextremevarietiesandgrainphenotypesforthetwoBBMhaplotypes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/332ebb7498f849984a0e3a47.xlsx"},{"id":101249203,"identity":"aa3a61f9-2794-44d1-8c4b-6dbff3a77f80","added_by":"auto","created_at":"2026-01-27 17:15:04","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":11942,"visible":true,"origin":"","legend":"Dataset 10","description":"","filename":"SupplementaryData10.Primersusedinthisstudy.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/ee7d5a7d119c0954602258b8.xlsx"},{"id":101296828,"identity":"af839f0c-91c7-4549-a718-2eead2df2b4a","added_by":"auto","created_at":"2026-01-28 09:21:17","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":10655,"visible":true,"origin":"","legend":"Dataset 6","description":"","filename":"SupplementaryData6.DAPseqidentifiedmotif.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/76e1d00623ab81371894c6de.xlsx"},{"id":101296874,"identity":"2051859f-66f9-4df4-92aa-264dab41c0f7","added_by":"auto","created_at":"2026-01-28 09:22:22","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":285320,"visible":true,"origin":"","legend":"Dataset 5","description":"","filename":"SupplementaryData5.ThelistDAPseqpeakanno.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/90efc8d3935b9fe9a7e38fd7.xlsx"},{"id":101297773,"identity":"5f8f22f3-3b1c-4f7f-834d-ccba3b3e04cb","added_by":"auto","created_at":"2026-01-28 09:28:44","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":1039055,"visible":true,"origin":"","legend":"Supplementary Figure","description":"","filename":"SupplementaryFig.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/2d7f901716da68611b188d8e.pdf"},{"id":101297708,"identity":"e20248fb-54e3-4a3c-9072-440fd3b19c49","added_by":"auto","created_at":"2026-01-28 09:28:41","extension":"xlsx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":709103,"visible":true,"origin":"","legend":"Dataset 3","description":"","filename":"SupplementaryData3.Listofdifferentiallyexpressedgenes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/840d4b16c46c6ffec01ac580.xlsx"},{"id":101297564,"identity":"04836487-0e3d-45c2-901a-b5c9dd7b3bca","added_by":"auto","created_at":"2026-01-28 09:27:57","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":38836,"visible":true,"origin":"","legend":"Dataset 8","description":"","filename":"SupplementaryData8.DNApulldownidentifiedTFs.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/1cc90d589f9fa855255dbd81.xlsx"},{"id":101249206,"identity":"7de96625-9b8e-43c9-a746-432c03f1cd8b","added_by":"auto","created_at":"2026-01-27 17:15:04","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":43905,"visible":true,"origin":"","legend":"Dataset 1","description":"","filename":"SupplementaryData1.ListofTFinthespatialtranscriptomicandsinglecelltranscriptomic.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/2909aed6b18c0f9a1c84c2b7.xlsx"},{"id":101297490,"identity":"27a6fb49-302e-475c-b6da-dcaf44535bbb","added_by":"auto","created_at":"2026-01-28 09:27:22","extension":"xlsx","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":11530,"visible":true,"origin":"","legend":"Dataset 7","description":"","filename":"SupplementaryData7.EmbryotranscriptomederivedDEGswithTaBBMB1DAPseqdatasets.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/8a0b4cff105c987da7032b0e.xlsx"},{"id":101249204,"identity":"3974c27c-f6e6-48c9-b188-f49f70a5c8ac","added_by":"auto","created_at":"2026-01-27 17:15:04","extension":"xlsx","order_by":10,"title":"","display":"","copyAsset":false,"role":"supplement","size":12437,"visible":true,"origin":"","legend":"Dataset 2","description":"","filename":"SupplementaryData2.Listofstarchsynthesisgenesinthe12DAPgrainRNAseq.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/0f26ddbbfd811101b4efdebf.xlsx"},{"id":101249211,"identity":"30a99978-f367-40f5-810a-05cce2d2059b","added_by":"auto","created_at":"2026-01-27 17:15:04","extension":"xlsx","order_by":11,"title":"","display":"","copyAsset":false,"role":"supplement","size":226591,"visible":true,"origin":"","legend":"Dataset 4","description":"","filename":"SupplementaryData4.ListofdifferentiallyexpressedGObetweenamiRBBMsandFielder.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8619315/v1/27d46a6e9257d9094eb5ffee.xlsx"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"The TaBBM-TaWRKY41-TacAGPS1a module affects starch synthesis and grain quality by regulating embryo and endosperm development in wheat","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"","lastPublishedDoi":"10.21203/rs.3.rs-8619315/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8619315/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"The BABY BOOM (BBM) AP2/ERF transcription factor is a key regulator of plant cell totipotency and embryogenesis, yet its function during zygotic development in monocots remains poorly defined. Here, using single-cell and spatial transcriptomic analyses in wheat, we show that BBM is specifically expressed in the embryo and in adjacent endosperm domains, where it coordinately regulates embryo and endosperm development. Upstream, the AT-hook transcription factor TaAHL10-B1 controls TaBBM-B1 expression, whereas downstream TaBBM-B1 directly associates with TaWRKY41-B1 to regulate TacAGPS1a-A1, which encodes a core enzyme in starch biosynthesis, thereby influencing grain nutrient accumulation and size. Natural polymorphisms in both promoter and coding regions fine-tune these regulatory interactions. Introgression of the large-grain TaBBM-B1 haplotype into small-grain wheat varieties significantly increased grain size. Together, our findings define a TaBBM-B1–TaWRKY41-B1–TacAGPS1a-A1 regulatory module that integrates embryonic growth with endosperm nutrient allocation to determine grain size, revealing an unexpected role for BBM in monocots and providing a molecular framework for improving wheat yield.","manuscriptTitle":"The TaBBM-TaWRKY41-TacAGPS1a module affects starch synthesis and grain quality by regulating embryo and endosperm development in wheat","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-27 17:14:58","doi":"10.21203/rs.3.rs-8619315/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":"4fdf8bcf-6962-4fba-be6a-c57cb4713c88","owner":[],"postedDate":"January 27th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":61264104,"name":"Biological sciences/Plant sciences/Plant development/Plant embryogenesis"},{"id":61264105,"name":"Biological sciences/Plant sciences/Plant reproduction/Seed development"}],"tags":[],"updatedAt":"2026-02-06T15:45:38+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-27 17:14:58","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8619315","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8619315","identity":"rs-8619315","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}