A novel chromosomal fragment deletion in the APRR2 repeated locus modulates dark sterm color in Cucurbita pepo

A novel chromosomal fragment deletion in the APRR2 repeated locus modulates dark sterm color in Cucurbita pepo | 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 A novel chromosomal fragment deletion in the APRR2 repeated locus modulates dark sterm color in Cucurbita pepo Lei Zhu, Yong Wang, Zhenli Zhang, Deju Hu, Zanlin Wang, Jianbin Hu, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1613427/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 4 You are reading this latest preprint version Abstract Stem color is an important agronomic trait in zucchini ( Cucurbita pepo , C. pepo ) for robust seedings and high yield. However, the gene controlling this trait has not been characterized. This study identified a single locus accounting for dark green stem color in C. pepo ( CpDsc-1 ). Genetic analysis of this trait in segregation populations derived from two parental lines (line 296 with dark green stem and line 274 with light green stem) revealed that it was controlled by a single dominant gene (dark green vs. light green). Using the bulked segregant analysis method, CpDsc-1 was mapped to a 2.09 Mb interval on chromosome 15. Then this region was further narrowed down to 65.2 kb using linkage analysis in the F 2 population. Sequencing analysis revealed a 14 kb deletion between Cp4.1LG15g03420 and Cp4.1LG15g03360 , encoding a two-component response regulator-like protein (APRR2). The incomplete structures of the two APRR2 genes and the abnormal chloroplasts in line 274 might be the main reason for the light green phenotype. Gene expression pattern analysis showed that only Cp4.1LG15g03420 was upregulated in line 296. The subcellular localization analysis indicated that Cp4.1LG15g03420 was a nuclear gene. Furthermore, a co-dominant marker G4563 (93% accuracy rate) and a co-segregation marker Fra3 were established in 111 diverse germplasms, and both were tightly linked with the color trait. This study provide new insight into the chlorophyll regulation pathway, and these markers would be valuable for marker-assisted selection in zucchini breeding. Cucurbita pepo Dark green stem color mapping Two-component response regulator-like protein Full Text Supplementary Files SupplementaryInformationSIallFigSandTables.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 09 May, 2022 Reviewers invited by journal 09 May, 2022 Editor assigned by journal 03 May, 2022 First submitted to journal 01 May, 2022 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-1613427","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":104671881,"identity":"bc4cfa81-8af3-4d45-a977-d9a44922f232","order_by":0,"name":"Lei Zhu","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Lei","middleName":"","lastName":"Zhu","suffix":""},{"id":104671882,"identity":"79bf891c-4705-4987-baa6-288857ae515c","order_by":1,"name":"Yong Wang","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Yong","middleName":"","lastName":"Wang","suffix":""},{"id":104671883,"identity":"f8a1b5c3-4196-49db-832c-e915630a4851","order_by":2,"name":"Zhenli Zhang","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Zhenli","middleName":"","lastName":"Zhang","suffix":""},{"id":104671884,"identity":"74034710-97db-4240-977b-06065db4f6b0","order_by":3,"name":"Deju Hu","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Deju","middleName":"","lastName":"Hu","suffix":""},{"id":104671885,"identity":"ad0f64c8-8814-4656-835f-90f6a20f2e79","order_by":4,"name":"Zanlin Wang","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Zanlin","middleName":"","lastName":"Wang","suffix":""},{"id":104671886,"identity":"27a46377-3928-4a89-b711-d27e16e20ec0","order_by":5,"name":"Jianbin Hu","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jianbin","middleName":"","lastName":"Hu","suffix":""},{"id":104671887,"identity":"641e82c7-3172-4b6e-9051-e75ae221b91f","order_by":6,"name":"Changsheng Ma","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Changsheng","middleName":"","lastName":"Ma","suffix":""},{"id":104671888,"identity":"7ce06475-144a-4c0d-b471-8887a5200fca","order_by":7,"name":"Luming Yang","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Luming","middleName":"","lastName":"Yang","suffix":""},{"id":104671889,"identity":"72696daf-6a17-432e-8996-5f703503f918","order_by":8,"name":"Shouru Sun","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA1UlEQVRIiWNgGAWjYHAC5gcf/9gkwDhEaWEznNmQRpoWBmnOhsMkaJHvP/vAmHHH+Tx+6eZnEgwV1okN7GcP4NVicCPd4HHhmdvFknOOmUkwnElPbODJS8CvRYKNwXgG2+3EDTcSzCQY2w4nNkjwGBBw2DEGaR62c4n7b6R/k2D8R4QWhgNpDNK8bQcSN0jkAG1pIEKLwY00NsMZZ5ITZ9zIKbZIOJZu3MaTQ9BhzA8+VNgl9s9I33jjQ421bD/7GQIOQwEJQMxGgvpRMApGwSgYBTgAAAnARbSGrJ2lAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-2730-4413","institution":"Henan Agricultural University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Shouru","middleName":"","lastName":"Sun","suffix":""},{"id":104671890,"identity":"293c2cd3-acfc-4cc2-ab3c-71ac97968ec2","order_by":9,"name":"Yanman Li","email":"","orcid":"","institution":"Henan Agricultural University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Yanman","middleName":"","lastName":"Li","suffix":""}],"badges":[],"createdAt":"2022-05-01 09:03:37","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-1613427/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-1613427/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":21400385,"identity":"f5af176c-7091-4d8f-830c-5b6a9fa554e8","added_by":"auto","created_at":"2022-05-12 16:02:29","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":948333,"visible":true,"origin":"","legend":"","description":"","filename":"ManuscriptV15.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1613427/v1_covered.pdf"},{"id":21400384,"identity":"4086b641-cb00-4305-b988-6f87ea4d0d2c","added_by":"auto","created_at":"2022-05-12 16:02:24","extension":"docx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":161510,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryInformationSIallFigSandTables.docx","url":"https://assets-eu.researchsquare.com/files/rs-1613427/v1/599dab91514a2ba69e913521.docx"}],"financialInterests":"","formattedTitle":"A novel chromosomal fragment deletion in the APRR2 repeated locus modulates dark sterm color in Cucurbita pepo","fulltext":[{"header":"Full Text","content":"This preprint is available for \u003ca href='/article/rs-1613427/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e."}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":true,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"theoretical-and-applied-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"taag","sideBox":"Learn more about [Theoretical and Applied Genetics](https://www.springer.com/journal/122)","snPcode":"122","submissionUrl":"https://submission.nature.com/new-submission/122/3","title":"Theoretical and Applied Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":" Cucurbita pepo, Dark green stem color, mapping, Two-component response regulator-like protein","lastPublishedDoi":"10.21203/rs.3.rs-1613427/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1613427/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Stem color is an important agronomic trait in zucchini ( Cucurbita pepo , C. pepo ) for robust seedings and high yield. However, the gene controlling this trait has not been characterized. This study identified a single locus accounting for dark green stem color in C. pepo ( CpDsc-1 ). Genetic analysis of this trait in segregation populations derived from two parental lines (line 296 with dark green stem and line 274 with light green stem) revealed that it was controlled by a single dominant gene (dark green vs. light green). Using the bulked segregant analysis method, CpDsc-1 was mapped to a 2.09 Mb interval on chromosome 15. Then this region was further narrowed down to 65.2 kb using linkage analysis in the F 2 population. Sequencing analysis revealed a 14 kb deletion between Cp4.1LG15g03420 and Cp4.1LG15g03360 , encoding a two-component response regulator-like protein (APRR2). The incomplete structures of the two APRR2 genes and the abnormal chloroplasts in line 274 might be the main reason for the light green phenotype. Gene expression pattern analysis showed that only Cp4.1LG15g03420 was upregulated in line 296. The subcellular localization analysis indicated that Cp4.1LG15g03420 was a nuclear gene. Furthermore, a co-dominant marker G4563 (93% accuracy rate) and a co-segregation marker Fra3 were established in 111 diverse germplasms, and both were tightly linked with the color trait. This study provide new insight into the chlorophyll regulation pathway, and these markers would be valuable for marker-assisted selection in zucchini breeding.","manuscriptTitle":"A novel chromosomal fragment deletion in the APRR2 repeated locus modulates dark sterm color in Cucurbita pepo","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2022-05-12 16:02:22","doi":"10.21203/rs.3.rs-1613427/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2022-05-09T21:10:56+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2022-05-09T16:06:21+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2022-05-03T17:49:35+00:00","index":"","fulltext":""},{"type":"submitted","content":"Theoretical and Applied Genetics","date":"2022-05-01T05:02:30+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"theoretical-and-applied-genetics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"taag","sideBox":"Learn more about [Theoretical and Applied Genetics](https://www.springer.com/journal/122)","snPcode":"122","submissionUrl":"https://submission.nature.com/new-submission/122/3","title":"Theoretical and Applied Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"8a0ffc99-851a-4074-a898-bfe98dfb22ef","owner":[],"postedDate":"May 12th, 2022","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2022-09-05T07:14:21+00:00","versionOfRecord":[],"versionCreatedAt":"2022-05-12 16:02:22","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-1613427","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-1613427","identity":"rs-1613427","version":["v1"]},"buildId":"ehx78VzkSd0WSzXnipQa-","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}