Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean | 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 Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean Tatiana Garcia, Jorge Duitama, Stephanie Zullo, Juanita Gil, Andrea Ariani, and 8 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-95762/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 29 Jan, 2021 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Lima bean ( Phaseolus lunatus L. ) is one of the five domesticated Phaseolus bean crops, which are essential sources of dietary proteins for human consumption. Compared to common bean ( P. vulgaris ), it shows a wider range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations and its phenotypic plasticity make Lima bean a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. Lima bean is also an excellent model to study convergent evolution of the adaptive domestication syndrome due to its dual domestication in Mesoamerica and the Andes. Combining long and short read sequencing technologies with a dense genetic map from a biparental population, we obtained the first chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models showed high diversity among 1,917 genes with conserved domains related to disease resistance. Structural comparison across 21,180 orthologs with common bean revealed high genome synteny and two large intrachromosomal rearrangements. Speciation between P. lunatus and P. vulgaris occurred about six million years ago according to nucleotide evolution between these orthologs. Population genomic analysis of GBS data for 482 wild and domesticated accessions from the Mesoamerican and Andean gene pools provided novel evidence on population structure at a finer geographical scale. Results show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. A new wild cluster of diversity was found in the Colombian Andes and a separate genetic cluster was observed for Mesoamerican landraces of the Peninsula of Yucatan in Mexico. This study also documents genome wide patterns of selection and haplotype introgression events among gene pools. Analysis of RNA-seq data obtained from wild and domesticated accessions at two different pod developmental stages revealed 4,275 differentially expressed genes, which could be related to pod dehiscence and seed development. We expect that the present resources serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide new tools and information for breeding for climate change resiliency of different domesticated species. Epigenetics & Genomics Plant Molecular Biology and Genetics Adaptations and Phenotypic Plasticity Food Security Climate Change Convergent Evolution Haplotype Introgression Events Figures Figure 1 Figure 2 Figure 3 Figure 4 Full Text Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the latest manuscript can be downloaded and accessed as a PDF. Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryMaterials.pdf Supplementary materials SupplementaryTable1LinkageMap.xlsx Supplementary table 1 SupplementaryTable2RecombRates.xlsx Supplementary table 2 SupplementaryTable3RepeatAnnotation.xlsx Supplementary table 3 SupplementaryTable4QTL.xlsx Supplementary table 4 SupplementaryTable5GenesAgronomicTraits.xlsx Supplementary table 5 SupplementaryTable6RGenes.xlsx Supplementary table 6 SupplementaryTable7Accessions.xlsx Supplementary table 7 SupplementaryTable8StructureK6.xlsx Supplementary table 8 SupplementaryTable9DiversityStats.xlsx Supplementary table 9 SupplementaryTable10FstBetweenPops.xlsx Supplementary table 10 SupplementaryTable11Introgressions.xlsx Supplementary table 11 SupplementaryTable12DEGs.xlsx Supplementary table 12 Cite Share Download PDF Status: Published Journal Publication published 29 Jan, 2021 Read the published version in Nature Communications → 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-95762","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":3891073,"identity":"d13e6187-798c-4571-bbd9-39d72ea6629d","order_by":0,"name":"Tatiana Garcia","email":"","orcid":"","institution":"Universidad Nacional de Colombia","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Tatiana","middleName":"","lastName":"Garcia","suffix":""},{"id":3891074,"identity":"fbf86cab-90fa-48c9-9215-828a07aea820","order_by":1,"name":"Jorge Duitama","email":"","orcid":"https://orcid.org/0000-0002-9105-6266","institution":"Universidad de los Andes","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jorge","middleName":"","lastName":"Duitama","suffix":""},{"id":3891075,"identity":"e7d4ecdc-dcb6-4750-9649-4540f64b7dcd","order_by":2,"name":"Stephanie Zullo","email":"","orcid":"","institution":"University of California Davis","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Stephanie","middleName":"","lastName":"Zullo","suffix":""},{"id":3891076,"identity":"644ed6a8-d221-41be-9e74-2bb1c9cef81d","order_by":3,"name":"Juanita Gil","email":"","orcid":"https://orcid.org/0000-0002-8333-4254","institution":"Universidad de los Andes","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Juanita","middleName":"","lastName":"Gil","suffix":""},{"id":3891077,"identity":"2bef8f80-7622-4e40-9b75-544f6acb846e","order_by":4,"name":"Andrea Ariani","email":"","orcid":"","institution":"University of California Davis","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Andrea","middleName":"","lastName":"Ariani","suffix":""},{"id":3891078,"identity":"911081dd-6b74-4f62-b4aa-92ce31e4b3fa","order_by":5,"name":"Sarah Dohle","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Sarah","middleName":"","lastName":"Dohle","suffix":""},{"id":3891079,"identity":"791d124f-97cd-4133-99e2-7eff6032069c","order_by":6,"name":"Antonia Palkovic","email":"","orcid":"","institution":"University of California Davis","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Antonia","middleName":"","lastName":"Palkovic","suffix":""},{"id":3891080,"identity":"7640a3e9-c243-4120-88b0-35ea03b99c52","order_by":7,"name":"Paola Skeen","email":"","orcid":"https://orcid.org/0000-0003-3463-4231","institution":"Universidad Nacional de Colombia","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Paola","middleName":"","lastName":"Skeen","suffix":""},{"id":3891081,"identity":"2ab0bca2-f592-47e8-bb1d-7c976aa65ff7","order_by":8,"name":"Clara Bermudez-Santana","email":"","orcid":"https://orcid.org/0000-0003-4290-8204","institution":"Universidad Nacional de Colombia","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Clara","middleName":"","lastName":"Bermudez-Santana","suffix":""},{"id":3891082,"identity":"c66915ea-b73c-4675-b8ef-f5a274e9a63c","order_by":9,"name":"Daniel Debouck","email":"","orcid":"","institution":"International Center for Tropical Agriculture (CIAT)","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Daniel","middleName":"","lastName":"Debouck","suffix":""},{"id":3891083,"identity":"df8701cb-5239-4716-858a-cb3b11cc1641","order_by":10,"name":"Jaime Martinez Castillo","email":"","orcid":"","institution":"Centro de Investigación Científica de Yucatán (CICY)","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jaime","middleName":"Martinez","lastName":"Castillo","suffix":""},{"id":3891084,"identity":"6b6beba5-0c39-4f38-9e57-87ff4c3774df","order_by":11,"name":"Paul Gepts","email":"","orcid":"https://orcid.org/0000-0002-1056-4665","institution":"University of California, Davis","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Paul","middleName":"","lastName":"Gepts","suffix":""},{"id":3891085,"identity":"21552d0c-4676-4b0c-8f77-e5cf09f1d09e","order_by":12,"name":"Maria Chacón-Sánchez","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA2klEQVRIiWNgGAWjYDACZgY2CIO9AUgUAPEBorXwgJQaEKOFAaZFIoFILbrtzM8e/KixyZOf+cbswQ8DBjm+GwmMHz7g0WJ2mM3csOdYWrHB7Rwgw4DBWPJGArPkDLxaeNgkeBsOJ26QzjGT4DFgSNxwI4GNmYeAFsm/QC3zZ54xk/xjwFBPlBZpkC0NN3jMpIG2JBgQ1sJmJi1zLC1xw5m0MmkZAwnDmWceNuP3y/nDzyTf1Ngkzm8/vE3yTYWNPN/x5IN4QwwdSAAxYwMJGkbBKBgFo2AUYAMAC85Ho/mrAiwAAAAASUVORK5CYII=","orcid":"","institution":"National University of Colombia","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Maria","middleName":"","lastName":"Chacón-Sánchez","suffix":""}],"badges":[],"createdAt":"2020-10-21 00:50:45","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-95762/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-95762/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41467-021-20921-1","type":"published","date":"2021-01-29T05:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":3241856,"identity":"da0a3876-97f2-47d8-98ce-1be5d3e7c458","added_by":"auto","created_at":"2020-10-28 13:48:06","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1012632,"visible":true,"origin":"","legend":" a. Genetic distance (cM) and recombination rate (cM/Mbp) by physical position (Mbp) on the Phaseolus lunatus reference genome for the UC 92 - UC Haskell RIL population. b. Chromosome lengths and pericentromeric regions. c. Density of repetitive elements. d. Density of gene models. e. Density of SNPs. f-i. LOD scores of QTL for four different traits screened in the RIL population. Colored zones represent LOD scores greater than 3 for determinacy (green), flowering time (blue), hundred seed weight (red) and volatile cyanide (yellow). j. Phenotypic distribution of traits in the RIL population with parental phenotypes represented by vertical lines.","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/76e87fd33e0b2635b2e2f1d0.png"},{"id":3241858,"identity":"755bc95d-d87f-42a2-929e-3e9580163016","added_by":"auto","created_at":"2020-10-28 13:48:06","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":816552,"visible":true,"origin":"","legend":"a. Ks and b. Ka/Ks statistics for P. lunatus and G. max paralogs, as well as orthologs between P. lunatus and P. vulgaris and orthologs between P. lunatus and V. unguiculata. c. Chromosome by chromosome synteny between P. lunatus and P. vulgaris for detailed visualization of structural rearrangements. d. Number of homologs of resistance genes by chromosome. e. NJ Radial tree diagram showing genetic variability among LRR type resistance genes. Light blue are proteins with domains NB-ARC and LRR, purple are proteins with domains TIR, NB-ARC and LRR, orange are proteins with the TIR and LRR domains.","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/2937f10093b3ac373eaf7731.png"},{"id":3241860,"identity":"c573e7de-2b39-477f-a735-fb141c3c073b","added_by":"auto","created_at":"2020-10-28 13:48:07","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":761908,"visible":true,"origin":"","legend":"a. STRUCTURE analysis of the genetic variability between 482 wild and domesticated Lima bean accessions collected across the Americas. Wild accessions are organized (from left to right) into a south-north geographic pattern. DOM: domesticated. MEX: Mexico. GUA: Guatemala. CR: Costa Rica. COL: Colombia. b. Linkage disequilibrium decay within different subgroups of wild and domesticated accessions. DOM: domesticated, DOM-AND: Andean landraces. c. Radial clustering of the 482 accessions according to the analysis performed by fineSTRUCTURE. Major gene pools are shown by different colors (purple cluster: wild MI from northern-western Mexico; pink cluster: wild MI from southern-western Mexico; medium blue cluster: domesticated MI from South America; dark blue cluster: domesticated MI from Mexico and Central America (CA); light blue cluster: domesticated MI from Yucatan Peninsula; yellow cluster: AII gene pool; red cluster: AI gene pool; green cluster: MII gene pool from Yucatan, central america and Colombia; light green cluster: MII gene pool from southern and central Mexico). d. Distribution of chromosomal segments contributed by different gene pools in a set of 15 wild and domesticated accessions. Wild accessions are marked in bold.","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/a1ac73bc2e1abb9994ed39b0.png"},{"id":3241862,"identity":"03818764-8f35-4d5e-b946-c4a3f6006914","added_by":"auto","created_at":"2020-10-28 13:48:07","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":765315,"visible":true,"origin":"","legend":"a. Heatmap of normalized expression values within genes with differential expression. The left dendrogram corresponds to an unsupervised hierarchical clustering of the genes based on the normalized expression values. b. Expression trajectories of the gene PlPDH1 in the domesticated accession (blue) and the wild accession (red) across two developmental times. c. Number of genes with differential expression between one wild and one domesticated accession and between two developmental times. d. Concept map of functional categories enriched for genes more expressed in the second developmental time only in the wild accession. ","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/eb0d704779a30b9659b9aec0.png"},{"id":15784281,"identity":"b6f9025a-c86d-4322-b2f6-d4e4183ae05a","added_by":"auto","created_at":"2021-11-22 15:49:24","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3239589,"visible":true,"origin":"","legend":"","description":"","filename":"LimaBeanGenomicsNatComm20201019.pdf","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1_covered.pdf"},{"id":13549139,"identity":"670835b8-c943-43f9-8556-de79051112f7","added_by":"auto","created_at":"2021-09-17 02:19:57","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3234556,"visible":true,"origin":"","legend":"","description":"","filename":"LimaBeanGenomicsNatComm20201019.pdf","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1_covered.pdf"},{"id":3241789,"identity":"f6050b38-89d9-448b-9f21-b8f2dbe310fa","added_by":"auto","created_at":"2020-10-28 13:47:45","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2685641,"visible":true,"origin":"","legend":"","description":"","filename":"LimaBeanGenomicsNatComm20201019.pdf","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1_stamped.pdf"},{"id":3241857,"identity":"31b75587-53a5-4f0d-8aa5-e951be56cb92","added_by":"auto","created_at":"2020-10-28 13:48:06","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":7137633,"visible":true,"origin":"","legend":"Supplementary materials","description":"","filename":"SupplementaryMaterials.pdf","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/2d315eede2f8a84e9be4cb47.pdf"},{"id":3241859,"identity":"cdc68d48-4241-43ed-ba75-d5fc79a11c0b","added_by":"auto","created_at":"2020-10-28 13:48:06","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":6405,"visible":true,"origin":"","legend":"Supplementary table 1","description":"","filename":"SupplementaryTable1LinkageMap.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/7fd3faaf96782a36ccb5382e.xlsx"},{"id":3241861,"identity":"71fde6e3-f5e3-497e-902d-ed0cf33c0855","added_by":"auto","created_at":"2020-10-28 13:48:07","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":6340,"visible":true,"origin":"","legend":"Supplementary table 2","description":"","filename":"SupplementaryTable2RecombRates.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/c5cdbe75d70f26c3dc9908bc.xlsx"},{"id":3241863,"identity":"3c60820c-3a2f-4085-9eeb-52beb7abe306","added_by":"auto","created_at":"2020-10-28 13:48:07","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":5325,"visible":true,"origin":"","legend":"Supplementary table 3","description":"","filename":"SupplementaryTable3RepeatAnnotation.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/6c2868dc03f83167160f56ac.xlsx"},{"id":3241864,"identity":"4ba2a274-59c5-479f-b3d0-17b82490a43b","added_by":"auto","created_at":"2020-10-28 13:48:07","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":5660,"visible":true,"origin":"","legend":"Supplementary table 4","description":"","filename":"SupplementaryTable4QTL.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/ac063b10006c4d3455d5060c.xlsx"},{"id":3241865,"identity":"a8c58a0e-5c73-4a67-a3d5-7b35abbe752a","added_by":"auto","created_at":"2020-10-28 13:48:08","extension":"xlsx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":16072,"visible":true,"origin":"","legend":"Supplementary table 5","description":"","filename":"SupplementaryTable5GenesAgronomicTraits.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/913ebcdd0dc599173f22670e.xlsx"},{"id":3241866,"identity":"3b26d2cd-5841-4738-b7e4-cb54743b35bd","added_by":"auto","created_at":"2020-10-28 13:48:08","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":134339,"visible":true,"origin":"","legend":"Supplementary table 6","description":"","filename":"SupplementaryTable6RGenes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/4488b0e7553d895e5b611f1c.xlsx"},{"id":3241867,"identity":"83a11c6a-e9c4-4cf7-8288-254d1681e8fa","added_by":"auto","created_at":"2020-10-28 13:48:08","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":46782,"visible":true,"origin":"","legend":"Supplementary table 7","description":"","filename":"SupplementaryTable7Accessions.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/f9e76e01295af14f290ff23b.xlsx"},{"id":3241868,"identity":"5d2b6fa9-c184-431f-9ec1-3b89e23988d6","added_by":"auto","created_at":"2020-10-28 13:48:08","extension":"xlsx","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":41935,"visible":true,"origin":"","legend":"Supplementary table 8","description":"","filename":"SupplementaryTable8StructureK6.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/36d99e50ffd703b80591757b.xlsx"},{"id":3241869,"identity":"5ddfa32f-fb8e-430e-954d-e28de49ee29c","added_by":"auto","created_at":"2020-10-28 13:48:08","extension":"xlsx","order_by":10,"title":"","display":"","copyAsset":false,"role":"supplement","size":6183,"visible":true,"origin":"","legend":"Supplementary table 9","description":"","filename":"SupplementaryTable9DiversityStats.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/c11de0ebc0bd5642309c407d.xlsx"},{"id":3241870,"identity":"85f999b7-0629-42f9-999c-f6d1ca37f92b","added_by":"auto","created_at":"2020-10-28 13:48:08","extension":"xlsx","order_by":11,"title":"","display":"","copyAsset":false,"role":"supplement","size":5452,"visible":true,"origin":"","legend":"Supplementary table 10","description":"","filename":"SupplementaryTable10FstBetweenPops.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/32d391c1704ea939dda3bf13.xlsx"},{"id":3241871,"identity":"fb2bc3d6-fad2-45b0-bf4b-689e637f1c87","added_by":"auto","created_at":"2020-10-28 13:48:09","extension":"xlsx","order_by":12,"title":"","display":"","copyAsset":false,"role":"supplement","size":14393,"visible":true,"origin":"","legend":"Supplementary table 11","description":"","filename":"SupplementaryTable11Introgressions.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/7eb98e66880a6b820a9982f0.xlsx"},{"id":3241872,"identity":"d6546f51-cdf4-49a6-9c8f-548f36a5f963","added_by":"auto","created_at":"2020-10-28 13:48:09","extension":"xlsx","order_by":13,"title":"","display":"","copyAsset":false,"role":"supplement","size":1130212,"visible":true,"origin":"","legend":"Supplementary table 12","description":"","filename":"SupplementaryTable12DEGs.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-95762/v1/0ee7ff22a71d0b9a6ef94a55.xlsx"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"\u003cb\u003eComprehensive genomic resources related to domestication and crop improvement traits in Lima bean\u003c/b\u003e","fulltext":[{"header":"Full Text","content":"Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the latest manuscript can be downloaded and \u003ca href='/article/rs-95762/latest.pdf' target='_blank'\u003e accessed 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":false,"isPdf":false,"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":"Adaptations and Phenotypic Plasticity, Food Security, Climate Change, Convergent Evolution, Haplotype Introgression Events","lastPublishedDoi":"10.21203/rs.3.rs-95762/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-95762/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eLima bean (\u003ci\u003ePhaseolus lunatus L.\u003c/i\u003e) is one of the five domesticated \u003ci\u003ePhaseolus\u003c/i\u003e bean crops, which are essential sources of dietary proteins for human consumption. Compared to common bean (\u003ci\u003eP. vulgaris\u003c/i\u003e), it shows a wider range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations and its phenotypic plasticity make Lima bean a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. Lima bean is also an excellent model to study convergent evolution of the adaptive domestication syndrome due to its dual domestication in Mesoamerica and the Andes. Combining long and short read sequencing technologies with a dense genetic map from a biparental population, we obtained the first chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models showed high diversity among 1,917 genes with conserved domains related to disease resistance. Structural comparison across 21,180 orthologs with common bean revealed high genome synteny and two large intrachromosomal rearrangements. Speciation between \u003ci\u003eP. lunatus\u003c/i\u003e and \u003ci\u003eP. vulgaris\u003c/i\u003e occurred about six million years ago according to nucleotide evolution between these orthologs. Population genomic analysis of GBS data for 482 wild and domesticated accessions from the Mesoamerican and Andean gene pools provided novel evidence on population structure at a finer geographical scale. Results show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. A new wild cluster of diversity was found in the Colombian Andes and a separate genetic cluster was observed for Mesoamerican landraces of the Peninsula of Yucatan in Mexico. This study also documents genome wide patterns of selection and haplotype introgression events among gene pools. Analysis of RNA-seq data obtained from wild and domesticated accessions at two different pod developmental stages revealed 4,275 differentially expressed genes, which could be related to pod dehiscence and seed development. We expect that the present resources serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of \u003ci\u003ePhaseolus\u003c/i\u003e species under domestication and provide new tools and information for breeding for climate change resiliency of different domesticated species.\u003c/p\u003e","manuscriptTitle":"Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2020-10-28 13:41:35","doi":"10.21203/rs.3.rs-95762/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":"55f63dd2-d63a-4626-a293-aa3b1e7e3a34","owner":[],"postedDate":"October 28th, 2020","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":904722,"name":"Epigenetics \u0026 Genomics"},{"id":904723,"name":"Plant Molecular Biology and Genetics"}],"tags":[],"updatedAt":"2021-11-22T15:46:39+00:00","versionOfRecord":{"articleIdentity":"rs-95762","link":"https://doi.org/10.1038/s41467-021-20921-1","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2021-01-29 05:00:00","publishedOnDateReadable":"January 29th, 2021"},"versionCreatedAt":"2020-10-28 13:41:35","video":"","vorDoi":"10.1038/s41467-021-20921-1","vorDoiUrl":"https://doi.org/10.1038/s41467-021-20921-1","workflowStages":[]},"version":"v1","identity":"rs-95762","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-95762","identity":"rs-95762","version":["v1"]},"buildId":"7rjqhiLT3MXkJMwkYKINL","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}