Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato

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dc.contributor.authorHardigan, Michael Alanen
dc.contributor.authorLaimbeer, F. Parker E.en
dc.contributor.authorNewton, Linseyen
dc.contributor.authorCrisovan, Emilyen
dc.contributor.authorHamilton, John P.en
dc.contributor.authorVaillancourt, Brieanneen
dc.contributor.authorWiegert-Rininger, Krystleen
dc.contributor.authorWood, Joshua C.en
dc.contributor.authorDouches, David S.en
dc.contributor.authorFarre, Eva M.en
dc.contributor.authorVeilleux, Richard E.en
dc.contributor.authorBuell, C. Robinen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2018-01-05T18:55:20Zen
dc.date.available2018-01-05T18:55:20Zen
dc.date.issued2017-11-14en
dc.description.abstractCultivated potatoes (Solanum tuberosum L.), domesticated from wild Solanum species native to the Andes of southern Peru, possess a diverse gene pool representing more than 100 tuber-bearing relatives (Solanum section Petota). A diversity panel of wild species, landraces, and cultivars was sequenced to assess genetic variation within tuber-bearing Solanum and the impact of domestication on genome diversity and identify key loci selected for cultivation in North and South America. Sequence diversity of diploid and tetraploid S. tuberosum exceeded any crop resequencing study to date, in part due to expanded wild introgressions following polyploidy that captured alleles outside of their geographic origin. We identified 2,622 genes as under selection, with only 14–16% shared by North American and Andean cultivars, showing that a limited gene set drove early improvement of cultivated potato, while adaptation of upland (S. tuberosum group Andigena) and lowland (S. tuberosum groups Chilotanum and Tuberosum) populations targeted distinct loci. Signatures of selection were uncovered in genes controlling carbohydrate metabolism, glycoalkaloid biosynthesis, the shikimate pathway, the cell cycle, and circadian rhythm. Reduced sexual fertility that accompanied the shift to asexual reproduction in cultivars was reflected by signatures of selection in genes regulating pollen development/gametogenesis. Exploration of haplotype diversity at potato’s maturity locus (StCDF1) revealed introgression of truncated alleles from wild species, particularly S. microdontum in long-day–adapted cultivars. This study uncovers a historic role of wild Solanum species in the diversification of long-day–adapted tetraploid potatoes, showing that extant natural populations represent an essential source of untapped adaptive potential.en
dc.description.versionPublished versionen
dc.format.extentE9999 - E10008 (10) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1073/pnas.1714380114en
dc.identifier.issn0027-8424en
dc.identifier.issue46en
dc.identifier.urihttp://hdl.handle.net/10919/81546en
dc.identifier.volume114en
dc.language.isoenen
dc.publisherNational Academy of Sciencesen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000415173300034&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectpotatoen
dc.subjectdiversityen
dc.subjectdomesticationen
dc.subjectintrogressionen
dc.subjectadaptationen
dc.subjectsucrose-phosphate synthaseen
dc.subjectsnf1-related protein-kinasesen
dc.subjectanaphase-promoting complexen
dc.subjectcopy number variationen
dc.subjectcircadian clocken
dc.subjectchloroplast dnaen
dc.subjecthigher-plantsen
dc.subjectfruit-growthen
dc.subjectphytophthora-infestansen
dc.subjectdecreased expressionen
dc.titleGenome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potatoen
dc.title.serialProceedings of the National Academy of Sciences of the United States of Americaen
dc.typeArticle - Refereeden
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Horticultureen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Fralin Affiliated Facultyen

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