Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

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dc.contributor.authorSharma, Sanjeev Kumaren
dc.contributor.authorBolser, Danielen
dc.contributor.authorde Boer, Janen
dc.contributor.authorSonderkaer, Madsen
dc.contributor.authorAmoros, Walteren
dc.contributor.authorCarboni, Martin Federicoen
dc.contributor.authorD'Ambrosio, Juan Martinen
dc.contributor.authorde la Cruz, Germanen
dc.contributor.authorDi Genova, Alexen
dc.contributor.authorDouches, David S.en
dc.contributor.authorEguiluz, Mariaen
dc.contributor.authorGuo, Xiaoen
dc.contributor.authorGuzman, Franken
dc.contributor.authorHackett, Christine A.en
dc.contributor.authorHamilton, John P.en
dc.contributor.authorLi, Guangcunen
dc.contributor.authorLi, Yingen
dc.contributor.authorLozano, Robertoen
dc.contributor.authorMaass, Alejandroen
dc.contributor.authorMarshall, Daviden
dc.contributor.authorMartinez, Dianaen
dc.contributor.authorMcLean, Karenen
dc.contributor.authorMejia, Niloen
dc.contributor.authorMilne, Lindaen
dc.contributor.authorMunive, Susanen
dc.contributor.authorNagy, Istvanen
dc.contributor.authorPonce, Olgaen
dc.contributor.authorRamirez, Manuelen
dc.contributor.authorSimon, Reinharden
dc.contributor.authorThomson, Susan J.en
dc.contributor.authorTorres, Yerisfen
dc.contributor.authorWaugh, Robbieen
dc.contributor.authorZhang, Zhonghuaen
dc.contributor.authorHuang, Sanwenen
dc.contributor.authorVisser, Richard G. F.en
dc.contributor.authorBachem, Christian W. B.en
dc.contributor.authorSagredo, Borisen
dc.contributor.authorFeingold, Sergio E.en
dc.contributor.authorOrjeda, Gisellaen
dc.contributor.authorVeilleux, Richard E.en
dc.contributor.authorBonierbale, Meridethen
dc.contributor.authorJacobs, Jeanne M. E.en
dc.contributor.authorMilbourne, Danen
dc.contributor.authorMartin, David Michael Alanen
dc.contributor.authorBryan, Glenn J.en
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2019-12-23T17:29:15Zen
dc.date.available2019-12-23T17:29:15Zen
dc.date.issued2013-11en
dc.description.abstractThe genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new similar to 936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (similar to 93%) of the 723 Mb genome assembly and 37,482 (similar to 96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal pseudomolecules.en
dc.description.notesWe thank Andrzej Kilian (Diversity Arrays Technology, Australia) for DArT genotyping of the DMDD mapping population. We acknowledge Peter E. Hedley and Clare Booth (The James Hutton Institute, UK) for help with SNP genotyping. We thank S. B. Divito (Instituto Nacional de Tecnologia Agropecuaria, Balcarce, Argentina) for technical assistance. We are also grateful to Luke Ramsay and Peter E. Hedley (The James Hutton Institute, UK) for comments on the manuscript. AFLP and WGP are (registered) trademarks owned by KeyGene N.V. We acknowledge the funding made available by the Potato Genome Sequencing grant, UK [Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS), Department for Environment, Food and Rural Affairs (DEFRA), Agriculture and Horticulture Development Board (AHDB)-Potato Council, Biotechnology and Biological Sciences Research Council (BBSRC, Grant BB/F012640)]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative and the New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs), CBSG (Centre for BioSystems Genomics), STW (Netherlands Technology Foundation grant 07796), The Netherlands; Teagasc Core Funding, DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYT (Fondap 1509007, Basal CMM, PBCT-PSD-03), CIRIC INRIA, INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA, PE/09/02 MINCyT-CONCyTEC, 2010-2011, Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds) and Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA SEDI/AE-305 /09 (2008-2012), Proyecto Bilateral Argentina, Per; FINCyT (099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008), Prestamo BID no. 1663/OC-PE, Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru, Peruvian Ministry of Agriculture, Technical Secretariat of coordination with the CGIAR, Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC), Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru).en
dc.description.sponsorshipPotato Genome Sequencing grant, UK; Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS); Department for Environment, Food and Rural Affairs (DEFRA)Department for Environment, Food & Rural Affairs (DEFRA); Agriculture and Horticulture Development Board (AHDB)-Potato Council; Biotechnology and Biological Sciences Research Council (BBSRC)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative; New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs); CBSG (Centre for BioSystems Genomics); STW (Netherlands Technology Foundation), The Netherlands [07796]; Teagasc Core Funding; DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYTComision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) [Fondap 1509007, PBCT-PSD-03]; CONICYT (Basal CMM); CIRIC INRIA; INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA [PE/09/02 MINCyT-CONCyTEC]; Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds); Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA [SEDI/AE-305 /09]; Proyecto Bilateral Argentina, Per; FINCyT [099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008)]; Prestamo BID [1663/OC-PE]; Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru; Peruvian Ministry of Agriculture, Technical Secretariat of coordination; CGIAR; Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC); Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru); Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640/1]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1534/g3.113.007153en
dc.identifier.eissn2160-1836en
dc.identifier.issue11en
dc.identifier.pmid24062527en
dc.identifier.urihttp://hdl.handle.net/10919/96207en
dc.identifier.volume3en
dc.language.isoenen
dc.publisherGenetics Society of Americaen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectSolanaceaeen
dc.subjectgenome anchoringen
dc.subjectscaffold orientationen
dc.subjectsequence-tagged sitesen
dc.subjectpseudomoleculesen
dc.subjectpotatoen
dc.subjectgenetic mapen
dc.subjectphysical mapen
dc.titleConstruction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Mapsen
dc.title.serialG3-Genes Genomes Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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