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Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps

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dc.contributor.author Sanjeev Kumar Sharma
dc.contributor.author Daniel Bolser
dc.contributor.author Jan de Boer
dc.contributor.author Mads Sønderkær
dc.contributor.author Walter Amoros
dc.contributor.author Martin Federico Carboni
dc.contributor.author Juan Martín D’Ambrosio
dc.contributor.author German de la Cruz
dc.contributor.author Alex Di Genova
dc.contributor.author David S Douches
dc.contributor.author Maria Eguiluz
dc.contributor.author Xiao Guo
dc.contributor.author Frank Guzman
dc.contributor.author Christine A Hackett
dc.contributor.author John P Hamilton
dc.contributor.author Guangcun Li
dc.contributor.author Ying Li
dc.contributor.author Roberto Lozano
dc.contributor.author Alejandro Maass
dc.contributor.author David Marshall
dc.contributor.author Diana Martinez
dc.contributor.author Karen McLean
dc.contributor.author Nilo Mejía
dc.contributor.author Linda Milne
dc.contributor.author Susan Munive
dc.contributor.author Istvan Nagy
dc.contributor.author Olga Ponce
dc.contributor.author Manuel Ramirez
dc.contributor.author Reinhard Simon
dc.contributor.author Susan J Thomson
dc.contributor.author Yerisf Torres
dc.contributor.author Robbie Waugh
dc.contributor.author Zhonghua Zhang
dc.contributor.author Sanwen Huang
dc.contributor.author Richard G F Visser
dc.contributor.author Christian W B Bachem
dc.contributor.author Boris Sagredo
dc.contributor.author Sergio E Feingold
dc.contributor.author Gisella Orjeda
dc.contributor.author Richard E Veilleux
dc.contributor.author Merideth Bonierbale
dc.contributor.author Jeanne M E Jacobs
dc.contributor.author Dan Milbourne
dc.contributor.author David Michael Alan Martin
dc.contributor.author Glenn J Bryan
dc.date.accessioned 2022-01-04T20:29:58Z
dc.date.available 2022-01-04T20:29:58Z
dc.date.issued 2013
dc.identifier.uri https://hdl.handle.net/20.500.12866/10469
dc.description.abstract The 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 ~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 (~93%) of the 723 Mb genome assembly and 37,482 (~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_US
dc.language.iso eng
dc.publisher Genetics Society of America
dc.relation.ispartofseries G3: Genes, Genomes, Genetics
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject nonhuman en_US
dc.subject genotype en_US
dc.subject Biological Markers en_US
dc.subject Internet en_US
dc.subject genetic marker en_US
dc.subject species difference en_US
dc.subject computer model en_US
dc.subject genomic DNA en_US
dc.subject Anchoring scaffold en_US
dc.subject centromere en_US
dc.subject chromosome 4 en_US
dc.subject chromosome inversion en_US
dc.subject Chromosome Mapping en_US
dc.subject Chromosomes, Plant en_US
dc.subject diploidy en_US
dc.subject gene mapping en_US
dc.subject genetic linkage en_US
dc.subject genetic map en_US
dc.subject Genetic map en_US
dc.subject genome anchoring en_US
dc.subject Genome, Plant en_US
dc.subject molecule en_US
dc.subject Orientation en_US
dc.subject physical map en_US
dc.subject Physical map en_US
dc.subject plant chromosome en_US
dc.subject plant DNA en_US
dc.subject plant genetics en_US
dc.subject plant genome en_US
dc.subject potato en_US
dc.subject pseudomolecules en_US
dc.subject Pseudomolecules potato en_US
dc.subject scaffold orientation en_US
dc.subject segregation distortion en_US
dc.subject sequence tagged site en_US
dc.subject sequence-tagged sites en_US
dc.subject Sequencetagged sites en_US
dc.subject Solanaceae en_US
dc.subject Solanaceae genome en_US
dc.subject Solanum tuberosum en_US
dc.subject tomato en_US
dc.subject User-Computer Interface en_US
dc.title Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1534/g3.113.007153
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.06.07
dc.relation.issn 2160-1836

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