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

Sanjeev Kumar Sharma, Daniel Bolser, Jan de Boer, Mads Sønderkær, Walter Amoros, Martin Federico Carboni, Juan Martín D'Ambrosio, German de la Cruz, Alex Di Genova, David S Douches, Maria Eguiluz, Xiao Guo, Frank Guzman, Christine A Hackett, John P Hamilton, Guangcun Li, Ying Li, Roberto Lozano, Alejandro Maass, David MarshallDiana Martinez, Karen McLean, Nilo Mejía, Linda Milne, Susan Munive, Istvan Nagy, Olga Ponce, Manuel Ramirez, Reinhard Simon, Susan J Thomson, Yerisf Torres, Robbie Waugh, Zhonghua Zhang, Sanwen Huang, Richard G F Visser, Christian W B Bachem, Boris Sagredo, Sergio E Feingold, Gisella Orjeda, Richard E Veilleux, Merideth Bonierbale, Jeanne M E Jacobs, Dan Milbourne, David Michael Alan Martin, Glenn J Bryan

Research output: Contribution to journalArticle

130 Citations (Scopus)
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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".

Original languageEnglish
Pages (from-to)2031-47
Number of pages17
JournalG3: Genes, Genomes, Genetics
Volume3
Issue number11
DOIs
Publication statusPrint publication - 6 Nov 2013

Keywords

  • Biomarkers/metabolism
  • Chromosome Mapping/standards
  • Chromosomes, Plant/genetics
  • Genome, Plant
  • Internet
  • Solanum tuberosum/genetics
  • User-Computer Interface

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