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

2013; Genetics Society of America; Volume: 3; Issue: 11 Linguagem: Inglês

10.1534/g3.113.007153

2160-1836

Sanjeev Sharma, Dan Bolser, Jan de Boer, Mads Sønderkær, Walter Amorós, Martín Carboni, Juan Martín D’Ambrosio, Germán De la Cruz, Alex Di Genova, David S. Douches, María Eguiluz, Xiao Guo, Frank Guzmán, Christine A. Hackett, John P. Hamilton, Guangcun Li, Ying Li, Roberto Lozano, Alejandro Maass, David Marshall, D Martinez, Karen McLean, Nilo Mejía, Linda Milne, Susan Munive, István Nagy, Olga Ponce, Manuel Ramírez, Reinhard Simon, Susan Thomson, Yerisf Torres, Robbie Waugh, Zhonghua Zhang, Sanwen Huang, Richard G. F. Visser, C. Bachem, Boris Sagredo, Sérgio Enrique Feingold, Gisella Orjeda, Richard E. Veilleux, Merideth Bonierbale, Jeanne M. E. Jacobs, Dan Milbourne, David Martin, Glenn J. Bryan,

Chromosomal and Genetic Variations

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".