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Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps
Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps
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Fecha
2013
Autores
Sharma, SK
Bolser, D
de Boer, J
Sonderkaer, M
Amoros, W
Carboni, MF
D'Ambrosio, JM
de la Cruz, G
Di Genova, A
Douches, DS
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Genetics Society of America
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Abstracto
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
marker2based 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”.
Descripción
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).
Palabras clave
Pseudomolecules potato,
Genetic map,
Anchoring scaffold