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Istvan Nagy

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

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskning

  • Sanjeev Kumar Sharma, Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Storbritannien
  • Daniel Bolser, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Storbritannien
  • Jan de Boer, Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Wageningen, Holland
  • Mads Sønderkær, Aalborg Universitet, Danmark
  • Walter Amoros, International Potato Center (CIP), Lima, Peru
  • Martin Federico Carboni, Laboratorio de Agrobiotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA) cc276 (7620) Balcarce, Argentina
  • Juan Martín D'Ambrosio, Laboratorio de Agrobiotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA) cc276 (7620) Balcarce, Argentina
  • German de la Cruz, Laboratorio de Agrobiotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA) cc276 (7620) Balcarce, Argentina
  • Alex Di Genova, Mathomics, Centro de Regulación Genómica & Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
  • David S Douches, Department of Crop and Soil Sciences, Michigan State University, East Lansing, Michigan, USA
  • Maria Eguiluz, Genomics Research Unit, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima , Peru
  • Xiao Guo, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, Kina
  • Frank Guzman, Genomics Research Unit, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima , Peru
  • Christine A Hackett, Biomathematics and Statistics Scotland, Dundee DD2 5DA, United Kingdom, Storbritannien
  • John P Hamilton, Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
  • Guangcun Li, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, Kina
  • Ying Li, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, Kina
  • Roberto Lozano, Genomics Research Unit, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima , Peru
  • Alejandro Maass, Mathomics, Centro de Regulación Genómica & Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
  • David Marshall, Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, Storbritannien
  • Diana Martinez, Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Storbritannien
  • Karen McLean, Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Storbritannien
  • Nilo Mejía, INIA-La Platina, Santiago, Chile
  • Linda Milne, Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, Storbritannien
  • Susan Munive, International Potato Center (CIP), Lima, Peru
  • Istvan Nagy
  • Olga Ponce, Genomics Research Unit, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima , Peru
  • Manuel Ramirez, Genomics Research Unit, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima , Storbritannien
  • Reinhard Simon, International Potato Center (CIP), Lima, Peru
  • Susan J Thomson, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, Kina
  • Yerisf Torres, Genomics Research Unit, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima , Peru
  • Robbie Waugh, *Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Storbritannien
  • Zhonghua Zhang, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, Kina
  • Sanwen Huang, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, Kina
  • Richard G F Visser, Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Wageningen, Holland
  • Christian W B Bachem, Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Wageningen, Holland
  • Boris Sagredo, INIA-Rayentué, Rengo, Chile
  • Sergio E Feingold, Laboratorio de Agrobiotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA) cc276 (7620) Balcarce, Argentina
  • Gisella Orjeda, Genomics Research Unit, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima , Peru
  • Richard E Veilleux, Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
  • Merideth Bonierbale, International Potato Center (CIP), Lima, Peru
  • Jeanne M E Jacobs, The New Zealand Institute for Plant & Food Research Ltd., Christchurch, New Zealand
  • Dan Milbourne, Crops Environment and Land Use Programme, Teagasc, Carlow, Irland
  • David Michael Alan Martin, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Storbritannien
  • Glenn J Bryan, Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Storbritannien
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".
OriginalsprogEngelsk
TidsskriftG3: Genes, Genomes, Genetics (Bethesda)
Vol/bind3
Nummer11
Sider (fra-til)2031-2047
Antal sider17
ISSN2160-1836
DOI
StatusUdgivet - nov. 2013
Eksternt udgivetJa

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