Repositorio
Institucional

Bryan, Glenn J

Sharma, Sanjeev Kumar

Bolser, Daniel

de Boer, Jan

Sonderkaer, Mads

Amoros, Walter

Carboni, Martin Federico

D'Ambrosio, Juan Martin

de la Cruz, German

Di Genova, Alex

Douches, David S.

Eguiluz, Maria

Guo, Xiao

Guzman, Frank

Hackett, Christine A.

Hamilton, John P.

Li, Guangcun

Li, Ying

Lozano, Roberto

Maass, Alejandro

Marshall, David

Martinez, Diana

McLean, Karen

Mejia, Nilo

Milne, Linda

Munive, Susan

Nagy, Istvan

Ponce, Olga

Ramirez, Manuel

Simon, Reinhard

Thomson, Susan J.

Torres, Yerisf

Waugh, Robbie

Zhang, Zhonghua

Huang, Sanwen

Visser, Richard G. F.

Bachem, Christian W. B.

Sagredo, Boris

Feingold, Sergio E.

Orjeda, Gisella

Veilleux, Richard E.

Bonierbale, Merideth

Jacobs, Jeanne M. E.

Milbourne, Dan

Martin, David Michael Alan

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

GENETICS SOCIETY AMERICA

G3-GENES GENOMES GENETICS

en

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 similar to 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 (similar to 93%) of the 723 Mb genome assembly and 37,482 (similar to 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.

Artículo original

We thank Andrzej Kilian (Diversity Arrays Technology, Australia) for DArT genotyping of the DMDD mapping population. We acknowledge Peter E. Hedley and Clare Booth (The James Hutton Institute, UK) for help with SNP genotyping. We thank S. B. Divito (Instituto Nacional de Tecnologia Agropecuaria, Balcarce, Argentina) for technical assistance. We are also grateful to Luke Ramsay and Peter E. Hedley (The James Hutton Institute, UK) for comments on the manuscript. AFLP and WGP are (registered) trademarks owned by KeyGene N.V. We acknowledge the funding made available by the Potato Genome Sequencing grant, UK [Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS), Department for Environment, Food and Rural Affairs (DEFRA), Agriculture and Horticulture Development Board (AHDB)-Potato Council, Biotechnology and Biological Sciences Research Council (BBSRC, Grant BB/F012640)]

New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative and the New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand

NMEA (Netherlands Ministry of Economic Affairs), CBSG (Centre for BioSystems Genomics), STW (Netherlands Technology Foundation grant 07796), The Netherlands

Teagasc Core Funding, DAFF-Research Stimulus Fund, Ireland

International Potato Center (CIP-CGIAR)/CRP RTB, Peru

CONICYT (Fondap 1509007, Basal CMM, PBCT-PSD-03), CIRIC INRIA, INIA-Ministry of Agriculture of Chile, Chile

FEMCIDI OEA, PE/09/02 MINCyT-CONCyTEC, 2010-2011, Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds) and Ministerio de Ciencia y Tecnologia (MINCyT), Argentina

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).

Agradecemos a Andrzej Kilian (Diversity Arrays Technology, Australia) por la genotipificación DArT de la población de mapeo DMDD. Agradecemos a Peter E. Hedley y Clare Booth (The James Hutton Institute, Reino Unido) por su ayuda con la genotipificación de SNP. Agradecemos a S. B. Divito (Instituto Nacional de Tecnologia Agropecuaria, Balcarce, Argentina) por su asistencia técnica. También agradecemos a Luke Ramsay y Peter E. Hedley (The James Hutton Institute, Reino Unido) por sus comentarios sobre el manuscrito. AFLP y WGP son marcas comerciales (registradas) propiedad de KeyGene N.V. Agradecemos la financiación proporcionada por la subvención de secuenciación del genoma de la papa, Reino Unido [División de Servicios Analíticos y de Ciencias Rurales y Ambientales del Gobierno Escocés (RESAS), Departamento de Medio Ambiente, Alimentación y Asuntos Rurales (DEFRA), Junta de Desarrollo de Agricultura y Horticultura (AHDB)-Consejo de la Papa, Consejo de Investigación de Biotecnología y Ciencias Biológicas (BBSRC, Subvención BB/F012640)]

New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative y New Zealand Institute for Plant & Food Research Ltd Capability Fund, Nueva Zelanda

NMEA (Ministerio de Asuntos Económicos de los Países Bajos), CBSG (Centre for BioSystems Genomics), STW (Netherlands Technology Foundation subvención 07796), Países Bajos

Teagasc Core Funding, DAFF-Research Stimulus Fund, Irlanda

International Papato Center (CIP-CGIAR)/CRP RTB, Perú

CONICYT (Fondap 1509007, Basal CMM, PBCT-PSD-03), CIRIC INRIA, INIA-Ministerio de Agricultura de Chile, Chile

FEMCIDI OEA, PE/09/02 MINCyT-CONCyTEC, 2010-2011, Instituto Nacional de Tecnología Agropecuaria (INTA-Core Funds) y Ministerio de Ciencia y Tecnología (MINCyT), Argentina

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 Innovación Agraria, Ministerio de Agricultura del Perú, Ministerio de Agricultura del Perú, Secretaría Técnica de coordinación con el CGIAR, Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica, Perú (CONCYTEC), Fondo Especial Multilateral del Consejo Interamericano para el Desarrollo Integral (FEMCIDI-Perú).

10.1534/g3.113.007153

pdf

Solanaceae

genome anchoring

scaffold orientation

sequence-tagged sites

pseudomolecules

potato

genetic map

physical map

TOMATO

DNA

MICROSATELLITES

IDENTIFICATION

CENTROMERES

Solanáceas

anclaje del genoma

orientación del andamiaje

sitios marcados con secuencias

pseudomoléculas

patata

mapa genético

mapa físico

TOMATE

ADN

MICROSATÉLITES

IDENTIFICACIÓN

CENTRÓMEROS

Solanaceae

genome anchoring

scaffold orientation

sequence-tagged sites

pseudomolecules

potato

genetic map

physical map

TOMATO

DNA

MICROSATELLITES

IDENTIFICATION

CENTROMERES

Solanáceas

anclaje del genoma

orientación del andamiaje

sitios marcados con secuencias

pseudomoléculas

patata

mapa genético

mapa físico

TOMATE

ADN

MICROSATÉLITES

IDENTIFICACIÓN

CENTRÓMEROS

Biotecnología agrícola

Genética y Herencia

Fitomejoramiento y protección vegetal

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

G3-GENES GENOMES GENETICS

dorada

verde

acceso abierto

acceso abierto

PMID 24062527

en

Artículo original

versión publicada

Potato Genome Sequencing grant, UK#Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS)#Department for Environment, Food and Rural Affairs (DEFRA)#Agriculture and Horticulture Development Board (AHDB)-Potato Council#Biotechnology and Biological Sciences Research Council (BBSRC) BB/F012640#New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative#New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand#NMEA (Netherlands Ministry of Economic Affairs)#CBSG (Centre for BioSystems Genomics)#STW (Netherlands Technology Foundation), The Netherlands 07796#Teagasc Core Funding#DAFF-Research Stimulus Fund, Ireland#International Potato Center (CIP-CGIAR)/CRP RTB, Peru#CONICYT Fondap 1509007, PBCT-PSD-03#CONICYT (Basal CMM)#CIRIC INRIA#INIA-Ministry of Agriculture of Chile, Chile#FEMCIDI OEA PE/09/02 MINCyT-CONCyTEC#Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds)#Ministerio de Ciencia y Tecnologia (MINCyT), Argentina#Proyecto FEMCIDI-OEA SEDI/AE-305 /09#Proyecto Bilateral Argentina, Per#FINCyT 099-FINCyT-EQUIP-2009#FINCyT 076-FINCyT-PIN-2008#Prestamo BID 1663/OC-PE#Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru#Peruvian Ministry of Agriculture, Technical Secretariat of coordination#CGIAR#Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC)#Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru)#BBSRC BB/F013280/1, BB/F012640/1 Funding Source: UKRI#Biotechnology and Biological Sciences Research Council BB/F012640/1, BB/F013280/1 Funding Source: researchfish

Potato Genome Sequencing grant, UK

Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS)

Department for Environment, Food and Rural Affairs (DEFRA)

Agriculture and Horticulture Development Board (AHDB)-Potato Council

Biotechnology and Biological Sciences Research Council (BBSRC) BB/F012640

New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative

New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand

NMEA (Netherlands Ministry of Economic Affairs)

CBSG (Centre for BioSystems Genomics)

STW (Netherlands Technology Foundation), The Netherlands 07796

Teagasc Core Funding

DAFF-Research Stimulus Fund, Ireland

International Potato Center (CIP-CGIAR)/CRP RTB, Peru

CONICYT Fondap 1509007, PBCT-PSD-03

CONICYT (Basal CMM)

CIRIC INRIA

INIA-Ministry of Agriculture of Chile, Chile

FEMCIDI OEA PE/09/02 MINCyT-CONCyTEC

Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds)

Ministerio de Ciencia y Tecnologia (MINCyT), Argentina

Proyecto FEMCIDI-OEA SEDI/AE-305 /09

Proyecto Bilateral Argentina, Per

FINCyT 099-FINCyT-EQUIP-2009

FINCyT 076-FINCyT-PIN-2008

Prestamo BID 1663/OC-PE

Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru

Peruvian Ministry of Agriculture, Technical Secretariat of coordination

CGIAR

Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC)

Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru)

BBSRC BB/F013280/1, BB/F012640/1 Funding Source: UKRI

Biotechnology and Biological Sciences Research Council BB/F012640/1, BB/F013280/1 Funding Source: researchfish

GENETICS SOCIETY AMERICA

2160-1836

2031

2047

Genética y herencia

Genetics & Heredity

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WOS:000327241900011