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 Marshall; Diana 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

doi:10.1534/g3.113.007153

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 (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

219 Citations (Scopus)

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 language	English
Pages (from-to)	2031-2047
Number of pages	17
Journal	G3: Genes \| Genomes \| Genetics
Volume	3
Issue number	11
DOIs	https://doi.org/10.1534/g3.113.007153
Publication status	Published - Nov 2013

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Sharma, S. K., Bolser, D., de Boer, J., Sønderkær, M., Amoros, W., Carboni, M. F., D'Ambrosio, J. M., de la Cruz, G., Di Genova, A., Douches, D. S., Eguiluz, M., Guo, X., Guzman, F., Hackett, C. A., Hamilton, J. P., Li, G., Li, Y., Lozano, R., Maass, A., ... Bryan, G. J. (2013). Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3: Genes | Genomes | Genetics, 3(11), 2031-2047. https://doi.org/10.1534/g3.113.007153

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

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 \textasciitilde{}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 (\textasciitilde{}93\%) of the 723 Mb genome assembly and 37,482 (\textasciitilde{}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{"}.",

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

year = "2013",

month = nov,

doi = "10.1534/g3.113.007153",

language = "English",

volume = "3",

pages = "2031--2047",

journal = "G3: Genes | Genomes | Genetics",

publisher = "Genetics Society of America",

number = "11",

}

Sharma, SK, Bolser, D, de Boer, J, Sønderkær, M, Amoros, W, Carboni, MF, D'Ambrosio, JM, de la Cruz, G, Di Genova, A, Douches, DS, Eguiluz, M, Guo, X, Guzman, F, Hackett, CA, Hamilton, JP, Li, G, Li, Y, Lozano, R, Maass, A, Marshall, D, Martinez, D, McLean, K, Mejía, N, Milne, L, Munive, S, Nagy, I, Ponce, O, Ramirez, M, Simon, R, Thomson, SJ, Torres, Y, Waugh, R, Zhang, Z, Huang, S, Visser, RGF, Bachem, CWB, Sagredo, B, Feingold, SE, Orjeda, G, Veilleux, RE, Bonierbale, M, Jacobs, JME, Milbourne, D, Martin, DMA & Bryan, GJ 2013, 'Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps', G3: Genes | Genomes | Genetics, vol. 3, no. 11, pp. 2031-2047. https://doi.org/10.1534/g3.113.007153

TY - JOUR

T1 - Construction of reference chromosome-scale pseudomolecules for potato

T2 - integrating the potato genome with genetic and physical maps

AU - Sharma, Sanjeev Kumar

AU - Bolser, Daniel

AU - de Boer, Jan

AU - Sønderkær, Mads

AU - Amoros, Walter

AU - Carboni, Martin Federico

AU - D'Ambrosio, Juan Martín

AU - de la Cruz, German

AU - Di Genova, Alex

AU - Douches, David S

AU - Eguiluz, Maria

AU - Guo, Xiao

AU - Guzman, Frank

AU - Hackett, Christine A

AU - Hamilton, John P

AU - Li, Guangcun

AU - Li, Ying

AU - Lozano, Roberto

AU - Maass, Alejandro

AU - Marshall, David

AU - Martinez, Diana

AU - McLean, Karen

AU - Mejía, Nilo

AU - Milne, Linda

AU - Munive, Susan

AU - Nagy, Istvan

AU - Ponce, Olga

AU - Ramirez, Manuel

AU - Simon, Reinhard

AU - Thomson, Susan J

AU - Torres, Yerisf

AU - Waugh, Robbie

AU - Zhang, Zhonghua

AU - Huang, Sanwen

AU - Visser, Richard G F

AU - Bachem, Christian W B

AU - Sagredo, Boris

AU - Feingold, Sergio E

AU - Orjeda, Gisella

AU - Veilleux, Richard E

AU - Bonierbale, Merideth

AU - Jacobs, Jeanne M E

AU - Milbourne, Dan

AU - Martin, David Michael Alan

AU - Bryan, Glenn J

PY - 2013/11

Y1 - 2013/11

N2 - 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".

AB - 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".

U2 - 10.1534/g3.113.007153

DO - 10.1534/g3.113.007153

M3 - Article

C2 - 24062527

VL - 3

SP - 2031

EP - 2047

JO - G3: Genes | Genomes | Genetics

JF - G3: Genes | Genomes | Genetics

IS - 11

ER -

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

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