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6. Genome sequence and analysis of the tuber crop potato

Author

Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Zhang, Bo, Mu, Desheng, Ni, Peixiang, Zhang, Gengyun, Yang, Shuang, Li, Ruiqiang, Wang, Jun, Orjeda, Gisella, Guzman, Frank, Torres, Michael, Lozano, Roberto, Ponce, Olga, Martinez, Diana, De la Cruz, Germán, Chakrabarti, S. K., Patil, Virupaksh U., Skryabin, Konstantin G., Kuznetsov, Boris B., Ravin, Nikolai V., Kolganova, Tatjana V., Beletsky, Alexey V., Mardanov, Andrei V., Di Genova, Alex, Bolser, Daniel M., Martin, David M. A., Li, Guangcun, Yang, Yu, Kuang, Hanhui, Hu, Qun, Xiong, Xingyao, Bishop, Gerard J., Sagredo, Boris, Mejía, Nilo, Zagorski, Wlodzimierz, Gromadka, Robert, Gawor, Jan, Szczesny, Pawel, Huang, Sanwen, Zhang, Zhonghua, Liang, Chunbo, He, Jun, Li, Ying, He, Ying, Xu, Jianfei, Zhang, Youjun, Xie, Binyan, Du, Yongchen, Qu, Dongyu, Bonierbale, Merideth, Ghislain, Marc, del Rosario Herrera, Maria, Giuliano, Giovanni, Pietrella, Marco, Perrotta, Gaetano, Facella, Paolo, O’Brien, Kimberly, Feingold, Sergio E., Barreiro, Leandro E., Massa, Gabriela A., Diambra, Luis, Whitty, Brett R., Vaillancourt, Brieanne, Lin, Haining, Massa, Alicia N., Geoffroy, Michael, Lundback, Steven, DellaPenna, Dean, Buell, Robin C., Sharma, Sanjeev Kumar, Marshall, David F., Waugh, Robbie, Bryan, Glenn J., Destefanis, Marialaura, Nagy, Istvan, Milbourne, Dan, Thomson, Susan J., Fiers, Mark, Jacobs, Jeanne M. E., Nielsen, Kåre L., Sønderkær, Mads, Iovene, Marina, Torres, Giovana A., Jiang, Jiming, Veilleux, Richard E., Bachem, Christian W. B., de Boer, Jan, Borm, Theo, Kloosterman, Bjorn, van Eck, Herman, Datema, Erwin, te Lintel Hekkert, Bas, Goverse, Aska, van Ham, Roeland C. H. J., and Visser, Richard G. F.

Published
2011
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9. Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

Author

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, 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, and Bryan, Glenn J.

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 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.

Published
2013
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10. Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

Author

School of Plant and Environmental Sciences, 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, Bryan, Glenn J., School of Plant and Environmental Sciences, 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, and Bryan, Glenn J.

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 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.

Published
2013

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

Author

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

Published
2013
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12. Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

Author

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 RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, and Bryan GJ

Subjects
Biomarkers metabolism, Chromosomes, Plant metabolism, Genome, Plant, Internet, User-Computer Interface, Chromosome Mapping standards, Chromosomes, Plant genetics, Solanum tuberosum genetics
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".

Published
2013
Full Text
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