American Journal of Potato Research

, Volume 93, Issue 1, pp 21–32 | Cite as

A Toolbox of Potato Genetic and Genomic Resources

  • Cory D. Hirsch
  • C. Robin BuellEmail author
  • Candice N. Hirsch
Invited Review


Access to genetic and genomic resources can greatly facilitate biological understanding of plant species leading to improved crop varieties. While model plant species such as Arabidopsis have had nearly two decades of genetic and genomic resource development, many major crop species have seen limited development of these resources due to the large, complex nature of their genomes. Cultivated potato is among the ranks of crop species that, despite substantial worldwide acreage, have seen limited genetic and genomic tool development. As technologies advance, this paradigm is shifting and a number of tools are being developed for important crop species such as potato. This review article highlights numerous tools that have been developed for the potato community with a specific focus on the reference de novo genome assembly and annotation, genetic markers, transcriptomics resources, and newly emerging resources that extend beyond a single reference individual.


Genome assembly Genome annotation Markers Transcriptomics 


El acceso a los recursos genéticos y genómicos puede facilitar en gran medida el entendimiento biológico de las especies de plantas, lo que conduce a variedades mejoradas de cultivos. Mientras que el modelo de las especies de plantas como Arabidopsis ha tenido cerca de dos décadas de desarrollo de recursos genéticos y genómicos, muchas especies de cultivos principales han visto desarrollo limitado de estos recursos debido a la naturaleza grande, compleja, de sus genomios. La papa cultivada está ubicada entre las especies de plantas que a pesar de su superficie substancial mundial, ha visto limitado el desarrollo de las herramientas genéticas y genómicas. A medida que avanzan las tecnologías, este paradigma está girando y se han estado desarrollando un número de herramientas para especies importantes de cultivo tales como la papa. Este artículo de revisión resalta las numerosas herramientas que se han desarrollado para la comunidad de la papa con un enfoque específico en la referencia de ensamblaje y registro de genomio de novo, marcadores genéticos, recursos transcriptómicos, y nuevas fuentes emergentes que se extienden más allá de la referencia de un único individuo.



This work was supported by a National Science Foundation National Plant Genome Initiative Postdoctoral Fellowship in Biology (Grant No. 1202724) to CDH, a National Science Foundation Plant Genome Research Program award (ISO-1237969) to CRB, and by funds from the U.S. Department of Agriculture, National Institute of Food and Agriculture, Agriculture and Food Research Initiative Plant Breeding, Genetics, and Genome grant (2009-85606-05673) to CRB.


  1. Anderson, J.E., M.B. Kantar, T.Y. Kono, F. Fu, A.O. Stec, Q. Song, P.B. Cregan, J.E. Specht, B.W. Diers, S.B. Cannon, L.K. McHale, and R.M. Stupar. 2014. A roadmap for functional structural variants in the soybean genome. Genes, Genomes, Genetics 4: 1307–1318.Google Scholar
  2. Anithakumari, A.M., J. Tang, H.J. van Eck, R.G. Visser, J.A. Leunissen, B. Vosman, and C.G. van der Linden. 2010. A pipeline for high throughput detection and mapping of SNPs from EST databases. Molecular Breeding 26: 65–75.PubMedCentralCrossRefPubMedGoogle Scholar
  3. Aversano, R., F. Contaldi, M.R. Ercolano, V. Grosso, M. Iorizzo, F. Tatino, L. Xumerle, A. Dal Molin, C. Avanzato, A. Ferrarini, M. Delledonne, W. Sanseverino, R.A. Cigliano, S. Capella-Gutierrez, T. Gabaldon, L. Frusciante, J.M. Bradeen, and D. Carputo. 2015. The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives. The Plant Cell 27: 954–968.CrossRefPubMedGoogle Scholar
  4. Bae, J., D. Halterman, and S. Jansky. 2008. Development of a molecular marker associated with Verticillium wilt resistance in diploid interspecific potato hybrids. Molecular Breeding 22: 61–69.CrossRefGoogle Scholar
  5. Belhaj, K., A. Chaparro-Garcia, S. Kamoun, N.J. Patron, and V. Nekrasov. 2015. Editing plant genomes with CRISPR/Cas9. Current Opinion in Biotechnology 32: 76–84.CrossRefPubMedGoogle Scholar
  6. Borm, T.J. 2008. Construction and use of a physical map of potato. PhD, Wageningen Univ.Google Scholar
  7. Bortesi, L., and R. Fischer. 2015. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnology Advances 33: 41–52.CrossRefPubMedGoogle Scholar
  8. Buckler, E.S., J.B. Holland, P.J. Bradbury, C.B. Acharya, P.J. Brown, C. Browne, E. Ersoz, S. Flint-Garcia, A. Garcia, J.C. Glaubitz, M.M. Goodman, C. Harjes, K. Guill, D.E. Kroon, S. Larsson, N.K. Lepak, H. Li, S.E. Mitchell, G. Pressoir, J.A. Peiffer, M.O. Rosas, T.R. Rocheford, M.C. Romay, S. Romero, S. Salvo, H. Sanchez Villeda, H.S. da Silva, Q. Sun, F. Tian, N. Upadyayula, D. Ware, H. Yates, J. Yu, Z. Zhang, S. Kresovich, and M.D. McMullen. 2009. The genetic architecture of maize flowering time. Science 325: 714–718.CrossRefPubMedGoogle Scholar
  9. Camire, M.E., S. Kubow, and D.J. Donnelly. 2009. Potatoes and human health. Critical Reviews in Food Science and Nutrition 49: 823–840.CrossRefPubMedGoogle Scholar
  10. Carputo, D., D. Alioto, R. Aversano, R. Garramone, V. Miraglia, C. Villano, and L. Frusciante. 2013. Genetic diversity among potato species as revealed by phenotypic resistances and SSR markers. Plant Genetic Resources 11: 131–139.CrossRefGoogle Scholar
  11. Chia, J.M., C. Song, P.J. Bradbury, D. Costich, N. de Leon, J. Doebley, R.J. Elshire, B. Gaut, L. Geller, J.C. Glaubitz, M. Gore, K.E. Guill, J. Holland, M.B. Hufford, J. Lai, M. Li, X. Liu, Y. Lu, R. McCombie, R. Nelson, J. Poland, B.M. Prasanna, T. Pyhajarvi, T. Rong, R.S. Sekhon, Q. Sun, M.I. Tenaillon, F. Tian, J. Wang, X. Xu, Z. Zhang, S.M. Kaeppler, J. Ross-Ibarra, M.D. McMullen, E.S. Buckler, G. Zhang, Y. Xu, and D. Ware. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics 44: 803–807.CrossRefPubMedGoogle Scholar
  12. Clasen, B.M., T.J. Stoddard, S. Luo, Z.L. Demorest, J. Li, F. Cedrone, R. Tibebu, S. Davison, E.E. Ray, A. Daulhac, A. Coffman, A. Yabandith, A. Retterath, W. Haun, N.J. Baltes, L. Mathis, D.F. Voytas, and F. Zhang. 2015. Improving cold storage and processing traits in potato through targeted gene knockout. Plant Biotechnology Journal. doi: 10.1111/pbi.12370.Google Scholar
  13. Colton, L.M., H.I. Groza, S.M. Wielgus, and J. Jiang. 2006. Marker-assisted selection for the broad-spectrum potato late blight resistance conferred by gene RB derived from a wild potato species. Crop Science 46: 589–594.CrossRefGoogle Scholar
  14. Crookshanks, M., J. Emmersen, K.G. Welinder, and K.L. Nielsen. 2001. The potato tuber transcriptome: Analysis of 6077 expressed sequence tags. Federation of European Biochemical Societies Letters 506: 123–126.CrossRefPubMedGoogle Scholar
  15. de Boer, J.M., E. Datema, X. Tang, T.J. Borm, E.H. Bakker, H.J. van Eck, R.C. van Ham, H. de Jong, R.G. Visser, and C.W. Bachem. 2015. Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin. BioMed Central Genomics 16: 374.PubMedCentralPubMedGoogle Scholar
  16. de Haan, S., J. Núñez, M. Bonierbale, M. Ghislain, and J. van der Maesen. 2013. A simple sequence repeat (SSR) marker comparison of a large in- and ex-situ potato landrace cultivar collection from Peru reaffirms the complementary nature of both conservation strategies. Diversity 5: 505–521.CrossRefGoogle Scholar
  17. Dong, F., J. Song, S.K. Naess, J.P. Helgeson, C. Gebhardt, and J. Jiang. 2000. Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theoretical and Applied Genetics 101: 1001–1007.CrossRefGoogle Scholar
  18. Douches, D., C.N. Hirsch, N.C. Manrique-Carpintero, A.N. Massa, J. Coombs, M. Hardigan, D. Bisognin, W. De Jong, and C.R. Buell. 2014. The contribution of the Solanaceae Coordinated Agricultural Project to potato breeding. Potato Research 57: 215–224.CrossRefGoogle Scholar
  19. Duangpan, S., W. Zhang, Y. Wu, S.H. Jansky, and J. Jiang. 2013. Insertional mutagenesis using Tnt1 retrotransposon in potato. Plant Physiology 163: 21–29.PubMedCentralCrossRefPubMedGoogle Scholar
  20. Feingold, S., J. Lloyd, N. Norero, M. Bonierbale, and J. Lorenzen. 2005. Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theoretical and Applied Genetics 111: 456–466.CrossRefPubMedGoogle Scholar
  21. Felcher, K.J., J.J. Coombs, A.N. Massa, C.N. Hansey, J.P. Hamilton, R.E. Veilleux, C.R. Buell, and D.S. Douches. 2012. Integration of two diploid potato linkage maps with the potato genome sequence. PloS One 7, e36347.PubMedCentralCrossRefPubMedGoogle Scholar
  22. Flinn, B., C. Rothwell, R. Griffiths, M. Lague, D. DeKoeyer, R. Sardana, P. Audy, C. Goyer, X.Q. Li, G. Wang-Pruski, and S. Regan. 2005. Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries. Plant Molecular Biology 59: 407–433.CrossRefPubMedGoogle Scholar
  23. Gan, X., O. Stegle, J. Behr, J.G. Steffen, P. Drewe, K.L. Hildebrand, R. Lyngsoe, S.J. Schultheiss, E.J. Osborne, V.T. Sreedharan, A. Kahles, R. Bohnert, G. Jean, P. Derwent, P. Kersey, E.J. Belfield, N.P. Harberd, E. Kemen, C. Toomajian, P.X. Kover, R.M. Clark, G. Ratsch, and R. Mott. 2011. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419–423.CrossRefPubMedGoogle Scholar
  24. Gebhardt, C., D. Mugniery, E. Ritter, F. Salamini, and E. Bonnel. 1993. Identification of RFLP markers closely linked to the H1 gene conferring resistance to Globodera rostochiensis in potato. Theoretical and Applied Genetics 85: 541–544.CrossRefPubMedGoogle Scholar
  25. Ghislain, M., J. Núñez, M. Rosario Herrera, J. Pignataro, F. Guzman, M. Bonierbale, and D. Spooner. 2009. Robust and highly informative microsatellite-based genetic identity kit for potato. Molecular Breeding 23: 377–388.CrossRefGoogle Scholar
  26. Gong, Z., Y. Wu, A. Koblížková, G.A. Torres, K. Wang, M. Iovene, P. Neumann, W. Zhang, P. Novák, C.R. Buell, J. Macas, and J. Jiang. 2012. Repeatless and repeat-based centromeres in potato: implications for centromere evolution. The Plant Cell 24: 3559–3574.PubMedCentralCrossRefPubMedGoogle Scholar
  27. Hackett, C.A., K. McLean, and G.J. Bryan. 2013. Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PloS One 8, e63939.PubMedCentralCrossRefPubMedGoogle Scholar
  28. Hackett, C.A., J.E. Bradshaw, and G.J. Bryan. 2014. QTL mapping in autotetraploids using SNP dosage information. Theoretical and Applied Genetics 127: 1885–1904.PubMedCentralCrossRefPubMedGoogle Scholar
  29. Hamilton, J.P., C.N. Hansey, B.R. Whitty, K. Stoffel, A.N. Massa, A. Van Deynze, W.S. De Jong, D.S. Douches, and C.R. Buell. 2011. Single nucleotide polymorphism discovery in elite North American potato germplasm. BioMed Central Genomics 12: 302.PubMedCentralPubMedGoogle Scholar
  30. Hardigan, M.A., J. Bamberg, C.R. Buell and D.S. Douches. 2015. Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota. The Plant Genome 8.Google Scholar
  31. Haynes, F.L. 1964. Pachytene chromosomes of solanum canasense. Journal of Heredity 55: 168–173.Google Scholar
  32. He, L., J. Liu, G. Torres, H. Zhang, J. Jiang, and C. Xie. 2013. Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species. Chromosome Research 21: 5–13.CrossRefPubMedGoogle Scholar
  33. Heldak, J., M. Bezo, V. Stefunova, and A. Gallikova. 2007. Selection of DNA markers for detection of extreme resistance to Potato virus Y in tetraploid potato (Solanum tuberosum L.) F1 progenies. Czech Journal of Genetics and Plant Breeding 43: 125–134.Google Scholar
  34. Hirsch, C.D., J.P. Hamilton, K.L. Childs, J. Cepela, E. Crisovan, B. Vaillancourt, C.N. Hirsch, M. Habermann, B. Neal and C.R. Buell. 2014a. Spud DB: A resource for mining sequences, genotypes, and phenotypes to accelarate potato breeding. The Plant Genome 7. doi:  10.3835/plantgenome2013.12.0042.
  35. Hirsch, C.N., C.D. Hirsch, K. Felcher, J. Coombs, D. Zarka, A. Van Deynze, W. De Jong, R.E. Veilleux, S. Jansky, P. Bethke, D.S. Douches, and C.R. Buell. 2013. Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries. Genes, Genomes, Genetics 3: 1003–1013.Google Scholar
  36. Hirsch, C.N., J.M. Foerster, J.M. Johnson, R.S. Sekhon, G. Muttoni, B. Vaillancourt, F. Penagaricano, E. Lindquist, M.A. Pedraza, K. Barry, N. de Leon, S.M. Kaeppler, and C.R. Buell. 2014b. Insights into the maize pan-genome and pan-transcriptome. The Plant Cell 26: 121–135.PubMedCentralCrossRefPubMedGoogle Scholar
  37. Hosaka, K., and R. Hanneman Jr. 1998. Genetics of self-compatibility in a self-incompatible wild diploid potato species Solanum chacoense. 1. Detection of an S locus inhibitor (Sli) gene. Euphytica 99: 191–197.CrossRefGoogle Scholar
  38. International Rice Genome Sequencing, P. 2005. The map-based sequence of the rice genome. Nature 436: 793–800.CrossRefGoogle Scholar
  39. Iovene, M., T. Zhang, Q. Lou, C.R. Buell, and J. Jiang. 2013. Copy number variation in potato - an asexually propagated autotetraploid species. Plant Journal 75: 80–89.CrossRefPubMedGoogle Scholar
  40. Jansky, S.H., Y.S. Chung, and P. Kittipadukal. 2014. M6: A diploid potato inbred line for use in breeding and genetics research. Journal of Plant Registrations 8: 195–199.CrossRefGoogle Scholar
  41. Kasai, K., Y. Morikawa, V.A. Sorri, J.P. Valkonen, C. Gebhardt, and K.N. Watanabe. 2000. Development of SCAR markers to the PVY resistance gene Ry adg based on a common feature of plant disease resistance genes. Genome 43: 1–8.CrossRefPubMedGoogle Scholar
  42. Kawchuk, L.M., D.R. Lynch, J. Thomas, B. Penner, D. Sillito, and F. Kulcsar. 1996. Characterization of Solanum tuberosum simple sequence repeats and application to potato cultivar identification. American Potato Journal 73: 325–335.CrossRefGoogle Scholar
  43. Lightbourn, G., and R. Veilleux. 2007. Production and evaluation of somatic hybrids derived from monoploid potato. American Journal of Potato Research 84: 425–435.CrossRefGoogle Scholar
  44. Lu, F., M.C. Romay, J.C. Glaubitz, P.J. Bradbury, R.J. Elshire, T. Wang, Y. Li, Y. Li, K. Semagn, X. Zhang, A.G. Hernandez, M.A. Mikel, I. Soifer, O. Barad, and E.S. Buckler. 2015. High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications 6: 6914.PubMedCentralCrossRefPubMedGoogle Scholar
  45. Mahfouz, M.M., A. Piatek, and C.N. Stewart Jr. 2014. Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. Plant Biotechnology Journal 12: 1006–1014.CrossRefPubMedGoogle Scholar
  46. Manrique-Carpintero, N.C., J.G. Tokuhisa, I. Ginzberg, J.A. Holliday, and R.E. Veilleux. 2013. Sequence diversity in coding regions of candidate genes in the glycoalkaloid biosynthetic pathway of wild potato species. Genes, Genomes, Genetics 3: 1467–1479.Google Scholar
  47. Manrique-Carpintero, N.C., J.G. Tokuhisa, I. Ginzberg, and R.E. Veilleux. 2014. Allelic variation in genes contributing to glycoalkaloid biosynthesis in a diploid interspecific population of potato. Theoretical and Applied Genetics 127: 391–405.CrossRefPubMedGoogle Scholar
  48. Massa, A.N., K.L. Childs, H. Lin, G.J. Bryan, G. Giuliano, and C.R. Buell. 2011. The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. PloS One 6, e26801.PubMedCentralCrossRefPubMedGoogle Scholar
  49. Massa, A.N., K.L. Childs and C.R. Buell. 2013. Abiotic and biotic stress responses in Solanum tuberosum Group Phureja DM1-3 516 R44 as measured through whole transcriptome sequencing. Plant Genome 6.Google Scholar
  50. Massa, A.N., N.C. Manrique-Carpintero, J.J. Coombs, D.G. Zarka, A.E. Boone, W.W. Kirk, C.A. Hackett, G.J. Bryan, and D.S. Douches. 2015. Genetic linkage mapping of economically important traits in cultivated tetraploid potato (Solanum tuberosum L.). Genes, Genomes, Genetics 5:2357–2364.Google Scholar
  51. McCord, P.H., B.R. Sosinski, K.G. Haynes, M.E. Clough, and G.C. Yencho. 2011. QTL mapping of internal heat necrosis in tetraploid potato. Theoretical and Applied Genetics 122: 129–142.CrossRefPubMedGoogle Scholar
  52. Milbourne, D., R.C. Meyer, A.J. Collins, L.D. Ramsay, C. Gebhardt, and R. Waugh. 1998. Isolation, characterisation and mapping of simple sequence repeat loci in potato. Molecular and General Genetics 259: 233–245.CrossRefPubMedGoogle Scholar
  53. Mok, D.W.S., H. Lee, and S.J. Peloquin. 1974. Identification of potato chromosomes with Giesma. American Potato Journal 51: 337–341.CrossRefGoogle Scholar
  54. Munoz-Amatriain, M., S.R. Eichten, T. Wicker, T.A. Richmond, M. Mascher, B. Steuernagel, U. Scholz, R. Ariyadasa, M. Spannagl, T. Nussbaumer, K.F. Mayer, S. Taudien, M. Platzer, J.A. Jeddeloh, N.M. Springer, G.J. Muehlbauer, and N. Stein. 2013. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biology 14: R58.PubMedCentralCrossRefPubMedGoogle Scholar
  55. Pandey, K.K. 1962. Interspecific incompatibility in Solanum species. American Journal of Botany 49: 874–882.CrossRefGoogle Scholar
  56. Paz, M.M., and R.E. Veilleux. 1999. Influence of culture medium and in vitro conditions on shoot regeneration in Solanum phureja monoploids and fertility of regenerated doubled monoploids. Plant Breeding 118: 53–57.CrossRefGoogle Scholar
  57. Peiffer, J.A., M.C. Romay, M.A. Gore, S.A. Flint-Garcia, Z. Zhang, M.J. Millard, C.A. Gardner, M.D. McMullen, J.B. Holland, P.J. Bradbury, and E.S. Buckler. 2014. The genetic architecture of maize height. Genetics 196: 1337–1356.PubMedCentralCrossRefPubMedGoogle Scholar
  58. Petolino, J.F. 2015. Genome editing in plants via designed zinc finger nucleases. In Vitro Cellular and Developmental Biology - Plant 51: 1–8.PubMedCentralCrossRefPubMedGoogle Scholar
  59. Potato Genome Sequencing Consortium. 2011. Genome sequence and analysis of the tuber crop potato. Nature 475: 189–195.CrossRefGoogle Scholar
  60. Redon, R., S. Ishikawa, K.R. Fitch, L. Feuk, G.H. Perry, T.D. Andrews, H. Fiegler, M.H. Shapero, A.R. Carson, W. Chen, E.K. Cho, S. Dallaire, J.L. Freeman, J.R. Gonzalez, M. Gratacos, J. Huang, D. Kalaitzopoulos, D. Komura, J.R. MacDonald, C.R. Marshall, R. Mei, L. Montgomery, K. Nishimura, K. Okamura, F. Shen, M.J. Somerville, J. Tchinda, A. Valsesia, C. Woodwark, F. Yang, J. Zhang, T. Zerjal, J. Zhang, L. Armengol, D.F. Conrad, X. Estivill, C. Tyler-Smith, N.P. Carter, H. Aburatani, C. Lee, K.W. Jones, S.W. Scherer, and M.E. Hurles. 2006. Global variation in copy number in the human genome. Nature 444: 444–454.PubMedCentralCrossRefPubMedGoogle Scholar
  61. Rensink, W., A. Hart, J. Liu, S. Ouyang, V. Zismann, and C.R. Buell. 2005a. Analyzing the potato abiotic stress transcriptome using expressed sequence tags. Genome 48: 598–605.CrossRefPubMedGoogle Scholar
  62. Rensink, W.A., S. Iobst, A. Hart, S. Stegalkina, J. Liu, and C.R. Buell. 2005b. Gene expression profiling of potato responses to cold, heat, and salt stress. Functional and Integrative Genomics 5: 201–207.CrossRefPubMedGoogle Scholar
  63. Ronning, C.M., S.S. Stegalkina, R.A. Ascenzi, O. Bougri, A.L. Hart, T.R. Utterbach, S.E. Vanaken, S.B. Riedmuller, J.A. White, J. Cho, G.M. Pertea, Y. Lee, S. Karamycheva, R. Sultana, J. Tsai, J. Quackenbush, H.M. Griffiths, S. Restrepo, C.D. Smart, W.E. Fry, R. Van Der Hoeven, S. Tanksley, P. Zhang, H. Jin, M.L. Yamamoto, B.J. Baker, and C.R. Buell. 2003. Comparative analyses of potato expressed sequence tag libraries. Plant Physiology 131: 419–429.PubMedCentralCrossRefPubMedGoogle Scholar
  64. Ruiz de Galarreta, J.I., L. Barandalla, R. Lorenzo, J. Gonzalez, D.J. Rios, and E. Ritter. 2007. Microsatellite variation in potato landraces from the island of La Palma. Spanish Journal of Agricultural Research 5: 186–192.CrossRefGoogle Scholar
  65. Schatz, M.C., L.G. Maron, J.C. Stein, A. Hernandez Wences, J. Gurtowski, E. Biggers, H. Lee, M. Kramer, E. Antoniou, E. Ghiban, M.H. Wright, J.M. Chia, D. Ware, S.R. McCouch, and W.R. McCombie. 2014. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology 15: 506.PubMedCentralPubMedGoogle Scholar
  66. Schnable, P.S., D. Ware, R.S. Fulton, J.C. Stein, F. Wei, S. Pasternak, C. Liang, J. Zhang, L. Fulton, T.A. Graves, P. Minx, A.D. Reily, L. Courtney, S.S. Kruchowski, C. Tomlinson, C. Strong, K. Delehaunty, C. Fronick, B. Courtney, S.M. Rock, E. Belter, F. Du, K. Kim, R.M. Abbott, M. Cotton, A. Levy, P. Marchetto, K. Ochoa, S.M. Jackson, B. Gillam, W. Chen, L. Yan, J. Higginbotham, M. Cardenas, J. Waligorski, E. Applebaum, L. Phelps, J. Falcone, K. Kanchi, T. Thane, A. Scimone, N. Thane, J. Henke, T. Wang, J. Ruppert, N. Shah, K. Rotter, J. Hodges, E. Ingenthron, M. Cordes, S. Kohlberg, J. Sgro, B. Delgado, K. Mead, A. Chinwalla, S. Leonard, K. Crouse, K. Collura, D. Kudrna, J. Currie, R. He, A. Angelova, S. Rajasekar, T. Mueller, R. Lomeli, G. Scara, A. Ko, K. Delaney, M. Wissotski, G. Lopez, D. Campos, M. Braidotti, E. Ashley, W. Golser, H. Kim, S. Lee, J. Lin, Z. Dujmic, W. Kim, J. Talag, A. Zuccolo, C. Fan, A. Sebastian, M. Kramer, L. Spiegel, L. Nascimento, T. Zutavern, B. Miller, C. Ambroise, S. Muller, W. Spooner, A. Narechania, L. Ren, S. Wei, S. Kumari, B. Faga, M.J. Levy, L. McMahan, P. Van Buren, M.W. Vaughn, K. Ying, C.-T. Yeh, S.J. Emrich, Y. Jia, A. Kalyanaraman, A.-P. Hsia, W.B. Barbazuk, R.S. Baucom, T.P. Brutnell, N.C. Carpita, C. Chaparro, J.-M. Chia, J.-M. Deragon, J.C. Estill, Y. Fu, J.A. Jeddeloh, Y. Han, H. Lee, P. Li, D.R. Lisch, S. Liu, Z. Liu, D.H. Nagel, M.C. McCann, P. SanMiguel, A.M. Myers, D. Nettleton, J. Nguyen, B.W. Penning, L. Ponnala, K.L. Schneider, D.C. Schwartz, A. Sharma, C. Soderlund, N.M. Springer, Q. Sun, H. Wang, M. Waterman, R. Westerman, T.K. Wolfgruber, L. Yang, Y. Yu, L. Zhang, S. Zhou, Q. Zhu, J.L. Bennetzen, R.K. Dawe, J. Jiang, N. Jiang, G.G. Presting, S.R. Wessler, S. Aluru, R.A. Martienssen, S.W. Clifton, W.R. McCombie, R.A. Wing, and R.K. Wilson. 2009. The B73 maize genome: Complexity, diversity, and dynamics. Science 326: 1112–1115.CrossRefPubMedGoogle Scholar
  67. Sharma, S.K., D. Bolser, J. de Boer, M. Sonderkaer, W. Amoros, M.F. Carboni, J.M. D’Ambrosio, G. de la Cruz, A. Di Genova, D.S. Douches, M. Eguiluz, X. Guo, F. Guzman, C.A. Hackett, J.P. Hamilton, G. Li, Y. Li, R. Lozano, A. Maass, D. Marshall, D. Martinez, K. McLean, N. Mejia, L. Milne, S. Munive, I. Nagy, O. Ponce, M. Ramirez, R. Simon, S.J. Thomson, Y. Torres, R. Waugh, Z. Zhang, S. Huang, R.G. Visser, C.W. Bachem, B. Sagredo, S.E. Feingold, G. Orjeda, R.E. Veilleux, M. Bonierbale, J.M. Jacobs, D. Milbourne, D.M. Martin, and G.J. Bryan. 2013. Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps. Genes, Genomes, Genetics 3: 2031–2047.Google Scholar
  68. Sliwka, J., H. Jakuczun, M. Chmielarz, A. Hara-Skrzypiec, I. Tomczynska, A. Kilian, and E. Zimnoch-Guzowska. 2012a. Late blight resistance gene from Solanum ruiz-ceballosii is located on potato chromosome X and linked to violet flower colour. BioMed Central Genetics 13: 11.PubMedCentralPubMedGoogle Scholar
  69. Sliwka, J., H. Jakuczun, M. Chmielarz, A. Hara-Skrzypiec, I. Tomczynska, A. Kilian, and E. Zimnoch-Guzowska. 2012b. A resistance gene against potato late blight originating from Solanum x michoacanum maps to potato chromosome VII. Theoretical and Applied Genetics 124: 397–406.PubMedCentralCrossRefPubMedGoogle Scholar
  70. Spooner, D.M., J. Núñez, G. Trujillo, M. del Rosario Herrera, F. Guzmán, and M. Ghislain. 2007. Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proceedings of the National Academy of Sciences 104: 19398–19403.CrossRefGoogle Scholar
  71. Sprink, T., J. Metje, and F. Hartung. 2015. Plant genome editing by novel tools: TALEN and other sequence specific nucleases. Current Opinion in Biotechnology 32: 47–53.CrossRefPubMedGoogle Scholar
  72. Stich, B., C. Urbany, P. Hoffmann, and C. Gebhardt. 2013. Population structure and linkage disequilibrium in diploid and tetraploid potato revealed by genome-wide high-density genotyping using the SolCAP SNP array. Plant Breeding 132: 718–724.CrossRefGoogle Scholar
  73. Swaminathan, M.S. 1954. Nature of polyploidy in some 48-chromosome species of the genus Solanum, section tuberarium. Genetics 39: 59–76.PubMedCentralPubMedGoogle Scholar
  74. Tang, X., J. Boer, H. Eck, C. Bachem, R.F. Visser, and H. Jong. 2009. Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosome Research 17: 899–915.PubMedCentralCrossRefPubMedGoogle Scholar
  75. Tanksley, S.D., M.W. Ganal, J.P. Prince, M.C. de Vicente, M.W. Bonierbale, P. Broun, T.M. Fulton, J.J. Giovannoni, S. Grandillo, G.B. Martin, et al. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141–1160.PubMedCentralPubMedGoogle Scholar
  76. Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635–641.CrossRefGoogle Scholar
  77. Torres, G.A., Z. Gong, M. Iovene, C.D. Hirsch, C.R. Buell, G.J. Bryan, P. Novák, J. Macas, and J. Jiang. 2011. Organization and evolution of subtelomeric satellite repeats in the potato genome. Genes, Genomes, Genetics 1: 85–92.Google Scholar
  78. Traini, A., M. Iorizzo, H. Mann, J.M. Bradeen, D. Carputo, L. Frusciante, and M.L. Chiusano. 2013. Genome microscale heterogeneity among wild potatoes revealed by diversity arrays technology marker sequences. International Journal of Genomics 2013: 257218.PubMedCentralCrossRefPubMedGoogle Scholar
  79. van Os, H., S. Andrzejewski, E. Bakker, I. Barrena, G.J. Bryan, B. Caromel, B. Ghareeb, E. Isidore, W. de Jong, P. van Koert, V. Lefebvre, D. Milbourne, E. Ritter, J.N. van der Voort, F. Rousselle-Bourgeois, J. van Vliet, R. Waugh, R.G. Visser, J. Bakker, and H.J. van Eck. 2006. Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173: 1075–1087.PubMedCentralCrossRefPubMedGoogle Scholar
  80. Visser, R.F., C.B. Bachem, J. Boer, G. Bryan, S. Chakrabati, S. Feingold, R. Gromadka, R.H.J. Ham, S. Huang, J.E. Jacobs, B. Kuznetsov, P. Melo, D. Milbourne, G. Orjeda, B. Sagredo, and X. Tang. 2009. Sequencing the potato genome: Outline and first results to come from the elucidation of the sequence of the world’s third most important food crop. American Journal of Potato Research 86: 417–429.CrossRefGoogle Scholar
  81. Wang, L., Z. Zeng, W. Zhang, and J. Jiang. 2014. Three potato centromeres are associated with distinct haplotypes with or without megabase-sized satellite repeat arrays. Genetics 196: 397–401.PubMedCentralCrossRefPubMedGoogle Scholar
  82. Zhu, W., S. Ouyang, M. Iovene, K. O’Brien, H. Vuong, J. Jiang, and C.R. Buell. 2008. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BioMed Central Genomics 9: 286.PubMedCentralPubMedGoogle Scholar
  83. Zuluaga, A.P., M. Sole, H. Lu, E. Gongora-Castillo, B. Vaillancourt, N. Coll, C.R. Buell, and M. Valls. 2015. Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii. BioMed Central Genomics 16: 246.PubMedCentralPubMedGoogle Scholar

Copyright information

© The Potato Association of America 2015

Authors and Affiliations

  • Cory D. Hirsch
    • 1
  • C. Robin Buell
    • 2
    Email author
  • Candice N. Hirsch
    • 3
  1. 1.Department of Plant BiologyUniversity of MinnesotaSaint PaulUSA
  2. 2.Department of Plant BiologyMichigan State UniversityEast LansingUSA
  3. 3.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulUSA

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