Russian Journal of Genetics: Applied Research

, Volume 7, Issue 7, pp 736–743 | Cite as

Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding

  • I. V. Bykova
  • N. A. Shmakov
  • D. A. Afonnikov
  • A. V. Kochetov
  • E. K. Khlestkina
Article
  • 23 Downloads

Abstract

In recent years, marker-assisted selection (MAS) has been intensively used to increase the efficiency of potato breeding. Large-scale studies of the potato genome and genes exploiting next-generation sequence (NGS) approaches are required for the widespread application of MAS as well as genomic selection and genomic editing (the newest approach for creating potato plants with the desired properties). In this review, the trends in potato NGS-based research are overviewed and the related Internet resources are systematized. Special attention is given to the peculiarities of the models and approaches used in genetic studies of potato, taking into account the complex organization of its genome and a high level of heterozygosity. In genetic studies diploids, including diploid potato species, artificially obtained heterozygous dihaploids, and homozygous double monoploids, are often used. The availability of artificially created diploid forms played a fundamental role in sequencing the potato genome, which was completed in 2011. The activities of the Potato Genome Sequencing Consortium (PGSC) included not only constructing genome libraries, sequencing, assembling and annotating the genome but also genome sequence-based investigations uncovering the features of the potato genome’s evolution, SNP identification, analysis of genes and gene networks regulating resistance to phytopathogens, and the technological characteristics. An important outcome of genome sequencing was the identification of more than 8000 SNPs and approbation of the genotyping-by-sequencing (GBS) method on potato, which is the basis for the genomic selection of potato and for the discovery of economically important genes using genome wide association studies (GWAS). Optimizing the existing bioinformatic tools to support these studies, taking into account the peculiarities of the potato genome’s organization, are carried out. This review analyzes the databases containing the results of sequencing the potato genome and transcriptome, as well as the accompanying resources. This information should prove useful while planning comparative assays of the potato transcriptome or applying DNA-markers. The sequencing of the genome, as well as the transcriptomes and microRNomes, of the cultivated potato and its wild relatives, on one hand, is of fundamental interest, assisting in detecting the features of the genome’s evolution, ontogenetic development, and mechanisms of various environmental stress responses. On the other hand, it is the basis for a wide range of practical applications for developing effective genomic and gene-specific markers and marker-assisted breeding of new potato cultivars with the desired properties.

Keywords

databases genes genome markers potato RNA-Seq Solanum tuberosum sequencing transcriptome 

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References

  1. Ali, A., Alexandersson, E., Sandin, M., Resjö, S., Lenman, M., Hedley, P., Levander, F., and Andreasson, E., Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions, BMC Genomics, 2014, vol. 15, nos. 1, p. 497. doi 10.1186/1471-2164-15-497CrossRefPubMedPubMedCentralGoogle Scholar
  2. Andersson, M., Turesson, H., Nicolia, A., Falt, A., Samuelsson, M., and Hofvander, P., Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts, Plant Cell Rep., 2016, vol. 36, no. 1, pp. 117–128. doi 10.1007/s00299-016-2062-3CrossRefPubMedPubMedCentralGoogle Scholar
  3. Baebler, Š., Witek, K., Petek, M., Stare, K., Tušek-Žnidarič, M., Pompe-Novak, M., Renaut, J., Szajko, K., Strzelczyk-Żyta, D., Marczewski, W., Morgiewicz, K., Gruden, K., and Hennig, J., Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potato, J. Exp. Bot., 2014, vol. 65, no. 4, pp. 1095–1109.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bhogale, S., Mahajan, A.S., Natarajan, B., Rajabhoj, M., Thulasiram, H.V., and Banerjee, A.K., MicroRNA156: A potential graft-transmissible microRNA that modulates plant architecture and tuberization in Solanum tuberosum ssp. andigena, Plant Physiol., 2014, vol. 164, no. 2, pp. 1011–1027. doi 10.1104/pp.113.230714CrossRefPubMedGoogle Scholar
  5. Bortesi, L. and Fischer, R., The CRISPR/Cas9 system for plant genome editing and beyond, Biotechnol. Adv., 2015, vol. 33, no. 1, pp. 41–52. doi 10.1016/j.biotechadv.2014.12.006CrossRefPubMedGoogle Scholar
  6. Burra, D.D., Berkowitz, O., Hedley, P.E., Morris, J., Resjö, S., Levander, F., Liljeroth, E., Andreasson, E., and Alexandersson, E., Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans, BMC Plant Biol., 2014, vol. 14, p. 254. doi 10.1186/s12870-014-0254-yCrossRefPubMedPubMedCentralGoogle Scholar
  7. Butler, N.M. and Douches, D.S., Sequence-specific nucleases for genetic improvement of potato, Am. J. Potato Res., 2016, vol. 93, no. 4, pp. 303–320. doi 10.1007/s12230-016-9513-9CrossRefGoogle Scholar
  8. Butler, N.M., Atkins, P.A., Voytas, D.F., and Douches, D.S., Generation and inheritance of targeted mutations in potato (Solanum tuberosum L.) using the CRISPR/Cas system, PLoS ONE, 2015, vol. 10, no. 12. doi 10.1371/journal.pone.0144591Google Scholar
  9. Carvallo, M.A., Pino, M.T., Jeknić, Z., Zou, C., Doherty, C.J., Shiu, S.H., Chen, T.H.H., and Thomashow, M.F., A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana, J. Exp. Bot., 2011, vol. 62, no. 11, pp. 3807–3819.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Chi, M., Liu, C., Su, Y., Tong, Y., and Liu, H., Bioinformatic prediction of upstream microRNAs of PPO and novel microRNAs in potato, Can. J. Plant Sci., 2015, vol. 95, no. 5, pp. 871–877. doi 10.1139/CJPS-2014-308CrossRefGoogle Scholar
  11. Clough, E. and Barrett, T., The gene expression omnibus database, Methods Mol. Biol., 2016, vol. 1418, pp. 93–110. doi 10.1007/978-1-4939-3578-9_5CrossRefPubMedPubMedCentralGoogle Scholar
  12. Evers, D., Legay, S., Lamoureux, D., Hausman, J.F., Hoffmann, L., and Renaut, J., Towards a synthetic view of potato cold and salt stress response by transcriptomic and proteomic analyses, Plant Mol. Biol., 2012, vol. 78, nos. 4–5, pp. 503–514. doi 10.1007/s11103-012-9879-0CrossRefPubMedGoogle Scholar
  13. Felcher, K.J., Coombs, J.J., Massa, A.N., Hansey, C.N., Hamilton, J.P., Veilleux, R.E., Buell, C.R., and Douches, D.S., Integration of two diploid potato linkage maps with the potato genome sequence, PLoS ONE, 2012, vol. 7, no. 4. doi 10.1371/journal.pone.0036347Google Scholar
  14. Frades, I., Abreha, K.B., Proux-Wéra, E., Lankinen, A., Andreasson, E., and Alexandersson, E., A novel workflow correlating RNA-Seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones, Front. Plant Sci., 2015, vol. 6, p. 718. doi 10.3389/fpls.2015.00718CrossRefPubMedPubMedCentralGoogle Scholar
  15. Gálvez, J.H., Tai, H.H., Lagüe, M., Zebarth, B.J., and Strömvik, M.V., The nitrogen responsive transcriptome in potato (Solanum tuberosum l.) reveals significant gene regulatory motifs, Sci. Rep., 2016, vol. 6, p. 26090. doi 10.1038/srep26090CrossRefPubMedPubMedCentralGoogle Scholar
  16. Gebhardt, C., Bridging the gap between genome analysis and precision breeding in potato, Cell, 2013, vol. 29, no. 4, pp. 248–256. doi 10.1016/j.tig.2012.11.006Google Scholar
  17. Gong, L., Zhang, H., Gan, X., Zhang, L., Chen, Y., Nie, F., Shi, L., Li, M., Guo, Z., Zhang, G., and Song, Y., Transcriptome profiling of the potato (Solanum tuberosum L.) plant under drought stress and water-stimulus conditions, PLoS ONE, 2015, vol. 10, no. 5. doi 10.1371/journal.pone.0128041Google Scholar
  18. Hamilton, J.P., Hansey, C.N., Whitty, B.R., Stoffel, K., Massa, A.N., Deynze, A., De Jong, W., David, S., Douches, D.S., and Buell, C.R., Single nucleotide polymorphism discovery in elite north american potato germplasm, BMC Genomics, 2011, vol. 12, p. 302. doi 10.1186/1471-2164-12-302CrossRefPubMedPubMedCentralGoogle Scholar
  19. Hirsch, C.D., Hamilton, J.P., Childs, K.L., Cepela, J., Crisovan, E., Vaillancourt, B., Hirsch, C.N., Habermann, M., Neal, B., and Buell, C.R., Spud DB: A resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding, Plant Genome, 2014, vol. 7, no. 1. doi 10.3835/plantgenome2013.12.0042Google Scholar
  20. Hougas, R.W., Peloquin, S.J., and Ross, R.W., Haploids of the common potato, J. Hered., 1958, vol. 49, pp. 103–106.CrossRefGoogle Scholar
  21. Jupe, F., Pritchard, L., Etherington, G.J., Mackenzie, K., Cock, P.J.A., Wright, F., Sharma, S.K., Bolser, D., Bryan, G.J., Jones, J.D.G., and Hein, I., Identification and localization of the NB-LRR gene family within the potato genome, BMC Genomics, 2012, vol. 13, p. 75. doi 10.1186/1471-2164-13-75CrossRefPubMedPubMedCentralGoogle Scholar
  22. Khlestkin, V.K., Pel’tek, S.E., and Kolchanov, N.A., Target genes for obtaining potato (Solanum tuberosum L.) cultivars with desired starch properties, S.-Kh. Biol., 2017, vol. 52, no. 1, pp. 25–36. doi 10.15389/agrobiology.2017.1.25rusGoogle Scholar
  23. Khlestkina, E.K. and Shumny, V.K., Prospects for application of breakthrough technologies in breeding: The CRISPR/Cas9 system for plant genome editing, Russ. J. Genet., 2016, vol. 52, no. 7, pp. 676–687.CrossRefGoogle Scholar
  24. Khlestkina, E.K., Genomic editing as a time machine, or domestication for a couple of years, Nauka Pervykh Ruk, 2016, vol. 71–72, pp. 72–75.Google Scholar
  25. Khlestkina, E.K., Shumny, V.K., and Kolchanov, N.A., Marker-oriented selection and examples of its application in other countries, Dostizh. Nauki Tekh. APK, 2016, vol. 52, no. 7, pp. 774–787.Google Scholar
  26. Kolchanov, N.A., Kochetov, A.V., Salina, E.A., Pershina, L.A., Khlestkina, E.K., and Shumny, V.K., Status and prospects of marker-assisted and genomic plant breeding, Herald Russ. Acad. Sci., 2017, vol. 87, no. 2, pp. 125–131.CrossRefGoogle Scholar
  27. Kolesnikov, N., Hastings, E., Keays, M., Melnichuk, O., Tang, Y.A., Williams, E., Dylag, M., Kurbatova, N., Brandizi, M., Burdett, T., Megy, K., Pilicheva, E., Rustici, G., Tikhonov, A., Parkinson, H., Petryszak, R., Sarkans, U., and Brazma, A., ArrayExpress update–simplifying data submissions, Nucleic Acids Res., 2015, vol. 43, no. D1, pp. D1113–D1116. doi 10.1093/nar/gku1057CrossRefPubMedGoogle Scholar
  28. Kozomara, A. and Griffiths-Jones, S., miRBase: Annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res., 2013, vol. 42, no. D1, pp. D68–D73. doi 10.1093/nar/gkt1181CrossRefPubMedPubMedCentralGoogle Scholar
  29. Lakhotia, N., Joshi, G., Bhardwaj, A.R., Bhardwaj, A.R., Katiyar-Agarwal, S., Agarwal, M., Jagannath, A., Goel, S., and Kumar, A., Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing, BMC Plant Biol., 2014, vol. 14, p. 6. doi 10.1186/1471-2229-14-6CrossRefPubMedPubMedCentralGoogle Scholar
  30. Limantseva, L., Mironenko, N., Shuvalov, O., Antonova, O., Khiutti, A., Novikova, L., Afanasenko, O., Spooner, D., and Gavrilenko, T., Characterization of resistance to Globodera rostochiensis pathotype Ro1 in cultivated and wild potato species accessions, Plant Breed., 2014, vol. 133, pp. 660–665. doi 10.1111/pbr.12195CrossRefGoogle Scholar
  31. Liu, Y., Lin-Wang, K., Deng, C., Warran, B., Wang, L., Yu, B., Yang, H., Wang, J., Espley, R.V., Zhang, J., Wang, D., and Allan, A.C., Comparative transcriptome analysis of white and purple potato to identify genes involved in anthocyanin biosynthesis, PLoS ONE, 2015, vol. 10, no. 6. doi 10.1371/journal.pone.0129148CrossRefGoogle Scholar
  32. Martin, A., Adam, H., Díaz-Mendoza, M., and Zurczak, M., González-Schain, N.D., and Suárez-López, P., Grafttransmissible induction of potato tuberization by the microRNA miR172, Development, 2009, vol. 136, no. 17, pp. 2873–2881. doi 10.1242/dev.031658CrossRefPubMedGoogle Scholar
  33. Massa, A.N., Childs, K.L., Lin, H., Bryan, G.J., Giuliano, G., and Buell, C.R., The transcriptome of the reference potato genome Solanum tuberosum group phureja clone DM1-3 516R44, PLoS ONE, 2011, vol. 6, no. 10. doi 10.1371/journal.pone.0026801Google Scholar
  34. Nowicki, M., Foolad, M.R., Nowakowska, M., and Kozik, E.U., Potato and tomato late blight caused by Phytophthora infestans: An overview of pathology and resistance breeding, Plant Dis., 2012, vol. 96, no. 1, pp. 4–17. doi 10.1094/PDIS-05-11-0458CrossRefGoogle Scholar
  35. Petek, M., Rotter, A., Kogovšek, P., Baebler, Š., Mithöfer, A., and Gruden, K., Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack, Mol. Ecol., 2014, vol. 23, no. 21, pp. 5378–5391. doi 10.1111/mec.12932CrossRefPubMedPubMedCentralGoogle Scholar
  36. Ramakrishnan, A.P., Ritland, C.E., Blas Sevillano, R.H., and Riseman, A., Review of potato molecular markers to enhance trait selection, Am. J. Potato Res., 2015, vol. 92, no. 4, pp. 455–472. doi 10.1007/s12230-015-9455-7CrossRefGoogle Scholar
  37. Rensink, W.A., Lee, Y., Liu, J., Iobst, S., Ouyang, S., and Buell, C.R., Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts, BMC Genomics, 2005, vol. 6, p. 124. doi 10.1186/1471-2164-6-124CrossRefPubMedPubMedCentralGoogle Scholar
  38. Rickert, A.M., Kim, J.H., Meyer, S., Nagel, A., Ballvora, A., Oefner, P.J., and Gebhardt, C., First generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome, Plant Biotechnol., 2003, vol. 1, pp. 399–410. doi 10.1046/j.1467-7652.2003.00036.xCrossRefGoogle Scholar
  39. Rogozina, E.V., Khavkin, E.E., Sokolova, E.A., Kuznetsova, M.A., Gavrilenko, T.A., Limantseva, L.A., Biryukova, V.A., Chalaya, N.A., Dzhons, R.V., and Dil, K.L., The clone collection of wild species and interspecies potato hybrids, studied by the phytopathological method and using DNA markers, Tr. Prikl. Bot. Genet. Sel., 2013, vol. 174, pp. 23–32.Google Scholar
  40. Rogozina, E.V., Shuvalov, O.Yu., Antonova, O.Yu., and Gavrilenko, T.A., Interspecies and intraspecies variety of potatoes for resistance to the Y-virus, S.-Kh. Biol., 2012, vol. 5, pp. 64–69. doi 10.15389/agrobiology.2012.5.64rusGoogle Scholar
  41. Rosyara, U.R., De Jong, W.S., Douches, D.S., and Endelman, J.B., Software for genome-wide association studies in autopolyploids and its application to potato, Plant Genome, 2016, vol. 9, no. 2. doi 10.3835/plantgenome2015.08.0073Google Scholar
  42. Simko, I., Haynes, K.G., and Jones, R.W., Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers, Genetics, 2006, vol. 173, no. 4, pp. 2237–2245. doi.106.060905 doi 10.1534/geneticsCrossRefPubMedPubMedCentralGoogle Scholar
  43. Slater, A.T., Cogan, N.O.I., and Forster, J.W., Cost analysis of the application of marker-assisted selection in potato breeding, Mol. Breed., 2013, vol. 32, no. 2, pp. 299–310. doi 10.1007/s11032-013-9871-7CrossRefGoogle Scholar
  44. Slater, A.T., Cogan, N.O.I., Forster, J.W., Hayes, B.J., and Daetwyler, H.D., Improving genetic gain with genomic selection in autotetraploid potato, Plant Genome, 2016, vol. 9, no. 3. doi 10.3835/plantgenome2016.02.0021 SolCAP 2016. http://solcap.msu.edu/potato_infinium.shtml. Accessed October 8, 2016.Google Scholar
  45. Stare, T., Ramšak, Ž., Blejec, A., Stare, K., Turnšek, N., Weckwerth, W., Wienkoop, S., Vodnik, D., and Gruden, K., Bimodal dynamics of primary metabolism-related responses in tolerant potato–Potato virus Y interaction, BMC Genomics, 2015, vol. 16, nos. 1, p. 716. doi 10.1186/s12864-015-1925-2CrossRefPubMedPubMedCentralGoogle Scholar
  46. Szcześniak, M.W. and Makałowska, I., miRNEST 2.0: A database of plant and animal microRNAs, Nucleic Acids Res., 2014, vol. 42, pp. D74–D77. doi 10.1093/nar/gkt1156CrossRefPubMedGoogle Scholar
  47. The Potato Genome Sequencing Consortium, Genome sequence and analysis of the tuber crop potato, Nature, 2011, vol. 475, pp. 189–195. doi 10.1038/nature10158CrossRefGoogle Scholar
  48. The RNAcentral Consortium, RNAcentral: A comprehensive database of non-coding RNA sequences, Nucl. Acids Res., 2017, vol. 45, no. D1, pp. D128–D134. doi 10.1093/nar/gkw1008CrossRefGoogle Scholar
  49. Uitdewilligen, J.G.A.M.L., Wolters, A.-M.A., D’hoop, B.B., Borm, T.J.A., Visser, R.G.F., and Van Eck, H.J., A nextgeneration sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato, PLoS ONE, 2013, vol. 8, no. 5. doi 10.1371/journal.pone.0062355Google Scholar
  50. Van Os, H., Andrzejewski, S., Bakker, E., Barrena, I., Bryan, G.J., Caromel, B., Ghareeb, B., Isidore, E., de Jong, W., van Koert, P., Lefebvre, V., Milbourne, D., Ritter, E., Rouppe van der Voort, J.N.A.M., Rousselle-Bourgeois, F., et al., 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, 2006, vol. 173, pp. 1075–1087. doi 10.1534/genetics.106.055871CrossRefPubMedPubMedCentralGoogle Scholar
  51. Veilleux, R.E., Booze-Daniels, J., and Pehu, E., Another culture of a 2n pollen producing clone of Solanum phureja Juz. & Buk, Can. J. Genet. Cytol., 1985, vol. 27, pp. 559–564.CrossRefGoogle Scholar
  52. Visser, R.G.F., Bachem, C.W.B., de Boer, J.M., Bryan, G.J., Chakrabati, S.K., Feingold, S., Gromadka, R., van Ham, R.C.H.J., Huang, S., Jacobs, J.M.E., Kuznetsov, B., de Melo, P.E., Milbourne, D., Orjeda, G., Sagredo, B., and Tang, X., 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, Am. J. Potato Res., 2009, vol. 86, pp. 417–429. doi 10.1007/s12230-009-9097-8CrossRefGoogle Scholar
  53. Wang, S., Zhang, S., Wang, W., Xiong, X., Meng, F., and Cui, X., Efficient targeted mutagenesis in potato by the CRISPR/Cas9 system, Plant Cell Rep., 2015, vol. 34, no. 9, pp. 1473–1476. doi 10.1007/s00299-015-1816-7CrossRefPubMedGoogle Scholar
  54. Zhang, N., Yang, J., Wang, Z., Wen, Y., Wang, J., He, W., Liu, B., Si, H., and Wang, D., Identification of novel and conserved microRNAs related to drought stress in potato by deep sequencing, PLoS ONE, 2014, vol. 9, no. 4. doi 10.1371/journal.pone.0095489Google Scholar
  55. Zhang, R., Marshall, D., Bryan, G.J., and Hornyik, C., Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing, PLoS ONE, 2013, vol. 8, no. 2. doi 10.1371/journal.pone.0057233Google Scholar
  56. Zhang, W., Luo, Y., Gong, X., Zeng, W., and Li, S., Computational identification of 48 potato microRNAs and their targets, Comput. Biol. Chem., 2009, vol. 33, no. 1, pp. 84–93. doi 10.1016/j.compbiolchem.2008.07.006CrossRefPubMedGoogle Scholar
  57. Zuluaga, P.A., Solé, M., Lu, H., Góngora-Castillo, E., Vaillancourt, B., Coll, N., Buell, C.R., and Valls, M., Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii, BMC Genomics, 2015, vol. 16, nos. 1, p. 246. doi 10.1186/s12864-015-1460-1CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2017

Authors and Affiliations

  • I. V. Bykova
    • 1
  • N. A. Shmakov
    • 1
    • 2
  • D. A. Afonnikov
    • 1
    • 2
  • A. V. Kochetov
    • 1
    • 2
  • E. K. Khlestkina
    • 1
  1. 1.Institute of Cytology and Genetics, Siberian BranchRussian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia

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