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Development of KASP Markers for the Potato Virus Y Resistance Gene Rychc Using Whole-Genome Resequencing Data

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Abstract

Potato virus Y is the most important potato virus worldwide, affecting tuber yield and quality. The resistance gene Rychc, derived from the potato wild relative Solanum chacoense, provides broad spectrum and durable resistance to the virus and has been used to develop resistant cultivars. Several DNA markers have been developed and have contributed to the efficient selection of resistant individuals. In this study, we developed Kompetitive Allele Specific PCR markers for Rychc using whole-genome resequencing data for a diverse set of 25 PVY susceptible cultivars and a Rychc-positive clone. Marker Ry_4099 targets two variants in the 3ʹ-UTR and was able to discriminate all five allele dosages in a tetraploid test population. Marker Ry_3331 targets two variants in Exon 4 and, although it only provides presence/absence information, it discriminates between the two known resistant alleles of Rychc. These markers will greatly contribute to efficient development of resistant cultivars.

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Data Availability

Whole-genome sequence data for 98H20-5 is available from the DDBJ Sequence Read Archive (DRA) under BioProject ID PRJDB16925.

References

  • Adams, M. J., J. F. Antoniw, and C. M. Fauquet. 2005. Molecular criteria for genus and species discrimination within the family Potyviridae. Archives of Virology 150: 459–479. https://doi.org/10.1007/s00705-004-0440-6.

    Article  CAS  PubMed  Google Scholar 

  • Akai, K., K. Asano, C. Suzuki, E. Shimosaka, S. Tamiya, T. Suzuki, T. Takeuchi, and T. Ohki. 2023. De novo genome assembly of the partial homozygous dihaploid potato identified PVY resistance gene Rychc derived from Solanum chacoense. Breeding Science. https://doi.org/10.1270/jsbbs.22078.

    Article  PubMed  PubMed Central  Google Scholar 

  • Andrade, C. M., C. A. B. P. Pinto, S. R. R. de Paula Ribeiro, and L. S. Peixouto. and X.M. De Souza Vilela. 2009. Potato clones with multiple copies of the Ryadg allele conferring resistance to PVY. Crop Breeding and Applied Biotechnology 9: 286–292.

  • Asama, K., H. Ito, N. Murakami, and T. Itoh. 1982. New potato variety Konafubuki. Bulletin of the Hokkaido Prefectural Agricultural Experiment Station 48: 75–84.

    Google Scholar 

  • Bethke, P. C., D. A. Halterman, D. M. Francis, J. M. Jiang, D. S. Douches, A. O. Charkowski, and J. Parsons. 2022. Diploid potatoes as a catalyst for change in the potato industry. American Journal of Potato Research 99: 337–357. https://doi.org/10.1007/s12230-022-09888-x.

    Article  Google Scholar 

  • Bradshaw, J. E. 2022. Breeding diploid F1 hybrid potatoes for propagation from botanical seed (TPS): comparisons with theory and other crops. Plants 11: https://doi.org/10.3390/plants11091121.

  • Brunt, A. A. 2001. Potyviruses. In Virus and virus-like diseases of potatoes and production of seed-potatoes, eds. G. Loebenstein, P. H. Berger, and A. A. Brunt. 77–86. Lawson: Dordrecht: Springer Science + Business Media Dordrecht.

    Chapter  Google Scholar 

  • Chen, X. W., D. Lewandowska, M. R. Armstrong, K. Baker, T. Y. Lim, M. Bayer, B. Harrower, K. McLean, F. Jupe, K. Witek, A. K. Lees, J. D. Jones, G. J. Bryan, and I. Hein. 2018. Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies. Theoretical and Applied Genetics 131: 1287–1297. https://doi.org/10.1007/s00122-018-3078-6.

    Article  CAS  PubMed  Google Scholar 

  • Chen, N., W. W. Zhu, J. F. Xu, S. G. Duan, C. S. Bian, J. Hu, W. X. Wang, G. C. Li, and L. P. Jin. 2019. Molecular marker development and primary physical map construction for the tuber shape ro gene locus in diploid potato (Solanum tuberosum L). Molecular Breeding 39: https://doi.org/10.1007/s11032-018-0913-z.

  • Clot, C. R., C. Polzer, C. Prodhomme, C. Schuit, C. J. M. Engelen, R. C. B. Hutten, and H. J. van Eck. 2020. The origin and widespread occurrence of Sli-based self-compatibility in potato. Theoretical and Applied Genetics 133: 2713–2728. https://doi.org/10.1007/s00122-020-03627-8.

    Article  CAS  PubMed  Google Scholar 

  • Cockerham, G. 1943. Potato breeding for virus resistance. Annals of Applied Biology 30: 105–108. https://doi.org/10.1111/j.1744-7348.1943.tb06166.x.

    Article  Google Scholar 

  • Danecek, P., J. K. Bonfield, J. Liddle, J. Marshall, V. Ohan, M. O. Pollard, A. Whitwham, T. Keane, S. A. McCarthy, R. M. Davies, and H. Li. 2021. Twelve years of SAMtools and BCFtools. Gigascience 10. https://doi.org/10.1093/gigascience/giab008.

  • DeYoung, B. J., and R. W. Innes. 2006. Plant NBS-LRR proteins in pathogen sensing and host defense. Nature Immunology 7: 1243–1249. https://doi.org/10.1038/ni1410.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duxbury, Z., C. H. Wu, and P. T. Ding. 2021. A comparative overview of the intracellular guardians of plants and animals: NLRs in innate immunity and beyond. Annual Review of Plant Biology, Vol 72, 2021 72: 155–184. https://doi.org/10.1146/annurev-arplant-080620-104948.

  • Elison, G. L., R. G. Novy, and J. L. Whitworth. 2021. Russet potato breeding clones with extreme resistance to potato virus Y conferred by Rychc as well as resistance to late blight and cold-induced sweetening. American Journal of Potato Research 98: 411–419. https://doi.org/10.1007/s12230-021-09852-1.

    Article  CAS  Google Scholar 

  • Endelman, J. B., and S. H. Jansky. 2016. Genetic mapping with an inbred line-derived F2 population in potato. Theoretical and Applied Genetics 129: 935–943. https://doi.org/10.1007/s00122-016-2673-7.

    Article  CAS  PubMed  Google Scholar 

  • Fujimatsu, M., H. Hashizume, T. Fudan, Y. Koma, R. Sanetomo, S. Ono, and K. Hosaka. 2018. Harimaru: a new potato variety for a local specialty. Breeding Science 68: 284–288. https://doi.org/10.1270/jsbbs.17109.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garrison, E., and G. Marth. 2012. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:12073907.

  • Hardigan, M. A., F. P. E. Laimbeer, L. Newton, E. Crisovan, J. P. Hamilton, B. Vaillancourt, K. Wiegert-Rininger, J. C. Wood, D. S. Douches, E. M. Farre, R. E. Veilleux, and C. R. Buell. 2017. Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. Proceedings of the National Academy of Sciences of the United States of America 114: E9999–E10008. https://doi.org/10.1073/pnas.1714380114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hosaka, K., Y. Hosaka, M. Mori, T. Maida, and H. Matsunaga. 2001. Detection of a simplex RAPD marker linked to resistance to potato virus Y in a tetraploid potato. American Journal of Potato Research 78: 191–196.

    Article  CAS  Google Scholar 

  • Jansky, S. H., A. O. Charkowski, D. S. Douches, G. Gusmini, C. Richael, P. C. Bethke, D. M. Spooner, R. G. Novy, H. De Jong, W. S. De Jong, J. B. Bamberg, A. L. Thompson, B. Bizimungu, D. G. Holm, C. R. Brown, K. G. Haynes, V. R. Sathuvalli, R. E. Veilleux, J. C. Miller, J. M. Bradeen, and J. M. Jiang. 2016. Reinventing potato as a diploid inbred line-based crop. Crop Science 56: 1412–1422. https://doi.org/10.2135/cropsci2015.12.0740.

    Article  CAS  Google Scholar 

  • Jones, R. 1990. Strain group specific and virus specific hypersensitive reactions to infection with potyviruses in potato cultivars. Annals of Applied Biology 117: 93–105.

    Article  Google Scholar 

  • Jones, J. D. G., R. E. Vance, and J. L. Dangl. 2016. Intracellular innate immune surveillance devices in plants and animals. Science 354: https://doi.org/10.1126/science.aaf6395.

  • Kante, M., H. Lindqvist-Kreuze, L. Portal, M. David, and M. Gastelo. 2021. Kompetitive Allele Specific PCR (KASP) markers for potato: An effective tool for increased genetic gains. Agronomy-Basel 11. https://doi.org/10.3390/agronomy11112315.

  • Karasev, A. V., and S. M. Gray. 2013. Continuous and emerging challenges of potato virus Y in potato. Annual Review of Phytopathology 51 51: 571–586. https://doi.org/10.1146/annurev-phyto-082712-102332.

    Article  CAS  PubMed  Google Scholar 

  • Kaushik, S. K., R. Sharma, I. D. Garg, B. P. Singh, S. K. Chakrabarti, V. Bhardwaj, and S. K. Pandey. 2013. Development of a triplex (YYYy) parental potato line with extreme resistance to potato virus Y using marker assisted selection. Journal of Horticultural Science & Biotechnology 88: 580–584.

    Article  CAS  Google Scholar 

  • Knaus, B. J., and N. J. Grunwald. 2017. VCFR: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources 17: 44–53. https://doi.org/10.1111/1755-0998.12549.

    Article  CAS  PubMed  Google Scholar 

  • Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997.

  • Li, G. G., J. J. Shao, Y. W. Wang, T. F. Liu, Y. H. Tong, S. Jansky, C. H. Xie, B. T. Song, and X. K. Cai. 2022. Rychc confers extreme resistance to potato virus Y in potato. Cells 11. https://doi.org/10.3390/cells11162577.

  • Lindhout, P., D. Meijer, T. Schotte, R. C. B. Hutten, and R. G. F. Visser. 2011. Eck, and H.J. van Towards F1 hybrid seed potato breeding. Potato Research 54: 301–312.

  • MacKenzie, T. D. B., M. S. Fageria, X. Z. Nie, and M. Singh. 2014. Effects of crop management practices on current-season spread of potato virus Y. Plant Disease 98: 213–222. https://doi.org/10.1094/pdis-04-13-0403-re.

    Article  PubMed  Google Scholar 

  • Meade, F., S. Byrne, D. Griffin, C. Kennedy, F. Mesiti, and D. Milbourne. 2020. Rapid development of KASP markers for disease resistance genes using pooled whole-genome resequencing. Potato Research 63: 57–73. https://doi.org/10.1007/s11540-019-09428-x.

    Article  CAS  Google Scholar 

  • Mori, K., N. Mukojima, T. Nakao, S. Tamiya, Y. Sakamoto, N. Sohbaru, K. Hayashi, H. Watanuki, K. Nara, K. Yamazaki, T. Ishii, and K. Hosaka. 2012. Germplasm Release: Saikai 35, a male and female fertile breeding line carrying Solanum phureja-derived cytoplasm and potato cyst nematode resistance (H1) and potato virus Y resistance (Rychc) genes. American Journal of Potato Research 89: 63–72. https://doi.org/10.1007/s12230-011-9221-4.

    Article  Google Scholar 

  • Mori, K., K. Asano, S. Tamiya, T. Nakao, and M. Mori. 2015. Challenges of breeding potato cultivars to grow in various environments and to meet different demands. Breeding Science 65: 3–16. https://doi.org/10.1270/jsbbs.65.3.

    Article  PubMed  PubMed Central  Google Scholar 

  • Munoz, F. J., R. L. Plaisted, and H. D. Thurston. 1975. Resistance to potato virus Y in Solanum tuberosum spp. andigena. American Potato Journal 52: 107–115. https://doi.org/10.1007/bf02852043.

    Article  Google Scholar 

  • Ohki, T., M. Sano, K. Asano, T. Nakayama, and T. Maoka. 2018. Effect of temperature on resistance to Potato virus Y in potato cultivars carrying the resistance gene Rychc. Plant Pathology 67: 1629–1635. https://doi.org/10.1111/ppa.12862.

    Article  CAS  Google Scholar 

  • Okonechnikov, K., O. Golosova, M. Fursov, and U. Team. 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28: 1166–1167. https://doi.org/10.1093/bioinformatics/bts091.

    Article  CAS  PubMed  Google Scholar 

  • Pham, G. M., J. P. Hamilton, J. C. Wood, J. T. Burke, H. N. Zhao, B. Vaillancourt, S. J. Ou, J. M. Jiang, and C. R. Buell. 2020. Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience 9: https://doi.org/10.1093/gigascience/giaa100.

  • Robinson, J. T., H. Thorvaldsdottir, W. Winckler, M. Guttman, E. S. Lander, G. Getz, and J. P. Mesirov. 2011. Integrative genomics viewer. Nature Biotechnology 29: 24–26. https://doi.org/10.1038/nbt.1754.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakamoto, Y., K. Mori, Y. Matsuo, N. Mukojima, W. Watanabe, N. Sobaru, S. Tamiya, T. Nakao, K. Hayashi, H. Watanuki, K. Nara, K. Yamazaki, and M. Chaya. 2017. Breeding of a new potato variety ‘Nagasaki Kogane’ with high eating quality, high carotenoid content, and resistance to diseases and pests. Breeding Science 67: 320–326. https://doi.org/10.1270/jsbbs.16168.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sato, M., K. Nishikawa, K. Komura, and K. Hosaka. 2006. Potato virus Y resistance gene, Rychc, mapped to the distal end of potato chromosome 9. Euphytica 149. https://doi.org/10.1007/s10681-006-9090-y.

  • Semagn, K., R. Babu, S. Hearne, and M. Olsen. 2014. Single nucleotide polymorphism genotyping using Kompetitive Allele specific PCR (KASP): overview of the technology and its application in crop improvement. Molecular Breeding 33: 1–14. https://doi.org/10.1007/s11032-013-9917-x.

    Article  CAS  Google Scholar 

  • Sorensen, P. L., G. Christensen, H. S. Karki, and J. B. Endelman. 2023. A KASP marker for the potato late blight resistance gene RB/Rpi-blb1. American Journal of Potato Research 100: 240–246. https://doi.org/10.1007/s12230-023-09914-6.

    Article  CAS  Google Scholar 

  • Strachan, S. M., M. R. Armstrong, A. Kaur, K. M. Wright, T. Y. Lim, K. Baker, J. Jones, G. Bryan, and V. Blok. and I. Hein. 2019. Mapping the H2 resistance effective against Globodera Pallida pathotype Pa1 in tetraploid potato. Theoretical and Applied Genetics 132: 1283–1294. https://doi.org/10.1007/s00122-019-03278-4.

  • Su, Y., M. Viquez-Zamora, D. den Uil, J. Sinnige, H. Kruyt, J. Vossen, and P. Lindhout. 2020. Heusden, and S. van Introgression of genes for resistance against Phytophthora infestans in diploid potato. American Journal of Potato Research 97: 33–42. https://doi.org/10.1007/s12230-019-09741-8.

  • Uitdewilligen, J., A. M. A. Wolters, B. B. D’Hoop, T. J. A. Borm, and R. G. F. Visser. and H.J. van Eck. 2013. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. Plos One 8. https://doi.org/10.1371/journal.pone.0062355.

  • Valkonen, J. P. T. 1997. Novel resistances to four potyviruses in tuber-bearing potato species, and temperature-sensitive expression of hypersensitive resistance to potato virus Y. Annals of Applied Biology 130: 91–104. https://doi.org/10.1111/j.1744-7348.1997.tb05785.x.

    Article  Google Scholar 

  • Valkonen, J. P. T. 2015. Elucidation of virus-host interactions to enhance resistance breeding for control of virus diseases in potato. Breeding Science 65: 69–76. https://doi.org/10.1270/jsbbs.65.69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Valkonen, J. P. T., M. M. Kyle, and S. A. Slack. 1996. Comparison of resistance to potyviruses within Solanaceae: infection of potatoes with tobacco etch potyvirus and peppers with potato A and Y potyviruses. Annals of Applied Biology 129: 25–38. https://doi.org/10.1111/j.1744-7348.1996.tb05728.x.

    Article  Google Scholar 

  • Yamakawa, H., E. Haque, M. Tanaka, H. Takagi, K. Asano, E. Shimosaka, K. Akai, S. Okamoto, K. Katayama, and S. Tamiya. 2021. Polyploid QTL-seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole-genome resequencing. Plant Biotechnology Journal 19: 2040–2051. https://doi.org/10.1111/pbi.13633.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, C. Z., Z. M. Yang, D. Tang, Y. H. Zhu, P. Wang, D. W. Li, G. T. Zhu, X. Y. Xiong, Y. Shang, and C. H. Li. and S.W. Huang. 2021. Genome design of hybrid potato. Cell 184: 3873–3883. https://doi.org/10.1016/j.cell.2021.06.006.

  • Zheng, C. Z., R. R. Amadeu, P. R. Munoz, and J. B. Endelman. 2021. Haplotype reconstruction in connected tetraploid F1 populations. Genetics 219: https://doi.org/10.1093/genetics/iyab106.

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Acknowledgements

We thank Dr. Kazuyoshi Hosaka, Obihiro University of Agriculture and Veterinary Medicine, and Dr. Xingkui Cai, Huazhong Agricultural University, for providing 98H20-5 and sequence information of Rychc-2, respectively. We also thank Dr. Kotaro Akai, Hokkaido Agricultural Research Center, National Agricultural Research Organization, and Grace Christensen, University of Wisconsin-Madison, for helpful suggestions on the research. This study was supported by grants from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics-Based Technology for Agricultural Improvement [SFC3002]), and USDA NIFA Award 2021-34141-35447.

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  1. Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Kenji Asano & Jeffrey B. Endelman

  2. Division of Large-Scale Upland Farming Research, Hokkaido Agricultural Research Center, National Agricultural Research Organization, Memuro, Hokkaido, 082-0081, Japan

    Kenji Asano

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  1. Kenji Asano
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KA designed the study, conducted the experiments, wrote the original draft, and edited the manuscript. JBE contributed methods, data, and germplasm, supervised the project, reviewed, and edited the manuscript.

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Correspondence to Kenji Asano.

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Asano, K., Endelman, J.B. Development of KASP Markers for the Potato Virus Y Resistance Gene Rychc Using Whole-Genome Resequencing Data. Am. J. Potato Res. (2024). https://doi.org/10.1007/s12230-024-09944-8

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