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Article

The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida

1
Cellular and Molecular Sciences Group, James Hutton Institute, Dundee DD2 5DA, UK
2
School of Biology, University of St Andrews, North Haugh, St Andrews KY16 9TZ, UK
3
Agriculture and Agri-Food Canada, 430 boul. Gouin, St-Jean-sur-Richelieu, QC J3B 3E6, Canada
4
School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TZ, UK
5
Information and Computational Sciences Group, James Hutton Institute, Dundee DD2 5DA, UK
6
School of Life Sciences, Division of Plant Sciences at the JHI, University of Dundee, Dundee DD2 5DA, UK
7
Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-766 Warsaw, Poland
*
Author to whom correspondence should be addressed.
Genes 2020, 11(12), 1429; https://doi.org/10.3390/genes11121429
Received: 16 October 2020 / Revised: 24 November 2020 / Accepted: 25 November 2020 / Published: 28 November 2020
(This article belongs to the Special Issue Genomics of Plant-Nematode Interactions)
Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) Globodera pallida, the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, GpaV (from Solanum vernei) and H3 from S. tuberosum ssp. andigena CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify Avirulence (Avr) genes in G. pallida populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate Avr genes. Most of the variant calls determining selection were associated with H3-selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in G. pallida. View Full-Text
Keywords: potato cyst nematodes; Globodera pallida; next generation sequencing; target enrichment sequencing; whole genome sequencing; selection; virulence; effectors potato cyst nematodes; Globodera pallida; next generation sequencing; target enrichment sequencing; whole genome sequencing; selection; virulence; effectors
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MDPI and ACS Style

Varypatakis, K.; Véronneau, P.-Y.; Thorpe, P.; Cock, P.J.A.; Lim, J.T.-Y.; Armstrong, M.R.; Janakowski, S.; Sobczak, M.; Hein, I.; Mimee, B.; Jones, J.T.; Blok, V.C. The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida. Genes 2020, 11, 1429. https://doi.org/10.3390/genes11121429

AMA Style

Varypatakis K, Véronneau P-Y, Thorpe P, Cock PJA, Lim JT-Y, Armstrong MR, Janakowski S, Sobczak M, Hein I, Mimee B, Jones JT, Blok VC. The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida. Genes. 2020; 11(12):1429. https://doi.org/10.3390/genes11121429

Chicago/Turabian Style

Varypatakis, Kyriakos; Véronneau, Pierre-Yves; Thorpe, Peter; Cock, Peter J.A.; Lim, Joanne T.-Y.; Armstrong, Miles R.; Janakowski, Sławomir; Sobczak, Mirosław; Hein, Ingo; Mimee, Benjamin; Jones, John T.; Blok, Vivian C. 2020. "The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida" Genes 11, no. 12: 1429. https://doi.org/10.3390/genes11121429

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