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The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida

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The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida. / Varypatakis, Kyriakos; Véronneau, Pierre-Yves ; Thorpe, Peter; Cock, Peter J A ; Tze- Yin Lim, Joanne; Armstrong, Miles R.; Janakowski, Sławomir; Sobczak, Mirosław ; Hein, Ingo; Mimee, Benjamin; Jones, John; Blok, Vivian.

In: Genes, Vol. 11, No. 12, 1429, 28.11.2020.

Research output: Contribution to journalArticlepeer-review

Harvard

Varypatakis, K, Véronneau, P-Y, Thorpe, P, Cock, PJA, Tze- Yin Lim, J, Armstrong, MR, Janakowski, S, Sobczak, M, Hein, I, Mimee, B, Jones, J & Blok, V 2020, 'The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida', Genes, vol. 11, no. 12, 1429. https://doi.org/10.3390/genes11121429

APA

Varypatakis, K., Véronneau, P-Y., Thorpe, P., Cock, P. J. A., Tze- Yin Lim, J., Armstrong, M. R., Janakowski, S., Sobczak, M., Hein, I., Mimee, B., Jones, J., & Blok, V. (2020). The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida. Genes, 11(12), [1429]. https://doi.org/10.3390/genes11121429

Vancouver

Varypatakis K, Véronneau P-Y, Thorpe P, Cock PJA, Tze- Yin Lim J, Armstrong MR et al. The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida. Genes. 2020 Nov 28;11(12). 1429. https://doi.org/10.3390/genes11121429

Author

Varypatakis, Kyriakos ; Véronneau, Pierre-Yves ; Thorpe, Peter ; Cock, Peter J A ; Tze- Yin Lim, Joanne ; Armstrong, Miles R. ; Janakowski, Sławomir ; Sobczak, Mirosław ; Hein, Ingo ; Mimee, Benjamin ; Jones, John ; Blok, Vivian. / The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida. In: Genes. 2020 ; Vol. 11, No. 12.

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@article{ad6cc4eb238e460db7823a0ba1c41195,
title = "The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida",
abstract = "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. ",
keywords = "Potato cyst nematodes, Globodera pallida, Next generation sequencing, Target enrichment sequencing, Whole genome sequencing, Selection, Virulence, Effectors",
author = "Kyriakos Varypatakis and Pierre-Yves V{\'e}ronneau and Peter Thorpe and Cock, {Peter J A} and {Tze- Yin Lim}, Joanne and Armstrong, {Miles R.} and S{\l}awomir Janakowski and Miros{\l}aw Sobczak and Ingo Hein and Benjamin Mimee and John Jones and Vivian Blok",
note = "This work was funded through an AHDB PhD award, the USDA GLOBAL Project and by the Rural and Environmental Science and Analytical Services division of the Scottish Government. Bioinformatics and computational analyses for the generation of the new G. pallida genome assembly were supported by the University of St Andrews Bioinformatics Unit, which is funded by a Wellcome Trust ISSF award (grant 105621/Z/14/Z).",
year = "2020",
month = nov,
day = "28",
doi = "10.3390/genes11121429",
language = "English",
volume = "11",
journal = "Genes",
issn = "2073-4425",
publisher = "MDPI",
number = "12",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - The genomic impact of selection for virulence against resistance in the potato cyst nematode, Globodera pallida

AU - Varypatakis, Kyriakos

AU - Véronneau, Pierre-Yves

AU - Thorpe, Peter

AU - Cock, Peter J A

AU - Tze- Yin Lim, Joanne

AU - Armstrong, Miles R.

AU - Janakowski, Sławomir

AU - Sobczak, Mirosław

AU - Hein, Ingo

AU - Mimee, Benjamin

AU - Jones, John

AU - Blok, Vivian

N1 - This work was funded through an AHDB PhD award, the USDA GLOBAL Project and by the Rural and Environmental Science and Analytical Services division of the Scottish Government. Bioinformatics and computational analyses for the generation of the new G. pallida genome assembly were supported by the University of St Andrews Bioinformatics Unit, which is funded by a Wellcome Trust ISSF award (grant 105621/Z/14/Z).

PY - 2020/11/28

Y1 - 2020/11/28

N2 - 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.

AB - 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.

KW - Potato cyst nematodes

KW - Globodera pallida

KW - Next generation sequencing

KW - Target enrichment sequencing

KW - Whole genome sequencing

KW - Selection

KW - Virulence

KW - Effectors

U2 - 10.3390/genes11121429

DO - 10.3390/genes11121429

M3 - Article

VL - 11

JO - Genes

JF - Genes

SN - 2073-4425

IS - 12

M1 - 1429

ER -

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