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

Kyriakos Varypatakis, Pierre-Yves Véronneau, Peter Thorpe, Peter J. A. Cock, Joanne Tze-Yin Lim, Miles R. Armstrong, Sławomir Janakowski, Miroslaw Sobczak, Ingo Hein, Benjamin Mimee, John T. Jones, Vivian C. Blok (Lead / Corresponding author)

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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.
Original languageEnglish
Article number1429
Number of pages20
JournalGenes
Volume11
Issue number12
DOIs
Publication statusPublished - 28 Nov 2020

Keywords

  • potato cyst nematodes
  • Globodera pallida
  • next generation sequencing
  • target enrichment sequencing
  • whole genome sequencing
  • selection
  • virulence
  • effectors
  • Whole genome sequencing
  • Selection
  • Virulence
  • Next generation sequencing
  • Target enrichment sequencing
  • Potato cyst nematodes
  • Effectors

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