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
SN - 2073-4425
VL - 11
JO - Genes
JF - Genes
IS - 12
M1 - 1429
ER -