A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual

Sebastian Eves-van den Akker (Lead / Corresponding author), Catherine J. Lilley, Alex Reid, Jon Pickup, Eric Anderson, Peter J. A. Cock, Mark Blaxter, Peter E. Urwin, John T. Jones, Vivian C. Blok

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Abstract

Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen-informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species.
We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK, and adopt a metagenetics approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach we describe the distribution of G. pallida mitotypes across Scotland with field-scale resolution. Most fields contain a single mitotype, one fifth contain a mix of mitotypes, and less than 3 % contain all three mitotypes. Within mixed fields we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying "pathoscape". Finally, we assess mitotype distribution at the level of the individual cyst, and provide evidence of "hybrids". This study provides a method for accurate, quantitative and high throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant-parasite.
Original languageEnglish
Pages (from-to)5842-5851
Number of pages10
JournalMolecular Ecology
Volume24
Issue number23
Early online date26 Nov 2015
DOIs
Publication statusPublished - Dec 2015

Keywords

  • Potato cyst nematode
  • Metagenetics
  • Mitotype
  • Diversity
  • Distribution

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    Eves-van den Akker, S., Lilley, C. J., Reid, A., Pickup, J., Anderson, E., Cock, P. J. A., Blaxter, M., Urwin, P. E., Jones, J. T., & Blok, V. C. (2015). A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual. Molecular Ecology, 24(23), 5842-5851. https://doi.org/10.1111/mec.13434