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

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 metagenetic 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.

Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion

“…mals(Bik et al, 2012;Capra et al, 2016;Eves-van den Akker et al, 2015;Gómez-Rodríguez, Crampton-Platt, Timmermans, Baselga, & Vogler, 2015;Griffiths et al, 2018). We show significantly positive correlations between all methods when focusing on seven functionally diverse nematode taxa targeted by qPCR and between most taxa recovered by HTS and MorphoID.…”

“…While morphological identification represents the most commonly applied technique to determine identities and abundances soil nematode communities, molecular analyses in form of high‐throughput sequencing that are commonplace to study microbes (Geisen, ; Prosser, ) are now applied more often on animals (Bik et al., ; Capra et al., ; Eves‐van den Akker et al., ; Gómez‐Rodríguez, Crampton‐Platt, Timmermans, Baselga, & Vogler, ; Griffiths et al., ). We show significantly positive correlations between all methods when focusing on seven functionally diverse nematode taxa targeted by qPCR and between most taxa recovered by HTS and MorphoID.…”

“…Molecular methods also allow high‐throughput differentiation of morphologically indistinguishable taxa to species or even sub‐species level (Eves‐van den Akker et al., ). For instance, we identified eight genera with HTS within the morphologically hardly distinguishable family Rhabditidae (Floyd et al., ; Powers, ).…”

Technological advancements and their importance for nematode identification

“…Genomic information at all levels has been utilised for identifying nematodes, from DNA sequence, the structure of molecules, and genetic mutations to the presence versus absence of genes (Subbotin and Moens, 2007). At the protein level, isozyme analysis (Esbenshade and Triantaphyllou, 1990;Payan and Dickson, 1990), two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (2-D SDS-PAGE) (Ferris et al, 1994), monoclonal or polyclonal antibodies-base serological techniques (Jones et al, 1988;Schots et al, 1990) and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) (Perera et al, 2009) are the methods that have been utilised for distinguishing nematodes at species or subspecific levels ( Table 1).…”

Increased virulence of Globodera pallida during repeated rearing on different resistant potato cultivars explained by a simple model

“…Every year in spring, without the host, about 30% of the eggs hatch spontaneously. When potatoes are grown again, the surviving eggs will hatch, leading to a new reproduction cycle (Seinhorst et al, 1995;Been & Schomaker, 2000;Eves-van den Akker et al, 2015).…”