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

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...

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Autores principales: Eves‐van den Akker, Sebastian, Lilley, Catherine J., Reid, Alex, Pickup, Jon, Anderson, Eric, Cock, Peter J.A., Blaxter, Mark, Urwin, Peter E., Jones, John T., Blok, Vivian C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981918/
https://www.ncbi.nlm.nih.gov/pubmed/26607216
http://dx.doi.org/10.1111/mec.13434
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author Eves‐van den Akker, Sebastian
Lilley, Catherine J.
Reid, Alex
Pickup, Jon
Anderson, Eric
Cock, Peter J.A.
Blaxter, Mark
Urwin, Peter E.
Jones, John T.
Blok, Vivian C.
author_facet Eves‐van den Akker, Sebastian
Lilley, Catherine J.
Reid, Alex
Pickup, Jon
Anderson, Eric
Cock, Peter J.A.
Blaxter, Mark
Urwin, Peter E.
Jones, John T.
Blok, Vivian C.
author_sort Eves‐van den Akker, Sebastian
collection PubMed
description 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.
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spelling pubmed-49819182016-08-26 A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual Eves‐van den Akker, Sebastian Lilley, Catherine J. Reid, Alex Pickup, Jon Anderson, Eric Cock, Peter J.A. Blaxter, Mark Urwin, Peter E. Jones, John T. Blok, Vivian C. Mol Ecol ORIGINAL ARTICLES 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. John Wiley and Sons Inc. 2015-11-26 2015-12 /pmc/articles/PMC4981918/ /pubmed/26607216 http://dx.doi.org/10.1111/mec.13434 Text en © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle ORIGINAL ARTICLES
Eves‐van den Akker, Sebastian
Lilley, Catherine J.
Reid, Alex
Pickup, Jon
Anderson, Eric
Cock, Peter J.A.
Blaxter, Mark
Urwin, Peter E.
Jones, John T.
Blok, Vivian C.
A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
title A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
title_full A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
title_fullStr A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
title_full_unstemmed A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
title_short A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
title_sort metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
topic ORIGINAL ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981918/
https://www.ncbi.nlm.nih.gov/pubmed/26607216
http://dx.doi.org/10.1111/mec.13434
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