Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

Frank N. Martin (Lead / Corresponding author), Yonghong Zhang, David E. L. Cooke (Lead / Corresponding author), Mike D. Coffey, Niklaus J. Grünwald, William E. Fry

Research output: Contribution to journalArticle

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Abstract

In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 P. infestans isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of P. infestans.

Original languageEnglish
Article numbere0208606
Pages (from-to)1-24
Number of pages24
JournalPLoS ONE
Volume14
Issue number1
DOIs
Publication statusPublished - 2 Jan 2019

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Phytophthora infestans
Mitochondrial DNA
Haplotypes
haplotypes
mitochondrial DNA
Pathogens
Restriction Fragment Length Polymorphisms
Population
restriction fragment length polymorphism
DNA sequences
Polymerase Chain Reaction
Assays
Association reactions
Phylogeography
genetic variation
South America
pathogens
Practice Management
phylogeography
Solanum tuberosum

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Martin, F. N., Zhang, Y., Cooke, D. E. L., Coffey, M. D., Grünwald, N. J., & Fry, W. E. (2019). Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs. PLoS ONE, 14(1), 1-24. [e0208606]. https://doi.org/10.1371/journal.pone.0208606
Martin, Frank N. ; Zhang, Yonghong ; Cooke, David E. L. ; Coffey, Mike D. ; Grünwald, Niklaus J. ; Fry, William E. / Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs. In: PLoS ONE. 2019 ; Vol. 14, No. 1. pp. 1-24.
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Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs. / Martin, Frank N. (Lead / Corresponding author); Zhang, Yonghong; Cooke, David E. L. (Lead / Corresponding author); Coffey, Mike D.; Grünwald, Niklaus J.; Fry, William E.

In: PLoS ONE, Vol. 14, No. 1, e0208606, 02.01.2019, p. 1-24.

Research output: Contribution to journalArticle

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