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

Authors: Martin, Frank; ZHANG, YONGHONG - University Of California; COOKE, DAVID - The James Hutton Institute; COFFEY, MICHAEL - University Of California; Grunwald, Niklaus - Nik; FRY, WILLIAM - Cornell University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/20/2018
Publication Date: 1/2/2019
Citation: Martin, F.N., Zhang, Y., Cooke, D.E.L., Coffey, M.D., Grunwald, 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):e0208606. https://doi.org/10.1371/journal.pone.0208606.
DOI: https://doi.org/10.1371/journal.pone.0208606

Interpretive Summary: This manuscript describes the development of additional molecular markers for studying differences in the mitochondrial genome and comparing the results to nuclear genotypes of Phytophthora infestans, the pathogen responsible for late blight. The research provides additional tools for studying the population genetics and biology of this important pathogen of potato.

Technical Abstract: The potato late blight pathogen, Phytophthora infestans, spread as a succession of clonal lineages in many parts of the world. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen dissemination at local and global scales. This, in turn, helps to optimize 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 improved discrimination from four types with the PCR RFLP method to 37 mtDNA haplotypes. Two main lineages, I and II were defined; group II comprised two distinct clusters with eight haplotypes corresponding to the RFLP type IIa and four haplotypes resolved within type IIb. Within type I, 26 mtDNA haplotypes were defined, but the association between the RFLP-based Ia and Ib types and sequence-based mtDNA haplotyping was less clear. Some isolates defined as type Ib clustered alongside type Ia isolates, suggesting homoplasy (i.e., independent origins of the same RFLP type). 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 was observed: US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers provide insights on evolutionary questions relating to the diversity, phylogeography, and the origins and spread of clonal lineages of P. infestans.