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

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.

Genotypic and phenotypic characterization of Phytophthora infestans in South Korea during 2009–2016 reveals clonal reproduction and absence of EU_13_A2 genotype

“…The KR_2_A2 genotype included only nine isolates, found in 2011, 2013, and 2015 in Gyeongnam Province, and grouped into three MLGs. This was also almost identical to A2 mating type isolates previously reported (Martin et al , 2019) from tomato in South Korea in 2007 (P15149) and potato in Japan (P6155, P6167) (Table ).…”

“…The SIB‐1 genotype included 31 isolates grouped into six MLGs. It had an almost identical SSR profile to two isolates previously reported from Russia as early as 2005 (P12030 and P12053; Martin et al , 2019) (Table ) and its match to the SIB‐1 clone (Elansky et al . , 2001; Guo et al .…”

“…The SSR genotype defined as KR_1_A1 in this study is unrelated to the KR‐1 genotype of A2 mating type defined by Gotoh et al (2005). Samples from the Riverside Phytophthora collection (https://phytophthora.ucr.edu/) provide some insights, with the following matching SSR fingerprints identified (Martin et al , 2019): clone KR_1_A1 isolate P15101 from South Korea in 2007 (mtDNA type IIa), clone KR_2_A2 isolates P6155 and P6167 from Japan and P15149 from South Korea in 2007 (mtDNA type IIa), and SIB‐1 isolates P12053 and P12030 from Murmansk in northwest Russia in 2005 (mtDNA type IIa). This is further confirmation that these clones have been present on solanaceous crops over a wide geographical region for over a decade.…”

Mitochondrial Genome Sequence ofPhytophthora sansomeanaand Comparative Analysis ofPhytophthoraMitochondrial Genomes

“…Inconsistencies in annotation have been observed. Mitochondrial genomes have been use to study the population of P. infestans [19][20][21][22] as well as resolving the phylogenetic relationship of Phytophthora species [15,23]. Molecular information from P. sansomeana is limited.…”

Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA

“…Yuan et al (2017) [192] showed that the ancestral expansion of inverted repeats resulted in gene duplication in the Pythiales and Saprolegniales compared with the Peronosporales. It has been indicated that whole mitogenome analysis appears to provide a view of the evolutionary history and phylogeography of the oomycetes and a comparison of sequence data from herbaria and living organisms can detect evolutionary events leading to the divergence of this important group of pathogens [192,193].…”