Genetic structure and population diversity of Phytophthora infestans strains in Pacific western Canada

Abstract

Late blight caused by Phytophthora infestans is an economically important disease of potato and tomato worldwide. In Canada, an increase in late blight incidence and severity coincided with changes in genetic composition of P. infestans. We monitored late blight incidence on tomato and potato in Pacific western and eastern Canada between 2019 and 2022, identified genotypes of P. infestans, and examined their population genetic diversity. We identified four major existing genotypes US11, US17, US8, and US23 as well as 25 new genotypes. The US11 genotype was dominant in Pacific western Canada, accounting for 59% of the total population. We discovered the US17 genotype for the first time in Canada. We revealed a higher incidence of late blight and quite diverse genotypes of P. infestans in Pacific western Canada than in eastern Canada. We found high genetic diversity of P. infestans population from Pacific western Canada, as evidenced by the high number of multilocus genotypes, high values of genetic diversity indices, and emergence of 25 new genotypes. Considering the number of disease incidence, the detection of diverse known genotypes, the emergence of novel genotypes, and the high number of isolates resistant to metalaxyl-m (95%) from Pacific western Canada, the region could play a role in establishing sexual recombination and diverse populations, which could ultimately pose challenges for late blight management. Therefore, continuous monitoring of P. infestans populations in Pacific western region and across Canada is warranted. Key points • Genotypes of P. infestans in Pacific western were quite diverse than in eastern Canada. • We discovered US17 genotype for the first time in Canada and identified 26 novel genotypes. • Approximately 95% of P. infestans isolates were resistant to metalaxyl-m.

Machine Learning-Based Identification of Mating Type and Metalaxyl Response in Phytophthora infestans Using SSR Markers

“…Molecular marker technology has advanced our understanding in plant pathology research [69]. Among different classes of molecular markers, SSR markers have been widely used in numerous applications in plant pathology, such as genotyping pathogen populations, genetic diversity studies, monitoring changes in pathogen populations, phylogeny, parentage analyses, and reproductive biology of various plant pathogens [6,[70][71][72][73]. This can be attributed to their multi-allelic nature, co-dominant inheritance (an important feature when analyzing the populations of diploid organisms such as P. infestans), relative abundance, repeatability, good genome coverage [74,75], and genotyping, which can be quickly completed by multiplexing all the pairs of SSR primers in a single reaction [76].…”

Modern Breeding Strategies and Tools for Durable Late Blight Resistance in Potato

“…It has the largest and most complex genome of the chromalveolates (240 megabases), with 74% of it as proliferative repetitive DNA [ 179 ]. In Canada, Babarinde et al [ 180 ] found that 25 new genotypes are emerging, as well as the already existing US11, US17, US8, and US23. Also, to illustrate this pathogen’s high evolutive ability, Shen et al [ 181 ] analysed the sequence of only one effector (Avr1) of 111 Chinese P. infestans isolates, during a short period (2010–2011), and found that nearly 80% of the isolates have undergone a point mutation.…”