Highly Diverse Phytophthora infestans Populations Infecting Potato Crops in Pskov Region, North-West Russia

Abstract

There is limited understanding of the genetic variability in Phytophthora infestans in the major potato cultivation region of north-western Russia, where potato is grown primarily by small households with limited chemical treatment of late blight. In this study, the mating type, sensitivity to metalaxyl, and genotype and population genetic diversity (based on 12 simple sequence repeat (SSR) markers) of 238 isolates of P. infestans from the Pskov region during the years 2010−2013 were characterized. The aim was to examine the population structure, phenotypic and genotypic diversity, and the prevalent reproductive mode of P. infestans, as well as the influence of the location, time, and agricultural management practices on the pathogen population. The frequency of the A2 mating was stable over the four seasons and ranged from 33 to 48% of the sampled population. Both mating types occurred simultaneously in 90% of studied fields, suggesting the presence of sexual reproduction and oospore production in P. infestans in the Pskov region. Metalaxyl-sensitive isolates prevailed in all four years (72%), however, significantly fewer sensitive isolates were found in samples from large-scale conventional fields. A total of 50 alleles were detected in the 141 P. infestans isolates analyzed for genetic diversity. Amongst the 83 SSR multilocus genotypes (MLGs) detected, 65% were unique and the number of MLGs varied between locations from 3 to 20. These results, together with the high genotypic diversity observed in all the locations and the lack of significance of linkage disequilibrium, suggest that sexual recombination is likely responsible for the unique MLGs and the high genetic diversity found in the Pskov region population, resembling those of north-eastern European populations.

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

“…SSR markers were used to characterize P. infestans isolates from Estonia, Pskov region (Russia) (published previously by [6,27], and Poland (published previously by [50,51]. These isolates were genotyped based on the following 12 SSR markers: D13, G11, Pi04, Pi4B, Pi63, Pi70, SSR2, Pi02, SSR4, SSR6, SSR8, and SSR11.…”

“…Potatoes (Solanum tuberosum, Solanaceae) are one of the most significant vegetables worldwide [1]. Late blight Phytophthora infestans (P. infestans) is a pathogen that affects field-grown potatoes and tomatoes all over the world and has historically been common in many countries [2][3][4][5][6][7][8]. Throughout the growing season, P. infestans can cause water-soaked lesions on the plant leaves, stems, and fruits, with an overall effect of reducing yield quality and quantity [9,10].…”

“…A better understanding of the population dynamics in P. infestans has been made possible by diversity studies that take into account both phenotypic and genotypic markers [6,[13][14][15][16]. Mating type, virulence spectrum, and metalaxyl/mefenoxam resistance are frequent phenotypic markers [17,18].…”

“…Mating type, virulence spectrum, and metalaxyl/mefenoxam resistance are frequent phenotypic markers [17,18]. Molecular markers such as simple sequence repeat (SSR) markers, amplified fragment length polymorphism (AFLP), and random fragment length polymorphism (RFLP) are commonly employed in P. infestans studies due to their high repeatability [6,17,19]. P. infestans has two mating types, A1 and A2, and it can reproduce both asexually and sexually.…”

“…Since the 1970s, phenylamide fungicides (initially, the racemic mixture of metalaxyl was used prior to the introduction of its biologically active enantiomer R-metalaxyl (also known as mefenoxam)) have made substantial contributions to the efficient management of P. infestans [6,12,18,26,27]. However, fungicide resistance to late blight is a problem that is getting worse due to the introduction of novel strains that are tolerant or resistant to metalaxyl.…”