Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology

Abstract

Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study were US-8 (n = 28), US-11 (n = 27), US-23 (n = 166), and US-24 (n = 36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94%), with the remaining isolates collected from 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.

Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing

“…It has been suggested that higher mismatch rates among replicates are associated with lower read depth [ 70 ]. For diploid organisms, filtering for minimum read depth from four to seven has been used to reduce error rates [ 25 , 70 ]. For the haploid C .…”

“…These methods enable sequencing of a targeted genome fraction for a large number of individuals thereby reducing ascertainment bias through simultaneous marker discovery and genotyping [ 12 , 14 ]. Population genomics approaches can improve population genetics studies through generating multitudes of polymorphic markers that better reflect the genome-wide genetic diversity of populations [ 13 , 24 ]; and enhance resolution to identify fine-scale genetic variation [ 25 – 27 ] or detect rare recombination events [ 28 ].…”

“…When using only a handful of microsatellite loci, a clone is defined as a unique multi-locus genotype (MLG) [ 30 , 31 ]. However, sequencing and SNP calling errors and missing data in RRS genotyping techniques result in identification of genetically identical individuals as different MLGs [ 25 , 29 , 32 ]. Moreover, in populations where clonal reproduction predominates, accumulation of somatic mutations over generations results in genetically non-identical individuals within clones, which may be more readily differentiated through high throughput genotyping methods with improved resolution.…”

Novel insights on colonization routes and evolutionary potential of Colletotrichum kahawae, a severe pathogen of Coffea arabica

“…Moreover, no vegetative compatibility group was found in Ck (He et al, 1998;Várzea et al, 2002). Clonal populations have been shown to have a demographic advantage not only because of the ability of a single individual to colonize an empty habitat, avoiding the risk of not finding a mating partner, but also because of the ability to produce a large number of offspring and quickly disperse them into an environment to which they are already adapted (Bazin et al, 2014;Dutech et al, 2012Dutech et al, , 2017Hansen et al, 2016). However, the absence of genetic recombination may decrease the adaptation potential in a changing environment, because new genotypes may emerge only by mutation .…”

Genetic Diversity and Population Structure of Races ofFusarium oxysporumCausing Cotton Wilt

“…Depending on coverage, this approach allows for the identification of hundreds to thousands of single nucleotide polymorphisms (SNPs) among a large sample of individuals, thus providing high resolution of genetic differences among individuals. GBS has previously been used in population analyses of plant pathogens to identify novel genetic diversity in high-diversity organisms, identify cryptic sexual recombination among clonal pathogens, and conduct genome-wide-association-studies (GWAS) linking quantitative trait nucleotides (QTNs) with pathogen virulence and mycotoxin production ( Milgroom et al 2014 ; Hansen et al 2016 ; Talas et al 2016 ).…”