Variation In Pathogen Populations Research Articles

Population genetics of Phytophthora species based on short sequence repeat (SSR) marker: a review of its importance and recent studies

Phytophthora is a genus of oomycete (water molds) whose member species mostly live as plant pathogens and have been reported to cause enormous economic losses on crops worldwide. In recent years, population genetics of Phytophthora pathogens have been broadly studied to evaluate their adaptive evolution. Population genetic studies focus on analyzing the level of genetic diversity and the structure of the pathogen population. A population’s genetic diversity is proportional to its evolutionary potential. The generation and maintenance of genetic variation in pathogen populations are influenced by the biology of the pathogen and its host, environments, agricultural practices, and human activities. Understanding the population genetics of plant pathogens allows us to track the dynamic of the pathogen population and their adaptive ability, assisting the development of sustainable disease management strategies. This review presents the importance of population genetics, short sequence repeat (SSR) marker utilization in population genetic studies, and recent population genetics studies of Phytophthora pathogens related to agricultural practices.

Practical Applications of China A-Shares: Strategic Allocation to Market and Factor Premiums

<h3>Abstract</h3> <h3>Background</h3> <i>Colletotrichum graminicola</i>, the causal agent of maize anthracnose, is an important crop disease worldwide. Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. The genus <i>Colletotrichum</i> is largely recognized as asexual, but several species have been reported to have a sexual cycle. Here, we employed a population genomics approach to investigate the genetic diversity and reproductive biology of <i>C. graminicola</i> isolates infecting maize. We sequenced 108 isolates of <i>C. graminicola</i> collected in 14 countries using restriction site-associated DNA sequencing (RAD-Seq) and whole-genome sequencing (WGS). <h3>Results</h3> Clustering analyses based on single-nucleotide polymorphisms showed populational differentiation at a global scale, with three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen, and geographic subdivision. Distinct levels of genetic diversity were observed between these clades, suggesting different evolutionary histories. Intra and inter-continental migration was predicted between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality and evidence of genetic recombination were detected from the analysis of linkage disequilibrium and the pairwise homoplasy index (PHI) test for clonality. We show evidence that even if rare (possibly due to losses of sex and meiosis-associated genes) <i>C. graminicola</i> can undergo sexual recombination based on lab assays and genomic analyses. <h3>Conclusions</h3> Our results support hypotheses of intra and intercontinental pathogen migration and genetic recombination with great impact on <i>C. graminicola</i> population structure.

Infection, genetics, and evolution of Trichinella: Historical insights and applications to molecular epidemiology

Genetic variation in pathogen populations provides the means to answer questions in disease ecology and transmission, illuminating interactions between genetic traits, environmental exposures, and disease. Such studies elucidate the phylogeny, evolution, transmission and pathogenesis of viruses, bacteria and parasites. Here, we review how such studies have fostered understanding of the biology and epidemiology of zoonotic nematode parasites in the genus Trichinella spp., which impose considerable economic and health burdens by infecting wildlife, livestock, and people. To use such data to define ongoing chains of local transmission and source traceback, researchers first must understand the extent and distribution of genetic variation resident in regional parasite populations. Thus, genetic variability illuminates a population's past as well as its present. Here we review how such data have helped define population dynamics of Trichinella spp. in wild and domesticated hosts, creating opportunities to harness genetic variation in the quest to prevent, track, and contain future outbreaks.

Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada

BackgroundClubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Alberta, Canada in 2003. Genetic resistance to clubroot in an adapted canola cultivar has been available since 2009, but resistance breakdown was detected in 2013 and new pathotypes are increasing rapidly. Information on genetic similarity among pathogen populations across Canada could be useful in estimating the genetic variation in pathogen populations, predicting the effect of subsequent selection pressure on changes in the pathogen population over time, and even in identifying the origin of the initial pathogen introduction to canola in Alberta.ResultsThe genomic sequences of 43 strains (34 field collections, 9 single-spore isolates) of P. brassicae from Canada, the United States, and China clustered into five clades based on SNP similarity. The strains from Canada separated into four clades, with two containing mostly strains from the Prairies (provinces of Alberta, Saskatchewan, and Manitoba) and two that were mostly from the rest of Canada or the USA. Several strains from China formed a separate clade. More than one pathotype and host were present in all four Canadian clades. The initial pathotypes from canola on the Prairies clustered separately from the pathotypes on canola that could overcome resistance to the initial pathotypes. Similarly, at one site in central Canada where resistance had broken down, about half of the genes differed (based on SNPs) between strains before and after the breakdown.ConclusionClustering based on genome-wide DNA sequencing demonstrated that the initial pathotypes on canola on the Prairies clustered separately from the new virulent pathotypes on the Prairies. Analysis indicated that these ‘new’ pathotypes were likely present in the pathogen population at very low frequency, maintained through balancing selection, and increased rapidly in response to selection from repeated exposure to host resistance.

Variation and correlations between sexual, asexual and natural enemy resistance life-history traits in a natural plant pathogen population

BackgroundUnderstanding the mechanisms by which diversity is maintained in pathogen populations is critical for epidemiological predictions. Life-history trade-offs have been proposed as a hypothesis for explaining long-term maintenance of variation in pathogen populations, yet the empirical evidence supporting trade-offs has remained mixed. This is in part due to the challenges of documenting successive pathogen life-history stages in many pathosystems. Moreover, little is understood of the role of natural enemies of pathogens on their life-history evolution.ResultsWe characterize life-history-trait variation and possible trade-offs in fungal pathogen Podosphaera plantaginis infecting the host plant Plantago lanceolata. We measured the timing of both asexual and sexual stages, as well as resistance to a hyperparasite of seven pathogen strains that vary in their prevalence in nature. We find significant variation among the strains in their life-history traits that constitute the infection cycle, but no evidence for trade-offs among pathogen development stages, apart from fast pathogen growth coninciding with fast hyperparasite growth. Also, the seemingly least fit pathogen strain was the most prevalent in the nature.ConclusionsWe conclude that in the nature environmental variation, and interactions with the antagonists of pathogens themselves may maintain variation in pathogen populations.

Role of Temperature and Coinfection in Mediating Pathogen Life-History Traits.

Understanding processes maintaining variation in pathogen life-history traits is a key challenge in disease biology, and of importance for predicting when and where risks of disease emergence are highest. Pathogens are expected to encounter tremendous levels of variation in their environment – both abiotic and biotic – and this variation may promote maintenance of variation in pathogen populations through space and time. Here, we measure life-history traits of an obligate fungal pathogen at both asexual and sexual stages under both single infection and coinfection along a temperature gradient. We find that temperature had a significant effect on all measured life-history traits while coinfection only had a significant effect on the number of sexual resting structures produced. The effect of temperature on life-history traits was both direct as well as mediated through a genotype-by-temperature interaction. We conclude that pathogen life-history traits vary in their sensitivity to abiotic and biotic variation in the environment.

Limited morphological, physiological and genetic diversity of Phytophthora palmivora from cocoa in Papua New Guinea

In Papua New Guinea (PNG) cocoa (Theobroma cacao) is one of the most important cash crops grown in the tropical lowland and island regions. As in most cocoa‐growing areas, phytophthora black pod and canker cause significant yield losses. Cocoa breeding activities in PNG are focused in East New Britain province where disease control recommendations are also developed. This study tested the hypothesis that there was no diversity in the Phytophthora palmivora population causing black pod on cocoa by characterizing the variation in pathogen populations within and between the five major cocoa‐growing areas. Diseased pods were sampled hierarchically from the five locations and additional isolates were collected from soil, stem and leaf lesions, or retrieved from culture collections. Morphological characters showed continuous variation within the range described for P. palmivora. Genetic analysis revealed that the isolates belonged to one dominant clonal lineage, with restricted distributions of several other subpopulations. Lowest diversities were found in the geographically isolated Karkar Island and East Sepik province. Soil isolates showed greater genetic diversity than isolates from cocoa lesions. Intra‐farm variation was as much as inter‐farm or inter‐province variation. Both mating types were detected, although no strong evidence of sexual recombination was observed. The analysis revealed limited geographic, temporal or host specialization, suggesting continuous selection for pathogenicity from a genetic pool of P. palmivora. These findings have significant implications on the deployment of cocoa genotypes, enforcement of inter‐province quarantine and sustainable disease management strategies.

Polymorphic SSR markers for Plasmopara obducens (Peronosporaceae), the newly emergent downy mildew pathogen of Impatiens (Balsaminaceae).

Premise of the study:Simple sequence repeat (SSR) markers were developed for Plasmopara obducens, the causal agent of the newly emergent downy mildew disease of Impatiens walleriana.Methods and Results:A 202-Mb draft genome assembly was generated from P. obducens using Illumina technology and mined to identify 13,483 SSR motifs. Primers were synthesized for 62 marker candidates, of which 37 generated reliable PCR products. Testing of the 37 markers using 96 P. obducens samples showed 96% of the markers were polymorphic, with 2−6 alleles observed. Observed and expected heterozygosity ranged from 0.000−0.892 and 0.023−0.746, respectively. Just 17 markers were sufficient to identify all multilocus genotypes.Conclusions:These are the first SSR markers available for this pathogen, and one of the first molecular resources. These markers will be useful in assessing variation in pathogen populations and determining the factors contributing to the emergence of destructive impatiens downy mildew disease.

A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter.

The increasing availability of hundreds of whole bacterial genomes provides opportunities for enhanced understanding of the genes and alleles responsible for clinically important phenotypes and how they evolved. However, it is a significant challenge to develop easy-to-use and scalable methods for characterizing these large and complex data and relating it to disease epidemiology. Existing approaches typically focus on either homologous sequence variation in genes that are shared by all isolates, or non-homologous sequence variation - focusing on genes that are differentially present in the population. Here we present a comparative genomics approach that simultaneously approximates core and accessory genome variation in pathogen populations and apply it to pathogenic species in the genus Campylobacter. A total of 7 published Campylobacter jejuni and Campylobacter coli genomes were selected to represent diversity across these species, and a list of all loci that were present at least once was compiled. After filtering duplicates a 7-isolate reference pan-genome, of 3,933 loci, was defined. A core genome of 1,035 genes was ubiquitous in the sample accounting for 59% of the genes in each isolate (average genome size of 1.68 Mb). The accessory genome contained 2,792 genes. A Campylobacter population sample of 192 genomes was screened for the presence of reference pan-genome loci with gene presence defined as a BLAST match of ≥70% identity over ≥50% of the locus length - aligned using MUSCLE on a gene-by-gene basis. A total of 21 genes were present only in C. coli and 27 only in C. jejuni, providing information about functional differences associated with species and novel epidemiological markers for population genomic analyses. Homologs of these genes were found in several of the genomes used to define the pan-genome and, therefore, would not have been identified using a single reference strain approach.

Regression-based ranking of pathogen strains with respect to their contribution to natural epidemics.

Genetic variation in pathogen populations may be an important factor driving heterogeneity in disease dynamics within their host populations. However, to date, we understand poorly how genetic diversity in diseases impact on epidemiological dynamics because data and tools required to answer this questions are lacking. Here, we combine pathogen genetic data with epidemiological monitoring of disease progression, and introduce a statistical exploratory method to investigate differences among pathogen strains in their performance in the field. The method exploits epidemiological data providing a measure of disease progress in time and space, and genetic data indicating the relative spatial patterns of the sampled pathogen strains. Applying this method allows to assign ranks to the pathogen strains with respect to their contributions to natural epidemics and to assess the significance of the ranking. This method was first tested on simulated data, including data obtained from an original, stochastic, multi-strain epidemic model. It was then applied to epidemiological and genetic data collected during one natural epidemic of powdery mildew occurring in its wild host population. Based on the simulation study, we conclude that the method can achieve its aim of ranking pathogen strains if the sampling effort is sufficient. For powdery mildew data, the method indicated that one of the sampled strains tends to have a higher fitness than the four other sampled strains, highlighting the importance of strain diversity for disease dynamics. Our approach allowing the comparison of pathogen strains in natural epidemic is complementary to the classical practice of using experimental infections in controlled conditions to estimate fitness of different pathogen strains. Our statistical tool, implemented in the R package StrainRanking, is mainly based on regression and does not rely on mechanistic assumptions on the pathogen dynamics. Thus, the method can be applied to a wide range of pathogens.

Global status of wheat leaf rust caused by Puccinia triticina

Leaf rust caused by Puccinia triticina is the most common and widely distributed of the three wheat rusts. Losses from leaf rust are usually less damaging than those from stem rust and stripe rust, but leaf rust causes greater annual losses due to its more frequent and widespread occurrence. Yield losses from leaf rust are mostly due to reductions in kernel weight. Many laboratories worldwide conduct leaf rust surveys and virulence analyses. Most currently important races (pathotypes) have either evolved through mutations in existing populations or migrated from other, often unknown, areas. Several leaf rust resistance genes are cataloged, and high levels of slow rusting adult plant resistance are available in high yielding CIMMYT wheats. This paper summarizes the importance of leaf rust in the main wheat production areas as reflected by yield losses, the complexity of virulence variation in pathogen populations, the role cultivars with race-specific resistance play in pathogen evolution, and the control measures currently practiced in various regions of the world.

Genetic basis of crown rust resistance in perennial ryegrass, breeding strategies, and genetic variation among pathogen populations: a review

Crown rust caused by the fungus Puccinia coronata f. sp. lolii is probably the most serious disease of perennial ryegrass (Lolium perenne L.). Breeding for resistance to crown rust is a major component of most perennial ryegrass improvement programs. This paper reviews the genetic basis of resistance to crown rust in perennial ryegrass, existing breeding strategies and their progress, and genetic variation in pathogen populations. Resistance to crown rust in perennial ryegrass appears to be controlled by both major and minor genes. Breeding for resistance to crown rust has traditionally been approached from a quantitative perspective (polygenic system), and phenotypic recurrent selection is by far the most commonly used method of selection. There appears to be considerable variation in the pathogen population which may impact on breeding progress. Owing to the present lack of information on the host–pathogen interaction system of this economically important disease, a basic model to study the L. perenne–P. coronata f. sp. lolii interaction system is presented. Its application in a breeding program is discussed.

Genetic Analysis of a Single Urediniospore Culture of Cronartium Quercuum f. sp. fusiforme, Using Random Amplified Polymorphic DNA Markers

Random amplified polymorphic DNA markers were developed for Cronartium quercuum f. sp. fusiforme, causal agent of fusiform rust disease on pines in the southern United States. Genetic linkages were identified between 103 marker loci in a population of 48 gametothalli and drops of spermatia produced from a single urediniospore culture. A preliminary genetic linkage map with eight linkage groups and 12 linked pairs is presented. Based on the extent of linkage detected among loci, the size of the nuclear genome of C. q. f. sp. fusiforme is estimated to be approximately 5100 recombination units. The 103 marker loci characterized are estimated to provide approximately 40% coverage of the genome. The random amplified polymorphic DNA markers may be of immediate utility in fingerprint identification of laboratory cultures and field isolates for epidemiological studies. Even this preliminary genetic linkage map has great potential for aiding in studies on the host-pathogen interaction in fusiform rust disease and monitoring variation in pathogen populations.

Genetic Analysis of a Single Urediniospore Culture ofCronartium QuercuumF. Sp.Fusiforme, Using Random Amplified Polymorphic Dna Markers

Random amplified polymorphic DNA markers were developed for Cronartium quercuum f. sp. fusiforme, causal agent of fusiform rust disease on pines in the southern United States. Genetic linkages were identified between 103 marker loci in a population of 48 gametothalli and drops of spermatia produced from a single urediniospore culture. A preliminary genetic linkage map with eight linkage groups and 12 linked pairs is presented. Based on the extent of linkage detected among loci, the size ofthe nuclear genome of C. q. f. sp. fusiforme is estimated to be approximately 5100 recombination units. The 103 marker loci characterized are estimated to provide approximately 40% coverage ofthe genome. The random amplified polymorphic DNA markers may be of immediate utility in fingerprint identification of laboratory cultures and field isolates for epidemiological studies. Even this preliminary genetic linkage map has great potential for aiding in studies on the host-pathogen interaction in fusiform rust disease and monitoring variation in pathogen populations.