High Virulence Diversity Research Articles

Relationship of Colletotrichum lindemuthianum races and resistance loci in the Phaseolus vulgaris L. genome

AbstractAnthracnose caused by Colletotrichum lindemuthianum is one of the most critical diseases in the common bean (Phaseolus vulgaris L.). The characterization and localization of pathogenic fungal races are essential for understanding pathogen population dynamics and developing resistant cultivars. Here, we discussed the relationship between the diversity of C. lindemuthianum and common bean resistance genes against anthracnose disease. Indeed, several studies using a system of 12 differential bean cultivars have been carried out since 1991 to monitor anthracnose, reporting the constant appearance of new races. Colletotrichum lindemuthianum shows high virulence diversity, with 298 races distributed across 29 countries. In Brazil, we identified 89 races, with races 73, 65, and 81 as the most frequent. Moreover, we highlighted the common bean gene clusters, their unique location on chromosomes, and their relationship with races and resistance genes. The genetic mapping studies, molecular markers linked to anthracnose resistance alleles, and the specific races were integrated on the seven‐chromosome map using the reference genome of common bean. Recently, the ease of use of genome sequences and the development of molecular technologies have allowed molecular markers for marker‐assisted selection applied to anthracnose‐resistant cultivars. As a result, it is feasible that Mesoamerican genes Co‐5, Co‐42, Co‐6, Co‐16, and Co‐17, and the Andean genes Co‐12, Co‐14, Co‐Bf, Co‐15, Co‐AC, and CoPv01CDRK are well known to confer resistance to most races reported in Brazil and around the world. Thus, pyramiding these genes through molecular markers can help reduce the time and cost of introducing resistance genes in commercial common bean cultivars.

Occurrence of anthracnose pathogen races and resistance genes in common bean across 30 years in Brazil

Anthracnose caused by Colletotrichum lindemuthianum is one of the most critical diseases in the common bean (Phaseolus vulgaris L.). The characterization and localization of pathogenic fungal races are essential for understanding pathogen population dynamics and recommending strategies to develop resistant cultivars. As resistant genotypes are the most economical and ecologically safe means of controlling plant diseases, there have been efforts to characterize resistance genes in common bean. Several studies using a system of 12 differential bean cultivars have been carried out to monitor anthracnose since 1991, reporting the constant appearance of new fungal races. C. lindemuthianum shows high virulence diversity. The objective of the present study was to review the relationship between C. lindemuthianum races and the common bean pathogenic processes involved in the risk of developing anthracnose disease. As a result, 89 races occurred in Brazil, wherein 73, 65, and 81 of C. lindemuthianum are the most frequent. Furthermore, we built a map with the anthracnose resistance loci, molecular markers, and their respective physical position. The accessibility to the genomes and sequencing technologies permits molecular markers for marker-assisted selection applied to anthracnose-resistant cultivars. This study could be used as a reference for future resistance mapping studies and as a guide for selecting resistance loci in breeding programs aiming to develop common bean cultivars with durable anthracnose resistance.

Genome assisted molecular typing and pathotyping of rice blast pathogen, Magnaporthe oryzae, reveals a genetically homogenous population with high virulence diversity

Genome sequence-driven molecular typing tools have the potential to uncover the population biology and genetic diversity of rapidly evolving plant pathogens like Magnaporthe oryzae. Here, we report a new molecular typing technique -a digitally portable tool for population genetic analysis of M. oryzae to decipher the genetic diversity. Our genotyping tool exploiting allelic variations in housekeeping and virulence genes coupled with pathotyping revealed a prevalence of genetically homogenous populations within a single-field and plant niches such as leaf and panicle. The M. oryzae inciting leaf-blast and panicle-blast were confirmed to be genetically identical with no or minor nucleotide polymorphism in 17 genomic loci analyzed. Genetic loci such as Mlc1, Mpg1, Mps1, Slp1, Cal, Ef-Tu, Pfk, and Pgk were highly polymorphic as indicated by the haplotype-diversity, the number of polymorphic sites, and the number of mutations. The genetically homogenous single field population showed high virulence variability or diversity on monogenic rice differentials. The study indicated that the genetic similarity displayed by the isolates collected from a particular geographical location had no consequence on their virulence pattern on rice differentials carrying single/multiple resistance genes. The data on virulence diversity showed by the identical Sequence Types (STs) is indicative of no congruence between polymorphic virulence genes-based pathotyping and conserved housekeeping genes-based genotyping.

Multilocus sequence typing and virulence genotyping of Streptococcus suis serotype 9 isolates revealed high genetic and virulence diversity.

Streptococcus suis is an important swine pathogen that can cause a variety of diseases. Streptococcus suis serotype 9 (SS9) is a prevalent serotype, but limited information is available. Here, we studied and compared 30 SS9 isolates, including 24 isolates from China between year 2004 and 2013, 5 isolates from Vietnam and a serotype reference isolate from Denmark. A multilocus sequence typing (MLST) analysis was performed to exploit the genetic relationships between those isolates. The phylogenetic tree based on the MLST data divides those isolates into two clades (I and II), revealing different evolutionary paths of collected strains. A virulence genotyping analysis was performed by detecting 23 virulence-related genes; the clustering result also revealed two clusters (I and II), highly in accordance with MLST analysis result, showing that phylogenetic relatedness led to the presence of similar virulence genotypes. Murine model infection experiment was performed to assess the virulence of those strains in cluster I and cluster II, which displayed high virulence diversity even within a same cluster/ST. Notably, ST 243 could be regarded as an ST with high virulence potential in SS9. In conclusion, this study has revealed high genetic and virulence diversity in SS9 isolates.

Identification of Eighteen Berberis Species as Alternate Hosts of Puccinia striiformis f. sp. tritici and Virulence Variation in the Pathogen Isolates from Natural Infection of Barberry Plants in China

ABSTRACT The wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) population in China has been reported to be a distinct genetic group with higher diversity than those in many other countries. Genetic recombination in the P. striiformis f. sp. tritici population has been identified with molecular markers but whether sexual reproduction occurs in China is unknown. In this study, we surveyed barberry plants for infection by rust fungi in the stripe rust "hotspot" regions in Gansu, Sichuan, and Shaanxi provinces; collected barberry plants and inoculated plants of 20 Berberis spp. with germinated teliospores under controlled greenhouse conditions for susceptibility to P. striiformis f. sp. tritici; and tested P. striiformis f. sp. tritici isolates obtained from aecia on naturally infected barberry plants on the wheat genotypes used to differentiate Chinese P. striiformis f. sp. tritici races to determine virulence variations. Different Berberis spp. were widely distributed and most surveyed plants had pycnia and aecia of rust fungi throughout the surveyed regions. In total, 28 Berberis spp. were identified during our study. From 20 Berberis spp. tested with teliospores of P. striiformis f. sp. tritici from wheat plants, 18 species were susceptible under greenhouse conditions. Among 3,703 aecia sampled from barberry plants of three species (Berberis shensiana, B. brachypoda, and B. soulieana) under natural infections in Gansu and Shaanxi provinces, four produced P. striiformis f. sp. tritici uredinia on susceptible wheat 'Mingxian 169'. Sequence of the internal transcribed spacer (ITS) regions of the four isolates from barberry shared 99% identity with the P. striiformis f. sp. tritici sequences in the National Center for Biotechnology Information database. The four isolates had virulence patterns different from all previously reported races collected from wheat plants. Furthermore, 82 single-uredinium isolates obtained from the four barberry isolates had high virulence diversity rates of 9.0 to 28.1%, indicating that the diverse isolates were produced through sexual reproduction on barberry plants under natural conditions. In addition to P. striiformis f. sp. tritici, sequence analysis of polymerase chain reaction products of the ITS regions and inoculation tests on wheat identified P. graminis (the stem rust pathogen). Our results indicated that P. striiformis f. sp. tritici can infect some Berberis spp. under natural conditions, and the sexual cycle of the fungus may contribute to the diversity of P. striiformis f. sp. tritici in China.

Development of an efficient method for assessing resistance to the net type of net blotch (Pyrenophora teres f. teres) in winter barley and mapping of quantitative trait loci for resistance

Breeding for resistance against Pyrenophora teres f. teres in barley is difficult due to the high virulence diversity of the pathogen and the fact that in field trials a simultaneous infection with Rhynchosporium commune, Puccinia hordei or Blumeria graminis f. sp. hordei often takes place. To avoid this, a so-called “summer hill trial” was developed in which winter barley is sown at the beginning of August at optimum conditions for P. teres infection. These trials allowed an unequivocal scoring of P. teres resistance. Using this approach, strong correlations of the results obtained in 3 years at two locations were observed and heritability was estimated at h 2 = 0.80 for the doubled haploid (DH) population Uschi × HHOR3073 and h 2 = 0.62 for (Post × Viresa) × HHOR9484. In parallel, genetic maps based on DArT, SSR and SNP markers were constructed, comprising 705.7 cM for the DH population Uschi × HHOR3073 and 1,035.8 cM for (Post × Viresa) × HHOR9484. In the population Uschi × HHOR3073, one quantitative trait locus (QTL) was detected on each of chromosomes 2H and 3H and two on chromosome 5H, explaining between 9.4 and 19.0 % of the phenotypic variance. In the population (Post × Viresa) × HHOR9484, three QTL were detected on chromosome 5H and one on chromosome 7H, explaining between 12.6 and 34.7 % of the phenotypic variance. These results show that the new summer hill trial design is best suited to obtain reliable phenotypic data for P. teres resistance under field conditions, as on the one hand already known QTL were confirmed and on the other hand new QTL were detected.

So Near and Yet so Far: The Specific Case of Ralstonia solanacearum Populations from Côte d'Ivoire in Africa

The genetic and phenotypic diversity of Côte d'Ivoire Ralstonia solanacearum strains was assessed on a 168-strain collection sampled on Solanaceae both in the southern lowlands and western highlands. Phylotypes I, II, and III were prevalent, though at unexpected frequencies. Phylotype I strains (87.5%) were genetically diverse and overrepresented in all agroecological areas, including highlands (AEZ III). Phylotype II strains (10.7%) only belonged to one tropical lowland-adapted broad host range lineage (IIA-35), whereas no highland-adapted potato brown rot (IIB-1) or Moko strains were detected. African phylotype III strains were rare (1.8%). They originated from a single Burkina Faso lineage (III-23) and were only found in lowlands. Three phylotype I strains were found harboring pRSC35, a plasmid identified in phylotype III strains in Cameroon. From pathogenicity tests performed on commercial varieties and tomato/eggplant/pepper references, the virulence diversity observed was high, with five pathoprofiles described. Eggplant accessions MM152 and EG203 and tomato HW7996 displayed the largest resistance spectrum and highest level. Two highly virulent phylotype I strains were able to bypass resistance of HW7996 and the eggplant reference AG91-25. Collectively, these points lead to the conclusion that the situation in Côte d'Ivoire is specific towards other African countries, and specifically from the Cameroon reference, and that within phylotype I can exist a high virulence diversity. This calls for similar studies in neighboring West African countries, linking R. solanacearum pathogen genetic diversity to strain virulence at the regional level, for the rationalization of regional resistance deployment strategies and future resistance durability studies.

The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off

RNA viruses exist in large intra-host populations which display great genotypic and phenotypic diversity. We analyze a model of viral competition between two viruses infecting a constantly replenished cell pool. We assume a trade-off between the ability of the virus to colonize new cells (cell killing rate or virulence) and its local competitiveness (replicative success within coinfected cells). We characterize the conditions that allow for viral spread by means of the basic reproductive number and show that a local coexistence equilibrium exists, which is asymptotically stable. At this equilibrium, the less virulent competitor has a reproductive advantage over the more virulent colonizer reflected by a larger equilibrium population size of the competitor. The equilibria at which one virus outcompetes the other one are unstable, i.e., a second virus is always able to permanently invade. We generalize the two-virus model to multiple viral strains, each displaying a different virulence. To account for the large phenotypic diversity in viral populations, we consider a continuous spectrum of virulences and present a continuum limit of this multiple viral strains model that describes the time evolution of an initial continuous distribution of virulence without mutations. We provide a proof of the existence of solutions of the model equations, analytically assess the properties of stationary solutions, and present numerical approximations of solutions for different initial distributions. Our simulations suggest that initial continuous distributions of virulence evolve toward a distribution that is extremely skewed in favor of competitors. At equilibrium, only the least virulent part of the population survives. The discrepancy of this finding in the continuum limit with the two-virus model is attributed to the skewed equilibrium subpopulation sizes and to the transition to a continuum. Consequently, in viral quasispecies with high virulence diversity, the model predicts collective virulence attenuation. This result may contribute to understanding virulence attenuation, which has been reported in several experimental studies.

Phytophthora infestans isolates from Northern China show high virulence diversity but low genotypic diversity

Phenotypic and genotypic characteristics of 48 Phytophthora infestans isolates, collected in five provinces in Northern China between 1997 and 2003, were determined and compared with reference isolates. Characterisation included mating type, virulence, mitochondrial DNA (mtDNA) haplotype and DNA fingerprinting patterns based on simple sequence repeats (SSR) and amplified fragment length polymorphisms (AFLP). All isolates had the A1 mating type, mtDNA haplotype IIa and an identical SSR genotype (designated as SG-01-01) that differed from SSR genotypes found in the reference isolates, including those representing the 'old' US-1 lineage that dominated the P. infestans population worldwide prior to 1980. In contrast, the virulence spectra were highly variable and virulence to all resistance genes present in the standard differential set (R1 to R11) was found. AFLP analysis revealed some diversity; eight different AFLP genotypes were found that could be grouped into two major clusters. This study shows that there is very little genotypic diversity in the P. infestans population in Northern China. The occurrence of many different races within this rather uniform population is discussed in the framework of recent insights into the molecular determinants of avirulence in potato-P. infestans'gene-for-gene' interactions.

Origin of the A2 Mating Type of Phytophthora infestans Outside Mexico

The first report of the A2 mating (compatibility) type of the potato late blight pathogen, Phytophthora infestans (Mont.) de Bary, outside Mexico was in Europe during 1984 (32) and, since then, the A2 has been found in many parts of the world (19,23). The four most likely hypotheses to explain the occurrence of the A2 mating type outside Mexico are that it (i) was always present, but undetected (58); (ii) was introduced by migration (62); (iii) arose by mutation or mitotic recombination; or (iv) arose by mating type change, either from exposure to fungicides or by induced selfing (39). Among these, the migration hypothesis is the only one with strong scientific support. However, this subject remains somewhat controversial, and alternative explanations for the origin of the A2 mating type of P. infestans outside Mexico still appear occasionally in the literature. Analyses of allozyme data provided the first unambiguous evidence that the A2 mating type in Europe and Japan was introduced by migration from Mexico (62). Numerous additional population genetic studies have fully supported the migration hypothesis (13, 15,18,23,25,40,44,55,63). In each location studied, the first detection of A2 isolates coincided with the appearance of new alleles at allozyme, DNA fingerprint, and mitochondrial DNA loci. Similar changes occurred with the recent appearance of the A2 mating type in the United States (29). Although the detection of new alleles sometimes preceded the A2 (1,25), the A2 never appeared without new alleles (19,23). The migration hypothesis was challenged recently by Ko (39), who proposed instead that mating type change was the origin of the A2 mating type of P. infestans outside Mexico. Ko’s (39) conclusion came from his result that self-fertilization could initiate mating type change. Unfortunately, the mating type change hypothesis in P. infestans was not tested using genetic markers, and no genetic mechanism was proposed by which mating type change could occur. Furthermore, the population genetic data that contradict the mating type change hypothesis were ignored. Part of the proof for the mating type change hypothesis was based on a number of early literature reports that supposedly stated that homothallic isolates of P. infestans were present outside Mexico prior to the 1950s. Unfortunately, these early references were cited without critical evaluation. It is well-known that heterothallic species of Phytophthora produce occasional oospores in single culture (4,21,53,64, 65). It is also quite well documented that oospores of P. infestans were found occasionally during the early part of this century in Europe and the United States (8,48). However, because these structures were produced only rarely and under specific conditions, the scientific consensus was that the sexual stage of P. infestans remained to be discovered. This did not change until the A2 mating type was found in Mexico during the 1950s (21,47,61). Because of the strong evidence for migration, the mating type change hypothesis has never been tested directly. Fortunately, this hypothesis provides testable predictions about the genetic background that should be present in A2 isolates outside Mexico. If the A2 originated by mating type change from A1 mating type populations, the first A2 isolates in each location should be identical, or nearly identical except for mating type, to the previously existing A1 isolates. Sexual reproduction after mating type change could generate new genotypes, but they still should contain only the alleles present in the original A1 populations. Because most populations throughout the world, until recently, were composed primarily, or exclusively, of a single clonal lineage (15,23,25), the mating type change hypothesis is easily testable using molecular markers. Identical multilocus genotypes (or changes limited to a rearrangement of alleles) before and after the occurrence of the A2 mating type would confirm the mating type change hypothesis. In contrast, if the A2 mating type originated by migration, A2 isolates could be similar, or very distinct, from the original A1 isolates, depending on the source population for the migrating genotypes. If the first A2 isolates were very different from isolates in the old A1 populations, the mating type change hypothesis would be rejected. Our purpose was to reanalyze previously published genotypic data to explicitly test the mating type change hypothesis for the origin of the A2 of P. infestans outside Mexico. A secondary goal was to evaluate the early literature to test Ko’s (39) conclusion that homothallic isolates of P. infestans were known outside Mexico prior to the 1950s. Finally, mating type segregations in self-fertilized progenies of P. infestans were analyzed to determine whether mating type change has been observed by other investigators.

The use of host resistance in disease management of rust in common bean

Bean rust, caused by Uramyces appendiculatus, is one of the major diseases in dry and snap bean production world-wide. Numerous advancements in disease management have been made to reduce rust losses. Host resistance is an important component of rust management. However, durability of disease resistance has often been short due to the use of single genes for resistance interacting with extremely high virulence diversity of the bean rust fungus. The challenge to increase durability of resistance has led to strategies such as gene pyramiding of race-specific resistance, selection and use of partial resistance, and investigation and discovery of leaf morphological features that may slow the rust epidemic. Germplasm with multiple sources of rust resistance has been developed in specific bean seed classes and released for public and commercial use in intensive production systems such as those in the United States. However, progress to develop rust resistant germplasm for the subsistence agriculture of Latin America and Africa where intercropping and mixed cultivars dominate the production system has been slow. Incorporation of high yielding, disease-resistant components as partial replacement in farmer's mixtures has the potential to reduce severity in the crop and increase yield in the presence of rust. This strategy would not erode the genetic diversity that is historically known to enhance resistance durability and for many years has given stability in production in the subsistent agriculture systems.