Selection of nematodes by resistant plants has implications for local adaptation and cross‐virulence

The variability of resistance durability in different potato genotypes harbouring the same resistance QTL but differing by their genetic background was explored. The indirect consequences of the resistance adaptation in terms of local (i.e. genotype‐specific) adaptation and cross‐virulence was also investigated. Following the virulence of the potato cyst nematode Globodera pallida in a long‐term experimental evolution protocol, the results showed that nematode populations were able to adapt to the resistance of four potato genotypes carrying the QTL GpaV from Solanum vernei, and that the plant genetic background has an impact upon the durability of resistance. The pattern of local adaptation observed here indicates that divergent selection has occurred during the experimental evolution performed from the same initial nematode population, and revealed a trade‐off between the adaptation to a resistant potato genotype and the adaptation to another resistant genotype differing in its genetic background. In terms of cross‐virulence between potato genotypes derived from different resistance sources (S. sparsipilum and S. spegazzinii), this study shows that the adaptation to resistance QTL GpaV_vrn does not necessarily allow the adaptation to collinear GpaV loci. The results presented here could be useful for predicting evolution of nematode populations in natural agro‐ecosystems and identifying durable strategies for resistance deployment.     

Impact of the genetic diversity of three cyst nematodes on the effectiveness of root exudates to induce hatching

European Journal of Plant Pathology - Cyst nematodes are sedentary endoparasites of plants which cause important economic losses worldwide. New nematode control measures are needed since the...     

Evidence of strong gene flow among French populations of the carrot cyst nematode Heterodera carotae

The recent ban of the most efficient chemical nematicides has left growers without methods for controlling the carrot cyst nematode Heterodera carotae. This phytoparasitic nematode species has a very narrow host range and causes severe crop losses in the main carrot-growing regions worldwide. The development of alternative means of management of H. carotae is thus essential, and knowledge is required about the adaptive abilities of H. carotae, which mainly depend on gene flow among populations. The goal of this study was to describe the genetic structure of H. carotae populations at the spatial scale of the main infested French carrot-producing region, i.e. Lower Normandy, and to disentangle the causes of the heterozygote deficit in this polyvoltine species. Microsatellite genotyping of populations collected at both the plant and field scales showed that: (i) the heterozygote deficit is mainly due to substructure; and (ii) there is strong gene flow among populations, leading to low F_ST and to no clear genetic structure at the spatial scale explored here. Soil transport through both agricultural machinery and the transport of leek seedlings is probably responsible for the very strong H. carotae migration among fields and production areas. Measures should be considered to limit the passive spread of H. carotae.     

Cucumber mosaic virus populations in Tunisian pepper crops are mainly composed of virus reassortants with resistance‐breaking properties

Cucumber mosaic virus is one of the most prevalent viruses in Tunisian pepper crops, where it has been detected in 68% of plants developing mosaic symptoms, making it essential to characterize the molecular and biological properties of local CMV populations. Two hundred and seventy‐eight isolates collected in the late 1990s, 2006 and 2008–2010 were characterized genetically. Isolates belonging to the three phylogenetic subgroups of CMV (IA, IB and II) were detected, but surprisingly, 90% of the isolates were reassortants between subgroups IA and IB, with two predominant haplotypes, IB‐IA‐IA and IB‐IA‐IB (nomenclature according to the subgrouping of the three genomic RNAs). The IB‐IA‐IA haplotype was present in all regions surveyed, while IB‐IA‐IB was observed only in northern Tunisia. This situation was unexpected, because CMV reassortants were previously thought to be counterselected in nature, and this raises the questions of the origin of IB strains in Tunisia and of the widespread distribution of these two reassortant types. Phylogenetic studies revealed low diversity within haplotypes, whatever the locality or the year of sampling. However, analysis of haplotype frequencies revealed a high genetic differentiation between CMV populations, which was better explained by the localities of sampling than by years. Geographic distances affected the differentiation of CMV populations, mainly between north and central Tunisia. When tested against a polygenic resistance to CMV movement in pepper, 55 of 57 isolates tested were able to break the resistance, indicating that this resistance would not be useful for controlling CMV in Tunisian pepper fields.     

Experimentally evolved populations of the potato cyst nematode Globodera pallida allow the targeting of genomic footprints of selection due to host adaptation

In the current agronomical context of pesticide use reduction, deciphering the genetic bases of pathogen adaptation to plant defences is of major importance to improve durability of resistance. Indeed, knowledge of virulence gene frequencies in pathogen populations could allow the prediction of resistance durability before deployment. Globodera pallida is a major pest of potato crops for which a promising resistance QTL, GpaV_vrn, has been identified in Solanum vernei. An experimental evolution study, in which G. pallida lineages evolved on resistant or susceptible potato genotypes for up to eight generations, previously showed that G. pallida was able to rapidly overcome GpaV_vrn resistance. However, it was not known if enough genetic mixing occurred in these lineages to be able to detect islands of differentiation in a genome scan approach. Here, this question was investigated using 53 polymorphic microsatellite markers distributed along the genome and three different tests based on genetic differentiation and heterozygosity. Eight outlier loci were identified, indicative of genomic regions putatively involved in host adaptation. Several loci were identified by multiple detection methods and/or in two independent adapted lineages. Some candidate genomic regions identified also seemed to be involved in overcoming resistance to nematodes in a plant genotype harbouring the same resistance QTL in a different genetic background. These results validate the feasibility of a genome scan approach on biological material coming from short experimental evolution, and encourage the use of a high coverage genome scan by whole genome resequencing.     

Phenotypic and Genomic Modifications Associated with <Emphasis Type="Italic">Globodera pallida</Emphasis> Adaptation to Potato Resistances

Studying phenotypic and genomic modifications associated with pathogen adaptation to resistance is a crucial step to better understand and anticipate resistance breakdown. This short review summarizes recent results obtained using experimentally evolved populations of the potato cyst nematode Globodera pallida. In a first step, the variability of resistance durability was explored in four different potato genotypes carrying the resistance quantitative trait loci (QTL) GpaV_vrn originating from Solanum vernei but differing by their genetic background. The consequences of the adaptation to resistance in terms of local adaptation, cross-virulence and virulence cost were then investigated. Finally, a genome scan approach was performed in order to identify the genomic regions involved in this adaptation. Results showed that nematode populations were able to adapt to the QTL GpaV_vrn, and that the plant genetic background has a strong impact on resistance durability. A trade-off between the adaptations to different resistant potato genotypes was detected, and we also showed that adaptation to the resistance QTL GpaV_vrn from S. vernei did not allow adaptation to the colinear locus from S. sparsipilum (GpaV_spl). Unexpectedly, the adaptation to resistance led to an increase of virulent individual’s fitness on a susceptible host. Moreover, the genome scan approach allowed the highlighting of candidate genomic regions involved in adaptation to host plant resistance. This review shows that experimental evolution is an interesting tool to anticipate the adaptation of pathogen populations and could be very useful for identifying durable strategies for resistance deployment.     

Assessment of fungicide resistance and pathogen diversity in Erysiphe necator using quantitative real-time PCR assays

BACKGROUND: Management of grapevine powdery mildew Erysiphe necator Schw. requires fungicide treatments such as sterol demethylation inhibitors (DMIs) or mitochondrial inhibitors (QoIs). Recently, reduction in the efficacy of DMIs or QoIs was reported in Europe and the United States. The aim of the present study was to develop real‐time qPCR tools to detect and quantify several CYP51 gene variants of E. necator: (i) A versus B groups (G37A) and (ii) sensitive versus resistant to sterol demethylase inhibitor fungicides (Y136F). RESULTS: The efficacy of the qPCR tools developed was better than the CAPS method, with a limit of 2 pg for E necator DNA, 0.06 ng for genetic group A and 1.4 ng for the DMI‐resistant allele. The detection limits of qPCR protocols (LOD) ranged from 0.72 to 0.85%, and the quantification limits (LOQ) ranged from 2.4 to 2.85% for the two alleles G47A and Y136F respectively. The application of qPCR to field isolates from French vineyards showed the presence of DMI‐resistant and/or QoI‐resistant alleles in French pathogen populations, linked to genetic group B. CONCLUSION: The real‐time PCR assay developed in this study provides a potentially useful tool for efficient quantification of different alleles of interest for fungicide monitoring and for population structure of E. necator. Copyright © 2010 Society of Chemical Industry     

Adaptation of Phytophthora infestans to Partial Resistance in Potato: Evidence from French and Moroccan Populations

ABSTRACT The use of partially resistant cultivars should become an essential component of a sustainable management strategy of potato late blight, caused by Phytophthora infestans. It is therefore important to determine to what extent P. infestans populations can be selected for increased aggressiveness by potato cultivars with different levels of partial resistance. To this end, we sampled P. infestans populations from France and Morocco, chosen as locations where late blight occurs regularly but which differ in the distribution of potato cultivars. Cross-inoculation experiments were used to determine the aggressiveness of all populations to potato cvs. Bintje (prevalent in France but not grown in Morocco) and Désirée (popular in Morocco but cultivated to a very small extent in France). French populations were more aggressive on cv. Bintje than on cv. Désirée, irrespective of the site they were sampled from. Their aggressiveness increased between early and late samplings, suggesting that both cultivars selected for increased aggressiveness during epidemics. By contrast, Moroccan populations were more aggressive on Désirée, regarded as partially resistant in Europe, than on Bintje, highly susceptible under European conditions. These data indicate that P. infestans populations adapt to locally dominant cultivars, irrespective of their resistance levels, and can therefore overcome polygenic, partial resistance. This adaptive pattern may render partial resistance nondurable if not properly managed.     

Spatio-temporal distribution of <Emphasis Type="Italic">Erysiphe necator</Emphasis> genetic groups and their relationship with disease levels in vineyards

The discovery of genetically distinct Erysiphe necator groups (A or B), with high phenotypic similarities, raises important questions about their coexistence. For plant pathogens, niche partitioning, allowing the coexistence on the same host (i.e. the same resource), might result from separation in space and/or time. We used a landscape genetic approach to study the geographic distribution of genetic groups of E. necator (distinguished by a SNP in the β-tubulin gene) at the spatial scale of the Languedoc-Roussillon region (southern France) and to assess the temporal succession of groups along the course of the 2007 epidemic. Spatial distribution revealed a high heterogeneity between vineyards: from 100% B to 100% A, with 62% and 38% of vineyards showing a majority of A and B isolates, respectively. Temporal isolation seems to be the major mechanism in the coexistence of the two genetic groups: all isolates collected towards the end of the epidemic belonged to group B, whatever the initial frequency of genetic groups. Our results confirm that both A or B isolates can lead to flag-shoot symptoms, and showed that group A isolates tend to disappear during the course of the epidemic, whereas group B isolates may be active during the entire epidemic and involved in further production of cleistothecia, when recombination takes place. For the first time, the relationship between the frequency of genetic groups and disease levels on leaves and clusters at the end of the epidemic was evaluated. We showed a strong relationship between the disease severity and the genetic composition of E. necator populations: the damage was more important when the epidemic was initiated by B isolates.     

Phenotypic and genotypic changes in French populations of Phytophthora infestans: are invasive clones the most aggressive?

The main objective of this investigation was to test the ‘always more aggressive’ hypothesis, often advocated to explain lineage replacements in clonal populations of the potato late blight oomycete Phytophthora infestans. To this end, genotypic and pathogenicity data on 1274 French isolates of P. infestans, collected over the period 2001–2008, were analysed. Overall, the populations sampled showed limited genetic diversity, with four multilocus lineages (1_A1, 2_A1, 8_A1 and 13_A2) accounting for over 80% of the isolates collected. As in other West European countries, drastic changes in these dominant clonal lineages were observed over the course of the 8 years, particularly in the appearance and propagation of the clone 13_A2. However, invasiveness of clones was not associated with higher aggressiveness; on the contrary, dominant clones had generally low or moderate aggressiveness relative to others present at the same time within the same populations. This finding challenges the link between invasive behaviour and increased aggressiveness often assumed for this biotrophic pathogen, and could reflect the existence of a trade‐off between intra‐season and inter‐season transmission. This would be consistent with the concept of inclusive fitness, which involves the abilities to both reproduce and survive.