Genetic and Pathogenicity Diversity of Aphanomyces euteiches Populations From Pea-Growing Regions in France

Abstract

Aphanomyces euteiches is an oomycete pathogen with a broad host-range on legumes that causes devastating root rot disease in many pea-growing countries and especially in France. Genetic resistance is a promising way to manage the disease since consistent QTL controlling partial resistance have been identified in near isogenic lines of pea. However, there are still no resistant pea varieties cultivated in France. This study aimed to evaluate the phenotypic and genetic diversity of A. euteiches populations from the major pea-growing regions in France. A collection of 205 isolates, from soil samples collected in infested pea fields located in five French regions, was established and genotyped using 20 SSR markers. Thirteen multilocus genotypes were found among the 205 isolates which displayed a low genotypic richness (ranged from 0 to 0.333). Two main clusters of isolates were identified using PCoA and STRUCTURE, including a predominant group comprising 88% of isolates and another group representing 12% of isolates mainly from the Bourgogne region. A subset of 34 isolates, representative of the fields sampled, was phenotyped for aggressiveness on a set of resistant and susceptible varieties of four legume hosts (pea, faba bean, vetch, alfalfa). Significant differences in disease severity were found among isolates and three groups of aggressiveness comprising 16, 17, and 2 isolates, respectively, were identified using HCA analysis. A higher diversity in pathogen aggressiveness was observed among isolates from Bourgogne, which included different legumes in its crop history. Little relationship was observed between genetic clusters and pathogenicity in the subset of 34 isolates, as expected using neutral markers. This study provides useful knowledge on the current state of low to moderate diversity among A. euteiches populations before resistant pea varieties are grown in France. New insights and hypotheses about the major factors shaping the diversity and evolution of A. euteiches are also discussed.

Keywords: Aphanomyces root rot; Pisum sativum; genetic structure; host specificity; legume crops.

Figure 1

(A) Geographical position of fields distributed in five regions and Bayesian analysis (STRUCTURE) of the corresponding isolates, with Bourgogne (BR) data. Assignment probabilities of A. euteiches isolates are presented for k = 2 and a delta k = 100. Each vertical dotted line separates isolates from each of the 17 sites. (B) Bayesian analysis of the corresponding isolates, without Bourgogne (BR) data. Assignment probabilities of A. euteiches isolates are presented for k = 3 and a delta k = 1,600. Each vertical dotted line separates isolates from each of the 13 sites.

Figure 2

Principal Coordinates Analysis (PCoA) conducted from SSR genotypic data on the A.euieiches isolates of the collection. (A) Analysis including all the fields. (B) Analysis performed without Bourgogne fields. Each color corresponds to regions: yellow Ile de France, green: Center, red: Bretagne, black: Nord Pas-de-Calais, blue: Bourgogne.

Figure 3

Minimum spanning network (MSN) of 19 haplotypes detected in the A. euteiches collection of 205 isolates. Each circle represents a unique haplotype and the colors represent the sampling fields. The circle size represents the haplotype frequency and the number of isolates was indicated in circles. Line widths and the shading represent relatedness of the haplotypes based on Nei's genetic distance.

Figure 4

PCA of LSMean disease severity data obtained on eight legume genotypes in response to inoculation with 34 isolates of A.euieiches. (A) Analysis included all the fields sites. (B) Analysis was performed without Bourgogne field sites. Each color correspond to group from the hierarchical clustering ascendant analysis: black, field sites from group A, red: field sites from group B and green, field sites from group C.