Isolates of the Diaporthe/Phomopsis (D/P) complex were collected in the main soybean producing area of Argentina during the 1996-97, 1997-98, and 1998-99 growing seasons. Twenty-three morphologic characters related to type of colonies, stroma, pycnidia and conidia, presence of perithecia, and asci length were studied by principal component analysis (PCA). Genomic DNA were analyzed by the random amplified polymorphic DNA (RAPD) technique. From both studies, 18 isolates were identified as D/P complex and grouped in four major taxa: (i) Diaporthe phaseolorum var. meridionalis, (ii) D. phaseolorum var. caulivora, (iii) D. phaseolorum var. sojae, and (iv) Phomopsis longicolla. In addition to distinguishing interspecific and intraspecific variability, molecular markers allowed the detection of differences among isolates within the same variety. Pathogenicity was assayed in the greenhouse, by the toothpick method, inoculating the D/P isolates to soybean genotypes carrying different resistance genes (Rdc1, Rdc2, Rdc3, and Rdc4) against soybean stem canker (SSC). Pathogenic analysis distinguished two main groups: (i) the SSC-producing isolates, including D. phaseolorum var. meridionalis and D. phaseolorum var. caulivora, and (ii) the non-SSC-producing isolates, including D. phaseolorum var. sojae and P. longicolla. Cultivar RA-702 (susceptible control) was compatible with both D. phaseolorum var. meridionalis and D. phaseolorum var. caulivora isolates; meanwhile, Tracy-M (Rdc1 and Rdc 2 genes) was incompatible with D. phaseolorum var. meridionalis but compatible with D. phaseolorum var. caulivora isolates. The fact that Rdc1 and Rdc2 together (as in Tracy-M) confer an almost immune reaction to all assayed isolates of D. phaseolorum var. meridionalis but were ineffective against the D. phaseolorum var. caulivora isolates evaluated suggests that the virulence or avirulence genes in D. phaseolorum var. meridionalis and D. phaseolorum var. caulivora are different. Moreover, physiological races of D. phaseolorum var. meridionalis were detected by using differential soybean genotypes carrying distinct single Rdc genes. As far as we know, this is the first report on the existence of physiological races of D. phaseolorum var. meridionalis in South America. Selective pressure due to deployment of resistant host cultivars may have changed the frequency of the virulence or avirulence genes within the population of D. phaseolorum var. meridionalis. On the whole, our results show that pathogenic variability of D. phaseolorum in the core soybean-producing area of Argentina is higher than previously recognized.

Phytophthora infestans is the causal organism of potato late blight, the most important disease in potato, the second most important arable crop in Europe. The P. infestans population in Europe is well known for its sudden changes in composition. Currently it is composed of a wide variety of genotypes, some of which are dominant clonal lines while others are rare or even unique to a year or location. Fungicides play a crucial role in the integrated control of late blight. Since its introduction in the Netherlands in 1992, fluazinam has been used in late blight control strategies in ware and starch potatoes. It has a broad spectrum of activity and is effective against a range of diseases including potato late blight. Fluazinam interrupts the pathogen cell's energy production process by an uncoupling effect on oxidative phosphorylation. It is considered to have a low resistance risk. Until recently, reduced efficacy against fluazinam was not detected in P. infestans surveys in Europe. In this paper we present the finding of a new clonal lineage (EU_33_A2) of P. infestans in the Netherlands and the reduced efficacy of fluazinam to control one of the EU_33_A2 isolates in field experiments carried out in 2011 and 2015 under high disease pressure. The potential effects of this finding on practical late blight control strategies are discussed.

Late blight disease, caused by the plant pathogen Phytophthora infestans, is one of the major threats for tomato and potato crops. Monitoring the populations of P. infestans is important to determine if there are changes in the sensitivity to fungicides and host preference. In this study, microsatellite markers and mitochondrial haplotypes were used to assess the genotype of isolates of P. infestans collected from tomato and potato plants in Colombia. Furthermore, sensitivity to three fungicides cymoxanil (penetrant fungicide), mefenoxam and fluopicolide (systemic fungicides) and tomato-potato host preference were evaluated. Mitochondrial haplotyping showed that isolates collected on tomato were from the genetic groups Ia and Ib, while isolates collected on potatoes belonged to group IIa. Microsatellite analyses showed that isolates from tomato form two groups, including the Ib mitochondrial haplotype which is genetically close to the US-1 clonal lineage and the Ia haplotype related to the EC-3 lineage, whereas Colombian isolates from potato formed a separate group. Furthermore, differences in sensitivity to fungicides were observed. Eighty-one percent of the isolates tested were resistant to mefenoxam with an EC50 value greater than 10 µg mL-1. Forty-two percent of the isolates showed an intermediate resistance to cymoxanil. The EC50 values ranged between 1 to 10 µg mL-1. For fluopicolide, 90% of the isolates were sensitive with EC50 values less than 1 µg mL-1. Host preference assays showed that potato isolates infected both host species. Thus, isolates that infect potatoes may pose a risk for tomato crops nearby.

In Colombia, late blight is considered one of the most limiting diseases on potato and tomato production. Recently, a new Phytophthora species, P. betacei, was described infecting tree tomato crops in the south of Colombia. However, the distribution and the host range of this new emerging pathogen in the country are unknown. The main aims of this study were to determine if this novel species is confined to the south of Colombia, to assess if P. betacei represents a genetically uniform clone across Colombia and to determine if in all regions there is a clear differentiation between the two Phytophthora species. Therefore, we characterized Phytophthora isolates obtained from tree tomato and potato crops in a central region of Colombia and compared them with the strains from the south. Initially, we evaluated the genetic differentiation among Phytophthora strains obtained from tree tomato and potato crops using simple sequence repeat markers. Results showed a strong population structure between P. infestans and P. betacei. However, we did not detect any genetic differentiation within P. infestans or P. betacei populations from different regions. Furthermore, we detected significant morphological differences among the species based on growth and sporangial morphology measurements. We also showed that strains of Phytophthora spp. are predominantly of the A1 mating type and belong to EC-1 and EC-3 clonal lineages for P. infestans and P. betacei, respectively. Our results describe the expanded geographical range of the new species of P. betacei in the central region of Colombia.

Pathogen variation plays an important role in the dynamics of infectious diseases. In this study, the genetic variation of 279 Phytophthora infestans isolates was assessed using a combination of 12 microsatellite simple-sequence repeat markers. Isolates were collected from 11 different potato cultivars in 11 different geographic localities of the central region of Colombia. The objective of this study was to determine whether populations were differentiated by host genotype or geographic origin. Within a single clonal lineage, EC-1, 76 genotypes were detected. An analysis of molecular variance attributed most of the variation to differences within host genotypes rather than among the host genotypes, suggesting that host cultivars do not structure the populations of the pathogen. Furthermore, the lack of a genetic population structure according to the host cultivar was confirmed by all of the analyses, including the Bayesian clustering analysis and the minimum spanning network that used the Bruvo genetic distance, which suggested that there are no significant barriers to gene flow for P. infestans among potato cultivars. According to the geographic origin, the populations of P. infestans were also not structured, and most of the variation among the isolates was attributed to differences within localities. Only some but not all localities in the north and west of the central region of Colombia showed some genetic differentiation from the other regions. The absence of sexual reproduction of this pathogen in Colombia was also demonstrated. Important insights are discussed regarding the genetic population dynamics of the P. infestans populations of the central region of Colombia that were provided by the results. In Colombia, there is a high genetic variation within the EC-1 clonal lineage with closely related genotypes, none dominant, that coexist in a wide geographic area and on several potato cultivars.