Evidence for Sexual Recombination in Didymella tanaceti Populations, and Their Evolution Over Spring Production in Australian Pyrethrum Fields

Evolution of the Genetic Structure of the Didymella tanaceti Population During Development of Succinate Dehydrogenase Inhibitor Resistance

Emergence of pathogens with decreased sensitivity to succinate dehydrogenase inhibitor fungicides is a global agronomical issue. Analysis of Didymella tanaceti isolates (n = 173), which cause tan spot of pyrethrum (Tanacetum cinerariifolium), collected prior to (2004 to 2005) and after (2009, 2010, 2012, and 2014) the commercial implementation of boscalid in Tasmanian pyrethrum fields identified that insensitivity developed over time and has become widespread. To evaluate temporal change, isolates were characterized for frequency of mutations in the succinate dehydrogenase (Sdh) B, C, and D subunits associated with boscalid resistance, mating type, and SSR genotype. All isolates from 2004 and 2005 exhibited wild-type (WT) Sdh alleles. Seven known Sdh substitutions were identified in isolates collected from 2009 to 2014. In 2009, 60.7% had Sdh substitutions associated with boscalid resistance in D. tanaceti. The frequency of WT isolates decreased over time, with no WT isolates identified in 2014. The frequency of the SdhB-H277Y genotype increased from 10.7 to 77.8% between 2009 and 2014. Genotypic evidence suggested that a shift in the population structure occurred between 2005 and 2009, with decreases in gene diversity (uh; 0.51 to 0.34), genotypic evenness (E5; 0.96 to 0.67), genotypic diversity (G; 9.3 to 6.8), and allele frequencies. No evidence was obtained to support the rapid spread of Sdh genotypes by clonal expansion of the population. Thus, insensitivity to boscalid has developed and become widespread within a diverse population within 4 years of usage. These results suggest that D. tanaceti can disperse insensitivity through repeated frequent mutation, sexual recombination, or a combination of both.

Population Biology and Genetic Variation of Spongospora subterranea f. sp. subterranea, the Causal Pathogen of Powdery Scab and Root Galls on Potatoes in South Africa

Spongospora subterranea f. sp. subterranea, causal agent of powdery scab and root galls of potatoes, occurs worldwide and is responsible for quality and yield losses in potato production in South Africa. Despite being one of the most important potato pathogens in South Africa, little information is available on the genetic structure and diversity of S. subterranea f. sp. subterranea, which could provide insight into the factors shaping its evolution and the role of inoculum sources in disease development. A total of 172 samples were collected from four potato growing regions in South Africa. An additional 27 samples obtained from Colombia were included for comparative purposes. The samples were screened against six informative microsatellite (simple-sequence repeat) markers. Of the 172 samples obtained from potato growing regions in South Africa, there were 75 multilocus genotypes (MLGs), only 16 of which were shared between potato growing regions, indicating substantial gene flow and countrywide dispersal of the pathogen. The presence of common MLGs among the root- and tuber-derived samples indicated a lack of specialization of S. subterranea f. sp. subterranea to either tuber or root infection. Nei's unbiased estimates of gene diversity for the clone-corrected data were low and ranged from 0.24 to 0.38. Analysis of molecular variance and discriminant analysis of principal components showed no population differentiation between different potato growing regions in South Africa and between root- and tuber-derived genotypes. The presence of MLGs, high considerable genotypic diversity, and failure to reject the null hypothesis of random mating in most populations are indicative of some kind of recombination, either sexual or asexual, in these S. subterranea f. sp. subterranea populations. Information from this study provides new insights into the genetic structure and diversity of S. subterranea f. sp. subterranea in South Africa. Continuous monitoring of the pathogen population dynamics will be helpful in implementing effective region-specific management strategies for the pathogen, especially in the development of resistant potato cultivars.

Population Structure of Colletotrichum tanaceti in Australian Pyrethrum Reveals High Evolutionary Potential

Colletotrichum tanaceti, the causal agent of anthracnose, is an emerging pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium) in Australia. A microsatellite marker library was developed to understand the spatio-genetic structure over three sampled years and across two regions where pyrethrum is cultivated in Australia. Results indicated that C. tanaceti was highly diverse with a mixed reproductive mode; comprising both sexual and clonal reproduction. Sexual reproduction of C. tanaceti was more prevalent in Tasmania than in Victoria. Little differentiation was observed among field populations likely due to isolation by colonization but most of the genetic variation was occurring within populations. C. tanaceti was likely to have had a long-distance gene and genotype flow among distant populations within a state and between states. Anthropogenic transmission of propagules and wind dispersal of ascospores are the most probable mechanisms of long-distance dispersal of C. tanaceti. Evaluation of putative population histories suggested that C. tanaceti most likely originated in Tasmania and expanded from an unidentified host onto pyrethrum. Victoria was later invaded by the Tasmanian population. With the mixed mode of reproduction and possible long-distance gene flow, C. tanaceti is likely to have a high evolutionary potential and thereby has ability to adapt to management practices in the future.

Multiple mutations across the succinate dehydrogenase gene complex are associated with boscalid resistance in Didymella tanaceti in pyrethrum

Failures in control of tan spot of pyrethrum, caused by Didymella tanaceti, has been associated with decreased sensitivity within the pathogen population to the succinate dehydrogenase inhibitor (SDHI) fungicide boscalid. Sequencing the SdhB, SdhC, and SdhD subunits of isolates with resistant and sensitive phenotypes identified 15 mutations, resulting in three amino acid substitutions in the SdhB (H277Y/R, I279V), six in the SdhC (S73P, G79R, H134R, H134Q, S135R and combined H134Q/S135R), and two in the SdhD (D112E, H122R). In vitro testing of their boscalid response and estimation of resistance factors (RF) identified isolates with wild-type (WT) Sdh genotypes were sensitive to boscalid. Isolates with SdhB-I279V, SdhC-H134Q and SdhD-D112E exhibited moderate resistance phenotypes (10 ≥ RF < 100) and isolates with SdhC-H134R exhibited very high resistance phenotypes (RF ≥ 1000). All other substitutions were associated with high resistance phenotypes (100 ≥ RF < 1000). High-resolution melt assays were designed and used to estimate the frequencies of substitutions in four field populations (n = 774) collected in August (pre-boscalid application) and November (post-boscalid application) 2012. The SdhB-H277Y, SdhC-H134R and SdhB-H277R genotypes were most frequently observed across populations at 56.7, 19.0, and 10.3%, respectively. In August 92.9% of D. tanaceti contained a substitution associated with decreased sensitivity. Following boscalid application, this increased to 98.9%, with no WT isolates detected in three fields. Overlaying previously obtained microsatellite and mating-type data revealed that all ten recurrent substitutions were associated with multiple genotypes. Thus, boscalid insensitivity in D. tanaceti appears widespread and not associated with clonal spread of a limited pool of individuals.