Evolution of High-Risk Isolates within the Australian Ascochyta rabiei Population and the Differential Defence Responses Instigated in Chickpea

Chickpea is a very important legume crop, playing a crucial role in global food security. However, yield and quality are significantly affected by many biotic and abiotic constraints. Among the biotic factors, Ascochyta blight caused by the necrotrophic fugal pathogen, Ascochyta rabiei (Pass.) Labr. (syn. Phoma rabiei) (Kovachevski) von Arx (Mycospaerella rabiei Kovachevski) is a major concern. The pathogen causes significant annual yield losses globally and is the major fungal disease constraint to production in Australia. In order to better inform for optimal management strategies for this pathogen, a comprehensive understanding of the fungal pathogen population and the host-pathogen interaction is necessary. The Australian Ascochyta rabiei population has low genotypic diversity with only one mating type detected to date, potentially precluding substantial evolution through sexual recombination. However, a large diversity in Australia in aggressiveness exists. In an effort to better understand the risk from selective adaptation to currently used resistance sources and chemical control strategies, the population was examined in detail. For this, a total of 598 isolates were quasi-hierarchically sampled between 2013 and 2015 across all major Australian chickpea growing regions and commonly grown host genotypes. These were molecularly compared at seven most informative microsatellite loci. Although a large number of haplotypes were identified (66), an overall low gene diversity (Hexp = 0.066) and genotypic diversity (D = 0.57) was detected, validating previous smaller studies. Almost 70% of the isolates assessed were of a single dominant and well adapted haplotype (ARH01). Members of this haplotype were present across all growing regions and on all host genotypes assessed, indicating a high degree of adaptation and fitness to survive. Disease screening on a differential host set, including three commonly deployed resistance sources, revealed distinct patterns in aggressiveness among the isolates. In total, 17% of all isolates were classified as highly aggressive and almost 75% of these were of the ARH01 haplotype. A similar pattern was observed at the host level, with 46% of all isolates collected from the commonly grown host genotype Genesis 090 (classified as “resistant” during the term of collection) identified as highly aggressive. Of these, 63% belonged to the ARH01 haplotype. The geographic hotspots within the industry with potential threat levels were also identified on the basis of detection of high risk isolates. In conclusion, the ARH01 haplotype represents a significant risk to the Australian chickpea industry, being not only widely adapted to the diverse agro-geographical environments of the Australian chickpea growing regions and cultivars sown, but also containing a disproportionately larger frequency of aggressive isolates, indicating fitness to survive and replicate on the best resistance sources in the Australian germplasm. This study has clearly demonstrated that the Australian Ascochyta rabiei population is diverse in its ability to cause disease on chickpea cultivars with isolates ranging from low to highly aggressive based on gross symptomolgy. In order to help inform strategic management of such a diverse population, knowledge on potential diversity in the infection and invasion processes of the pathogen and the A. rabiei-chickpea interaction was required. Therefore, an in-depth histopathology study was conducted with isolates with varying aggressiveness on four differential host genotypes. Highly replicated microscopy observations revealed significant differences in percentages, timings and rates of conidia germination and growth, and appressoria formation among isolates on all of the hosts assessed. In general, the previously characterised highly aggressive isolates germinated and penetrated faster than the low aggressive isolate. However, there were significance differences in these rates, indicating that some highly aggressive isolates are able to germinate and invade the host much faster than others and within the first 12 hours of contact. This difference continued through to development of disease symptomology which appeared earlier and more severely for aggressive isolates on the moderately resistant PBA HatTrick and susceptible Kyabra cultivars than on resistant hosts. This knowledge will inform disease management decisions including the potential to improve the timing and targeting of specific chemical controls to reduce the impact of this ubiquitous and pathogenically diverse pathogen.