Phytophthora root rot of chickpea: inoculum, pathogenicity and resistance phenotyping

Abstract

<p>Phytophthora root rot (PRR) caused by <i>Phytophthora medicaginis</i> is the major root disease of chickpea (<i>Cicer arietinum</i>) in north-eastern Australia. Improving resistance to <i>P. medicaginis</i> has been a high priority for Australian chickpea breeding. Despite this high priority the understanding of <i>P. medicaginis</i> population dynamics and relationship to yield loss, variation in <i>P. medicaginis</i> isolate aggressiveness and the most effective partial resistance phenotyping methods remain significant knowledge gaps.</p> <p>My research focused on four main areas. First, a qPCR method was developed to quantify <i>P. medicaginis</i> DNA in soil samples. The efficacy of <i>P. medicaginis</i> DNA soil concentrations at planting to predict PRR levels and yield loss in chickpea across a range of disease conducive environmental conditions was evaluated. <i>Phytophthora medicaginis</i> DNA concentrations at seeding could only predict PRR disease risk accurately for low to moderate disease conducive environmental conditions. </p> <p>Second, the prevalence and inoculum dynamics of <i>P. medicaginis</i> in chickpea cropping systems was evaluated. <i>Phytophthora medicaginis</i> DNA was detected in soil in over 30% of chickpea fields in regions where PRR disease occurs. Inoculum concentration declines were demonstrated following in-crop epidemics for the PRR very susceptible var. Sonali, in naturally infested stored soil, and in the postharvest period of the field experiment.</p> <p>Third, I evaluated the variation in <i>P. medicaginis</i> aggressiveness and the effects of the phenotyping system used on host genotype-isolate rankings. Results demonstrated an aggressiveness continuum among <i>P. medicaginis</i> isolates. Comparison of multiple phenotyping systems showed the level of aggressiveness of <i>P. medicaginis</i> isolates was affected by the phenotyping method and that phenotyping methods interact with both isolate and host genotype reactions.</p> <p>Finally, in-field genotype dependant soil <i>P. medicaginis</i> inoculum concentrations were evaluated for the identification of genotypes with high levels of partial resistance. Recombinant inbred lines (RIL) with high levels of PRR foliage symptoms had higher inoculum concentrations than RIL with low levels of foliage symptoms. Superior RIL with consistently low levels of foliage symptoms provided in-crop <i>P. medicaginis</i> soil inoculum concentrations relative to normalised yield loss across a putative partial resistance-tolerance spectrum</p> <p>This research identified a number of aspects of <i>P. medicaginis</i> biology relevant to understanding inoculum dynamics, in-field PRR development, isolate aggressiveness and host resistance phenotyping. Using <i>P. medicaginis</i> inoculum concentration to determine PRR disease risk in chickpea only showed promise in low to moderate disease conducive seasons. Monitoring in-field <i>P. medicaginis</i> populations is challenging due to post-epidemic inoculum decline. This means that the most reliable time to detect <i>P. medicaginis</i> inoculum is during chickpea cropping rather than from non-host break crops. To improve P. medicaginis resistance breeding practices aggressive P. medicaginis isolates can be selected alongside root reaction focused phenotyping methods. Genotype dependant soil <i>P. medicaginis</i> inoculum concentrations relative to normalised yield loss provide a useful method of identifying genotypes with high levels of partial resistance. Overall this research has provided outputs that contribute to PRR management through pathogen detection, quantification and resistance breeding methods.</p>