Aggressiveness of Phytophthora medicaginis on chickpea: Phenotyping method determines isolate ranking and host genotype-by-isolate interactions

Phytophthora medicaginis causing Phytophthora root rot of chickpea (Cicer arietinum) is an important disease, with genetic resistance using C. arietinum × Cicer echinospermum crosses as the main disease management strategy. We evaluated pathogenic variation in P. medicaginis populations with the aim of improving phenotyping methods for disease resistance. We addressed the question of individual isolate aggressiveness across four different seedling-based phenotyping methods conducted in glasshouses and one field-based phenotyping method. Our results revealed that a seedling media surface inoculation method used on a susceptible C. arietinum variety and a moderately resistant C. arietinum × C. echinospermum backcross detected the greatest variability in aggressiveness among 37 P. medicaginis isolates. Evaluations of different components of resistance, using our different phenotyping methods, revealed that differential pathogen–isolate reactions occur with some phenotyping methods. We found support for our hypotheses that the level of aggressiveness of P. medicaginis isolates depends on the phenotyping method, and that phenotyping methods interact with both isolate and host genotype reactions. Our cup-based root inoculation method showed promise as a non-field-based phenotyping method, as it provided significant correlations with genotype–isolate rankings in the field experiment for a number of disease parameters

An evaluation of Solanum nigrum and S. physalifolium biology and management strategies to reduce nightshade fruit contamination of process pea crops

The contamination of process pea (Pisum sativum L.) crops by the immature fruit of black nightshade (Solanum nigrum L.) and hairy nightshade (S. physalifolium Rusby var. nitidibaccatum (Bitter.) Edmonds) causes income losses to pea farmers in Canterbury, New Zealand. This thesis investigates the questions of whether seed dormancy, germination requirements, plant growth, reproductive phenology, or fruit growth of either nightshade species reveal specific management practices that could reduce the contamination of process peas by the fruit of these two weeds. The seed dormancy status of these weeds indicated that both species are capable of germinating to high levels (> 90%) throughout the pea sowing season when tested at an optimum germination temperature of 20/30 °C (16/8 h). However, light was required at this temperature regime to obtain maximum germination of S. nigrum. The levels of germination in the dark at 20/30 °C and at 5/20 °C, and in light at 5/20 °C, and day to 50 % germination analyses indicated that this species cycled from nondormancy to conditional dormancy throughout the period of investigation (July to December 2002). For S. physalifolium, light was not a germination requirement, and dormancy inhibited germination at 5/20 °C early in the pea sowing season (July and August). However, by October, 100% of the population was non-dormant at this test temperature. Two field trials showed that dark cultivation did not reduce the germination of either species. Growth trials with S. nigrum and S. physalifolium indicated that S. physalifolium, in a non-competitive environment, accumulated dry matter at a faster rate than S. nigrum. However, when the two species were grown with peas there was no difference in dry matter accumulation. Investigation of the flowering phenology and fruit growth of both species showed that S. physalifolium flowered (509 °Cd, base temperature (Tb) 6 °C) approximately 120 °Cd prior to S. nigrum (633 °Cd). The fruit growth rate of S. nigrum (0.62 mm/d) was significantly faster than the growth rate of S. physalifolium (0.36 mm/d). Because of the earlier flowering of S. physalifolium it was estimated that for seedlings of both species emerging on the same date that S. physalifolium could produce a fruit with a maximum diameter of 3 mm ~ 60 °Cd before S. nigrum. Overlaps in flowering between peas and nightshade were examined in four pea cultivars, of varying time to maturity, sown on six dates. Solanum physalifolium had the potential to contaminate more pea crops than S. nigrum. In particular, late sown peas were more prone to nightshade contamination, especially late sowings using mid to long duration pea cultivars (777-839 °Cd, Tb 4.5 °C). This comparison was supported by factory data, which indicated that contamination of crops sown in October and November was more common than in crops sown in August and September. Also, cultivars sown in the later two months had an ~ 100 °Cd greater maturity value than cultivars sown in August and September. Nightshade flowering and pea maturity comparisons indicated that the use of the thermal time values for the flowering of S. nigrum and S. physalifolium can be used to calculate the necessary weed free period required from pea sowing in order to prevent the flowering of these species. The earlier flowering of S. physalifolium indicates that this species is more likely to contaminate pea crops than is S. nigrum. Therefore, extra attention may be required where this species is present in process pea crops. The prevention of the flowering of both species, by the maintenance of the appropriate weed free period following pea sowing or crop emergence, was identified as potentially, the most useful means of reducing nightshade contamination in peas

Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories

Background: The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect this symbiotic relationship including abiotic conditions, plant genotype, and disruptions to host signalling/perception networks. In order to support improved nodule formation in chickpea, we investigated how plant genotype and soil nutrient availability affect chickpea nodule formation and nitrogen fixation. Further, using transcriptomic profiling, we sought to identify gene expression patterns that characterize highly nodulated genotypes. Results: A study involving six chickpea varieties demonstrated large genotype by soil nitrogen interaction effects on nodulation and further identified agronomic traits of genotypes (such as shoot weight) associated with high nodulation. We broadened our scope to consider 29 varieties and breeding lines to examine the relationship between soilborne disease resistance and the number of nodules developed and real-time nitrogen fixation. Results of this larger study supported the earlier genotype specific findings, however, disease resistance did not explain differences in nodulation across genotypes. Transcriptional profiling of six chickpea genotypes indicates that genes associated with signalling, N transport and cellular localization, as opposed to genes associated with the classical nodulation pathway, are more likely to predict whether a given genotype will exhibit high levels of nodule formation. Conclusions: This research identified a number of key abiotic and genetic factors affecting chickpea nodule development and nitrogen fixation. These findings indicate that an improved understanding of genotype-specific factors affecting chickpea nodule induction and function are key research areas necessary to improving the benefits of rhizobial symbiosis in chickpea

Chickpea Roots Undergoing Colonisation by Phytophthora medicaginis Exhibit Opposing Jasmonic Acid and Salicylic Acid Accumulation and Signalling Profiles to Leaf Hemibiotrophic Models

Hemibiotrophic pathogens cause significant losses within agriculture, threatening the sustainability of food systems globally. These microbes colonise plant tissues in three phases: a biotrophic phase followed by a biotrophic-to-necrotrophic switch phase and ending with necrotrophy. Each of these phases is characterized by both common and discrete host transcriptional responses. Plant hormones play an important role in these phases, with foliar models showing that salicylic acid accumulates during the biotrophic phase and jasmonic acid/ethylene responses occur during the necrotrophic phase. The appropriateness of this model to plant roots has been challenged in recent years. The need to understand root responses to hemibiotrophic pathogens of agronomic importance necessitates further research. In this study, using the root hemibiotroph Phytophthora medicaginis, we define the duration of each phase of pathogenesis in Cicer arietinum (chickpea) roots. Using transcriptional profiling, we demonstrate that susceptible chickpea roots display some similarities in response to disease progression as previously documented in leaf plant–pathogen hemibiotrophic interactions. However, our transcriptomic results also show that chickpea roots do not conform to the phytohormone responses typically found in leaf colonisation by hemibiotrophs. We found that quantified levels of salicylic acid concentrations in root tissues decreased significantly during biotrophy while jasmonic acid concentrations were significantly induced. This study demonstrated that a wider spectrum of plant species should be investigated in the future to understand the physiological changes in plants during colonisation by soil-borne hemibiotrophic pathogens before we can better manage these economically important microbes

Order of microbial succession affects rhizobia-mediated biocontrol efforts against Phytophthora root rot

The management of soilborne root diseases in pulse crops is challenged by a limited range of resistance sources and often a complete absence of in-crop management options. Therefore, alternative management strategies need to be developed. We evaluated disease limiting interactions between the rhizobia species Mesorhizobium ciceri, and the oomycete pathogen Phytophthora medicaginis, which causes Phytophthora root rot (PRR) of chickpea (Cicer arietinum). For the PRR susceptible var. Sonali plants, post-pathogen M. ciceri inoculation significantly improved probability of plant survival when compared to P. medicaginis infected plants only pre-inoculated with M. ciceri (75 % versus 35 %, respectively). Potential mechanisms for these effects were investigated: rhizobia inoculation benefits to plant nodulation were not demonstrated, but the highest nodule N-fixation activity of P. medicaginis inoculated plants occurred for the post-pathogen M. ciceri treatment; rhizobia inoculation treatment did not reduce lesion development but certain combinations of microbial inoculation led to significant reduction in root growth. Microcosm studies, however, showed that the presence of M. ciceri reduced growth of P. medicaginis isolates. Putative chickpea disease resistance gene expression was evaluated using qPCR in var. Sonali roots. When var. Sonali plants were treated with M. ciceri post-P. medicaginis inoculation, the gene regulation in the plant host became more similar to PRR moderately resistant var. PBA HatTrick. These results suggest that M. ciceri application post P. medicaginis inoculation may improve plant survival by inducing defense responses similar to a PRR moderately resistant chickpea variety. Altogether, these results indicate that order of microbial succession can significantly affect PRR plant survial in susceptible chickpea under controlled conditions and improved plant survival effects are due to a number of different mechanisms including improved host nutrition, through direct inhibiton of pathogen growth, as well as host defense priming

Productivity is negatively related to shoot growth across five mango cultivars in the seasonally wet-dry tropics of northern Australia

Introduction. Mango productivity is low in seasonally wet-dry tropical areas where breeding programs require information on factors affecting productivity of mango cultivars. Specifically, our study tested a novel hypothesis that, among Australian- and Florida-bred cultivars, the greater growth of vegetatively vigorous cultivars would contribute to lower levels of fruit production in comparison with less vegetatively vigorous cultivars, in a wet-dry tropical environment. Materials and methods. A field experiment was conducted on trees of the cultivars ‘Kensington Pride’ and ‘Strawberry’, both polyembryonic cultivars, and ‘Haden’, ‘Irwin’ and ‘Tommy Atkins’, all monoembryonic cultivars. Results. Shoot growth was recorded over two years; in both years the polyembryonic cultivars produced more new shoot length than the monoembryonic cultivars; ‘Irwin’ was the least vigorous cultivar in both years. Across cultivars, there was a negative relationship between normalised (by flowering intensity and canopy area) fruit number or yield and vegetative vigour as represented by new shoot length. Conclusion. The results supported the hypothesis that the greater shoot growth of vegetatively vigorous cultivars contributed to lower levels of fruit production in comparison with less vegetatively vigorous cultivars in a tropical environment. This is the first study which demonstrates that the extent of seasonal shoot growth had a fruit production cost for mango

Rapid and High Throughput Hydroponics Phenotyping Method for Evaluating Chickpea Resistance to Phytophthora Root Rot

Phytophthora root rot (PRR) is a major constraint to chickpea production in Australia. Management options for controlling the disease are limited to crop rotation and avoiding high risk paddocks for planting. Current Australian cultivars have partial PRR resistance, and new sources of resistance are needed to breed cultivars with improved resistance. Field- and glasshouse-based PRR resistance phenotyping methods are labour intensive, time consuming, and provide seasonally variable results; hence, these methods limit breeding programs’ abilities to screen large numbers of genotypes. In this study, we developed a new space saving (400 plants/m2), rapid (<12 days), and simplified hydroponics-based PRR phenotyping method, which eliminated seedling transplant requirements following germination and preparation of zoospore inoculum. The method also provided post-phenotyping propagation all the way through to seed production for selected high-resistance lines. A test of 11 diverse chickpea genotypes provided both qualitative (PRR symptoms) and quantitative (amount of pathogen DNA in roots) results demonstrating that the method successfully differentiated between genotypes with differing PRR resistance. Furthermore, PRR resistance hydroponic assessment results for 180 recombinant inbred lines (RILs) were correlated strongly with the field-based phenotyping, indicating the field phenotype relevance of this method. Finally, post-phenotyping high-resistance genotypes were selected. These were successfully transplanted and propagated all the way through to seed production; this demonstrated the utility of the rapid hydroponics method (RHM) for selection of individuals from segregating populations. The RHM will facilitate the rapid identification and propagation of new PRR resistance sources, especially in large breeding populations at early evaluation stages

Improved Phytophthora resistance in commercial chickpea (Cicer arietinum) varieties negatively impacts symbiotic gene signalling and symbiotic potential in some varieties

Breeding disease-resistant varieties is one of the most effective and economical means to combat soilborne diseases in pulse crops. Commonalities between pathogenic and mutualistic microbe colonization strategies, however, raises the concern that reduced susceptibility to pathogens may simultaneously reduce colonization by beneficial microbes. We investigate here the degree of overlap in the transcriptional response of the Phytophthora medicaginis susceptible chickpea variety „Sonali‟ to the early colonization stages of either Phytophthora, rhizobial bacteria or arbuscular mycorrhizal fungi. From a total of 6,476 genes differentially expressed in Sonali roots during colonization by any of the microbes tested, 10.2% were regulated in a similar manner regardless of whether it was the pathogenic oomycete or a mutualistic microbe colonizing the roots. Of these genes, 49.7% were oppositely regulated under the same conditions in the moderately Phytophthora resistant chickpea variety „PBA HatTrick‟. Chickpea varieties with improved resistance to Phytophthora also displayed lower colonization by rhizobial bacteria and mycorrhizal fungi leading to an increased reliance on N and P from soil. Together, our results suggest that marker-based breeding in crops such as chickpea should be further investigated such that plant disease resistance can be tailored to a specific pathogen without affecting mutualistic plant:microbe interactions

Hidden diversity of Macrophomina associated with broadacre and horticultural crops in Australia

Worldwide, most isolates of Macrophomina (Botryosphaeriaceae) have been attributed to the generalist phytopathogen M. phaseolina. Since 2014, three cryptic species of Macrophomina have been recognised by molecular methods. This study elucidates the taxonomy of Macrophomina species associated with broadacre and horticultural crops in Australia. A five-locus phylogenetic analysis of 80 isolates of Macrophomina from 28 plant species in Australia, combined with genealogical concordance phylogenetic species recognition and coalescent-based species delimitation approaches, found M. phaseolina, M. pseudophaseolina and supported the introduction of M. tecta sp. nov. Macrophomina phaseolina was the most frequently isolated (88%). Macrophomina pseudophaseolina is reported for the first time in Australia. Macrophomina tecta was isolated from stems of Sorghum bicolor and Vigna radiata with charcoal rot symptoms in New South Wales and Queensland. The potential for two or more Macrophomina species to co-infect the same host has implications for disease epidemiology and pathogen evolution. Future investigations into the distribution, biology, host range and population diversity of the new Macrophomina records are needed