Cause of Death: Phytophthora or Flood? Effects of Waterlogging on Phytophthora medicaginis and Resistance of Chickpea (Cicer arietinum)

Chickpea production in Australia is constrained by both waterlogging and the root disease Phytophthora root rot (PRR). Soil saturation is an important pre-condition for significant disease development for many soil-borne Phytophthora spp. In wet years, water can pool in low lying areas within a field, resulting in waterlogging, which, in the presence of PRR, can result in a significant yield loss for Australian chickpea varieties. In these circumstances, the specific cause of death is often difficult to discern, as the damage is rapid and the spread of PRR can be explosive in nature. The present study describes the impact of soil waterlogging on oxygen availability and the ability of P. medicaginis to infect chickpea plants. Late waterlogging in combination with PRR reduced the total plant biomass by an average of 94%; however, waterlogging alone accounted for 88% of this loss across three reference genotypes. Additional experiments found that under hypoxic conditions associated with waterlogging, P. medicaganis did not proliferate as determined by zoospore counts and DNA detection using qPCR. Consequently, minimizing waterlogging damage through breeding and agronomic practices should be a key priority for integrated disease management, as waterlogging alone results in plant stunting, yield loss and a reduced resistance to PRR.

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

Background Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between ‘Criollo de Morellos-334’ (CM-334), a resistant landrace from Mexico, and ‘Early Jalapeno’, a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. Results Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. Conclusions Results support the genetic complexity of the P. capsici–Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

Management of Phytophthora cinnamomi using fungicides and host plant defense inducers under drought conditions: A case-study of flowering dogwood

Phytophthora cinnamomi is considered one of the most destructive pathogens of ornamental crops. Different fungicides and host plant defense inducers were tested for their efficacy in managing Phytophthora root rot in drought conditions. In this study, the drought conditions were maintained by evaluating the moisture holding capacity of the pine bark in a 10.2 cm nursery container. Four controls and nine different treatments were used in two trials for this greenhouse study. All treatments were drench applied as a preventative or curative treatment. Seedlings were artificially inoculated with P. cinnamomi. Regular irrigation was carried out using overhead irrigation for one month after inoculation. Irrigation was regulated by drip irrigation after the first month. A moisture level of 15-18% of total moisture holding capacity was maintained using the gravimetric method throughout the drought period. Physiological parameters of the seedlings were recorded a week after seedlings were drought stressed. In both trials of preventative and curative treatments, all treatments were able to suppress the disease significantly except Orkestra Intrinsic. Orkestra Intrinsic had a disease severity statistically similar to the inoculated and stressed control in trial 1 of the curative treatment. Net photosynthesis, stomatal conductance, and leaf moisture potential were significantly greater in seedlings treated with Subdue MAXX, Signature Xtra and Empress Intrinsic in both trials of preventative and curative treatments. Effective quantum yield of Photosystem II was significantly lower in the inoculated stressed control in both trials of preventative and curative treatments. Net chlorophyll content through the SPAD meter showed higher values for Subdue MAXX treated seedlings compared to the non-inoculated non-stressed controls in trial 1 as both a curative and preventative application. In trial 2, Subdue MAXX and Signature Xtra were the best curative treatments, whereas Empress Intrinsic, Interface and Subdue MAXX were the best preventative treatments for higher chlorophyll content. This case study will help growers perform successful management of Phytophthora root rot in woody ornamental crops during drought or water deficit conditions.

Phenotyping for waterlogging tolerance as a proxy for Phytophthora medicaginis resistance in chickpea

Phytophthora root rot (PRR) caused by the soil-borne oomycete Phytophthora medicaginis is a significant constraint to chickpea (Cicer aretinium) production across the northern grains region of Australia. In flooded soil, which is conducive to PRR disease development, up to 70% yield loss can occur in the most resistant Australian cultivars. Incorporating waterlogging tolerance in soybean (Glycine max) has been shown to improve quantitative resistance to Phytophthora sojae. Root growth of three chickpea genotypes were assessed at the seedling stage under waterlogging, PRR and the combination of these abiotic and biotic constraints. Levels of waterlogging tolerance in chickpea are inherently low; yet selected genotypes displayed variability in root traits linked to improved waterlogging tolerance. The PRR moderately susceptible chickpea cultivar Yorker and PRR very susceptible Rupali demonstrated an eight-fold increase in early adventitious root growth from the epicotyl region under waterlogging stress, compared to the PRR resistant interspecific backcross genotype 04067-81-2-1-1 (C. echinospermum x C. aretinium*2). Selection for primary root depth, which was significantly greater in 04067-81-2-1-1 under waterlogging, appears to improve PRR resistance compared with root replacement traits. Soil-borne Phytophthora spp. are reportedly attracted to branch sites and leached exudates. We propose that compromised root barriers at emergence sites of adventitious roots under waterlogging conditions hasten hyphal entry, potentially increasing susceptibility to PRR. Hence, screening for root depth and absence of adventitious root development under waterlogged conditions may offer a novel proxy phenotyping method for PRR resistance traits at early stages of chickpea breeding.

The challenges of managing Phytophthora root rot in the nursery industry

For nearly 100 years, Phytophthora root rot (PRR) has been a severe problem in nurseries. Early surveys found only one or two Phytophthora species on any one host. However, recent surveys show that nurseries are impacted by increasingly complex Phytophthora communities that vary by host, nursery, and region. Individual community members have diverse biological characteristics and differ in their responses to disease control measures. These differences may shift community composition towards members that are less sensitive to treatment, thereby decreasing overall disease control. Together, this suggests that PRR is better approached as a disease complex rather than as a disease caused by a single entity. Yet, most experiments use only a single Phytophthora isolate and therefore overlook the potential for other community members to be less responsive to treatment. Successful control is further limited by a lack of data on the disease losses and soilborne inoculum levels encountered in the nursery industry, which are essential for establishing risks for infection, pathogen movement, and for evaluating disease control efficacy. Focused surveys with intensive sampling are needed to better characterize the Phytophthora communities occurring on major nursery crops. Experiments should utilize a representative set of species and isolates to ensure treatments are effective. The presence of diverse Phytophthora communities in the nursery industry makes it less likely that any one disease control tactic will be broadly effective. Instead, a combination of approaches that take into account the individual weaknesses of each community member will likely be necessary to achieve long-term PRR control.

Antagonistic Potential of Native Trichoderma spp. against Phytophthora cinnamomi in the Control of Holm Oak Decline in Dehesas Ecosystems

Phytophthora root rot caused by the pathogen Phytophthora cinnamomi is one of the main causes of oak mortality in Mediterranean open woodlands, the so-called dehesas. Disease control is challenging; therefore, new alternative measures are needed. This study focused on searching for natural biocontrol agents with the aim of developing integrated pest management (IPM) strategies in dehesas as a part of adaptive forest management (AFM) strategies. Native Trichoderma spp. were selectively isolated from healthy trees growing in damaged areas by P. cinnamomi root rot, using Rose Bengal selective medium. All Trichoderma (n = 95) isolates were evaluated against P. cinnamomi by mycelial growth inhibition (MGI). Forty-three isolates presented an MGI higher than 60%. Twenty-one isolates belonging to the highest categories of MGI were molecularly identified as T. gamsii, T. viridarium, T. hamatum, T. olivascens, T. virens, T. paraviridescens, T. linzhiense, T. hirsutum, T. samuelsii, and T. harzianum. Amongst the identified strains, 10 outstanding Trichoderma isolates were tested for mycoparasitism, showing values on a scale ranging from 3 to 4. As far as we know, this is the first report referring to the antagonistic activity of native Trichoderma spp. over P. cinnamomi strains cohabiting in the same infected dehesas. The analysis of the tree health status and MGI suggest that the presence of Trichoderma spp. might diminish or even avoid the development of P. cinnamomi, protecting trees from the worst effects of P. cinnamomi root rot.

Phosphonate treatment effects on Phytophthora root rot control, phosphite residues and Phytophthora cactorum inoculum in young apple orchards

Phytophthora root rot, caused by Phytophthora cactorum, is an economically important disease on young apple trees. Limited information is available on the effect of different phosphonate application methods and dosages on disease control, fruit- and root phosphite concentrations and soil- and root pathogen inoculum levels. Evaluation of phosphonate treatments in three apple orchard trials (two in the Grabouw and one in the Koue Bokkeveld region) showed that foliar sprays (ammonium- or potassium phosphonate), trunk sprays and trunk paints, were equally effective at increasing trunk diameter in one trial and yield in a second trial over a 25-month period. Foliar ammonium- and potassium phosphonate sprays (12 g phosphorous acid/tree), and two different dosages of the ammonium phosphonate sprays (~ 4.8 g or 12 g phosphorous acid/tree) were all equally effective at improving tree growth. The addition of a bark penetrant (polyether-polymethylsiloxane-copolymer) to trunk sprays did not improve the activity of trunk sprays. The low dosage ammonium phosphonate foliar spray (~4.8 g a.i./tree) was the only treatment that in general yielded significantly lower root phosphite concentrations than the other phosphonate treatments. Root phosphite concentrations were significantly positively correlated (P < 0.0001) with an increase in trunk diameter and negatively with P. cactorum root DNA quantities (P ≤ 0.001). Phosphite fruit residues were less than 31 ppm for all treatments, with the trunk paint treatment (80 g phosphorous acid/tree applied annually) yielding significantly lower residues than the higher dosage foliar sprays (~12 g a.i/tree). Twenty-one months post-treatment, most of the phosphonate treatments in all of the trials similarly significantly reduced P. cactorum DNA quantities estimated directly from roots, but not from soil based on soil baiting DNA analysis. Pathogen quantities in fine feeder roots did not differ significantly from those in higher-order roots (< 5 mm dia.). Phytophthora cactorum DNA quantities estimated using DNA quantification directly from roots were significantly correlated (P < 0.0001) with those obtained through root leaf baiting DNA analysis, and to a lesser extent with soil leaf baiting DNA quantities (P = 0.025).