Genome Resource of Raspberry Root Rot Pathogen Phytophthora gonapodyides.

Root rot of raspberry (Rubus idaeus), thought to be primarily caused by Phytophthora rubi, is an economically important disease in the western United States. The objectives of this study were to determine which Phytophthora species are involved in root rot, examine the efficacy of different isolation methods (cane, root, and root/soil baiting with young raspberry plants), and determine if pathogenicity, fungicide resistance, and/or genetic variation exists among P. rubi isolates collected from raspberry fields in Washington, Oregon, and California. Of 275 samples, direct isolation from cane material resulted in a greater number of P. rubi isolates (39%), whereas root/soil baiting yielded the least (11%). Sequencing of the internal transcribed spacer region of 210 of the total 597 collected Phytophthora isolates showed that all but one isolate (identified as P. bisheria) were P. rubi. Results of the pathogenicity and fungicide resistance to mefenoxam comparing 14 total isolates from Washington, Oregon, and California showed that isolates were similarly virulent against red raspberry and the EC50 frequency distributions showed no significant difference. These results, combined with amplified fragment length polymorphism results show that P. rubi isolates from Washington, Oregon, and California represent one large mixed population. This work provides novel insights into the isolation and biology of P. rubi in western U.S. raspberry production systems.

First report of Phytopythium helicoides causing crown and root rot of raspberry (Rubus Idaeus L.) in Mexico

Specific scopeThis standard describes the production of certified pathogen‐tested material ofRubus.Specific approval and amendmentFirst approved in 2004–09.Revised in 2009–09.

Phytophthora rubi has been reported as the primary causal agent of raspberry root rot (RRR) in the UK, resulting in severe economic losses. Recent observations suggest the RRR complex may be more diverse than previously thought. This study investigated the Peronosporales species present in UK raspberry plants and factors affecting their diversity and abundance. Eighty‐six symptomatic root and 86 cane samples were collected from seven farms in the UK in 2020 and 2021. Five additional samples were collected from blackberry roots. Symptomatic tissue was plated onto selective media, and resultant isolates were identified by ribosomal internal transcribed spacer (ITS) barcoding. Twelve isolates of five species of Phytophthora (P. citrophthora, P. pini, P. erythroseptica, P. cryptogea and P. pseudocryptogea) and seven isolates of two Phytopythium species (Pp. vexans and Pp. litorale) were collected. Isolate pathogenicity was assessed on detached leaves, with Pp. litorale and Pp. vexans exhibiting significantly higher pathogenicity on raspberry leaves than an isolate of P. rubi. High‐throughput sequencing of the ITS region of symptomatic root samples revealed farm location had a significant effect on Peronosporales community composition (p = 0.001), and both farm location and plant variety significantly affected the abundance of taxa (p < 0.002 and p < 2 × 10−16, respectively). This study presents Pp. vexans and Pp. litorale as new potential pathogens for further study. Furthermore, we recommend the inclusion of other Peronosporales species into resistance screens in raspberry breeding programmes to produce genotypes more resilient to community composition shifts in raspberry root pathospheres in the UK.

Phytophthora cryptogea was isolated from field plantings of the red raspberry cultivars Glen Clova, Canby and Willamette which showed wilting, dieback, stem lesions and root rotting. Pathogenicity of P. cryptogea to raspberry was demonstrated in glasshouse experiments. Twelve cultivars of raspberry were screened for resistance to the disease by growing them in artificially infested soil. Glen Clova and Canby were highly susceptible whilst Chilcotin, Nootka, Haida and Puyallup were resistant. Soil treatments with either metalaxyl, phosphorous acid or fosetyl aluminium controlled the disease. This is the first record of a phytophthora root rot of raspberry in Australia, and the first demonstrating the pathogenicity of P. cryptogea to raspberry.

Phytophthora fragariae Hickman, which causes strawberry red stele and raspberry root rot, is a quarantine organism for which specific and sensitive detection methods are required to test the health of planting material. Sequences of the internal transcribed spacer regions of the ribosomal gene repeat (rDNA) were used to develop primers for P. fragariae in a nested Polymerase Chain Reaction (PCR). The fungus was readily detected in infected but symptomless roots by nested, but not single-round, PCR. It was also detected in infested water samples obtained from the Dutch General Inspection Service by nested PCR. Detection of PCR products was at least 10-fold more sensitive by PCR-ELISA than by conventional visualisation on agarose gels.

Phytophthora frugariae causes red core root rot of strawberries. Although the disease is probably most acute in northern Europe, serious outbreaks have been reported from a number of Mediterranean countries, especially France and Italy. Leather rot of fruit and crown rot, which are caused by P. cuctorum, can also be severe problems in warmer climates. Both fungi survive in soil for long periods, but the most common form of spread is in diseased planting material. Sensitive tests have been developed to detect red core in planting material, and been used to effect in certification schemes. Root rot of raspberry has gained prominence in the last 10 years in Europe as raspberry growing has expanded, but the disease has been known for many years in France. Nine species of Phyfophthora have been recovered from affected plants, but two of these, one with affinities with P. megasperma, and P. cumbiuora, are responsible for most major outbreaks. The other species are only troublesome where drainage is poor. Again, spread is mainly in infected material. Few raspberries are resistant to root rot, but some wild RubuP spp., blackberries and raspberry x blackberry hybrids are resistant and may be useful in breeding programmes.

Analysis of RFLPs in nuclear and mitochondrial DNA and the taxonomy of Phytophthora fragariae

A homothallic semipapillate slow growing Phytophthora species associated with root rot of strawberries from greenhouse-grown plants in North Carolina, USA, root rot of roses in the Netherlands, and root rot of raspberry in Knoxfield, Australia, was identified. The main character of this organism is the production of paragynous antheridia with broad attachment to the oogonial wall. The morphology of the pathogen does not match that of any of the more than 85 described Phytophthora species. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA region (ITS1-5.8S-ITS2) of this taxon and those from other Phytophthora species from GenBank supports the conclusion that this organism is an unreported new species. In the phylogenetic tree with other reported Phytophthora species at the GenBank, the new species is more closely related to others in ITS clade 2 comprising semipapillate taxa including P. botryosa, P. citrophthora, P. colocasiae, P. meadii, P. citricola, P. inflata, P.tropicalis, P. capsici, Phytophthora sp. 'glovera' and P. multivesiculata. The most closely related species is P. multivesiculata isolated from Cymbidium orchid in the Netherlands. In this paper we describe the morphological characteristics and the phylogenetic relationships that support the description of this taxon as a new species Phytophthora bisheria sp. nov.

Identity, Virulence, and Isolation Frequency of Seven<i>Phytophthora</i>spp. Causing Root Rot of Raspberry in New York

Molecular characterization of Phytophthora isolates with non-papillate sporangia causing root rot of raspberry using mtDNA restriction fragment length polymorphisms

A homothallic semipapillate slow growing Phytophthora species associated with root rot of strawberries from greenhouse-grown plants in North Carolina, USA, root rot of roses in the Netherlands, and root rot of raspberry in Knoxfield, Australia, was identified. The main character of this organism is the production of paragynous antheridia with broad attachment to the oogonial wall. The morphology of the pathogen does not match that of any of the more than 85 described Phytophthora species. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA region (ITS1-5.8S-ITS2) of this taxon and those from other Phytophthora species from GenBank supports the conclusion that this organism is an unreported new species. In the phylogenetic tree with other reported Phytophthora species at the GenBank, the new species is more closely related to others in ITS clade 2 comprising semipapillate taxa including P. botryosa, P. citrophthora, P. colocasiae, P. meadii, P. citricola, P. inflata, P.tropicalis, P. capsici, Phytophthora sp. ‘glovera’ and P. multivesiculata. The most closely related species is P. multivesiculata isolated from Cymbidium orchid in the Netherlands. In this paper we describe the morphological characteristics and the phylogenetic relationships that support the description of this taxon as a new species Phytophthora bisheria sp. nov.

Zoospores and agar discs of the fungus causing raspberry root rot (Phytophthora fragariae) were used as inoculum to assess the resistance of raspberry genotypes in pot experiments. High zoospore concentrations resulted in more severe symptoms than low concentrations. There was a strong correlation between the results obtained with zoospores and with colonized agar discs as inocula. although disease was generally more severe with the former. The severity of root rot was correlated with a number of other symptoms, in particular growth reductions, stem lesions and leaf wilting, and some of these symptoms could possibly be used as measures of resistance. There was no evidence of physiological specialization with the range of isolates and raspberry genotypes used. Pot tests in general gave results which matched reported resistances in the field, and could be used to assess the resistance of breeding lines and selections.

The effects of raised beds, mulching, organic amendments and soil treatment with metalaxyl on raspberry root rot ( Phytophthora fragariae var. rubi ) were studied in a field experiment with two raspberry cultivars, Veten (highly susceptible) and Chilliwack, a less susceptible cultivar. Raised beds reduced the severity of root rot compared with flat beds. The best results for both cultivars were obtained with a combination of raised beds and metalaxyl treatment. As separate treatments, raised beds and metalaxyl had approximately the same effect. Mulching with grass or composted manure increased the severity of root rot.

Raspberry root rot and wilting complex (RRWC), primarily caused by Phytophthora rubi, is the most important disease for raspberry producers in Canada. There is currently little to no information on phenotypic diversity or sensitivity to metalaxyl-m of P. rubi isolates affecting raspberries in Canada. This study was conducted to understand the diversity in virulence and sensitivity to metalaxyl-m of P. rubi populations collected from diverse raspberry cultivars, fields, and locations during 2018–2020. All isolates of P. rubi (n = 24) were pathogenic on ‘Chemainus’ raspberry and showed significant variation (P < 0.05) in days to first foliar symptom development (DFSD) and progress in wilting index, as indicated by relative areas under disease progress curves (rAUDPC). Principal component analyses identified that root rot index, rAUDPC, DFSD, and percentage reduction in root length and weight were important variables in assessing pathogen virulence. Metalaxyl-m sensitivity was assessed using a radial growth assay and effective concentrations that inhibited 50% of mycelial growth (EC50) were determined for 44 isolates. The EC50 values ranged from 0.035–4.71 µg mL−1 with a mean value of 0.793 µg mL−1. About 61% of the isolates were very sensitive (EC50 values <0.20 µg mL−1), 25% of isolates were considered sensitive (EC50 values of 0.21–1.18 µg mL−1), and 14% of isolates showed reduced sensitivity to metalaxyl-m (EC50 value range of 1.19–4.71 µg mL−1). Knowledge of pathogen phenotypic diversity will be useful for raspberry breeders in screening genotypes against RRWC and the results of the fungicide sensitivity study will be useful in developing management strategies for RRWC.