Transcriptomic Evidence of a Link between Cell Wall Biogenesis, Pathogenesis, and Vigor in Walnut Root and Trunk Diseases

Crown gall disease (Agrobacterium tumefaciens), crown/root rot disease (Phytophthora spp.), root lesion disease (Pratylenchus vulnus) and tree vigor are key traits affecting the productivity and quality of walnuts in California. Unchallenged hybrid rootstocks were analyzed by RNA-seq to examine pre-formed factors affecting these traits. Enrichment analysis of the differentially expressed genes revealed that the increased expression of cell wall biogenesis-related genes plays a key role in susceptibility to A. tumefaciens, susceptibility to Phytophthora spp. and increased vigor. Analysis of the predicted subcellular loci of the encoded proteins revealed that many gene products associated with vigor and susceptibility were targeted to the plasma membrane and extracellular space, connecting these traits to sustaining barrier function. We observed that RNA processing and splicing, along with predicted nuclear targeting, were associated with resistance to A. tumefaciens, resistance to Phytophthora spp. and low vigor. Four genes within the J. microcarpa QTL region for resistance to A. tumefaciens and Phytophthora spp. were represented among our transcripts, with two of the genes being differentially expressed in association with resistance to A. tumefaciens and decreased vigor. No differential expression related to Phytophthora spp. or P. vulnus resistance was observed in this region. Additionally, the J. microcarpa haplotype expressed more transcripts associated with resistance to A. tumefaciens, Phytophthora spp. and low vigor, but not P. vulnus, than the J. regia haplotype. We also report unique and shared hormone and defense responses associated with each trait. This research suggests a link between cell wall biogenesis, vigor and critical root diseases of walnut.

Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrids

Soil-borne plant pathogens represent a serious threat that undermines commercial walnut (Juglans regia) production worldwide. Crown gall, caused by Agrobacterium tumefaciens, and Phytophthora root and crown rots, caused by various Phytophthora spp., are among the most devastating walnut soil-borne diseases. A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks. Here, resistance to A. tumefaciens, P. cinnamomi, and P. pini is mapped in the genome of Juglans microcarpa, a North American wild relative of cultivated walnut. Half-sib J. microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J. regia cv. Serr, producing 353 and 400 hybrids, respectively. Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens. Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J. microcarpa chromosome 4D and was associated with the same haplotype, designated as haplotype b, raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens. The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots.

Temporal Occurrence and Niche Preferences of Phytophthora spp. Causing Brown Rot of Citrus in the Central Valley of California

Brown rot of citrus fruit is caused by several species of Phytophthora and is currently of serious concern for the California citrus industry. Two species, Phytophthora syringae and P. hibernalis, are quarantine pathogens in China, a major export market for California citrus. To maintain trade and estimate the risk of exporting a quarantine pathogen, the distribution and frequency of Phytophthora spp. causing brown rot of orange in major growing areas of California was investigated. Symptomatic fruit were collected from navel (winter to late spring) and Valencia (late spring to summer) orange orchards from 2013 to 2015. Species identification of isolates was based on morphological characteristics, random amplified polymorphic DNA banding patterns, and sequencing of the internal transcribed spacer and the partial cox2/spacer/cox1 regions from axenic cultures, or directly on DNA from fruit tissue using a multiplex TaqMan quantitative polymerase chain reaction assay. In winter samplings, the incidence of P. syringae based on the number of fruit with Phytophthora spp. detection ranged from 73.6 to 96.1% for the two counties surveyed. The remaining isolates were identified as P. citrophthora. In late spring or summer, only P. citrophthora was recovered. P. hibernalis and P. nicotianae were not detected in any fruit with brown rot symptoms. These results indicate that P. syringae is currently an important brown rot pathogen of citrus fruit in California during the cooler seasons of the year. In winter 2016 and 2017, P. syringae was recovered by pear baiting at a high incidence from leaf litter and from a small number of rhizosphere soil or root samples but not from living leaves on the tree. In contrast, P. citrophthora was rarely found in leaf litter but was commonly detected in the rhizosphere. Thus, leaf litter is a major inoculum source for P. syringae and this species occupies a distinct ecological niche.

The avocado subgroup of Phytophthora citricola constitutes a distinct species, Phytophthora mengei sp. nov

Isolates from avocado tree cankers have been recognized as a distinct subgroup within the P. citricola complex since 1974, both morphologically and molecularly (isozyme and amplified fragment length polymorphism [AFLP] analyses). This subgroup is formally separated from P. citricola after comparative DNA fingerprinting and sequence analyses of the ITS region, as well as by morphological examinations. This new taxon is homothallic, produces plerotic oospores with paragynous antheridia and noncaducous semipapillate sporangia. Morphologically it differs from other species of Waterhouse group III by producing many large bizarre-shaped sporangia and smaller oogonia with asymmetric capitate antheridia. It belongs to clade 2 and is phylogenetically closer to P. siskiyouensis, P. capsici and P. tropicalis than to P. citricola. P. mengei can be easily differentiated from its relatives in the same clade and other species of this morpho-group by DNA fingerprints and sequence analysis. This new taxon is named Phytophthora mengei sp. nov.

Genetic Diversity in Populations of Phytophthora citricola Associated with Horticultural Crops in California

California populations of the plant pathogen Phytophthora citricola were examined for amplified fragment length polymorphism (AFLP), pathogenicity on almond, and sensitivity to mefenoxam. The characterizations of AFLP variation and mefenoxam sensitivity were based on 86 isolates (44 from almond, 11 from avocado, 3 from strawberry, 18 from walnut, and 10 from six other hosts). Cluster analysis of the AFLP data using the unweighted pair group method indicated a high level of genetic diversity among the isolates, and four main clusters were identified-one dominated by isolates from almond, another including all isolates from avocado, and two including isolates from several hosts other than avocado. Analysis of molecular variance revealed that 38.4 and 24.9% of the AFLP variation were associated with host and geographical factors, respectively. Of 24 isolates, including those from almond, avocado, strawberry, and walnut, 22 were aggressive on almond shoots; there was no evidence of host specificity. All but 1 of the 86 isolates grew at different rates on V8 juice medium amended with mefenoxam at 1 ppm, indicating partial tolerance to the fungicide. Isolates of P. citricola from California populations are genetically diverse, and much of the variation is associated with host and geography. These populations are all potentially pathogenic on almond and tolerant to mefenoxam.

Almond Replant Disease and Its Management with Alternative Pre-Plant Soil Fumigation Treatments and Rootstocks

Trials were conducted in orchards near Chico, CA and microplots near Parlier, CA to examine symptoms and control measures for a replant disease (RD) on almond (Prunus dulcis). In the orchard trials, areas with a recent history of severe RD were cleared, given soil fumigation treatments in the fall, and replanted with almond trees on various rootstocks the following winter. The replants in nonfumigated soil developed severe RD (stunting, wilting, chlorosis, defoliation) by the following summer, while those in most fumigated treatments remained healthy. Trees in nonfumigated soil developed smaller trunk diameters and fewer healthy roots ≤1 mm diameter, compared with the healthy trees. Almond developed RD on all rootstocks evaluated (Marianna 2624, Lovell, and Nemaguard), but the trees on Marianna 2624 were the most severely affected. Pre-plant tree-site (spot) fumigation treatments with methyl bromide (MB), chloropicrin (CP), 1,3-dichloropropene (1,3-D), 1,3-D + CP, iodomethane, and iodomethane + CP all prevented severe RD. Broadcast soil fumigation with CP also was effective, but broadcast MB and 1,3-D were ineffective. In microplots filled with RD-conducive soil, CP was more potent than MB for prevention of RD on Nemaguard peach. There was no association between nematodes and RD in orchard or microplot trials. The RD apparently was mediated by a biological agent(s) other than nematodes and can be prevented by appropriate fumigation with CP or other MB alternatives.

Genetic and Pathogenic Variation in Phytophthora cactorum Affecting Fruit and Nut Crops in California

Isolates of Phytophthora cactorum and 15 other species of Phytophthora were characterized according to their genomic DNA, pathogenicity, and sensitivity to mefenoxam. Amplified fragment length polymorphism (AFLP) analysis was completed for 132 isolates of P. cactorum (30 from almond, 86 from strawberry, 5 from walnut, and 11 from other hosts) and 22 isolates of 15 other Phytophthora spp. from various hosts. All 16 Phytophthora spp. were distinguishable by unique AFLP banding patterns. Cluster analysis of the AFLP data revealed high coefficients of genetic similarity (>0.9) among all California isolates of P. cactorum. Analysis of molecular variance indicated that, among all 132 isolates of P. cactorum, 30.8 and 24.5% of the AFLP variation was associated with hosts and geographical sources of isolates, respectively, whereas 15.0% of the variation was associated with isolate niche (i.e., an aerial plant part, portion of the root system, or soil). Among the 86 isolates of P. cactorum from strawberry, characterization by source in the production system (i.e., fruiting field or plant nursery) did not account for a significant proportion of the variation (0.6%, P = 0.204). In pathogenicity tests on strawberry plants (cv. Diamante) in a greenhouse, isolates of P. cactorum from hosts other than strawberry and an isolate from a strawberry fruit caused only negligible amounts of disease, but isolates from strawberry root systems were highly aggressive. On excised shoot segments of almond (cv. Drake), all isolates of P. cactorum originally from almond were pathogenic, and 8 of 17 isolates of the pathogen from other hosts caused significantly less disease than the almond isolates. All 132 isolates of P. cactorum were sensitive to mefenoxam at 1 ppm. Populations of P. cactorum in California apparently are mefenoxam sensitive and exhibit host specificity with relatively minor variation in genomic DNA. The genetic variation observed in P. cactorum included significant geographical and host origin components, which has implications for disease management approaches.

Phytophthora Leaf Spot and Foliar Blight of Pieris japonica Caused by Phytophthora citricola in California

During 2004, containerized nursery stock of lily-of-the-valley-bush (Pieris japonica 'Flamingo', family Ericaceae) in Santa Cruz County was affected by a foliar disease. Symptoms consisted of large leaf spots, many developing at the leaf tips that ranged in size from 1 to greater than 4 cm in diameter. Spots were dark brown to almost black, generally oval to round, visible from both sides of the leaf, and did not exhibit signs of any pathogen. Lesions typically expanded and affected the entire leaf, leaf petiole, and stems, resulting in blight-like symptoms. Severely affected leaves abscised from the plant. In advanced stages of the disease, the foliage of the plant was killed. These symptoms resembled those caused by the sudden oak death (SOD) pathogen, Phytophthora ramorum (3). A Phytophthora sp. was isolated consistently from symptomatic leaf tissue. However, the species was identified as P. citricola based on morphological traits that included the following: production of semipapillate, noncaducous sporangia that were irregular in shape and occasionally had more than one apex; presence of oospores with paragynous antheridia in single culture; and radiate to slightly petaloid colony morphology (1). P. ramorum and other fungi were not recovered. Pathogenicity of four representative isolates was confirmed by gently abrading the adaxial surfaces of attached leaves with a sterile wire brush, placing a colonized agar plug (5 mm in diameter) on the surface, misting the leaf with sterile water, and then covering the plug with a plastic cap that was secured with a wire clip. Control leaves were treated in the same manner but received sterile agar plugs. Plants were maintained in a greenhouse at 23 to 25°C. After 2 days, all leaves inoculated with the isolates exhibited dark brown lesions and by day 6, lesions measured 3 cm in diameter. P. citricola was reisolated from symptomatic lesions. Sterile plug control leaves developed no symptoms. The test was repeated and the results were similar. To our knowledge, this is the first report of P. citricola causing a foliar disease of Pieris japonica in California. P. citricola has been reported as a pathogen on Pieris spp. in Ohio (2). Our finding is important because P. ramorum causes very similar symptoms on this same host (3). The occurrence of these two foliar Phytophthora spp. on this ornamental plant may complicate P. ramorum field detection during inspections and laboratory confirmations as established by quarantine regulations. References: (1) D. C. Erwin and O. K. Ribeiro. Morphology and Identification of Phytophthora Species. Pages 96-144 in: Phytophthora Diseases Worldwide. The American Phytopathological Society, St. Paul, MN, 1996. (2) W. W. P. Gerlach et al. Phytopathology 64:1368, 1974. (3) P. W. Tooley et al. Plant Dis. 88:993, 2004.

Effects of Phosphonate and Mefenoxam Treatments on Development of Perennial Cankers Caused by Two Phytophthora spp. on Almond

Orchard experiments were conducted to evaluate chemical treatments for management of perennial cankers caused by Phytophthora cactorum and P. citricola on almond (Prunus dulcis) in the San Joaquin Valley of California. Single preventive foliar sprays with phosphonate were tested by wounding and inoculating tree trunks and branches with either pathogen at time intervals from 15 days to 5 months after spraying. One to 3 months after inoculation, resulting cankers were measured. Preventive foliar sprays with phosphonate in the fall or spring suppressed development of cankers for up to 5 months after treatment; mean canker lengths on the trees sprayed with phosphonate before inoculation were 22 to 98% smaller than those on trees that received no phosphonate. In subsequent tests, preventive chemigation with phosphonate in spring or summer also inhibited canker expansion. A curative topical treatment with either fosetyl-Al or mefenoxam on cankers caused by P. cactorum or P. citricola reduced canker expansion by 36 to 88%. Neither preventive nor therapeutic treatments eradicated the pathogens from the diseased tissues, but disease ratings made 1 year after the treatments indicated extended disease suppression. Phosphonate and mefenoxam treatments can effectively manage almond scion cankers caused by P. cactorum or P. citricola.

Comparison of Drip and Sprinkler Irrigation Systems for Applying Metam Sodium and Managing Stem Rot on Potato

Drip and sprinkler systems were compared for effectiveness as preplant metam sodium chemigation systems and conduciveness to late-season development of stem rot disease on potato. Sclerotia of Sclerotium rolfsii were used in a bioassay to test efficacy of metam sodium treatments. Drip application of metam sodium (532 liters/ha, 32.8% a.i.) through lines at 7 cm of depth in preformed beds (depths from bed top unless stated otherwise) killed all test sclerotia at 15-, 30-, or 46-cm depths. Drip application of the metam sodium through drip lines at 41 or 46 cm of depth resulted in 0 to 17 or 68 to 80% survival, respectively, of test sclerotia at 15 cm of depth; but all the sclerotia at 30 or 46 cm of depth were killed. Compared with the drip applications, sprinkler chemigation with metam sodium generally treated beds less effectively (8 to 100% of sclerotia survived at 15 cm, 62 to 100% at 30 or 46 cm). On flat ground, drip and sprinkler chemigation (metam sodium, 560 liters/ha) performed equally (4, 37, and 77% survival at 15-, 45-, and 75-cm depths, respectively). After potato planting and artificial soil infestation with S. rolfsii (5 to 6 weeks before harvest), subsurface drip-irrigated plots (line depth of 41 or 46 cm) had lower incidence of stem rot disease at harvest (13 to 23% on tubers) than that in sprinkler plots (56 to 62%). The low incidence of disease was associated with relatively dry surface soil. Subsurface drip chemigation with metam sodium in preformed plant beds does not consistently eradicate S. rolfsii sclerotia near the upper bed surface but, in an arid climate, it is less conducive than sprinkler irrigation to development of stem rot disease of potato.

Lethal Cankers Caused by Phytophthora spp. in Almond Scions: Specific Etiology and Potential Inoculum Sources

Etiology of a new lethal canker syndrome of almond trees was investigated in the San Joaquin Valley of California. Phytophthora citricola was isolated most frequently from cankers limited to the aboveground scion portions of trees; whereas P. cactorum usually was isolated from cankers originating at or below the soil surface. Repeated observations and isolations indicated that some of the cankers associated with each species were perennial. In pathogenicity tests, isolates of P. cactorum and P. citricola caused bark cankers in excised segments of almond shoots and branches, as well as root and crown rot on potted almond seedlings. Only P. citricola caused significant disease in root and crown tissues of peach seedlings. When pear fruits and almond seedlings were used as bait, P. cactorum and P. citricola were isolated from orchard soil, debris collected in natural depressions where scaffold branches and the tree trunk joined at a common point, and debris deposited on tree surfaces during nut harvest. Control strategies for Phytophthora diseases of almond should consider aboveground as well as belowground modes of attack by P. citricola and P. cactorum. Debris infested with these pathogens and deposited on trees during harvest may play a role in the disease epidemiology.