First Report of Phytophthora parsiana Causing Crown and Root Rot on Guayule in the United States

Guayule (Parthenium argentatum A. Gray) is a perennial shrub plant (approximately 50 cm in height) cultivated in the southwestern United States. It produces natural low-allergenic latex, resins and high-energy biofuel feedstock. During August 2021, a crown and root rot disease was observed on 2-year-old plants of direct-seeded guayule cultivar ‘Az 2’ in research plots located in Pinal county, Arizona, where a record 36 cm of rainfall fell during monsoon season. Symptoms included yellowing of leaves, wilting, and plant death. Average disease incidence was 16%. Isolation from necrotic crown and root tissues on 10% clarified V8-PARP (Jeffers and Martin 1986) yielded Phytophthora-like colonies. Three isolates were subcultured on V8 agar and chlamydospores and hyphal swellings were abundant in 2-week-old cultures. All three isolates produced abundant noncaducous and nonpapillate sporangia ranging from 33 to 54 μm × 20 to 39 μm (average 45.5 × 28.5 μm, n = 20) in soil water extract solution. Isolates did not produce oospores after 2 weeks on carrot agar at 20°C in the dark. Isolates had optimum vegetative growth at 30 oC and grew well at 35 oC. There was no growth at 5 and 40 oC. Genomic DNA was extracted from the mycelia of three isolates using DNeasy Plant Pro Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. The internal transcribed spacer (ITS) region of rDNA, mitochondrially encoded cytochrome c oxidase 1 (cox 1) gene, and beta-tubulin (β-tub) gene were amplified with primers ITS1/ITS4 (White et al., 1990), COXF4N/COXR4N and TUBUF2/TUBUR1 (Kroon et al., 2004) and the resulting 3 amplicons were sequenced (GenBank Accession No. OK438221, OK484426, and OK484427). A BLASTn search of 811-bp amplicon (OK438221) revealed 99% match (762/766) with ITS sequences MG865562 which was Phytophthora parsiana Ex-type CPHST BL 47 from Iran. BLAST analysis of the 867-bp amplicon (OK484427) showed 99% identity (866/867) with the COX 1 sequence of P. parsiana (KC733455) from Virginia. BLAST analysis of the 941-bp amplicon (OK484426) showed 99% identity (928/938) with the β-tub sequence of P. parsiana (AY659746). To fulfill Koch’s postulates, pathogenicity tests were conducted twice on 2-week-old ‘Az 2’ guayule seedlings grown in 10 plants per 1.9-liter pot filled with a steam-disinfested potting mix. Pots were placed in a plastic container and watered three times a week by flooding, to create waterlogged conditions. Plants were maintained in a greenhouse with 12 h day/12 h night (15-28 oC) and fertilized weekly with a 20-20-20 fertilizer at 1mg/ml. Fifty plants in 5 pots were challenged with a P. parsiana isolate by drenching each pot with 50 ml of a 1×105 zoospore/ml suspension. Fifty plants in 5 pots, serving as a control, received each 50 ml of distilled water. Symptoms of wilting, root rot, and plant death were observed 1 week afterward in inoculated plants, whereas control plants remained asymptomatic. P. parsiana was reisolated from necrotic roots of inoculated plants but not from control plants. To our knowledge, this is the first report of crown and root rot in guayule caused by P. parsiana in Arizona. P. parsiana is a species known for causing root rot on woody plants such as pistachio in California (Fichtner et al., 2016) and Iran (Mostowfizadeh-Ghalamfarsa et al., 2008). Arizona is home of desert woody guayule plant. P. parsiana may represent a significant barrier to commercialization of guayule for rubber in low desert areas of Arizona. The origin, distribution, and virulence of the pathogen on Arizona guayule is currently unknown. Disease resistance evaluation may help identify resistance in guayule germplasm that are useful in breeding for resistant cultivars.

Development of an SNP Assay for Marker-Assisted Selection of Soil-Borne Rhizoctonia Solani AG-2-2-IIIB Resistance in Sugar Beet

Rhizoctonia solani, causing Rhizoctonia crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs. We report the identification of a single-nucleotide polymorphism (SNP) marker linked to Rhizoctonia resistance using restriction site-associated DNA (RAD) sequencing of two geographically discrete sets of plant materials with different degrees of resistance/susceptibility to enable a wider selection of superior genotypes. The variant calling pipeline utilized SAMtools for variant calling and the resulting raw SNPs from RAD sequencing (15,988 and 22,439 SNPs) were able to explain 13.40% and 25.45% of the phenotypic variation in the two sets of material from different sources of origin, respectively. An association analysis was carried out independently on both the datasets and mutually occurring significant SNPs were filtered depending on their contribution to the phenotype using principal component analysis (PCA) biplots. To provide a ready-to-use marker for the breeding community, a systematic molecular validation of significant SNPs distributed across the genome was undertaken to combine high-resolution melting, Sanger sequencing, and rhAmp SNP genotyping. We report that RsBv1 located on Chromosome 6 (9000093 bp) is significantly associated with Rhizoctonia resistance (p < 0.01) and able to explain 10% of the phenotypic disease variance. The related SNP assay is thus ready for marker-assisted selection in sugar beet breeding for Rhizoctonia resistance.

First report of Pythium aphanidermatum causing crown and root rot on industrial hemp in China

In July 2020, symptoms of crown and root rot were observed on about 10% of 4-month-old plants of industrial hemp Cannabis sativa cultivar Yunma-1 in Weifang City, Shandong Province in eastern China (Fig 1). During this month, the local temperature ranged from 19-32°C, and the total precipitation was 148mm. The disease symptoms included leaf chlorosis, crown and root rot, stunted growth, and wilting (Figs. 1 and 2). The diseased stem and root tissues were collected and cut into fragments of 0.5cm each. The fragments were surface-sterilized by dipping into 1% NaClO for 1 min, rinsed in sterile water and plated on potato dextrose agar (PDA) and on oomycetes-selective medium PARP (Jeffers and Martin 1986). The plates were incubated at 25°C in the dark for 3 days and 18 total single-hyphal purified isolates were obtained for further analyses with 8 from PDA and 10 from PARP. The colonies of all 18 isolates were white, had abundant aerial hyphae, and were cottony in appearance, resembling Pythium spp (Watanabe 2002). The grass-leaf method (Van Der Plaats-Niterink 1981) induced their sexual reproduction. The size and shape of hyphae, oogonia, antheridia, and oospores were all consistent with those of Pythium aphanidermatum (Fig 3). DNA was extracted from three isolates and their internal transcribed spacer (ITS) regions of rDNA were amplified and sequenced using the primers ITS1/ITS4 (White et al. 1990). The ITS sequences of all three isolates were identical to each other (GenBank accession OK091124.1) and showed a 100% query coverage and 99.88% nucleotide sequence identity with that of type strain of P. aphanidermatum (GenBank accession AY598622.2). Pathogenicity tests were performed with three isolates on hemp cultivar B1. Sterile substrates were prepared in 2L-pots containing peat soil and vermiculite in a 2:1 ratio, with test hemp plants grown from rooted stem cuttings. Plants were kept in a greenhouse at 22 to 27°C under 16 h photoperiod, watered every two days (about 200ml each time) and supplied commercial nutrient solution once a week. A month after transplanting to pots, a wound of 1 mm deep and 10 mm long (made by a sterilized needle) on the surface of the root crown area of the main stem was inoculated with an 8-mm-diameter agar disk of mycelia grown on PDA for 4 days. Six plants were tested for each isolate and three plants were inoculated with sterile agar medium without mycelia as negative controls. The experiment was repeated twice. After one month, plants inoculated with P. aphanidermatum isolates showed the same disease symptoms as observed on field plants while all negative control plants remained disease-free. P. aphanidermatum was reisolated from the diseased tissue and confirmed to be identical to those inoculated based on ITS sequencing and colony morphology. To our knowledge, this is the first report of P. aphanidermatum causing crown and root rot on hemp in China. With an estimated 66,700 hectares hemp cultivation in China producing over US$1 billion worth of hemp fiber (McGrath 2020), this pathogen represents a serious threat to the hemp industry. This pathogen has been reported on hemp in the US and Canada (Beckerman et al. 2017; Punja et al. 2018). The origin of P. aphanidermatum on hemp in China and its relationship to those in North America remain to be examined.

Identification and characterization of Phytophthora species associated with crown and root rot of pistachio trees in California.

Pistachio is one of the most widely cultivated nut crops in California with approximately 115,000 hectares of bearing pistachio trees. In recent years, several orchards were identified with declining trees leading to substantial tree losses. Symptoms included trees with poor vigor, yellowing and wilting of leaves, crown rot and profuse gumming on the lower portion of trunks. Thirty-seven Phytophthora-like isolates were obtained from crown rot tissues in the rootstock of grafted pistachio trees and characterized by means of multi-locus phylogeny comprising ITS rDNA, beta-tubulin and mt cox1 sequence data. The analysis provided strong support for the delineation and identification of three Phytophthora species associated with declining pistachio trees, including Phytophthora niederhauserii, P. mediterranea and P. taxon walnut. Pathogenicity studies in potted UCBI rootstocks (clonal and seeded) confirmed that all three Phytophthora species can cause crown and root rot of pistachio, thus fulfilling Koch’s postulates. The widespread occurrence of Phytophthora crown rot in recently planted pistachio orchards and the high susceptibility of UCBI rootstocks suggest this disease constitute an emerging new threat to the pistachio industry of California. To the best of our knowledge, this study is the first to report P. niederhauserii, P. mediterranea and P. taxon walnut as causal agents of crown and root rots of pistachio.

Phylogeny and Pathogenicity of Phytophthora Species Associated with Artichoke Crown and Root Rot and Description of Phytophthora marrasii sp. nov.

Field surveys conducted on nine farms over a 2-year period showed the widespread presence of Phytophthora-related diseases on globe artichoke plants in the main growing area in Sardinia (Italy). Characteristic symptoms included wilting and necrosis of the outermost leaves and dark brown discoloration of stem tissues, as well as root rot. A total of 18 Phytophthora colonies belonging to three species were isolated and characterized. Based on morphological features and ITS sequence data, Phytophthora isolates were identified as P. crassamura (eight isolates) and P. cactorum (four isolates). Six isolates could not be assigned to any formally described species of Phytophthora and are therefore described here as Phytophthora marrasii sp. nov. The ITS phylogeny places P. marrasii in a terminal clade basal to the sister taxa (P. foliorum, P. hibernalis, P. lateralis, and P. ramorum) of the clade 8c. In particular, P. marrasii is phylogenetically related to P. foliorum, a species from which it differs in 62 nucleotides in the ITS region. At the same time, it can easily be distinguished morphologically from P. foliorum mainly because of the low minimum temperature for growth, the bigger and persistent non-papillate sporangia, and smaller oogonia. Pathogenicity tests confirmed that all three Phytophthora species are pathogenic on globe artichokes, which represent a new host for these pathogens.

Morphological and Molecular Characteristics of Fungal Species Associated with Crown Rot of Strawberry in South Korea

Crown and root rot is the most important and destructive strawberry diseases in Korea as it causessubstantial economic loss. In August 2020, a severe outbreak of crown and root rot on strawberries (Fragaria×ananassa Duch.) was observed in the greenhouse at Sangju, South Korea. Infected plantlets displayed browning rot within the crown and root, stunted growth, and poor rooting. Thirty fungal isolates were procured from the affected plantlet. Isolates were identified based on morphological characteristics and pathogenicity test as well as sequence data obtained from internal transcribed spacer, large subunit ribosomal ribonucleic acid, translation elongation factor,and RNA polymerase Ⅱ-second largest subunit. Results showed that thecrown and root rot of strawberry in Korea was caused by three distinct fungal species:Fusarium oxysporum species complex, F. solani species complex, andPlectosphaerella cucumerina. To the best of our knowledge,F. solani species complex andP. cucumerinaare reported for the first time as the causal agents of the crown and root rot of strawberryin South Korea.Pathogenicity tests confirmed that these isolates are pathogenic to strawberry.Understanding the composition and biology of the pathogen population will be helpful toprovide effectivecontrol strategies for the disease.