Integration of Rubus yellow net virus in the raspberry genome: A story centuries in the making.

Rubus yellow net virus (RYNV) belongs to genus Badnavirus. Badnaviruses are found in plants as endogenous, inactive or activatable sequences, and/or in episomal (infectious and active) forms. To assess the state of RYNV in Rubus germplasm, we sequenced the genomes of various cultivars and mined eight raspberry whole genome datasets. Bioinformatics analysis revealed the presence of a diverse array of endogenous RYNV (endoRYNV) sequences that differ significantly in their structure; some lineages have nearly complete, yet non-functional genomes whereas others have rudimentary, short sequence fragments. We developed assays to genotype the main lineages as well as the only known episomal lineage present in the United States. This study discloses the widespread presence of endoRYNVs in commercial raspberries, likely because breeding efforts have focused on a limited pool of germplasm that harbored endoRYNVs.

First Report of Berkeleyomyces basicola Causing Black Shoot Rot of Raspberry in Nursery Production in the United States and Worldwide.

Commercial production of raspberry (Rubus ideaus) transplants is almost exclusively accomplished through clonal propagation. One system involves forcing young shoots to grow from roots. The shoots are cut and rooted in propagation trays and referred to as tray plants. Sanitation is important during tray plant production as this method carries some risk due to contamination by substrate pathogens. In May 2021, a new disease was observed on raspberry tray plant cuttings at one nursery location in California, and observed again in 2022 and 2023 but at a much lesser extent. Multiple cultivars were affected; however, up to 70% mortality was observed on cv. RH740.1. In less affected cultivars, mortality ranged from 5-20%. Symptoms included chlorotic leaves, lack of rooting, and blackening at the basal end of shoots, followed by death of the cutting. Affected propagation trays had inconsistent foliage and patchy growth. Chains of chlamydospores (two to eight spores in each chain) similar in morphology to Thielaviopsis species (Shew and Meyer 1992) were observed at the cut end of symptomatic tray plants using a microscope. Isolates were retrieved by incubating tissue on surface-disinfested (1% NaOCl) carrot discs in a humid chamber for 5 days until greyish black mycelium was observed (Yarwood 1946). Mycelium was transferred to acidified potato dextrose agar and formed a gray to black compact mycelial colony with both endoconidia and chlamydospores. Endoconidia were catenulate, single-celled with slightly rounded ends, colorless, and 10-20 µm x 3-5 µm in size; dark-colored chlamydospores were 10-15 µm x 5-8 µm in size. The ITS region of isolates 21-006 and 22-024 was amplified with ITS5 and ITS4 primers using a 48°C annealing temperature (White et al. 1990), Sanger sequenced (GenBank accession OQ359100) and yielded 100% match to Berkeleyomyces basicola accession MH855452. Pathogenicity was confirmed by dipping 80 grams of roots of cv. RH740.1 into a suspension of 106 conidia/mL of isolate 21-006 for 15 min. For the non-inoculated control, 80 grams of roots were dipped in water. Roots were then planted into trays of coir (Berger, Watsonville, CA). Six weeks after inoculation, twenty-four shoots were harvested from each treatment, stuck into propagation trays filled with coir and maintained in a humid chamber for 14-days to induce rooting. Tray plants were then harvested and assessed for root development, black basal shoot tips, and presence of chlamydospores. Forty-two percent of cuttings from the inoculated treatment had rotten basal tips and failed to root, in comparison to 8% of the cuttings from the non-inoculated control. Chlamydospores were visualized only on shoots that emerged from inoculated roots and B. basicola was isolated only from cuttings originating from inoculated roots. Post-inoculation isolates were confirmed as B. basicola using methods described above. To our knowledge, this is the first report of B. basicola infecting raspberry. Confirmation of this pathogen on tray plants is significant because of the potential impact this disease may have in commercial nursery production worldwide. In 2021, the value of the harvested raspberry crop in the U.S. totaled $531 M, of which California represented $421 M (USDA 2022). The value of the 2021 crop was highest in the U.S. ($531 M), followed by Russia ($512 M), Spain ($405 M) and Mexico ($332 M) (FAO 2021).