Native Rubus Research Articles

Identification and characterization of the causal agent of powdery mildew on native salmonberry and thimbleberry plants in British Columbia

Salmonberry (Rubus spectabilis) and thimbleberry (Rubus nutkanus) are important native berry plants for Indigenous communities and restoration sites in the coastal region of British Columbia (BC). Compared to cultivated berry plants, information on the diseases impacting native berry plant species is limited. In late August 2022, powdery mildew symptoms and signs were observed on field plots of salmonberry and thimbleberry plants at the Agassiz Research and Development Centre, BC. The disease symptoms progressed until the end of September. The morphology of conidiophores and conidia when examined under a compound and scanning electron microscope showed they matched with those of Podosphaera aphanis. DNA from diseased foliage was subjected to PCR amplification with primers representing the internal transcribed spacer (ITS) region of rDNA followed by sequencing. The corresponding sequences from both hosts showed >99% similarity to P. aphanis in GenBank and grouped with several accessions of P. aphanis following phylogenetic analysis. In artificially inoculated trials conducted in the greenhouse, powdery mildew symptoms developed within 3−4 weeks post-inoculation and P. aphanis isolates from salmonberry and thimbleberry were cross-pathogenic to each host. To our knowledge, this is the first study characterizing the powdery mildew pathogen infecting salmonberry and thimbleberry and demonstrating cross-pathogenicity to both hosts. The outcomes from this study provide insight into the biology of the powdery mildew pathogen infecting native Rubus spp.

Comparative Analysis of Complete Chloroplast Genomes of Rubus in China: Hypervariable Regions and Phylogenetic Relationships.

With more than 200 species of native Rubus, China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese Rubus species (including varieties) from three of the eight sections reported in China, i.e., the sections Chamaebatus, Idaeobatus, and Malachobatus. Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 Rubus species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these Rubus plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: trnH-psbA, trnK-rps16, rps16-trnQ-psbK, petN-psbM, trnT-trnL, petA-psbJ, rpl16 intron, ndhF-trnL, and ycf1. Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these Rubus species. All sampled Rubus species formed a monophyletic group; however, sections Idaeobatus and Malachobatus were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within Rubus.

First Report of Gnomoniopsis idaeicola Causing Cane Wilt and Canker in Commercial Blackberry Fields in Oregon.

Oregon is the leading producer of blackberries in the United States (USDA 2021). In November 2020, we visited a seven-year-old, 5.6 HA field of thornless trailing cultivar 'Columbia Star' in Marion County, Oregon in response to grower reports of rapid plant death that they called 'Blackberry Collapse.' The pattern of disease in the field was semi-circular patches of dead plants. We estimate that ca. 17% of the plants were killed. Symptoms included fewer and stunted primocanes, floricane reddening, premature floricane senescence, or elliptical or irregular brown to purple cane lesions often near the base of necrotic petioles clasping the cane. Twenty-two cane lesions were collected, surface-disinfested, and placed on potato dextrose agar with streptomycin. In addition to common Rubus cane pathogens (Kalmusia coniothyrium, Botrytis spp., Diaporthe spp., and Seimatosporium lichenicola), Gnomoniopsis idaeicola was isolated from 23% of the samples. After isolation of G. idaeicola from 'Columbia Star', we also isolated the pathogen from symptomatic 'Black Diamond' blackberry in fields in Washington and Linn Counties in Oregon. G. idaeicola grew as white- to cream-colored circular colonies on the agar surface with sparse to dense aerial hyphae. Some isolates produced cream-colored exudate from irregular conidiomata. Conidia were single-celled, hyaline, oval to ellipsoid, and ranged from 4.9 to 6.9 µm long and 1.2 to 2.5 µm wide (n = 100). Perithecia and ascospores were not seen on canes or in culture; molecular methods were used to identify the fungus. Genomic DNA was extracted from nine isolates and β-tubulin, ITS region, and tef-1α were amplified using the primers and conditions described by Walker et al. (2010). Amplicons were Sanger sequenced in both directions by the Core Facilities of the Center for Quantitative Life Sciences of Oregon State University, Corvallis, OR. Sequences were deposited in GenBank (β-tubulin OK539758-OK539766; ITS OK348854-OK348862; tef-1α OK539767-OK539775). β-tubulin sequences (737 bp) were 100% identical to sequence of G. idaeicola from Rubus procerus, Oregon (GU320783). ITS sequences (518 bp) were 99.2 to 100% identical to G. idaeicola CBS125674T (GU320796). tef-1α sequences (860 bp) were 99.9 to 100% identical with reference sequences of G. idaeicola. Phylogenetic analyses of concatenated sequences using Tamura-Nei neighbor-joining (Tamura et al. 2004) confirmed identity. Pathogenicity of G. idaeicola isolates was tested in repeated experiments on four to five detached 'Black Diamond' primocanes and potted 'Columbia Star' plants with 4 mm hyphal plugs placed on fresh wounds and wrapped in parafilm; controls were treated with sterile agar plugs (Ellis et al. 1984; Stevanović et al. 2019). By 14 days, in each experiment, expanding necrotic lesions were observed on canes inoculated with G. idaeicola, but not with sterile agar plugs. ITS-sequence of fungi isolated from lesions confirmed identity as G. idaeicola, fulfilling Koch's postulate. G. idaeicola was described as a new species by Walker et al. (2010) from perithecia collected from wild Rubus spp. in the Pacific Northwest. Despite its presence on native Rubus, G. idaeicola has not been reported in commercial blackberry fields in OR. Stevanović et al. (2019) identified G. idaeicola as an important pathogen causing canker, wilt, and death of blackberry in Serbia. Surveys of Oregon blackberry fields for G. idaeicola are ongoing, along with research on the epidemiology and management of this emerging pathogen.

Surviving or thriving? Trade-offs between growth, defense, and reproduction in a native versus an invasive Rubus

Little is known about limits to reproduction in plants, especially as to how their other life history functions (growth and defense) may constrain reproductive investment. Understanding these constraints can help researchers refine best practices for cultivating species like Rubus (Rosaceae) that produce nutritious fruits as well as for controlling invasive species. Here, we sought to elucidate potential trade-offs between growth, defense, and reproduction in native Rubus allegheniensis Porter (common blackberry) and invasive Rubus phoenicolasius Maxim. (wineberry) while accounting for the effects of varying insect herbivory and resource availability levels. We observed traits related to physical defense (e.g., prickle intensity), growth (e.g., cane length), and floral reproduction (e.g., ripe fruits), as well as carbon availability (e.g., canopy cover). We then used multiple regressions to characterize relationships between these variables for both species. We found potential evidence for 2 induced defenses in the invasive wineberry. Also, 5 models returned significant results indicative of trade-offs between reproduction and growth, reproduction and defense, and defense and growth in a single or both species. Our results highlight the importance of understanding the defensive strategies utilized by these species because inducible defenses may result in trade-offs that could reduce yields and (or) increase the invasive potential of Rubus species.

North American species of Rubus L. (Rosaceae) described from European botanical gardens (1789-1823)

Native Rubus were brought from North America to European botanical gardens in the 18th and early 19th centuries, and some were described as new species. Limited knowledge of Rubus in that era, typically combined with brief descriptions, led to many incorrect interpretations, causing much confusion (especially in North America). We established a project to clarify the identity of these confusing species by reviewing types and descriptions along with comparative work involving modern collections. We identified seven putative North American Rubus species named from early European garden collections: R. villosus Aiton, R. vulpinus Poir., R. pensilvanicus Poir., R. flagellaris Willd., R. inermis Willd., R. heterophyllus Willd., and R. argutus Link, and four other names in the early European botanical literature of possible North American origin: R. decumbens Thunb., R. inermis Thunb., R. enslenii Tratt., and R. floridus Tratt. We affirmed the current applications of R. flagellaris, R. argutus, and R. enslenii. Rubus villosus is identical with R. leviculus L.H. Bailey, while the taxon to which R. villosus was generally applied in the 19th century, R. allegheniensis Porter, appears to be identical with R. vulpinus. Rubus heterophyllus Willd. was identified as an earlier name for R. plicatifolius Blanch. Rubus inermis Willd. is identical with R. ulmifolius Schott and must have originated in the Old World. Thunberg's other American Rubus, R. decumbens, can be identified as R. arundelanus Blanch. Rubus floridus remains a puzzle. If its type represents a sample of a determinate flowering branch from a large, mounding dewberry, it is closest to R. grimesii L.H. Bailey, but it could also have been taken from a side-branch from an unknown upright blackberry. Another name for which identity could not be definitively established is R. pensilvanicus. It is allied with R. allegheniensis, but its type is insufficient to determine if it is an extreme form of that species, a related taxon, or a hybrid of it with a species of section Arguti (Rydb.) L.H. Bailey. We propose the name, R. revealii sp. nov. for the corymbose to weakly racemose Arguti previously considered as R. pensilvanicus sensu L.H. Bailey. Herein, we lectotypify R. abactus L.H. Bailey, R. arundelanus, R. decumbens, R. grimesii, R. inermis Thunb., R. invisus (L.H. Bailey) Britton, and R. vulpinus, and designate neotypes for R. argutus and R. heterophyllus.

Diversity of Plants in Thickets of Invasive Sorbaria sorbifolia: Differences in the Effect on Aboveground Vegetation and Seed Bank

The diversity of aboveground vegetation of the herb–dwarf shrub layer and seedlings from the soil seed bank in the thickets of invasive shrub Sorbaria sorbifolia was evaluated in urbanized forests of the city of Yekaterinburg (the Middle Urals, Russia). Geobotanical releves and identification of seedlings from the soil seed bank were performed in different forest communities: thickets of invasive S. sorbifolia, thickets of native Rubus idaeus, and in forest communities without S. sorbifolia and R. idaeus. The effect observed in the presence of S. sorbifolia was as follows: the abundance of aboveground vegetation in the herb–dwarf shrub layer was lower by a factor of 10–20 or more; the taxonomic richness of the herb–dwarf shrub layer in the releve (α-diversity), by a factor of 6–8; and the total number of species recorded in the community group (γ-diversity), by a factor of 3. The disappearance of species under S. sorbifolia was selective. Relatively light-loving and relatively dry-loving species disappeared first, while more shade-loving and moisture-loving species were relatively resistant. The taxonomic richness and abundance of seedlings from the soil seed bank did not change depending on the abundance of S. sorbifolia. Approximately half of the identified seedling taxa were typical forest plants, while the others were only specific for the seed bank and did not occur in the vegetative state. It is concluded that the influence of S. sorbifolia on the vegetation of subordinate layers is due primarily to the direct competitive and habitat-transforming effect of the living S. sorbifolia phytomass.

Ecological implications of the replacement of native plant species in riparian systems: unexpected effects of Reynoutria japonica Houtt. leaf litter

In European rivers, one of the most invasive of terrestrial plant species, Reynoutria japonica Houtt. (Polygonaceae), is frequently found at the water-land interface. In this study, ecological effects of native species replacement by this invasive species was explored. In particular, we examined changes in leaf litter composition, and the subsequent impacts of their decomposition on riparian and in-stream plant community growth. We compared leaf litter from two riparian species, native Rubus fruticosus L. agg. (Rosaceae) and its spontaneous substitute along river corridors, R. japonica. Effects were assessed through phytotoxicity tests on (1) a terrestrial model plant species, the lettuce Lactuca sativa var. capitata L. (Asteraceae) and (2) a typical semi-aquatic riparian plant species growing in the same riparian zone, the watercress Nasturtium officinale R.Br. (Brassicaceae). Seedling root length measurement permitted calculation of a root length reduction index. The experiment was performed over a six-month decomposition period, with samples taken at five time intervals. Phytotoxic abilities of R. japonica were inconsistent over the decomposition period, leading to breaks in the regulatory processes of the structuring native species, R. fruticosus. Decomposition of R. japonica leaf litter led to the unexpected emergence of successive competition and facilitation interactions. This study showed distinct phytotoxic impacts from R. japonica leaf litter decomposition, causing ecological effects that differed from that of native species. In a context where R. japonica progressively replaces native riparian species, such impacts need to be considered further as R. japonica phytotoxicity does not steadily prevent other species with offset phenologies to establish, including invasive species.

The effect of multiple contamination of soil on LMW and MMW PAHs accumulation in the roots of Rubus fruticosus L. naturally growing near The Copper Mining and Smelting Complex Bor (East Serbia).

Samples of roots and spatial soils of native Rubus fruticosus L. were collected from the spots positioned at different distances from the copper smelter and city heating plants in the industrial zone of the town of Bor (Serbia) and subjected to chemical analyses in order to determine the content of several heavy metals, and 15 priority polycyclic aromatic hydrocarbons (PAHs). In this study, the results for 9 low and medium molecular weight PAHs (LMW and MMW PAHs) are represented and processed using the calculation of bio-concentration factors and statistical methods such as hierarchical cluster analysis and Pearson's correlation study with the aim of investigating the plant capabilities for their uptake from the soil and later accumulation into the root tissue, under the hostile circumstances of multiple contamination. The obtained data revealed different accumulation rates for the investigated PAHs and showed that in several cases, the contents of root PAHs were under the strong influence of present contaminants such as soil copper and some soil PAHs, indicating at the same time that R. fruticosus can regulate the processes of LMW and MMW PAHs extraction/accumulation using different mechanisms, depending on the existing environmental circumstances. The used mechanisms could be exploited in phytoremediation methods based not only on the extraction and concentration of PAHs in plant roots but also on PAH degradation or stabilization in the soil. Also, the results of this study confirmed that, except in the case of naphthalene and fluoranthene, there was no PAH pollution, which originated solely from the industrial zone.

Leaf Litter Decomposition of Nonnative Shrub Species in Nonnative and Native Shrub Environments: A Field Experiment with Three Rosaceae Shrubs

AbstractInvasion by nonnative plants may have ecosystem-wide effects, altering the decomposition rate of plant material via changes in litter quality or altered environment (abiotic conditions, associated biotic community), or both. Yet, the relative importance of these factors for decomposition rates is not clear. We studied decomposition using the leaves of related shrub species (nonnative Sorbaria sorbifolia and Rosa rugosa, native Rubus idaeus) with comparable physiognomy but different leaf characteristics and origin (alien vs. native) in patches formed by S. sorbifolia and Rubus idaeus in southwestern Finland. Decomposition of cellulose in the topsoils of the patches was also studied. Using litter bags, we found that S. sorbifolia leaf litter decomposed slowest and Rosa rugosa leaves fastest irrespective of patch type. Topsoils in S. sorbifolia patches were richer in carbon, nitrogen, and calcium than those of Rubus idaeus, but these differences did not affect decomposition rates. Very little decomposition appeared to happen during the winter but during the summer, microclimate had minor but significant effects on decomposition rates. Our results highlight the key role of litter source in the decomposition of plant material. Between-patch differences in abiotic conditions appear to play a minor role relative to litter quality.

Genetic diversity in the invasive Rubus phoenicolasius as compared to the native Rubus argutus using inter-simple sequence repeat (ISSR) markers

Invasive species are one of most significant factors in human-influenced global change. Management actions that prevent the spread and impacts of invasive species require knowledge of their ecological and genetic characteristics. The genetic characteristics of the invasive wine raspberry, Rubus phoenicolasius Maxim. (Rosaceae) and the native sawtooth blackberry, Rubus argutus Link, were examined in two forest habitats on the Maryland Coastal Plain. Using inter-simple sequence repeat (ISSR) markers we quantified the genetic diversity of both species. We analyzed genetic diversity using analysis of molecular variance (AMOVA) and found less genetic diversity in the invasive species, R. phoenicolasius, with variation between sites was 0.418 between sites and 0.075 within sites as compared to the native, R. argutus, where the variation between sites was 1.538 and 0.370 within sites. The lower genetic diversity in the invasive may be due to a history of limited introductions or frequent self-fertilization and clonal reproduction.

First Report of Black raspberry necrosis virus in Rubus canadensis in Tennessee.

Symptoms that resembled virus infection were observed on several smooth blackberry (Rubus canadensis L.) plants in the Great Smoky Mountain National Park (GSMNP) during a project carried out in the summer and fall of 2006 as part of All Taxa Biodiversity Inventory (ATBI) activities (2). Diseased specimens showed chlorosis and mottling as well as deformation of younger leaves. Symptomatic leaves were collected, and preliminary screening by double-antibody sandwich (DAS)-ELISA did not detect Tobacco ringspot virus (TRSV), Tomato ringspot virus (ToRSV), Tomato spotted wilt virus (TSWV), Raspberry bushy dwarf virus (RBDV), or Impatiens necrotic spot virus (INSV) in these samples. Double-stranded RNA (dsRNA) extracted from symptomatic leaves of two diseased specimens (GSM-1 and GSM-2) revealed two bands with sizes estimated at 7.5 and 6.5 kb. Purified dsRNAs from specimen GSM-1 were used as a template to generate random-primed cDNA clones. Several clones were sequenced and analysis of approximately 3 kb of contiguous sequence (GenBank Accession No. EU419645) revealed the presence of a single open reading frame encoding a protein containing the complete proteinase and partial polymerase domains. BLAST analysis showed that the virus from R. canadensis shared 77 and 87% nucleotide and amino acid sequence identity, respectively, with the recently described putative sadwavirus Black raspberry necrosis virus (BRNV) (GenBank Accession No. NC_008182) (1), suggesting that this virus is a distinct isolate of BRNV. The virus shared a lower degree of identity with the analogous sequences of other viruses belonging to the genus Sadwavirus, with only 48 and 37% identity with Strawberry mottle virus (GenBank Accession No. NC_003445) and Satsuma dwarf virus (GenBank Accession No. NC_003785), respectively. To our knowledge, this is the first report of BRNV in GSMNP and Tennessee, indicating that it may be widespread in native Rubus spp. through the southeastern United States.

Brambles: Downy mildew on wild and cultivatedRubusspecies in New Zealand

Abstract Eight wild blackberries, three native Rubus species, and nine Rubus cultivars were surveyed for natural infection with downy mildew (Peronspora sparsa Berk.) in the northern South Island of New Zealand. Most plants were found to be susceptible to infection. ‘Boysenberry’, ‘Youngberry’ and R. cissburiensis fruits and foliage where extremely susceptible. No infection was found on R. echinatus. For field management of bramble crops, wild blackberries (especially R. cissburiensis,) should be eliminated as a source of infection. Development of new disease-resistant cultivars to replace ‘Boysenberry’ and ‘Youngberry’ will make this source of infection from wild blackberries less important.