Genetic control of the reactions of raspberry to black raspberry necrosis, raspberry leaf mottle and raspberry leaf spot viruses

Black raspberry necrosis virus (BRNV) induces a severe apical necrosis in black raspberry (Rubus occidentalis) but fails to induce diagnostic symptoms in red raspberry. However, BRNV infection of F₁, F₂ and F₃ hybrids from the cross black raspberry × red raspberry induced mosaic symptoms of varying intensity but no typical apical necrosis. In a survey of 28 red raspberry cultivars, a few developed severe angular chlorotic leaf spots when infected with raspberry leaf mottle virus and a few others did so when infected with raspberry leaf spot virus. These reactions were determined by single dominant genes designated Lm and Ls respectively. The value of the different host reactions for controlling the effects and spread of these viruses is discussed.     

Rubus host range of rubus yellow net virus and its involvement with other aphid-borne latent viruses in inducing raspberry veinbanding mosaic disease

After graft inoculation with rubus yellow net virus (RYNV), 12 of 34 Rubus species and cultivars developed noticeable symptoms. R. macraei developed the most conspicuous symptoms and is recommended as an improved indicator plant. In attempts to determine the cause of raspberry veinbanding mosaic, a disease in which RYNV is involved, several European and North American red raspberry cvs were graft-inoculated with RYNV and three other aphid-borne viruses, black raspberry necrosis (BRNV), raspberry leaf mottle (RLMV) and raspberry leaf spot, singly and in all combinations. In periods of up to 4 yr, classical veinbanding mosaic symptoms developed in sensitive cvs only when they contained both RYNV and RLMV. These symptoms were intensified in plants co-infected with additional viruses. Veinbanding mosaic disease did not develop in any of 11 cvs infected with RYNV + BRNV, the combination of viruses previously assumed to be responsible for this disease in Britain and North America.     

Molecular detection and characterisation of black raspberry necrosis virus and raspberry bushy dwarf virus isolates in wild raspberries

Virus‐derived small interfering RNAs (siRNAs) were extracted from leaves of wild raspberries (Rubus idaeus) sampled from three different regions in Finland and subjected to deep sequencing. Assembly of the siRNA reads to contigs and their comparison to sequences in databases revealed the presence of the bipartite positive‐sense single‐stranded RNA viruses, raspberry bushy dwarf virus (RBDV, genus Idaeovirus), and black raspberry necrosis virus (BRNV, family Secoviridae) in 19 and 26 samples, respectively, including 15 plants coinfected with both viruses. Coverage with siRNA reads [21 and 22 nucleotides (nt)] was higher in BRNV‐FI (Finland) RNA1 (79%) than RNA2 (45%). In RBDV, the coverage of siRNA reads was 89% and 90% for RNA1 and RNA2, respectively. Average depth of coverage was 1.6–4.9 for BRNV and 16.5–36.5 for RBDV. PCR primers designed for RBDV and BRNV based on the contigs were used for screening wild raspberry and a few cultivated raspberry samples from different regions. Furthermore, the sequences of BRNV RNA1 and RNA2 were determined by amplification and sequencing of overlapping contigs (length 1000–1200 nt) except for the 3′ and 5′ ends of RNA1 and RNA2 covered by primers. RNA1 of the Finnish BRNV isolate (BRNV‐FI) was 80% and 86% identical to BRNV‐NA (USA) and BRNV‐Alyth (UK), respectively, whereas the identity of NA and Alyth was 79%. RNA2 of BRNV‐FI was 84% and 80% identical to BRNV‐NA and BRNV‐Alyth, respectively, whereas NA and Alyth were 82% identical. Hence, the strains detected in Finland differ from those reported in the UK and USA. Our results reveal the presence of BRNV in Finland for the first time. The virus is common in wild raspberries and nearly identical isolates are found in cultivated raspberries as well. The results show that wild raspberries in Finland are commonly infected with RBDV or BRNV or both viruses and thus are likely to serve as reservoirs of RBDV and BRNV for cultivated Rubus spp.     

Propagation of black raspberry necrosis virus (BRNV) in mixed culture with solanum nodiflorum mottle virus, and the production and use of BRNV antiserum

The concentration of particles of black raspberry necrosis virus (BRNV), which is normally extremely low in herbaceous plants, increased about 1000-fold when Nicotiana clevelandii plants were inoculated with a mixture of BRNV and an unrelated virus, solanum nodiflorum mottle (SNMV). In sap from N. clevelandii infected with the mixed culture, BRNV infectivity survived dilution to 10?⁴ but not 10?⁵, and storage for 6 but not 8 days at 20 ^oC, for 6 but usually not 10 days at 4 ^oC and for more than 13 days at – 15 ^oC. When plants were inoculated with the mixed culture, BRNV induced typical symptoms in several Chenopodium species and infected several previously unreported hosts. Purified preparations of particles of the mixed culture contained only a small proportion of BRNV particles, which sedimented in sucrose density gradients as two components, one, probably non-infective, of c. 505, and the other, infective, of 120-130S. An antiserum prepared to purified particles of the mixed culture was cross-absorbed with SNMV particles and used in indirect ELISA to detect BRNV in herbaceous plants infected with the mixed culture, and also in a wide range of Rubus species, cultivars and hybrids infected naturally, by grafting or by inoculation with the aphid Amphorophora idaei. The reliability of ELISA for detecting BRNV in raspberry leaves depended on the cultivar and time of year. Some cultivars, such as Glen Clova, had low concentrations of BRNV, which was detected reliably only in late spring/early summer, whereas other cultivars, such as Lloyd George and Mailing Enterprise, had greater BRNV concentrations. In small-scale surveys in eastern Scotland, BRNV was detected by ELISA in many raspberry cvs, including some that contain major gene resistance to the vector, A. idaei; in five of nine raspberry stocks entered for the Standard grade certificate but in none of five stocks entered for the Stock Cane certificate; and in 40% of wild raspberry and 14% of wild bramble plants growing near commercial raspberry crops. The significance of these findings for the control of BRNV is discussed.     

Virus infections reduce in vitro multiplication of ‘Malling Landmark’ raspberry

Summary Virus-infected plants are often symptomless and may be inadvertently used as explant sources in tissue culture research. Our objective was to determine the effect of virus infection on micropropagation. We studied the effects of single and multiple infections of three common raspberry viruses on the in vitro culture of ‘Malling Landmark’ red raspberry (Rubus idaeus L.). Virus-infected reaspberry plants were produced by leaf-graft inoculation from known-infected plants onto virus-free ‘Malling Landmark’. Single-virus source plants were infected with either tobacco streak ilarvirus (TSV), tomato ringspot nepovirus (TomRSV), or raspberry bushy dwarf idaeovirus (RBDV) and were free of other viruses as determined by enzyme-linked immunosorbent assay (ELISA) and bioassay. Virus-free, single, and multiple virus-infected ‘malling Landmark’ explants were initiated into culture and multiplied on Anderson's medium with 8.9 μM N⁶-benzyladenine (BA). At the end of the multiplication tests, ELISA reconfirmed virus infections. In vitro multiplication of ‘Malling Landmark’ was significantly reduced by multiple infections, and multiplication of plants infected with all three viruses (RBDV+TomRSV+TSV) was less than half that of virus free cultures. Shoot height and morphology of in vitro cultures were not influenced by virus infection. The greenhouse stock plant with the three-virus infection was stunted and yellow compared to the control and the other infected plants. Part of a thesis submitted by C.-W.V.T. in partial fulfilment of the requirements for the MS degree. The use of trade names in this publication does not imply endorsement by the U.S. Department of Agriculture or Oregon State University.     

The effect of resistance to Amphorophora rubi in raspberry (Rubus idaeus) on the spread of aphid-borne viruses

The effectiveness of resistance to the aphid Amphorophora rubi in restricting the spread of aphid-borne viruses was assessed in a field experiment using six genotypes of red raspberry. In one block of the experiment, the genotypes alternated with rows of virus-infected Mailing Jewel raspberry, and in the other they alternated with virus-free Mailing Jewel. During 4 years, the numbers of A. rubi and the amount of 52V virus spread in the two blocks were similar, suggesting that this virus was mostly introduced from outside the plots. Lloyd George and Mailing Jewel raspberry became heavily infested with A. rubi and were rapidly infected with raspberry leaf mottle, raspberry leaf spot and 52V viruses. Glen Clova and Norfolk Giant raspberry, which contain minor genes for resistance to A. rubi, were infested with fewer A. rubi and virus spread more slowly in these cultivars. A. rubi were rare on Mailing Orion and an East Mailing raspberry selection (888/49) which have genes A₁ and A₁₀ respectively for resistance to A.rubi, and these plants remained largely free of virus. The role of minor and major gene resistance to A. rubi in restricting virus spread is discussed. A few Macrosiphum euphorbiae and Myzus ornatus were recorded on several of the raspberry genotypes.     

Production and properties of monoclonal antibodies to Solanum nodiflorum mottle sobemovirus

Black raspberry necrosis virus (BRNV) reaches only very low concentrations in herbaceous plants and is difficult to maintain in culture. However, in a mixed culture with an unrelated virus, Solanum nodiflorum mottle (SNMV), in the genus Sobemovirus, the concentration of BRNV particles increases about 1000‐fold. In attempts to produce monoclonal antibodies (MAbs) to BRNV for diagnostic use, purified virus particles from the mixed virus culture were used as immunogen and the resultant antibodies screened against cultures of SNMV alone, BRNV+SNMV and healthy plant extracts. None of the virus‐specific MAbs obtained in this way was specific to BRNV but six were specific to SNMV. Although the original objective was not achieved, the SNMV MAbs were characterised and used to study serological properties of SNMV and other Sobemoviruses. Characterisation of the six SNMV MAbs showed that four were IgG3, one IgG1 and the other IgG2b. SNMV was detected by all six MAbs in ELISA, by five in Western blotting, by three in agarose gel double diffusion tests, but only one was suitable for trapping virus particles in immuno‐electron microscopy (IEM). In Western blotting using virus in sap extracts of Nicotiana clevelandii, each of the five MAbs detected a single major band of Mc. 31 000 in sap containing SNMV, and additional bands of lower mass attributed to degradation of coat protein. In various serological tests, no cross‐reactions were detected between SNMV and seven other viruses from the genus Sobemovirus. However, in IEM but not in Western blotting, significant cross‐reactions were observed between SNMV and Velvet tobacco mottle virus, another species from the genus Sobemovirus. The significance of these different findings is discussed.     

Further studies on the effect of resistance to Amphorophora idaei in raspberry (Rubus idaeus) on the spread of aphid-borne viruses

The rate of spread of viruses transmitted by the aphid Amphorophora idaei into genotypes of raspberry differing in resistance to infestation by A. idaei was studied in a field experiment which exposed plants to large numbers of infective aphids. Under these conditions, genotypes that are readily colonised by A. idaei were totally infected with virus after two to three growing seasons, whereas genotypes with a high degree of resistance were substantially free of virus after four growing seasons but 56% of plants were infected after seven seasons. Genotypes with intermediate resistance were also substantially free of virus after three seasons but 76% of plants were virus infected after seven seasons. The effectiveness of resistance to A. idaei in raspberry in restricting spread of viruses transmitted by this aphid is discussed.     

Detection of Sap-Transmissible Viruses by ELISA in Tissue-Propagated Plants of Red Raspberry during in vitro Culture

Apple mosaic virus and raspberry bushy dwarf virus were detected by ELISA in plantlets of red raspberry still growing in vitro. The plantlets were derived from explants which were excised from plants infected by either of the viruses mentioned. Detection by ELISA of prune dwarf virus in 4-month-old in vitro cultures of sour cherry was reported earlier. Thus, application of ELISA to tissue cultured plants in vitro seems to be an appropriate method for early detection of virus-infected plant cultures.     

Identification of Rubus yellow net virus as a distinct badnavirus and its detection by PCR in Rubus species and in aphids

Rubus yellow net virus (RYNV) infects Rubus species and cultivars worldwide and is an essential component of raspberry veinbanding mosaic (RVBMD), a virus disease complex that causes serious decline in plant vigour and productivity. The virus is transmitted, probably in a semi‐persistent manner, by the large raspberry aphid, Amphorophora idaei in Europe, and A. agathonica in North America. The particles of RYNV are bacilliform in shape and measure 80–150 × 25–30 nm, similar to those of badnaviruses. A1.7 kb fragment of the viral DNA was amplified by PCR and then directly sequenced. Analysis of this sequence suggests that RYNV is possibly a distinct species in the genus Badnavirus and is most closely related to Gooseberry vein banding associated virus (GVBAV) and Spiraea yellow leaf spot virus, two other badnaviruses described recently. Using the sequence derived from the PCR‐amplified viral DNA fragment, RYNV‐specific primers were designed and used in PCR to assay for RYNV in a range of Rubus germplasm infected with RYNV, with other unrelated viruses and virus‐like diseases found in Rubus, and in healthy plants. RYNV was detected in all glasshouse cultures of RYNV‐infected plants, whether alone or in complex infections with other viruses, but not from healthy Rubus plants, nor from plants infected with other viruses. It was also detected in field‐grown raspberry plants with and without symptoms of RVBMD and in raspberry plants infected with RYNV by viruliferous A. idaei. RYNV was also detected by PCR in A. idaei following access feeds on RYNV‐infected plants of 1 h or more. PCR failed to amplify DNA from gooseberry infected with GVBAV confirming the specificity of the RYNV analysis. PCR detection of RYNV in dormant raspberry buds allows assays to be made outside the natural growing season, providing a useful application for plant introduction and quarantine programmes.     

Infectibility and sensitivity of UK raspberry, blackberry and hybrid berry cultivars to Rubus viruses

Six blackberry or hybrid berry cultivars and 19 raspberry cultivars were assessed for their infectibility with, and sensitivity to, graft inoculation with 10 distinct viruses found infecting Rubus in the UK. Cultivars were grafted with each of, two isolates of the pollen borne raspberry bushy dwarf virus (RBDV), five aphid borne viruses: black raspberry necrosis, raspberry leaf mottle (RLMV), raspberry leaf spot (RLSV), rubus yellow net and raspberry vein chlorosis (RVCV); and isolates of the nematode transmitted nepoviruses, arabis mosaic, raspberry ringspot, strawberry latent ringspot and tomato black ring. All tested cultivars were infectible with a resistance breaking isolate of RBDV but only about half of that number with the Scottish type isolate of the virus. The raspberry cvs Autumn Bliss, and occasionally Glen Garry and Glen Prosen, developed leaf yellowing symptoms following infection with RBDV, but none of the other infected cultivars showed obvious leaf symptoms when kept in a heated glasshouse during the growing season. All tested cultivars were infectible with each of the four viruses transmitted in nature by the aphid, Amphorophora idaei. Most were infected symptomlessly, but seven cultivars developed severe leaf spotting symptoms due to infection with RLMV or RLSV. All but one of the raspberry cultivars were infectible with RVCV, which is transmitted in nature by the aphid Aphis idaei, and almost all infected plants developed leaf symptoms; only one of the hybrid berry or blackberry cultivars tested was infected with RVCV. In tests with the four nepoviruses, all tested cultivars, except Tummelberry, were infectible with at least one or more of these viruses. However, cultivars responded differently to challenge inoculation with different isolates of individual nepoviruses. Several cultivars developed chlorotic leaf mottling following infection with some nepovirus isolates. The implications of these results for virus control are discussed in the light of the changing pattern of virus and virus vector incidence in the UK.     

The multiplication of Longidorus elongatus (de Man) on different host plants with reference to virus transmission

In pot tests, Longidorus elongatus (de Man) populations increased rapidly on Fragaria vesca, Stellaria media, Mentha sativa and Lolium perenne and slightly on Brassica rapa (turnip var. White globe) and on Ribes nigrum; but on Rubus idaeus populations declined at the same rate as in fallow soil. Raspberry ringspot (RRV) and tomato black ring (TBRV) viruses were readily transmitted by L. elongatus to S. media, TBRV only was transmitted to L. perenne, and M. sativa became infected with neither virus. RRV was transmitted to R. idaeus var. Mailing Jewel, on which the nematode fed but evidently did not reproduce. In a field experiment L. perenne and Fragaria ananassa (strawberry) vars. Huxley and Redgauntlet were shown to be good hosts for L. elongatus and R. idaeus (raspberry) vars. Lloyd George and Mailing Jewel were confirmed as non-hosts, together with Rheum rhaponticum (rhubarb). Two periods of egg laying were detected each year in the Redgauntlet strawberry plots and these coincided with the growth of young roots during the late spring and autumn. The wide host range of L. elongatus among cultivated plants and weeds, together with its ability to survive long periods without food, precludes the use of crop rotation as a means of control. Chemical soil sterilization is considered the most effective means of control because it can greatly decrease L. elongatus populations and as the nematode multiplies slowly, even on favourable host plants, several years are likely to elapse before populations become large enough to spread viruses effectively from infector plants to susceptible crops.     

Association of different kinds of bacilliform particle with vein chlorosis and mosaic diseases of raspberry (Rubus idaeus)

Thin sections of diseased raspberry (Rubus idaeus) were examined by electron microscopy. Plants of the cv. Baumforth's B and of an aphid (Amphorophora rubi)-resistant breeding selection (6820/54), both infected with raspberry vein chlorosis virus (RVCV) but not with other detectable viruses, contained large bacilliform particles c. 430 × 65 nm. Particles occurred in the cytoplasm and perinuclear space of a small proportion of xylem parenchyma cells. They had an inner core c. 25–30 nm in diameter with cross-banding of periodicity 4·5 nm, and were bounded by an outer membrane. They are probably the particles of RVCV. Plants of cv. Mailing Jewel and of a selection (M14) both showing symptoms of raspberry mosaic (veinbanding) disease contained smaller bacilliform particles c. 125 × 30 nm, which occurred singly or in clusters in the cytoplasm of a small proportion of vascular parenchyma cells. It is not known which, if any, of the viruses associated with raspberry mosaic are represented by the particles.     

Unusual filamentous virus-like particles in symptomless blackberry associated with severe leaf curling in the virus indicator Rubus macraei, and anomalous data using a degenerate badnavirus primer in PCR of Rubus species

Electron microscopy of ultrathin sections of leaves of symptomless Himalaya Giant blackberry and of the virus indicator species, Rubus macraei, showing severe leaf curl symptoms following graft inoculation with scions from this blackberry, detected highly flexuous virus‐like particles with an unusual ‘beaded’ structure. Such particles were restricted to a few vascular cells and were distinct from P‐protein common in some such cells. This virus, provisionally named Hawaiian rubus leaf curl virus (HRLCV), symptomlessly infected a wide range of Rubus species and cultivars. Badnavirus‐like bacilliform particles were observed in some cells of a single R. macraei plant showing leaf curl symptoms following graft inoculation with the causal agent of this disease symptom from Himalaya Giant blackberry after passage through red raspberry, but not in any other material. PCR with primer sets for the badnaviruses Rubus yellow net virus and Gooseberry veinbanding associated virus, showed that no Rubus sources studied contained these viruses. However, using a sequence‐specific primer set designed from the sequence of the product generated with a badnavirus degenerate primer set, a specific product was amplified from healthy plants of all of 16 raspberry cultivars and two Rubus species, but not from 16 blackberry cultivars (including cv. Himalaya Giant). All of these sources were free from viruses known to occur in Rubus. Sequence analysis of this product showed no homology with any known badnavirus, or with any other published sequences. It seems most likely therefore that a region of the raspberry genome has been amplified using the degenerate badnavirus primer set and that it is absent from the blackberry genome.     

Seed-transmission of nematode-borne viruses

Transmission through seed of crop and weed plants seems to be characteristic of nematode-borne viruses. It occurred with tomato black ring virus (TBRV) in nineteen species (thirteen botanical families), with arabis mosaic virus (AMV) in thirteen species (eleven families), with raspberry ringspot virus (RRV) in six species (five families), and also, in more limited tests, with tomato ringspot, cherry leaf roll and tobacco rattle viruses. A remarkable feature was that infected seedlings, except those containing tobacco rattle virus, often appeared healthy. The occurrence and extent of seed-transmission depended on both the virus and the host plant. In many progenies more than 10%, and in some 100%, of seedlings were infected. The viruses were transmitted through at least two or three generations of seed of those host species tested. After 6 years' storage, TBRV- and RRV-containing seed of Capsella bursa-pastoris and Stellaria media germinated to give infected seedlings. In controlled crossing experiments with strawberry and raspberry, virus was transmitted to seed from both male and female parents but, at least in raspberry, the presence of competing virus-free pollen much decreased the ability of pollen from infected plants to set seed. There was no evidence that healthy mother plants became infected when their flowers were pollinated with infected pollen.     

The genome of black raspberry (Rubus occidentalis)

Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein‐coding genes, we identified 290 very recent small‐scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.     

The occurrence and distribution of isolates of raspberry bushy dwarf virus in England

The distribution of distinct isolates of raspberry bushy dwarf virus (RBDV) in Rubus in England was studied. Isolates similar in Rubus host range to the Scottish type isolate (D200) were largely confined to the old red raspberry (Rubus idaeus) cv. Norfolk Giant, but were also encountered in a single plant of an unidentified raspberry cultivar and in a clump of wild R. idaeus. Outside East Mailing Research Station (EMRS) RBDV isolates with wider Rubus host ranges than that of the type isolate were found only and exclusively in hybrid berries (Loganberry, clones LY59 and L654, and Tayberry) in which infection ranged from < 1% to 100%. The significance of these findings is discussed.     

STUDIES IN RUBUS VIRUS DISEASES I. A LATENT VIRUS OF NORFOLK GIANT RASPBERRY

A selection of Norfolk Giant raspberry is infected with a virus transmissible by Amphorophora rubi Kalt. after short feeding periods on infected plants and persisting for at least 18 1/2 hr. in the aphid. This virus is identified with one which is carried without symptoms by Norfolk Giant and Baumforth's Seedling B, and causes necrosis on Rubus henryi and mosaic symptoms on R. saxatilis , American black raspberry R. occidentalis (var. Cumberland) and the red raspberry varieties Chartham, Mailing Landmark and St Walfried. The virus is present in some commercial stocks of Baumforth's Seedling B, Burnetholm Seedling, and the Mailing varieties Enterprise, Notable and Promise. The name raspberry leaf mottle is proposed.     

The genetic structure of red raspberry (<Emphasis Type="Italic">Rubus idaeus</Emphasis> L.) populations in Lithuania

The red raspberry (Rubus idaeus L.) is widely distributed in Lithuania and occupies a range of habitats. The presence of coadapted gene pools in local populations of R. idaeus is a question of interest not only to plant scientists, but also to plant breeders. In this study, we investigated the genetic structure of R. idaeus and the influence of local habitats on the genetic diversity within and among populations. Nineteen populations of R. idaeus were sampled from different habitats in various agroclimatic subregions of Lithuania, and analyzed using RAPD markers. 113 RAPD bands were identified among 315 individuals; 84.31% of these were polymorphic. The mean values of Shannon’s information index for different populations ranged from 0.341 to 0.455. Nei’s gene diversity established within populations averaged 0.266. An AMOVA revealed 74% of genetic variation among individuals within populations of R. idaeus, and 23% among populations. The remaining genetic variation was distributed among populations from different agroclimatic subregions (3%). The results of this study suggest that the genetic structure of R. idaeus populations in Lithuania may be influenced partially by isolation by distance as well as by local environmental conditions.     

Non-invasive observation of the development of fungal infection in fruit

Summary The progression of infection caused by a fungal pathogen,Botrytis cinerea Pers.: Fr., in a fruit of red raspberry (Rubus idaeus L.) was followed by nuclear magnetic resonance (NMR) microscopic imaging over a 4 day period. It was found that a standard gradient echo sequence discriminated clearly between infected and healthy tissue as mycelium spread across the fruit from a single woundinoculated drupelet.