Bean Common Mosaic Research Articles

First Report of Bean Common Mosaic Virus Infecting Flowering Ginger (Alpinia purpurata) in Hawaii

First Report of Bean Common Mosaic Virus Infecting Flowering Ginger (<i>Alpinia purpurata</i>) in Hawaii

Illumina Sequencing Reveals the First Near-Complete Genome Sequence of Ugandan Passiflora Virus.

Here, we present the first near-complete genome of Ugandan Passiflora virus (UPV) sequenced from a symptomatic sample of KH7 passion fruit (Passiflora edulis Sims) variety. UPV had limited amino acid identity with other potyviruses known to cause passion fruit woodiness disease (PWD). The closest relationship (71.2% amino acid similarity) was with Bean common mosaic necrosis virus.

Detection of potyviruses infecting Iranian common beans using broad-spectrum antibodies and universal primer pairs

Six provinces of Iran were surveyed during 2012–2014 to detect potyviruses infecting common bean crops. A total of 277 leaf samples were collected from bean plants and some other legumes as well as weeds and wild legumes showing virus-like symptoms. Enzyme-linked immunosorbent assay (ELISA) using broad-spectrum potyvirus antibodies gave a positive reaction with 63 samples (22.7%). Moreover, a mixed colony of aphids (Aphis craccivora and A. fabae), collected from a locust tree plant (Robinia sp.), transmitted a potyvirus to young healthy bean plants; the infection was confirmed through serological assays. Partial nuclear inclusion b (NIb) and coat protein (CP) regions of the genomes of 19 ELISA-positive samples were amplified by reverse-transcription polymerase chain reaction (RT-PCR) using NIb and NWCIEN (or WCIEN) universal primer sets, respectively. Potyvirus species identification was confirmed by BLASTN and phylogenetic analyses followed by ELISA tests using virus-specific antibodies or biological assays. The results clearly showed the presence of Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), Bean yellow mosaic virus (BYMV) and Wisteria vein mosaic virus (WVMV) in the samples tested. Non-specific amplification of a Cucumovirus genome by using NIb primers was also recorded. The results showed the natural occurrence of a new potyvirus species (WVMV), and a new host for BYMV (Trifolium repens) in the mid-Eurasian region of Iran. Our findings indicate the capacity of the universal detection systems for fast and accurate detection of legume potyviruses in the country and for use in routine diagnostic assays.

A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya.

Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.

Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus.

Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.

Evaluation of Common Bean Cultivars Resistance to the Bean Common Mosaic Necrosis Virus in Western Kenya

The common bean (Phaseolus vulgaris), is a high protein crop and the main legume in the cropping system of western Kenya. Despite its importance, common bean yields are low (<1.0 t/ha) and declining. Bean Common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are the most common and most destructive and can cause a yield loss as high as 100%. In Kenya, limited cultivars and exotic genotypes with resistance to BCMV and BCMNV strains have been reported. Reports indicate BCMNV being a widespread virus compared to BCMV in western Kenya. This study therefore, sought to screen popular cultivars for resistance to the virus. Sixteen popularly grown bean cultivars together with cowpea (Vigna unguiculata), soybean (Glycine max) and groundnut (Arachis hypogaea) were planted in a green house in a completely randomized block design with three replicates. The plants were inoculated with BCMNV Enzyme Linked Immunosorbent Assay (ELISA) positive isolate at 3-leaf stage. Data was taken weekly for 3 weeks on type of symptoms expressed and number of plants infected. Ten bean cultivars were susceptible, 4 tolerant and 2 resistant. For improved yields of common bean, farmers should be advised to plant certified seeds for all legumes in the cropping system.

First Full Length Genome Sequence of Bean Common Mosaic Necrosis Virus (BCMNV) Isolated from Common Bean in Western Kenya

Bean common mosaic necrosis virus (BCMNV) is one of the most common and most destructive viruses of common bean and can cause a yield loss as high as 100%. The common bean (Phaseolus vulgaris L) is an important legume crop for food and cash in Kenya. In Kenya, there is inadequate documentation on the strains of the virus infecting common bean. This information is crucial in devising control measures. This study therefore, sought to characterize BCMNV isolates from western Kenya. Leafy samples showing virus-like symptoms were collected and analysed by Enzyme linked immunosorbent Assay (ELISA) and or next generation sequencing (NGS). Extraction of total RNA from ELISA positive samples was done using RNeasy Plant Mini Kit and NGS carried out following Illumina protocol to determine diversity of the virus. NGS data was trimmed and the sequence reads assembled into contigs, which were analyzed against virus sequence database. Phylogenetic analyses and comparisons were performed using MEGA7 program. The first complete genome sequence of Bean common mosaic virus (BCMNV) is reported from a Kenyan isolate. NGS technology revealed full-length sequence of BCMNV from an isolate BG 12 from Bungoma County with a genome of 9584 nt in length. Phylogenetic analysis of full-length sequences available through the Genbank clustered the isolate with the Tanzanian isolate strain TN-1 and two USA isolates, TN1a and NL-3K.

Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya.

Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.

Recovery of a Common Bean Landrace (Phaseolus vulgaris L.) for Commercial Purposes.

The “Caparrona” bean is a landrace that was grown largely in Monzón, and for that reason, it is also known by the name of “Caparrona de Monzón.” Historical references mention that in the thirties of the last century, Caparrona beans reached a production higher than 200,000 kg. Nevertheless, the increasing modernization of agriculture at the end of the 20th century enhanced its replacement by newer varieties. As a result, only a few local growers continued producing Caparrona beans mainly for family use. However, in recent years, the high demand for local products, grown with environmentally friendly farming techniques, has reawakened interest in this local bean. In order to recover the Caparrona bean crop, a study was conducted with the aim of assessing this landrace, along with all the processes, from collecting seeds to securing the in situ and ex situ conservation. Six bean samples were initially collected from local farmers and the traditional knowledge was also recorded. After the first seed-borne virus test, two samples were rejected because of the positive results for Bean Common Mosaic Virus (BCMV). The four remaining samples were evaluated in a randomized complete block design with three replications at two locations. All through the growth phase of the plants, samples were taken for a virus test. Two samples tested positive for BCMV and were discarded. Between the two healthy seed samples, regarding morphology, chemical composition, and agronomic data, no significant statistical differences were found. Therefore, both samples were selected for commercial production. The seeds obtained from the assays were transferred to a recently created producers’ association, which registered a private label to commercialize the Caparrona beans as a gourmet product. Seeds are also available from the Spanish BGHZ-CITA public genebank.

Description and genetic variation of a distinct species of Potyvirus infecting saffron (Crocus sativus L.) plants in major production regions in Iran

Saffron (Crocus sativus L.), a highly valuable crop famous for the unique taste, aroma, colour and medicinal properties of the stigmas, is widely cultivated in Iran. During 2011–2016, a total of 965 samples were randomly collected from six important saffron growing provinces of Iran to test for the presence of viruses. Assays revealed the presence of a distinct species of the genus Potyvirus, which has been tentatively named saffron latent virus (SaLV). Phylogenetic analysis of the SaLV complete genome sequence, 9,693 nucleotides (nt) excluding poly(A) tail, revealed that this virus grouped into Bean common mosaic virus subgroup in the genus Potyvirus with the closest relative being Bean common mosaic necrosis virus. A number of distinct plant species were evaluated for the host range of SaLV; Chenopodium amaranticolor and Chenopodium quinoa were found to be systemic hosts of SaLV. There were no nucleotide sites that indicated any recombination events, and the analysis of the coat protein (CP) sequence of 50 samples, collected from different geographical origins, did not show spatially structured diversity. Overall, our data shows strong negative selection pressure in CP, estimated by nucleotide sequences. The relevance of SaLV for saffron production in Iran remains to be established.

Molecular characterization and analysis of conserved potyviral motifs in bean common mosaic virus (BCMV) for RNAi-mediated protection.

Australian bean common mosaic virus (BCMV) isolates were sequenced, and the sequences were compared to global BCMV and bean common mosaic necrosis virus (BCMNV) sequences and analysed for conserved potyviral motifs to generate in planta RNA-interference (RNAi) resistance. Thirty-nine out of 40 previously reported potyvirus motifs were conserved among all 77 BCMV/BCMNV sequences. Two RNAi target regions were selected for dsRNA construct design, covering 920 bp of the nuclease inclusion b (NIb) protein and 461 bp of the coat protein (CP). In silico prediction of the effectiveness of these constructs for broad-spectrum defence against the 77 BCMV and BCMNV sequences was done via analysis of putative 21-nucleotide (nt) and 22-nt small-interfering RNAs (siRNAs) generated from the target regions. The effectiveness of both constructs for siRNA generation and BCMV RNAi-mediated resistance was validated in Nicotiana benthamiana transient assays.

Comprehensive Surveys of Bean common mosaic virus and Bean common mosaic necrosis virus and Molecular Evidence for Occurrence of Other Phaseolus vulgaris Viruses in Tanzania.

Virus diseases are among the main biotic factors constraining common bean (Phaseolus vulgaris L.) production in Tanzania. Disease management requires information on types, distribution, incidence, and genetic variation of the causal viruses, which is currently limited. Thus, a countrywide comprehensive survey was conducted. Use of a next-generation sequencing technique enabled simultaneous detection of 15 viruses belonging to 11 genera. De novo assembly resulted in many contigs, including complete or nearly complete sequences of Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), and Southern bean mosaic virus (SBMV). Some viruses (for example, SBMV and Tomato leaf curl Uganda virus-related begomovirus) were detected for the first time in common bean in Tanzania. Visually assessed virus-like disease incidence ranged from 0 to 98% but reverse-transcription polymerase chain reaction-based incidence of BCMV and BCMNV (7,756 samples) was mostly less than 40%. The Sanger-based nucleotide sequences encoding coat proteins of BCMV and BCMNV isolates were 90.2 to 100% and 97.1 to 100% identical to each other, respectively. Phylogenetic analysis showed that BCMV isolates were more diverse than BCMNV isolates. The information generated in this study will contribute to the development of molecular diagnostic tools and strategies for management of virus diseases nationally and internationally.

First Report of Bean Common Mosaic Necrosis Virus Infecting Soybean in Korea.

First Report of Bean Common Mosaic Necrosis Virus Infecting Soybean in Korea.

Звичайна мозаїка квасолі на Київщині: етіологія хвороби та ідентифікація збудника

Звичайна мозаїка квасолі на Київщині: етіологія хвороби та ідентифікація збудника

Viral Diseases of Crops in Nepal

Viral diseases are the important diseases next to the fungal and bacterial in Nepal. The increase in incidence and severity of viral diseases and emergence of new viral diseases causes the significant yield losses of different crops in Nepal. But the research and studies on plant viral diseases are limited. Most of the studies were focused in viral diseases of rice (Rice tungro virus and Rice dwarf virus), tomato (Yellow leaf curl virus) and potato (PVX and PVY). Maize leaf fleck virus and mosaic caused by Maize mosaic virus were recorded as minor disease of maize. Citrus Tristeza Virus is an important virus of citrus fruit in Nepal while Papaya ringspot potyvirus, Ageratum yellow vein virus (AYVV), Tomato leaf curlJava betasatellite and Sida yellow vein Chinaalphasatellite were recorded from the papaya fruit. The Cucumber mosaic virus (CMV) and Zucchini yellow mosaic potyvirus (ZYMV) are the viral diseases of cucurbitaceous crop reported in Nepal. Mungbean yellow mosaic India virus (MYMIV) found to infect the many crops Limabean, Kidney bean, blackgram and Mungbean. Bean common mosaic necrosis virus in sweet bean, Pea leaf distortion virus (PLDV), Cowpea aphid‐borne mosaic potyvirus (CABMV), Peanut bud necrosis virus (PBNV) in groundnut, Cucumber mosaic virus (CMV). Chili veinal mottle potyvirus (CVMV) and Tomatoyellow leaf curl gemini virus (TYLCV) were only reported and no any further works have been carried out. The 3 virus diseases Soyabean mosaic (SMV), Soybean yellow mosaic virus and Bud blight tobacco ring spot virus (TRSV) were found in soybean.Int. J. Appl. Sci. Biotechnol. Vol 6(2): 75-80

Recessive Resistance to Bean common mosaic virus Conferred by the bc-1 and bc-2 Genes in Common Bean (Phaseolus vulgaris) Affects Long-Distance Movement of the Virus.

Recessive resistance to Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris) is governed by four genes that include one strain-nonspecific helper gene bc-u, and three strain-specific genes bc-1, bc-2, and bc-3. The bc-3 gene was identified as an eIF4E translation initiation factor gene mediating resistance through disruption of the interaction between this protein and the VPg protein of the virus. The mode of action of bc-1 and bc-2 in expression of BCMV resistance is unknown, although bc-1 gene was found to affect systemic spread of a related potyvirus, Bean common mosaic necrosis virus. To investigate the possible role of both bc-1 and bc-2 genes in replication, cell-to-cell, and long-distance movement of BCMV in P. vulgaris, we tested virus spread of eight BCMV isolates representing pathogroups I, IV, VI, VII, and VIII in a set of bean differentials expressing different combinations of six resistance alleles including bc-u, bc-1, bc-12, bc-2, bc-22, and bc-3. All studied BCMV isolates were able to replicate and spread in inoculated leaves of bean cultivars harboring bc-u, bc-1, bc-12, bc-2, and bc-22 alleles and their combinations, while no BCMV replication was found in inoculated leaves of cultivar IVT7214 carrying the bc-u, bc-2, and bc-3 genes, except for isolate 1755a, which was capable of overcoming the resistance conferred by bc-2 and bc-3. In contrast, the systemic spread of all BCMV isolates from pathogroups I, IV, VI, VII, and VIII was impaired in common bean cultivars carrying bc-1, bc-12, bc-2, and bc-22 alleles. The data suggest that bc-1 and bc-2 recessive resistance genes have no effect on the replication and cell-to-cell movement of BCMV, but affect systemic spread of BCMV in common bean. The BCMV resistance conferred by bc-1 and bc-2 and affecting systemic spread was found only partially effective when these two genes were expressed singly. The efficiency of the restriction of the systemic spread of the virus was greatly enhanced when the alleles of bc-1 and bc-2 genes were combined together.

Registration of ‘Red Cedar’ Dark Red Kidney Bean

‘Red Cedar’ dark red kidney bean (Phaseolus vulgaris L.) (Reg. No. CV‐323, PI 685023), developed by Michigan State University AgBioResearch, was released in 2017 as an upright, full‐season cultivar that possesses acceptable canning quality and tolerance to common bacterial blight (CBB) and root rots. Red Cedar was developed using pedigree breeding method to the F4 generation followed by pure line selection for disease, agronomic, and quality traits. In 6 yr of field trials, Red Cedar yielded 3250 kg ha−1, flowered in 40 d, and matured in 101 d on average. Plants averaged 48 cm in height, with a lodging resistance score of 1.8 and seed weight of 55.8 g 100 seed−1. Red Cedar is resistant to race 73 of anthracnose, is partially resistant to local isolates of CBB, is sensitive to strain NL 3 of Bean common mosaic necrosis virus, and is susceptible to bean rust race 22:2. Red Cedar produces seed that meets industry standards for dry seed packaging and was rated satisfactory in overall canned bean quality in the dark red kidney bean seed class.

Registration of ‘Cayenne’ Small Red Bean

‘Cayenne’ small red bean (Phaseolus vulgaris L.) (Reg. No. CV‐322, PI 685022), developed by Michigan State University AgBioResearch, was released in 2017 as an upright, full‐season cultivar that possesses excellent canning quality and tolerance to common bacterial blight (CBB) and white mold. Cayenne was developed using the pedigree breeding method to the F4 generation followed by pure line selection for disease, agronomic, and quality traits. In 5 yr of field trials, Cayenne yielded 3357 kg ha−1, flowered in 45 d, and matured in 97 d on average. Plants averaged 52 cm in height, with lodging resistance score of 1.8 and seed weight of 36.1 g 100 seed−1. Cayenne combines high yield potential with resistance to lodging and high pod placement within plant structure, making it suitable for direct harvest under narrow‐row production systems. The upright architecture also contributes to avoidance of white mold, a disease that is intensified by narrow‐row production systems. Cayenne is partially resistant to local isolates of CBB, is resistant to strain NL 3 of Bean common mosaic necrosis virus, but is susceptible to race 73 of anthracnose, and to race 22:2 of bean rust. Cayenne produces seed that meets industry standards for packaging and was rated highest in overall canned bean quality in the small red bean seed class.

First Report of Cowpea mild mottle virus Infecting Cultivated and Wild Phaseolus in the Central-Western Region of Mexico

In the context of a regional project with the aim of identifying viruses infecting cultivated Phaseolus vulgaris (CB) and wild bean (WB): P. vulgaris, P. coccineus and P. leptostachyus species in the central-western region of Mexico, six leaves from 394 CB and 245 WB plants with (74%) and without (26%) viral symptoms were collected in the Mexican states of Guanajuato, Jalisco and Nayarit between 2013-2015. The symptoms observed were chlorotic lesions, mild and severe mottling, mild mosaics and leaf deformation. To identify the viruses, small RNA sequencing and an assembly technique was used (Kreuze, 2014). Small RNA (sRNA) reads with identity to Cowpea mild mottle virus (CPMMV) and Bean common mosaic necrosis virus (BCMNV) were identified in the sRNA library CN2Ls prepared from one sample of Phaseolus vulgaris cv. ‘Coranay’ collected in Nayarit state (CN2, NCBI BioProject: PRJNA362733), whose leaves exhibited mottling, mild mosaic and slight deformation symptoms. After bioinformatic processing and assembl...

Natural incidence of bean viruses in the northwest of Iran

Bean is considered as one of the most important legumes around the world. Viral diseases are a major yield reducing factor in bean production. Bean samples with virus-like symptoms like severe or mild mosaic, vein banding, leaf curling, blistering and necrosis were collected from different bean fields in Urmia (Northwest of Iran) during the growing seasons of 2013 and 2014. Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), Bean yellow mosaic virus (BYMV), Cucumber mosaic virus (CMV), Tomato spotted wilt virus (TSWV), Tomato mosaic virus (ToMV) and Tomato yellow leaf curl virus (TYLCV) were detected by double antibody sandwich enzyme-linked-immunosorbent assay. Mixed infection of BCMV and BCMNV were found. BCMNV was the most frequent virus in this region whereas BYMV and TYLCV were each detected just in one sample. This is the first report of BCMNV, BCMV, BYMV, TSWV, TMV and TYLCV incidence on bean in Urmia, Iran.