Bean Common Mosaic Virus Isolates Research Articles

Molecular Characterization of an Isolate of Bean Common Mosaic Virus First Identified in Gardenia Using Metatranscriptome and Small RNA Sequencing.

Gardenia (Gardenia jasminoides) is a popular and economically vital plant known for its ornamental and medicinal properties. Despite its widespread cultivation, there has been no documentation of plant viruses on gardenia yet. In the present study, gardenia leaves exhibiting symptoms of plant viral diseases were sampled and sequenced by both metatranscriptome and small RNA sequencing. As a consequence, bean common mosaic virus (BCMV) was identified in gardenia for the first time and named BCMV-gardenia. The full genome sequence of BCMV-gardenia is 10,054 nucleotides (nt) in length (excluding the poly (A) at the 3' termini), encoding a large polyprotein of 3,222 amino acids. Sequence analysis showed that the N-termini of the polyprotein encoded by BCMV-gardenia is less conserved when compared to other BCMV isolates, whereas the C-termini is the most conserved. Maximum likelihood phylogenetic analysis showed that BCMV-gardenia was clustered closely with other BCMV isolates identified outside the leguminous plants. Our results indicated that the majority of BCMV-gardenia virus-derived small interfering RNAs (vsiRNAs) were 21 nt and 22 nt, with 21 nt being more abundant. The first nucleotide at the 5' termini of vsiRNAs derived from BCMV-gardenia preferred U and A. The ratio of vsiRNAs derived from sense (51.1%) and antisense (48.9%) strands is approaching, and the distribution of vsiRNAs along the viral genome is generally even, with some hot spots forming in local regions. Our findings could provide new insights into the diversity, evolution, and host expansion of BCMV and contribute to the prevention and treatment of this virus.

Molecular Characteristics of Bean Common Mosaic Virus Occurring in Inner Mongolia, China.

Bean common mosaic virus (BCMV) was detected on common bean (Phaseolus vulgaris) plants showing wrinkled and/or narrow leaves, curling, shrinking and chlorosis of leaves, dwarfing of plants, and mottled pods in Inner Mongolia and named BCMV-22Huhe. Its genome has a size of 10,062 bp and was deposited in GenBank under the accession number OR778613. It is closely related to BCMV-Az (GenBank accession no. KP903372, in China) in the lineage of AzBMV. A recombination event was detected for BCMV-22Huhe among the 99 BCMV isolates published in the NCBI GenBank database, showing that BCMV-CJ25 (MK069986, found in Mexico) was a potential major parent, and the minor parent is unknown. This work is the first description of the occurrence of BCMV in Inner Mongolia, China.

Sword Bean (Canavalia gladiata): a new host of Bean common mosaic virus.

Sword bean (Canavalia gladiata) is an underutilized legume that has the potential to become an important food source owing to its wide range of nutritional and medicinal properties. In May 2023, symptoms induced by a possible virus infection such as mosaic, mottling and vein banding were observed on the leaves of about 20% of the Sword bean plants growing at the experimental research farm of the Indian Agricultural Research Institute in Pune, Maharashtra, India. Symptomatic and asymptomatic samples were screened by ELISA for the presence of Potyvirus, Cucumber mosaic virus and Tobacco mosaic virus. All symptomatic samples tested positive for Potyvirus in ELISA as well as in RT-PCR assay using the universal potyvirus primer pair (CPUP /P9502) which amplify c. 700bp of the partial coat protein region and 3'UTR. Asymptomatic samples tested negative for all tested viruses in both serological and molecular assays. BLASTn sequence analysis of the amplicons revealed that the sequence shares more than 98% identity with an Indian isolate of Bean common mosaic virus (BCMV). Sequence analysis enabled the identification of the Potyvirus as BCMV. Furthermore, the present Sword bean isolate clustered with other BCMV isolates in the phylogenetic analysis. In the present study, BCMV was found to be naturally infecting Sword bean for the first time in the world. This is of epidemiological importance, as BCMV is known to cause significant yield losses in legumes and could severely hamper Sword bean production.

First report of bean common mosaic virus naturally infecting yam bean (Pachyrhizus erosus) in China.

Yam bean (Pachyrhizus erosus), a high-yielding leguminous root crop with good nutritional value, is widely cultivated in southern China. In 2020, P. erosus (cv. Mumashan) plants exhibiting irregular yellow leaves and malformed seed pods (Supplementary Fig S1) were observed at Ningbo city, Zhejiang Province, China. To determine the causal agent(s) of the disease, symptomatic leaves (n=4) were collected for electron microscopy negative staining. Virus particles with a length of about 700nm, similar to viruses in the genus Potyvirus, were observed via transmission electron microscope (TEM), suggesting the presence a potyvirus(es). To further confirm which potyvirus(es) infected yam bean, total RNA was extracted from leaf samples of a total of six plants, including four symptomatic plants and two asymptomatic plants using TRIzol reagent (Invitrogen Carlsbad, CA, USA) according to the manufacturer's instructions. RNA was reverse-transcribed into cDNA with M4-T as the 3'-anchoring primer by ReverTra Ace® kit (Toyobo, Japan). Sprimer/M4 Potyviridae specific primers (Chen et al., 2001) were used for PCR analysis. A ~1,700-bp-long product was amplified from four symptomatic plants using KOD FX enzyme (Toyobo, Japan). No such band was amplified from the two asymptomatic plants. The PCR product (~1.7kb) amplified from a single symptomatic plant was ligated into the pEASY®-Blunt Zero vector (TransGen Bio, Beijing, China) and sequenced (Sangon Bio, Shanghai, China). The amplicon showed 99% nucleotide sequence identities with bean common mosaic virus (BCMV) isolate NKY021 (KJ807819). Subsequently, the complete nucleotide sequences of this BCMV isolate (referred as BCMV-NB) was amplified by overlapping RT-PCR and rapid amplification of cDNA ends with primers (Supplementary Table S1) designed from the sequence of BCMV isolate NKY021. The BCMV-NB full genome (Accession No. OL871237) consists of 10,053 nucleotides excluding the poly(A) tail and contains a large open reading frame encoding a polyprotein of 3222 amino acids. BLASTn analysis showed that BCMV-NB shared a sequence identity of 96.4% with BCMV isolate HZZB011 (KJ807815). Phylogenetic tree generated by Neighbour-Joining method revealing the BCMV-NB isolate was grouped together with Chinese isolates from Glycine max (Supplementary Fig S1). To test the infectivity of BCMV-NB, virus-free yam bean (cv. Mumashan) and Nicotiana benthamiana seedlings were mechanically inoculated with sap extracted from the symptomatic leaves of a BCMV-NB-infected yam bean plant. The inoculated yam bean plants developed typical BCMV mosaic and chlorotic symptoms at 16 days post inoculation (dpi), while Nicotiana benthamiana had no obvious symptoms at 10 or 20 dpi (Supplementary Fig S1). BCMV infections were confirmed in yam bean plants (infection rate 6/6) and N. benthamiana plants (infection rate 8/8) by RT-PCR at 16 dpi and 10 dpi, respectively. Twelve further P. erosus plants (cv. Mumashan) were collected from a field in Ningbo city and tested by RT-PCR with BCMV-specific primer pair BCMV CP (+)/(-) (Supplementary Table 1). Eight out of the 12 samples tested positive for BCMV by PCR-gel electrophoresis (Supplementary Fig S1) and Sanger sequencing, suggesting a high incidence of BCMV infection in this field. BCMV infection in yam bean has been reported from Indonesia (Damayanti et al., 2008) and Peru (Fuentes et al., 2012). To the best of our knowledge, this is the first report of BCMV naturally infecting yam bean in China. Thus, special attention and appropriate management strategies are needed to minimize the damage caused by BCMV to yam bean crops in China.

The first report of bean common mosaic virus (BCMV) infection of African yam bean (Sphenostylis stenocarpa) in Nigeria

African yam bean (Sphenostylis stenocarpa) is an underutilized crop that has the potential to contribute to sustainable food security. In October 2021, more than 90% African Yam Bean (AYB) plants showed typical virus symptoms of mosaic and necrosis in the grain legumes field of the Institute of Agricultural Research and Training (IAR&T), Nigeria. Subsequently, leaf samples were collected and tested by ELISA and PCR to identify the virus species. Anti-BCMV and anti-potyvirus antibodies both gave positive results when symptomatic leaves were tested, and PCR using primers designed to the coat protein gene of BCMV amplified a band of the expected size (469bp). The sequence of the PCR product was deposited in GenBank with the accession No. OL763314. The nucleotide sequence of the coat protein gene had 99% identity with BCMV isolate TN2 (KY044818). The identities of the nucleotide and amino acid sequence of the partial CP gene of the isolated virus relative to those of other potyviruses were 82.96-99.12% and 87.33-100%,, respectively. Phylogenetic analyses of the partial CP-nucleotide sequences grouped the isolate from this study (BCMV-IART-AYB) and BCMV-TN2 in the same cluster with other BCMV strains of the peanut stripe (PSt) and the blackeye cowpea (BlC) strains. In this study, we identified Bean commom mosaic virus (BCMV) infecting AYB for the first time in Nigeria and show that it has high nucleotide and amino acid identity with an Isolate of cowpea-infecting BCMV in India and China respectively than isolate in Nigeria.

A bean common mosaic virus-resistance gene in the soybean variant V94-5152 was mapped to the Rsv4 locus conferring resistance to soybean mosaic virus.

In the soybean variant V94-5152, a BCMV-resistance gene was mapped near to the region of SMV-resistance Rsv4 locus, raising a possibility that V94-5152 may rely on Rsv4 locus to resist against both SMV and BCMV. Both Soybean mosaic virus (SMV) and Bean common mosaic virus (BCMV) can induce soybean mosaic diseases, but few studies have explored soybean resistance against BCMV so far. In this study, V94-5152, a soybean variant resistant to BCMV and SMV, was crossed with a susceptible cultivar, Williams 82 to map the resistance gene. By inoculating 292 F2 individuals with a BCMV isolate HZZB011, a segregation ratio of 3 resistant: 1 susceptible was observed, suggesting that V94-5152 possesses a single-dominant resistance gene against BCMV-HZZB011. Bulk segregation analysis (BSA) then revealed that the resistance gene is closely linked to BARCSOYSSR_02_0617, a simple sequence repeat (SSR) marker on chromosome 2. Genotyping neighboring SSR markers among the 292 F2 individuals enabled us to draw a genetic linkage map, which indicated that the BCMV-resistance gene is located 0.2cM downstream of BARCSOYSSR_02_0617. Amplification and sequencing ten candidate genes (Glyma02g121300 to Glyma02g122200) around this marker then revealed four genes containing nonsynonymous changes or indels. Also, this location is near to the recently cloned SMV-resistance Rsv4 locus from the cultivar Peking. By obtaining ten more sequences of Rsv4 locus from cultivated and wild soybean materials, we further investigated the variation and evolutionary patterns of this virus-resistance locus. It was evident that positive selections had been acting on this locus, with one critical amino acid change (R55P) shared by all resistance soybeans tested.

A New Strain of Bean Common Mosaic Virus From Lima Bean (Phaseolus lunatus): Biological and Molecular Characterization.

Lima bean (Phaseolus lunatus) is a popular cultivated legume vegetable grown in the United States for dry bean or canned bean production. In 2017, two symptomatic P. lunatus plants exhibiting mosaic, vein banding, and growth retardation were collected in a public garden in Honolulu, HI. Both samples contained bean common mosaic virus (BCMV), and the two BCMV isolates were subjected to biological characterization on a panel of 11 differential cultivars of common bean (P. vulgaris), and to molecular characterization through whole genome sequencing. Both samples contained nearly identical BCMV sequences, named BCMV-A1, which, in turn, were 93% identical to the peanut stripe virus strain of BCMV. BCMV-A1 induced an unusually severe systemic necrosis in cultivar 'Dubbele Witte', and pronounced necrotic or chlorotic reaction in inoculated leaves of five other bean differentials. BCMV-A1 was able to partially overcome resistance alleles bc-1 and bc-2 expressed singly in common bean, inducing no systemic symptoms. Phylogenetic analysis of the BCMV-A1 sequence, and distinct biological reactions in common bean differentials suggested that BCMV-A1 represented a new lima bean strain of BCMV. In 2017, two BCMV isolates were collected in Idaho from common bean, and based on partial genome sequences were found 99% identical to the BCMV-A1 sequence. The data suggest that the lima bean strain of BCMV may have a wider circulation, including common bean as a host. This new strain of BCMV may thus pose a significant threat to common bean production.

Genetic variability and molecular evolution of Bean common mosaic virus populations in Iran: comparison with the populations in the world

Bean common mosaic virus (BCMV) is an important plant pathogen causing considerable economic loss to legume production worldwide. In this study, the molecular characterizations of four BCMV isolates from Iran were determined, and their genetic variation and phylogenetic relationship compared with those of 49 other from GenBank. The genome contained a single open reading frame encoding a polyprotein of 3221, 3222, 3201 and 3202 amino acids (aa) in Ir-MSC1, Ir-GoB, Ir-MJB, and Ir-MSC2, respectively. Phylogenetic analysis of the polyprotein nucleotide sequences revealed that all 53 BCMV isolates clustered into six phylogroups distinguishable according to their genetic distances, namely S (soybean), P (peanut), C (common bean) and also three other distinct groups (R1, R2, and R3) of isolates all of which were recombinant. Iranian BCMV isolates did not form a compact group in the phylogenetic trees and shared 82.7–97.0% nt and 98.6–98.9% aa sequence identity among themselves and 80.1–98.7% nt and 83.4–99.8% aa sequence identity with the 49 other BCMV isolates. Of the 53 BCMV isolates studied, 34 (including Ir-MSC1 and Ir-GoB) were found to be recombinants at multiple regions of the genomes. The 19 non-recombinant isolates fell into three main phylogroups (S, P, and C) and tended to be classified according to their original host (with some exceptions). Statistically highly significant genetic differentiation (FST > 0.80) and infrequent gene flow were detected between the three phylogroups, suggesting ancestral differentiation. The normalized values for dN-dS indicated different purifying selection pressures acting on each of cistrons, with the P1 and NIa-Pro being subjected to the weakest and strongest functional constraints, respectively. Some codons (mainly in P1 and P3 regions) were under positive selection. This study presents a comprehensive analysis of evolutionary forces shaping the genetic structure of BCMV with implications for international exchanges of propagating materials.

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.

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.

Botrytis fabae and Bean common mosaic virus (BCMV) are the most common diseases of Faba bean (Vicia faba L.) in TRNC

Surveys were conducted on the fields of faba bean culture in Turkish republic of North Cyprus (TRNC) during 2011-2013 indicated that Botrytis fabae and Bean common mosaic virus (BCMV) are the diseases that cause crop loss at economic level. During the field surveys 117 infected plants that have the symptoms of both diseases were collected from 38 different locations. Symptomatologic, morphologic and classic tests indicated that 96 of the faba bean samples had Chocolate spot disease caused by Botrytis fabae and the conidia lengths have been measured between 12.7-22.4 x 9.4-17.8 microns. Faba bean samples with virus symptoms that were collected from 38 locations. All samples were infected by Bean common mosaic potyvirus (BCMV) serologically (DAS-ELISA). The 850 bp section of BCMV isolates coat protein was increased using RT-PCR method. This section was sequenced directly using ClonJet and characterization was determined. According to Blast obtained from sequences 98% and 96 % resemblances with Mexican and Columbian isolates have been found.

First occurrence of bean common mosaic virus in soybean [Glycine max] from India

The incidence of Bean Common Mosaic Virus (BCMV) in soybean cultivated in western region of Tamil Nadu state, India, was confirmed by symptomatology and reverse transcription-polymerase chain reaction (RT-PCR). Sequence analysis showed nucleotide and amino acid identities of 100% for the isolate BCMV TN1 with BCMV isolate from China (GenBank Accession No. KJ807806) and the isolates soymosaic2 and soymosaic3 showed highest identity of 98.4% with the BCMV isolate (GenBank Accession No. KJ807807) in soybean from China. This is the first report on the emergence of BCMV in soybean in India.

BIOLOGICAL AND MOLECULAR CHARACTERISTICS OF BEAN COMMON MOSAIC VIRUS ISOLATES CIRCULATING IN COMMON BEAN IN IRAN

Bean common mosaic virus (BCMV) is one of the most widespread and economically important seed and aphid-transmitted viruses. During 2010-2011, a total of 2410 symptomatic bean (Phaseolus vulgaris) leaf samples were collected from nine provinces of Iran and checked by DAS-ELISA (double antibody sandwich enzyme-linked immunsorbent assay), resulting in detection of BCMV in 655 samples. Following biological purification, the reaction of 16 differential bean cultivars (belonging to 11 host groups) against five geographical BCMV isolates revealed the occurrence of five different BCMV pathogroups, PG- I, II, IV, V and VII, which were new for Iran. The response of five commonly cultivated bean genotypes against three BCMV pathotypes (I, II and IV) was evaluated by semi-quantitave ELISA and two genotypes, Chiti karaj and Jules, were characterized as highly sensitive and tolerant genotypes, respectively. Pathogenicity of three different BCMV pathotypes on five bean genotypes used in this study revealed that they all belong to host group-1. Amplification of the 3'-terminal region (comprising coat protein region and partial 3'-UTR) of four BCMV isolates was performed by reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis of nucleotide and deduced amino acid sequences of coat protein genes did not differentiate BCMV isolates by host, location and pathogenicity group.

IDENTIFIKASI MOLEKULER BEAN COMMON MOSAIC VIRUS YANG BERASOSIASI DENGAN PENYAKIT MOSAIK KUNING KACANG PANJANG

Molecular identification of bean common mosaic virus associated with yellow mosaic disease on yard long bean. Bean common mosaic virus (BCMV) has been reported as one of the causal agents of yellow mosaic disease on yard long bean in West Java and Central Java. Infected plants showed mosaic, yellowing, and mixture of yellow mosaic. The research was conducted to identify the diversity of BCMV associated with yellow mosaic disease based on coat protein (CP) gene sequences. Symptomatic leaf samples were collected from yard long bean growing areas in several districts in West Java (Bogor, Cirebon, Subang, and Indramayu), and several districts in Central Java (Tegal, Klaten, Solo, Yogjakarta, Sleman, and Magelang). Molecular detection using RT-PCR method was carried out by using specific primer to BCMV which will amplify the CP gene. DNA fragment, + 860 bp in size, was successfully amplified from 8 out of 13 leaf samples, i.e samples from three villages in Bogor District (Cangkurawok, Bubulak, Bojong), and five samples from District of Cirebon, Subang, Solo, Sleman, and Tegal. Sequence analysis of those DNA fragment showed that 4 isolates (Bogor-Cangkurawok, Subang, Solo and Sleman) had the highest homology to BCMV-BlC from Taiwan, whereas 2 isolates (Cirebon and Tegal) had the highest homology to BCMVNL1 from England. Further, phyllogenetic analysis revealed that those of 4 isolates were closely related to BCMV-BlC from Taiwan based on nucleotide as well as amino acid sequences; while those other 2 isolates were closely related to BCMV-NL1 from England based on nucleotide sequences but closely related to BCMV-BlC Y from China based on amino acid sequences. Phyllogenetic analysis showed that those of 6 BCMV isolates separated in two different clusters; 4 isolates (Bogor- Cangkurawok, Subang, Solo, and Sleman) in cluster 1 together with BCMV-BlC from Taiwan, while other 2 isolates (Cirebon and Tegal) in cluster 2 together with BCMV-NL1.

Characterization of Bean common mosaic virus and Bean common mosaic necrosis virus isolates in common bean growing areas in Turkey

Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are well-known legume-infecting potyviruses. The incidences of BCMV and BCMNV infections were determined by ELISA in 367 seed and leaf samples which were collected in 15 common bean-growing provinces of Turkey. Of the samples tested, 67 (18.2 %) occurred to be infected with BCMV, however only 5 (1.4 %) were infected with BCMNV. A total of 45 ELISA-positive samples were selected from single-virus infected ones to determine BCMV and BCMNV pathogenicity groups (PGs) by using a set of bean cultivars that contain different combinations of resistance genes. Some BCMV populations exhibiting unusual pathogenicity were identified. One of them, named TR-180, was found to overcome resistance conferred by bc-1, bc-1 2 , bc-2 and bc-2 2 recessive alleles in common bean and assigned to PG VII. This isolate shared high (99 %) sequence identity with previously identified BCMV RU-1 and RU-1-related strains (RU1-OR-B and RU1-OR-C) according to a BLAST analysis of the nucleotide sequences of RT-PCR amplified products comprising the complete coat protein and 3′ partial NIb regions. The isolates TR-203 and TR-256 produced a distinctive reaction pattern in the dominant I gene-bearing bean cultivars Amanda and Isabella at lower (<30 °C) temperatures and were classified into PG IVb. These isolates were found to be 99 % identical to US-1 strain based on 3′ terminal nucleotide sequences of the BCMV genome. A fourth isolate, TR-243, involved mixed BCMV populations, as confirmed by partial nucleotide sequence analysis; one was classified as belonging to PG VII being similar to TR-180, and another was assigned to PG IVb. In conclusion, on the basis of both the reactions of differential bean cultivars and ELISA results, most of BCMV isolates were assigned to pathogroup PG VII and BCMNV isolates to PG VIb. This study is the first to show that four recessive resistance alleles of common bean can be overcome by a single field isolate of BCMV, and that a wide range of BCMV pathogroups are present in Turkey.

Bean common mosaic virus Isolate Exhibits a Novel Pathogenicity Profile in Common Bean, Overcoming the bc-3 Resistance Allele Coding for the Mutated eIF4E Translation Initiation Factor.

Resistance against Bean common mosaic virus (BCMV) in Phaseolus vulgaris is governed by six recessive resistance alleles at four loci. One of these alleles, bc-3, is able to protect P. vulgaris against all BCMV strains and against other potyviruses; bc-3 was identified as the eIF4E allele carrying mutated eukaryotic translation initiation factor gene. Here, we characterized a novel BCMV isolate 1755a that was able to overcome bc-2 and bc-3 alleles in common bean. Thus, it displayed a novel pattern of interactions with resistance genes in P. vulgaris, and was assigned to a new pathogroup, PG-VIII. The IVT7214 cultivar supporting the replication of BCMV-1755a was found to have the intact homozygous bc-3 cleaved amplified polymorphic sequences marker and corresponding mutations in the eIF4E allele that confer resistance to BCMV isolates from all other pathogroups as well as to other potyviruses. The VPg protein of 1755a had seven amino acid substitutions relative to VPgs of other BCMV isolates unable to overcome bc-3. The 1755a genome was found to be a recombinant between NL1, US1 (both PG-I), and a yet unknown BCMV strain. Analysis of the recombination patterns in the genomes of NL1 and US1 (PG-I), NY15P (PG-V), US10 and RU1-OR (PG-VII), and 1755a (PG-VIII), indicated that P1/HC-Pro cistrons of BCMV strains may interact with most resistance genes. This is the first report of a BCMV isolate able to overcome the bc-3 resistance allele, suggesting that the virus has evolved mechanisms to overcome multiple resistance genes available in common bean.

A Recombinant of Bean common mosaic virus Induces Temperature-Insensitive Necrosis in an I Gene-Bearing Line of Common Bean.

The I gene is a single, dominant gene conferring temperature-sensitive resistance to all known strains of Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris). However, the closely related Bean common mosaic necrosis virus (BCMNV) induces whole plant necrosis in I-bearing genotypes of common bean, and the presence of additional, recessive genes is required to prevent this severe whole plant necrotic reaction caused by BCMNV. Almost all known BCMNV isolates have so far been classified as having pathotype VI based on their interactions with the five BCMV resistance genes, and all have a distinct serotype A. Here, we describe a new isolate of BCMV, RU1M, capable of inducing whole plant necrosis in the presence of the I gene, that appears to belong to pathotype VII and exhibits B-serotype. Unlike other isolates of BCMV, RU1M was able to induce severe whole plant necrosis below 30°C in bean cultivar Jubila that carries the I gene and a protective recessive gene bc-1. The whole genome of RU1M was cloned and sequenced and determined to be 9,953 nucleotides long excluding poly(A), coding for a single polyprotein of 3,186 amino acids. Most of the genome was found almost identical (>98%) to the BCMV isolate RU1-OR (also pathotype VII) that did not induce necrotic symptoms in 'Jubila'. Inspection of the nucleotide sequences for BCMV isolates RU1-OR, RU1M, and US10 (all pathotype VII) and three closely related sequences of BCMV isolates RU1P, RU1D, and RU1W (all pathotype VI) revealed that RU1M is a product of recombination between RU1-OR and a yet unknown potyvirus. A 0.8-kb fragment of an unknown origin in the RU1M genome may have led to its ability to induce necrosis regardless of temperature in beans carrying the I gene. This is the first report of a BCMV isolate inducing temperature-insensitive necrosis in an I gene containing bean genotype.

First Report of Bean common mosaic virus Infecting Mungbean (Vigna radiata) in China.

Bean common mosaic virus (BCMV) is a member of the genus Potyvirus and one of the numerous viruses that can infect Phaseolus vulgaris. In May of 2013, we planted more than 100 varieties of mungbean in fields and a greenhouse of Nanjing. Mungbean (Vigna radiata (Linn.) Wilczek.) with leaves displaying mosaic and shrinkage typical of viral infection was observed in a greenhouse and a field in Nanjing. About 60% of the varieties can be infected. The symptoms in some sources from Southeast Asian countries and wild germplasm are heavier, while the symptoms are lighter on the local varieties. It can be transmitted to mungbean via aphid or mechanical inoculation, or by seeds. The infected leaves were collected for electron micrograph analysis. Pinwheel inclusion and filamentous virus particles were observed, indicating a Potyvirus infection. To confirm the presence of Potyvirus infection, total RNA was extracted from plants from the greenhouse and field, and RT-PCR was performed using universal Potyvirus primers (Sprimer (+) 5'-GGXAAYAAYAGYGGXCAZCC-3'; X=A, G, C or T, Y=T or C, Z=A or G); M4T (5'-GTTTTCCCAGTCACGAC(T)-3'), which amplify a region of the 3' fragment of the RNA-dependent RNA polymerase of potyviruses (1). The 596-bp sequence was found to be 95% identical to the BCMV isolate HB (GenBank Accession No. KC478389.1). To confirm the presence of BCMV, three leaf samples were randomly collected and all were determined to be positive when subjected to ELISA using BCMV-specific antibodies. The virus infecting mungbean was identified as BCMV and the strain was named BCMV-JAAS (KJ866945). Using gene-specific primers (BCMV-cp-F: 5'-CAAAAGGACAAGGATTGAGGA, BCMV-cp-R: 3'-ACAACAAACATTGCCGTAGC) for the reported coat protein gene in BCMV, a 1,080-bp gene fragment was amplified from the total RNA of the isolate, and subsequent sequence analysis indicated that an 862-bp region contained the complete cp gene that encodes a 228 amino acid protein. The nucleotide sequences of the cp gene from the isolate shared 96% homology with the reported BCMV-HB. The phylogenetic trees based on the CP gene show that BCMV-JAAS (KJ866945) was most closely related to other Chinese BCMV isolates (KF439722.1 and AJ132145.1) followed by Azuki mosaic virus (AB012663.1) and Peanut stripe virus (U34972.1). These results indicate that the virus associated with the mosaic disease in mungbean is an isolate of BCMV. To our knowledge, this is the first report of BCMV infecting mungbean in China. BCMV affects a wide range of legume crops and can spread rapidly, causing serious harm. The discovery could effectively control BCMV and characterize the prevalent BCMV strains. Research utilizing whole-genome sequencing of the mungbean isolate is continuing and is currently being expanded to characterize the genetic diversity of the virus, assisting in the study of the evolution of the virus. Reference: (1) J. Chen and J. P. Chen. Chin. J. Virol. 18:372, 2002.

A genomic survey of thirty soybean-infecting bean common mosaic virus (BCMV) isolates from China pointed BCMV as a potential threat to soybean production

Widely known as a severe pathogen of bean plants, the bean common mosaic virus (BCMV) has been reported to infect soybeans only sporadically and the involved strains were all found in China regions. To explore variations among soybean-infecting BCMV strains, hundreds of soybean mosaic leave samples were collected throughout China, with a total of 30 BCMV isolates detected and their genomes sequenced. These newly obtained genomes, together with 16 other BCMV genomes available in GenBank were examined from multiple aspects to characterize BCMV evolutionary processes. Phylogenetic analysis showed that both soybean-infecting BCMVs (group I) and peanut-infecting BCMVs (group II) are distantly related to other BCMVs, suggesting ancestral differentiation and host adaptation. Genetic variation analysis showed that P1, P3 and 6K2 genes and the beginning portion of CP gene showed higher levels of variation relative to other genes. Moreover, selection analyses further confirmed that a number of sites within the P1 and P3 genes have suffered positive selection. These obtained BCMV sequences also exhibit high recombination frequencies, indicating a more dynamic evolutionary history. Finally, 12 different soybean cultivars were challenged with two BCMV isolates (DXH015 and HZZB011), with most of the cultivars successfully infected. These findings suggest that BCMV is indeed a potential threat to soybean production.

Recombinants of bean common mosaic virus (BCMV) and genetic determinants of BCMV involved in overcoming resistance in common bean.

Bean common mosaic virus (BCMV) exists as a complex of strains classified by reactions to resistance genes found in common bean (Phaseolus vulgaris); seven BCMV pathotypes have been distinguished thus far, numbered I to VII. Virus genetic determinants involved in pathogenicity interactions with resistance genes have not yet been identified. Here, we describe the characterization of two novel field isolates of BCMV that helped to narrow down these genetic determinants interacting with specific P. vulgaris resistance factors. Based on a biological characterization on common bean differentials, both isolates were classified as belonging to pathotype VII, similar to control isolate US10, and both isolates exhibited the B serotype. The whole genome was sequenced for both isolates and found to be 98 to 99% identical to the BCMV isolate RU1 (pathotype VI), and a single name was retained: BCMV RU1-OR. To identify a genetic determinant of BCMV linked to the BCMV pathotype VII, the whole genome was also sequenced for two control isolates, US10 and RU1-P. Inspection of the nucleotide sequences for BCMV RU1-OR and US10 (both pathotype VII) and three closely related sequences of BCMV (RU1-P, RU1-D, and RU1-W, all pathotype VI) revealed that RU1-OR originated through a series of recombination events between US10 and an as-yet-unidentified BCMV parental genome, resulting in changes in virus pathology. The data obtained suggest that a fragment of the RU1-OR genome between positions 723 and 1,961 nucleotides that is common to US10 and RU1-OR in the P1-HC-Pro region of the BCMV genome may be responsible for the ability to overcome resistance in bean conferred by the bc-2(2) gene. This is the first report of a virus genetic determinant responsible for overcoming a specific BCMV resistance gene in common bean.