Search Results (23)

Virus diseases are among the major constraints in the production of food legumes in Africa, causing substantial crop losses. Common bean mosaic and black root, cowpea mosaic, chickpea stunt, faba bean necrotic yellows and stunt, groundnut rosette, and soybean mosaic are the six diseases considered economically significant in Africa. Past research enabled the description of the main characteristics of the causal viruses, including particle and genome properties, modes of transmission, host range, and virus–vector relationships. Such information in many cases assisted in developing effective diagnostics and disease management methods such as host resistance, chemical vector control, and cultural practices. Integrating two or more of these approaches is usually more effective. The major challenge, however, remains ensuring the adoption of such recommendations at a sufficiently large scale by many farmers to have an impact over wider geographical areas. Future work should focus on scaling up the adoption of available control technologies and generating new information, including epidemiological data, to support future management decisions. Furthermore, since the occurrence and significance of viruses on food legumes in many African countries are still not studied, large-scale surveys to identify viruses, establish their distribution and impact, and working out suitable control measures are required. Full article

Bean common mosaic virus (BCMV; Potyvirus phaseovulgaris) is one of the primary viruses that severely impacts the yield and quality of common beans (Phaseolus vulgaris L.) and has a worldwide distribution. Utilizing small RNA sequencing and RT-PCR validation, this study identified widespread co-infection by multiple viruses in field-collected common bean samples, with BCMV being the dominant viral species. A novel isolate, designated DY9, was obtained from these field samples. Pathotype characterization confirmed DY9 as pathotype PG-III, while previous studies reported all other PG-III members as Bean common mosaic necrosis virus (BCMNV). Whole-genome sequencing and phylogenetic analysis revealed that DY9 was genetically closer to BCMV and diverged significantly from known PG-III isolates. Based on these findings, we constructed an infectious clone of DY9. To address the genetic instability of Potyvirus in the Escherichia coli (E. coli) expression system, we discovered that inserting Intron 2 (derived from the NiR gene of P. vulgaris, GenBank: U10419.1) at position 2431 of the HC-Pro gene and targeting Intron 1 (derived from the ST LS1 gene of Solanum tuberosum, GenBank: X04753.1) at position 4240 of the CI gene significantly improved the stability of the cloning vector. The clone was verified to systemically infect common bean plants and induce typical mosaic symptoms. Infectivity was validated through RT-PCR, RT-qPCR, Western blotting, and transmission electron microscopy. This study represents the first successful construction of an infectious clone for pathotype PG-III BCMV, providing a critical reverse genetics tool for dissecting viral pathogenesis and identifying resistance genes. These findings not only expand the genetic diversity of BCMV but also offer a methodological reference for constructing infectious clones of Potyvirus species. Full article

The common bean (Phaseolus vulgaris L.) is a vital food crop worldwide, particularly in Latin America, Asia, and Sub-Saharan Africa, due to its high levels of protein, fiber, and essential nutrients. However, it is susceptible to viral infections, especially from the Bean common mosaic virus and Bean common mosaic necrosis virus. While previous research has primarily focused on specific resistance genes, a broader understanding of the plant’s overall immune response remains limited. To investigate this, a study was conducted involving 51 infected leaf samples. RNA was extracted, and deep metatranscriptomic sequencing was performed using the Illumina MiSeq platform. The results indicated that several genes related to stress response, nitrogen metabolism, and biosynthesis pathways were activated during infection. Key defense mechanisms included pathogen recognition, the production of antimicrobial peptides, and changes in metabolic activity. The Mitogen-Activated Protein Kinase (MAPK) signaling pathway and enzymes like glycosyl transferases, which aid in building protective structures, played a significant role. These findings suggest that the bean’s defense system is complex and involves not only direct attacks on pathogens but also metabolic shifts and microbial interactions. Understanding these processes provides valuable insights for breeding stronger, disease-resistant, and climate-resilient bean varieties. Full article

Common bean (Phaseolus vulgaris L.), the world’s most widely grown legume crop, is not only of great commercial importance but is also a vital smallholder crop in low-to-medium-income countries. In sub-Saharan Africa common bean provides consumers with a major proportion of their dietary protein and micronutrients. However, productivity is constrained by viruses, particularly those vectored by aphids and whiteflies, and problems are further compounded by seed-borne transmission. We describe common bean’s major viral threats including the aphid-transmitted RNA viruses bean common mosaic virus and bean common mosaic necrosis virus, and the whitefly-transmitted begomoviruses bean golden mosaic virus and bean golden yellow mosaic virus and discuss how high-throughput sequencing is revealing emerging threats. We discuss how recent work on indirect and direct viral ‘manipulation’ of vector behaviour is influencing modelling of viral epidemics. Viral extended phenotypes also modify legume interactions with beneficial organisms including root-associated microbes, pollinators and the natural enemies of vectors. While problems with common bean tissue culture have constrained transgenic and gene editing approaches to crop protection, topical application of double-stranded RNA molecules could provide a practical protection system compatible with the wide diversity of common bean lines grown in sub-Saharan Africa. Full article

Common bean (Phaseolus vulgaris L.) is known for its high protein, dietary fiber, and various trace element contents, making it a widely grown leguminous crop globally. The bean common mosaic virus (BCMV) poses a significant threat to leguminous crop production, causing substantial yield reductions when common beans are infected. Widely occurring in mRNA, the m⁶A modification is vital for maintaining mRNA stability, facilitating splicing, enabling nuclear export, supporting polyadenylation, and initiating translation. Recent studies have identified the m⁶A regulatory gene family in various plant species, and its ability to regulate plant virus infection has been confirmed. There is currently insufficient information regarding the m⁶A regulatory gene family in beans and how it responds to BCMV infection. Consequently, we carried out a genome-wide characterization of the m⁶A regulatory gene family in common bean, which led to the identification of 31 potential regulatory gene members associated with m⁶A. According to evolutionary analysis, the increase in the bean m⁶A regulatory gene family appears to be linked to either whole-genome duplication or segmental duplication events. Subsequent investigations into the expression levels of these genes throughout different phases of BCMV infection showed that all candidate genes responded to the infection with various changes in expression. Moreover, we characterized the methyltransferase activity of PvMTA and validated the interactive relationship between mRNA adenosine methyltransferase A (MTA) and mRNA adenosine methyltransferase B (MTB) in common beans. Through overexpressing and silencing PvMTA, we further ascertained that this particular gene has a detrimental impact on the regulation of BCMV infection. This research provides fresh perspectives on the molecular processes that govern the interaction between the common bean and BCMV and aids progress in molecular bean breeding. Full article

Common bean (Phaseolus vulgaris L.) is a widely cultivated crop, representing an important protein source in the human diet in developing countries. The production of this crop faces serious challenges, such as virus diseases transmitted by the whitefly Bemisia tabaci. Although there is a lot of information about some of these viruses, most of what we know has been developed using model systems, such as tomato plants and tomato yellow leaf curl virus (TYLCV). There is still very little information on the most relevant common bean viruses, such as bean golden mosaic virus (BGMV), bean golden yellow mosaic virus (BGYMV), bean dwarf mosaic virus (BDMV), cowpea mild mottle virus (CPMMV), and bean yellow disorder virus (BnYDV). In this review, we discuss the available data in the most up-to-date literature and suggest future research avenues to contribute to the development of management tools for preventing or reducing the damage caused by viruses in this important crop. Full article

Agricultural pests can cause direct damage to crops, including chlorosis, loss of vigor, defoliation, and wilting. In addition, they can also indirectly damage plants, such as by transmitting pathogenic micro-organisms while feeding on plant tissues, affecting the productivity and quality of crops and interfering with agricultural production. Among the known arthropod pests, mites are highly prevalent in global agriculture, particularly those from the Tetranychidae family. The two-spotted spider mite, Tetranychus urticae, is especially notorious, infesting about 1600 plant species and causing significant agricultural losses. Despite its impact on agriculture, the virome of T. urticae is poorly characterized in the literature. This lack of knowledge is concerning, as these mites could potentially transmit plant-infecting viral pathogens, compromising food security and complicating integrated pest management efforts. Our study aimed to characterize the virome of the mite T. urticae by taking advantage of publicly available RNA deep sequencing libraries. A total of 30 libraries were selected, covering a wide range of geographic and sampling conditions. The library selection step included selecting 1 control library from each project in the NCBI SRA database (16 in total), in addition to the 14 unique libraries from a project containing field-collected mites. The analysis was conducted using an integrated de novo virus discovery bioinformatics pipeline developed by our group. This approach revealed 20 viral sequences, including 11 related to new viruses. Through phylogenetic analysis, eight of these were classified into the Nodaviridae, Kitaviridae, Phenuiviridae, Rhabdoviridae, Birnaviridae, and Qinviridae viral families, while three were characterized only at the order level within Picornavirales and Reovirales. The remaining nine viral sequences showed high similarity at the nucleotide level with known viral species, likely representing new strains of previously characterized viruses. Notably, these include the known Bean common mosaic virus (BCMV) and Phaseolus vulgaris alphaendornavirus 1, both of which have significant impacts on bean agriculture. Altogether, our results expand the virome associated with the ubiquitous mite pest T. urticae and highlight its potential role as a transmitter of important plant pathogens. Our data emphasize the importance of continuous virus surveillance for help in the preparedness of future emerging threats. Full article

Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their “centre of emergence”. We have compared over 700 of the complete genomic ORFs of the crop pandemic and the non-crop viruses in various ways. Only one-third of crop virus genomes are non-recombinant, but more than half the non-crop virus genomes are. Four of the viruses were from crops domesticated in the Old World (Africa to SE Asia), and the other five were from New World crops. There was a temporal signal in only three of the crop virus datasets, but it confirmed that the most recent common ancestors of all the crop viruses were before inter-continental marine trade started after 1492 CE, whereas all the crown clusters of the phylogenies are from after that date. The non-crop virus datasets are genetically more diverse than those of the crop viruses, and Tajima’s D analyses showed that their populations were contracting, and only one of the crop viruses had a significantly expanding population. dN/dS analyses showed that most of the genes and codons in all the viruses were under significant negative selection, and the few that were under significant positive selection were mostly in the PIPO-encoding region of the P3 protein, or the PIPO protein itself. Interestingly, more positively selected codons were found in non-crop than in crop viruses, and, as the hosts of the former were taxonomically more diverse than the latter, this may indicate that the positively selected codons are involved in host range determination; AlphaFold3 modelling was used to investigate this possibility. Full article

Protected geographical indications (PGIs) share health problems related to plant propagation material. The PGI “Faba de Lourenzá” encompasses a 1660 km² area in northern Galicia, Spain, renowned for its “Faba Galaica” (FG) and Faba do marisco” (FM) bean cultivars. The lack of certified virus-free seeds poses a challenge. From 2019 to 2023, seeds from 60 lots were tested for BCMV. Plants from several plots were tested periodically to develop disease progress curves (DPCs). Control methods (plots out PGI zone, virus-free seedlings, rogueing, corn borders, and intercropping) were tested. Yields in five plots were used to assess BCMV’s economic impact. Seed lots were 22.3% FG-infected and <5% FM-infected. The transmission rate of BCMV from infected FG plants to their seeds was 25.5 ± 5%, while for FM it was 12 ± 3%. FG yield losses were on average 31.6 ± 4.5%. Combining virus-free seedlings and infected plant removal in plots outside the PGI area proved effective at reducing infection rates; combining with intercropping resulted in the lowest incidence in an FG plot. Farmer training and off-site plot selection to produce healthy sowing beans are key to improving results. Full article

Analysis of the viromes of three symptomatic Fabaceae plants, i.e., red clover (Trifolium pratense L.), pea (Pisum sativum L.), and common bean (Phaseolus vulgaris L.), using high-throughput sequencing revealed complex infections and enabled the acquisition of complete genomes of a potyvirus, bean yellow mosaic virus (BYMV). Based on phylogenetic analysis, the Slovak BYMV isolates belong to two distinct molecular groups, i.e., VI (isolate FA40) and XI (isolates DAT, PS2). Five commercial pea genotypes (Alderman, Ambrosia, Gloriosa, Herkules, Senator) were successfully infected with the BYMV-PS2 inoculum and displayed similar systemic chlorotic mottling symptoms. Relative comparison of optical density values using semi-quantitative DAS-ELISA revealed significant differences among virus titers in one of the infected pea genotypes (Ambrosia) when upper fully developed leaves were tested. Immunoblot analysis of systemically infected Alderman plants showed rather uneven virus accumulation in different plant parts. The lowest virus accumulation was repeatedly detected in the roots, while the highest was in the upper part of the plant stem. Full article

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. Full article

Bean common mosaic virus from the genus Potyvirus has a wide range of hosts and a very negative impact on cultivated crops from the genus Phaseolus. The risk of viral infection of economically important crops increases even if the carriers of the virus are related plant species growing on agroecological interfaces. Such plant species have emerged as new hosts for BCMV, usually harboring novel genetic variants of the virus. A novel genetic variant of BCMV was isolated from a symptomatic crownvetch plant, where the presence of this virus was confirmed via Western blot analysis and via amino acid identities in peptide fragments of CI, HC-pro, and CP proteins using the nanoLC-ESI-Q-TOF. The novel BCMV SVK isolate differed from the most genetically similar one in 0.91% of nucleotides and 1.55% of amino acids. The highest number of amino acid substitutions (8.8% of amino acids) was in the P1 protein, followed by CP (2.44% of amino acids). Minor substitutions were in Hc-pro, CI, and Nib proteins. The symptomatic crownvetch plant was confirmed as a new host and carrier of the novel BCMV isolate. Full article

Wisteria vein mosaic virus (WVMV) is a member of the genus Potyvirus, found to be associated with the Wisteria mosaic disease (WMD). In 2022, severe symptoms resembling WMD were observed on the foliage of a Chinese wisteria (Wisteria sinensis) tree growing in Apulia (Italy). The presence of WVMV was ascertained by RT-PCR using the universal degenerate primers NIb2F/NIb3R in the NIb gene. Next, we derived the complete sequence of the CP gene. MAFFT pairwise alignment of the two target regions showed a high amino acid sequence identity of isolate Bari with other WVMV isolates, confirming they belonged to the same species. NIb phylogenetic analysis placed WVMV Bari within the lineage identified in the genus Potyvirus as the bean common mosaic virus supergroup. Closer analysis based on the CP gene showed that WVMV Bari was part of a sub-clade gathering all WVMV isolates within a larger clade clustering closely related species. An exploratory analysis of the genetic diversity and possible mechanisms underlying the evolution of geographic populations of WVMV was attempted. The analysis was based on the N-terminal coding region of CP, available for 20 isolates from Europe, Asia, and Oceania. A high diversity, mainly found in the European population, led to the identification of 16 different haplotypes. Based on the dN/dS ratio, the target region appears to be under negative selective pressure. Neutrality tests indicated a potential population expansion in Europe and a recent decrease in Asia. The two populations exhibited a high level of gene flow. We found that WVMV Bari may have originated from a recombination event in the NIb gene. To date, the presence of WVMV had never been reported on W. sinensis in Italy, and no molecular information was available on any Italian isolate. Our report draws attention to the further spread of WVMV in the European territory and its rising threat to the ornamental nursery sector. Full article

Bean common mosaic disease is one of the most destructive diseases of the common bean, which is one of the most important legumes worldwide. It is caused by two closely related potyviruses: bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV). Both viruses have spread to all the common bean-growing areas worldwide and have become a major challenge in bean production. In this review, we summarized the biology and diversity of BCMV and BCMNV, discussed the current knowledge on the resistance genes of BCMV, and finally pointed out the future prospects for the control of bean common mosaic disease. Full article

Country bean (Lablab purpureus L.), a popular vegetable in Bangladesh, is severely affected by insect pests and diseases. Farmers’ perceptions of insect pests, diseases, and their management are critical constraints to the establishment of an effective and sustainable pest management approach for this crop. A comprehensive survey was conducted with 300 country bean farmers from six districts of Bangladesh to assess farmers’ perceptions and knowledge of the insect pests and diseases of country bean, and their management practices. The survey results show that country bean farmers have been facing varying pest problems for more than ten years. They could identify eight pests and only one beneficial insect species in their fields, including thrips and jute weevil, as new pests. Among the pests, aphids and pod borers were common in all surveyed areas. More than 80% of farmers said their bean plants were severely affected by bean yellow mosaic virus and white mold diseases. Farmers also mentioned that insect pests and diseases together caused 30–40% yield losses of this crop. About 76% of the farmers solely depended on different chemical pesticides for the production of country bean. Growers frequently used insecticides from the organophosphorus and neonicotinoid groups, and fungicides from the triazole group, to manage pests associated with this crop. Farmers start applying pesticides from the seedling stages, at three-day intervals, maintaining only two- to four-day pre-harvest intervals (PHI). Our findings provide insight into the importance of developing sustainable pest management approaches for country bean production in Bangladesh. Full article