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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.

AIMS: Rice (Oryza sativa L.), wheat (Triticum aestivum L.) and common bean (Phaseolus vulgaris L.) are major staple food crops consumed worldwide. Zinc (Zn) deficiency represents a common micronutrient deficiency in human populations, especially in regions of the world where staple food crops are the main source of daily calorie intake. Foliar application of Zn fertilizer has been shown to be effective for enriching food crop grains with Zn to desirable amounts for human nutrition. For promoting adoption of this practice by growers, it is important to know whether foliar Zn fertilizers can be applied along with pesticides to wheat, rice and also common bean grown across different soil and environmental conditions. METHODS: The feasibility of foliar application of zinc sulphate (ZnSO₄.7H₂O) to wheat, rice and common bean in combination with commonly used five fungicides and nine insecticides was investigated under field conditions at the 31 sites-years of seven countries, i.e., China, India, Pakistan, Thailand, Turkey, Brazil and Zambia. RESULTS: Significant increases in grain yields were observed with foliar Zn/foliar Zn + pesticide (5.2–7.7 % of wheat and 1.6–4.2 % of rice) over yields with no Zn treatment. In wheat, as average of all experiments, higher grain Zn concentrations were recorded with foliar Zn alone (41.2 mg kg⁻¹) and foliar Zn + pesticide (38.4 mg kg⁻¹) as compared to no Zn treatment (28.0 mg kg⁻¹). Though the magnitude of grain Zn enrichment was lesser in rice than wheat, grain Zn concentrations in brown rice were significantly higher with foliar Zn (24.1 mg kg⁻¹) and foliar Zn + pesticide (23.6 mg kg⁻¹) than with no Zn (19.1 mg kg⁻¹). In case of common bean, grain Zn concentration increased from 68 to 78 mg kg⁻¹ with foliar Zn alone and to 77 mg kg⁻¹ with foliar Zn applied in combination with pesticides. Thus, grain Zn enrichment with foliar Zn, without or with pesticides, was almost similar in all the tested crops. CONCLUSIONS: The results obtained at the 31 experimental site-years of seven countries revealed that foliar Zn fertilization can be realized in combination with commonly-applied pesticides to contribute Zn biofortification of grains in wheat, rice and common bean. This agronomic approach represents a useful practice for the farmers to alleviate Zn deficiency problem in human populations.

Cold temperatures can be detrimental to crop survival and productivity. Breeding progress can be improved by understanding the molecular basis of low temperature tolerance. We investigated the key routes and critical metabolites related to low temperature resistance in cold-tolerant and -sensitive common bean cultivars 120 and 093, respectively. Many potential genes and metabolites implicated in major metabolic pathways during the chilling stress response were identified through transcriptomics and metabolomics research. Under chilling stress, the expression of many genes involved in lipid, amino acid, and flavonoid metabolism, as well as metabolite accumulation increased in the two bean types. Malondialdehyde (MDA) content was lower in 120 than in 093. Regarding amino acid metabolism, 120 had a higher concentration of acidic amino acids than 093, whereas 093 had a higher concentration of basic amino acids. Methionine accumulation was clearly higher in 120 than in 093. In addition, 120 had a higher concentration of many types of flavonoids than 093. Flavonoids, methionine and malondialdehyde could be used as biomarkers of plant chilling injury. Transcriptome analysis of hormone metabolism revealed considerably greater, expression of abscisic acid (ABA), gibberellin (GA), and jasmonic acid (JA) in 093 than in 120 during chilling stress, indicating that hormone regulation modes in 093 and 120 were different. Thus, chilling stress tolerance is different between 093 and 120 possibly due to transcriptional and metabolic regulation.

Background Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. Results We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean ( Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. Conclusions The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.

Background and Aims Common bacterial blight (CBB), caused by Xanthomonas phaseoli pv. phaseoli (Xpp), is a major disease affecting common bean production in Brazil. Understanding the survival of Xpp across various environments is essential for effective disease management. Methods This study assessed Xpp survival under different environmental conditions, including variations in soil type and temperature, and the phyllosphere and rhizosphere of crops and weeds. Results Xpp survived longest in clayey soils and at lower temperatures (15 °C). It exhibited prolonged survival in the phyllosphere of common beans (up to 70 days), while it survived minimally on non-host crops like cotton, maize, and soybean. Xpp survival was positively correlated with rainfall. In the rhizosphere, maximum survival occurred in pigeon pea (up to 42 days). Weeds showed varied survival rates, with the longest being 28 days in the phyllosphere of Cyperus rotundus, whereas other species supported the bacterium for 7 to 14 days. The maximum survival period of Xpp in the rhizosphere of weeds was 21 days, but in most species, it was only detected on the day the experiment was set up. Conclusion Crop rotation with non-host crops such as cotton, maize, and soybean appears effective in reducing Xpp inoculum in fields. Managing weed populations is also crucial, as many can harbor Xpp, contributing to disease persistence. These findings are integral to developing integrated disease management strategies.

Melatonin plays important roles in multiple stress responses; however, the downstream signaling pathway and molecular mechanism remain unclear. This study aimed to elucidate the transcriptional regulation of melatonin-induced salt stress tolerance in Phaseolus vulgaris L. and identify the key downstream transcription factors of melatonin through transcriptomic and metabolomic analyses. The melatonin-induced transcriptional network of hormones, transcription factors, and functional genes was established under both control and stress conditions. Among these, eight candidate transcription factors were identified via gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, one gene related to transmembrane transport of salts ( Phvul.004G177300 ). These genes may play a role in maintaining the cell structure and excreting sodium ions outside the cell or transporting them to the vacuoles for storage. Melatonin regulates the Phvul.009G210332 gene and metabolites C05642 (N-acetyl-N-2-formyl-5-methoxycanurine), C05643 (6-hydroxymelatonin), C05660 (5-methoxyindoleacetic acid) involved in tryptophan metabolism. The metabolites C05642 and C05643 were identified as decomposition products of tryptophan, indicating that exogenous melatonin entered the P. vulgaris tissue and was metabolized. Melatonin promotes the synthesis and metabolism of tryptophan, which is crucial to plant metabolism, growth, maintenance, and repair.

Salinity stress significantly threatens seed germination, plant growth, and agricultural productivity, necessitating effective mitigation strategies. This study evaluates the potential of salicylic acid (SA) pretreatment to alleviate the detrimental effects of salinity on common bean ( Phaseolus vulgaris ) genotypes. SA, a phenolic plant hormone, is crucial for regulating growth, stress responses, and essential physiological processes, including seed germination and ion transport. Previous research has established the general benefits of SA in enhancing stress tolerance, but the specific mechanisms and effects on common bean genotypes remain underexplored. This research focuses on the impact of salinity on the germination and seedling growth of various common bean genotypes, the efficacy of SA pretreatment in enhancing these genotypes' tolerance to salinity stress, and the underlying physiological and biochemical mechanisms, particularly involving the antioxidant defense system. The research was conducted in two phases: germination and seedling growth. Ten genotypes and two commercial varieties were exposed to varying salinity levels alongside SA concentrations to assess germination performance. Subsequently, six genotypes and one variety were evaluated for seedling growth under controlled and salt stress conditions (100 mM and 200 mM NaCl), with SA treatments at 0, 0.5, and 1 mM. Results revealed that salinity severely impaired germination traits, which were significantly enhanced by SA pretreatment. During the seedling growth phase, salinity stress resulted in reduced protein, chlorophyll, and carotenoid content, decreased potassium (K⁺) levels, and diminished water content, while increasing electrolyte leakage, malondialdehyde (MDA) levels, sodium (Na⁺) concentrations, enzyme activities, and proline levels. Importantly, SA pretreatment elevated chlorophyll and protein concentrations, improved water retention, and moderated K⁺ and Na⁺ levels, including their ratios under stress conditions. SA pretreatment also significantly enhanced the antioxidant defense system, reducing oxidative damage induced by salinity stress. Principal component analysis (PCA) successfully categorized the genotypes into semi-tolerant, tolerant, semi-sensitive, and sensitive classes based on their stress responses. Notably, the Jules variety exhibited exceptional resilience during both germination and seedling growth stages, indicating its potential as a superior candidate for cultivation in salt-affected regions. This study highlights SA pretreatment as an effective strategy to enhance salinity stress resilience in common bean genotypes. The novelty of this work lies in the detailed elucidation of SA's role in modulating antioxidant defenses and ion homeostasis in different genotypes, providing new insights into breeding programs and agricultural practices aimed at improving crop resilience and productivity in increasingly saline environments.

Vertical transmission, the transfer of pathogens across generations, is a critical mechanism for the persistence of plant viruses. The transmission mechanisms are diverse, involving direct invasion through the suspensor and virus entry into developing gametes before achieving symplastic isolation. Despite the progress in understanding vertical virus transmission, the environmental factors influencing this process remain largely unexplored. We investigated the complex interplay between vertical transmission of plant viruses and pollination dynamics, focusing on common bean ( Phaseolus vulgaris ). The intricate relationship between plants and pollinators, especially bees, is essential for global ecosystems and crop productivity. We explored the impact of virus infection on seed transmission rates, with a particular emphasis on bean common mosaic virus (BCMV), bean common mosaic necrosis virus (BCMNV), and cucumber mosaic virus (CMV). Under controlled growth conditions, BCMNV exhibited the highest seed transmission rate, followed by BCMV and CMV. Notably, in the field, bee-pollinated BCMV-infected plants showed a reduced transmission rate compared to self-pollinated plants. This highlights the influence of pollinators on virus transmission dynamics. The findings demonstrate the virus-specific nature of seed transmission and underscore the importance of considering environmental factors, such as pollination, in understanding and managing plant virus spread.

Background Physical seed dormancy is an important trait in legume domestication. Although seed dormancy is beneficial in wild ecosystems, it is generally considered to be an undesirable trait in crops due to reduction in yield and / or quality. The physiological mechanism and underlying genetic factor(s) of seed dormancy is largely unknown in several legume species. Here we employed an integrative approach to understand the mechanisms controlling physical seed dormancy in common bean ( Phaseolus vulgaris L.). Results Using an innovative CT scan imaging system, we were able to track water movements inside the seed coat. We found that water uptake initiates from the bean seed lens. Using a scanning electron microscopy (SEM) we further identified several micro-cracks on the lens surface of non-dormant bean genotypes. Bulked segregant analysis (BSA) was conducted on a bi-parental RIL (recombinant inbred line) population, segregating for seed dormancy. This analysis revealed that the seed water uptake is associated with a single major QTL on Pv03. The QTL region was fine-mapped to a 118 Kb interval possessing 11 genes. Coding sequence analysis of candidate genes revealed a 5-bp insertion in an ortholog of pectin acetylesterase 8 that causes a frame shift, loss-of-function mutation in non-dormant genotype. Gene expression analysis of the candidate genes in the seed coat of contrasting genotypes indicated 21-fold lower expression of pectin acetylesterase 8 in non-dormant genotype. An analysis of mutational polymorphism was conducted among wild and domesticated beans. Although all the wild beans possessed the functional allele of pectin acetylesterase 8 , the majority (77%) of domesticated beans had the non-functional allele suggesting that this variant was under strong selection pressure through domestication. Conclusions In this study, we identified the physiological mechanism of physical seed dormancy and have identified a candidate allele causing variation in this trait. Our findings suggest that a 5-bp insertion in an ortholog of pectin acetylesterase 8 is likely a major causative mutation underlying the loss of seed dormancy during domestication. Although the results of current study provide strong evidences for the role of pectin acetylesterase 8 in seed dormancy, further confirmations seem necessary by employing transgenic approaches.

Background Wall-associated kinases (WAKs) and WAK-like proteins (WAKLs) are receptor-like kinases implicated in plant perception of extracellular cues and immune signaling. In common bean ( Phaseolus vulgaris ), differential resistance to Colletotrichum lindemuthianum offers an opportunity to link structural variation in these receptors to functional outcomes. Results Here, we systematically characterize the WAK/WAKL gene family in P. vulgaris , integrating domain architecture, gene structure, phylogeny, synteny, and transcriptomic responses in resistant (Ouro Vermelho) versus susceptible (BRS Estilo) cultivars across infection time points. Using conserved domain annotation, PvWAKs and PvWAKLs were classified based on combinations of extracellular domains (EGF and GUB_WAK_bind) while retaining a conserved intracellular kinase core. Twenty-five distinct domains were identified, with specific sets being common or exclusive to each group, suggesting modular diversification of interaction interfaces. Phylogenetic and gene structure analyses revealed evolutionary patterns consistent with both conservation of signaling machinery and divergence in extracellular features. Integration with synteny supported retention of candidate orthologs across related species. RNA-Seq profiling at 0, 48, and 96 h post-inoculation uncovered complex, genotype- and time-dependent expression dynamics: subsets of PvWAK/WAKL genes were differentially expressed uniquely in resistant or susceptible backgrounds, while others displayed opposing temporal patterns, highlighting nuanced regulatory contributions to resistance. Combining structural and expression evidence yielded a prioritized list of PvWAK/WAKL candidates potentially underlying anthracnose resistance. Conclusions The study delineates how conserved kinase signaling is coupled to extracellular domain variability and dynamic expression to enable functional divergence within the WAK/WAKL family in P. vulgaris . The resulting candidate genes provide a focused basis for functional validation and may inform molecular breeding strategies for enhanced disease resistance.