Advancing common bean (Phaseolus vulgaris L.) disease detection with YOLO driven deep learning to enhance agricultural AI.

Common beans (CB), a vital source for high protein content, plays a crucial role in ensuring both nutrition and economic stability in diverse communities, particularly in Africa and Latin America. However, CB cultivation poses a significant threat to diseases that can drastically reduce yield and quality. Detecting these diseases solely based on visual symptoms is challenging, due to the variability across different pathogens and similar symptoms caused by distinct pathogens, further complicating the detection process. Traditional methods relying solely on farmers' ability to detect diseases is inadequate, and while engaging expert pathologists and advanced laboratories is necessary, it can also be resource intensive. To address this challenge, we present a AI-driven system for rapid and cost-effective CB disease detection, leveraging state-of-the-art deep learning and object detection technologies. We utilized an extensive image dataset collected from disease hotspots in Africa and Colombia, focusing on five major diseases: Angular Leaf Spot (ALS), Common Bacterial Blight (CBB), Common Bean Mosaic Virus (CBMV), Bean Rust, and Anthracnose, covering both leaf and pod samples in real-field settings. However, pod images are only available for Angular Leaf Spot disease. The study employed data augmentation techniques and annotation at both whole and micro levels for comprehensive analysis. To train the model, we utilized three advanced YOLO architectures: YOLOv7, YOLOv8, and YOLO-NAS. Particularly for whole leaf annotations, the YOLO-NAS model achieves the highest mAP value of up to 97.9% and a recall of 98.8%, indicating superior detection accuracy. In contrast, for whole pod disease detection, YOLOv7 and YOLOv8 outperformed YOLO-NAS, with mAP values exceeding 95% and 93% recall. However, micro annotation consistently yields lower performance than whole annotation across all disease classes and plant parts, as examined by all YOLO models, highlighting an unexpected discrepancy in detection accuracy. Furthermore, we successfully deployed YOLO-NAS annotation models into an Android app, validating their effectiveness on unseen data from disease hotspots with high classification accuracy (90%). This accomplishment showcases the integration of deep learning into our production pipeline, a process known as DLOps. This innovative approach significantly reduces diagnosis time, enabling farmers to take prompt management interventions. The potential benefits extend beyond rapid diagnosis serving as an early warning system to enhance common bean productivity and quality.

Metabolomic analysis reveals stress tolerance mechanisms in common bean (Phaseolus vulgaris L.) related to treatment with a biostimulant obtained from Corynebacterium glutamicum.

Microbial biostimulants have emerged as a sustainable alternative to increase the productivity and quality of important crops. Despite this, the effects of the treatment on plant metabolism are poorly understood. Thus, this study investigated the metabolic response of common bean (Phaseolus vulgaris) related to the treatment with a biostimulant obtained from the extract of Corynebacterium glutamicum that showed positive effects on the development, growth, and yield of crops previously. By untargeted metabolomic analysis using UHPLC-MS/MS, plants and seeds were subjected to treatment with the biostimulant. Under ideal growth conditions, the plants treated exhibited higher concentration levels of glutamic acid, nicotiflorin and glycosylated lipids derived from linolenic acid. The foliar application of the biostimulant under water stress conditions increased the chlorophyll content by 17% and induced the accumulation of flavonols, mainly quercetin derivatives. Also, germination seed assays exhibited longer radicle lengths for seeds treated compared to the untreated control even in the absence of light (13-18% increase, p-value <0.05). Metabolomic analysis of the seeds indicated changes in concentration levels of amino acids (tryptophan, phenylalanine, tyrosine, glutamine, and arginine) and their derivatives. The results point out the enhancement of abiotic stress tolerance and the metabolic processes triggered in this crop associated with the treatment with the biostimulant, giving the first insights into stress tolerance mechanisms in P. vulgaris.

Rhizobacteria control damping-off and promote growth of lima bean with and without co-inoculation with Rhizobium tropici CIAT899.

Rhizoctonia solani compromises the production of lima bean, an alternative and low-input food source in many tropical regions. Inoculation of bacterial strains has been used, but research on their biocontrol and growth promotion potential on lima bean is scarce. The objective of this study was to evaluate the effects of inoculation with rhizobacterial strains of the genera Bacillus, Brevibacillus, Paenibacillus, Burkholderia, Pseudomonas, and Rhizobium in combination or not with N2-fixing Rhizobium tropici on the control of damping-off disease and growth promotion in lima bean plants. Greenhouse experiments were conducted to evaluate the inoculation with bacterial strains with biocontrol potential in combination or not with R. tropici in substrate infected with R. solani CML 1846. Growth promotion of these strains was also assessed. Strains of Brevibacillus (UFLA 02-286), Pseudomonas (UFLA 02-281 and UFLA 04-885), Rhizobium (UFLA 04-195), and Burkholderia (UFLA 04-227) co-inoculated with the strain CIAT 899 (Rhizobium tropici) were the most effective in controlling R. solani, reducing the disease incidence in 47-60% on lima bean. The promising strains used in the biocontrol assays were also responsive in promoting growth of lima bean under disease and sterile conditions. A positive synergistic effect of co-inoculation of different genera contributed to plant growth, and these outcomes are important first steps to improve lima bean production.

Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere.

Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.

Comprehensive Analysis of Phaseolus vulgaris SnRK Gene Family and Their Expression during Rhizobial and Mycorrhizal Symbiosis.

Sucrose non-fermentation-related protein kinase 1 (SnRK1) a Ser/Thr protein kinase, is known to play a crucial role in plants during biotic and abiotic stress responses by activating protein phosphorylation pathways. SnRK1 and some members of the plant-specific SnRK2 and SnRK3 sub-families have been studied in different plant species. However, a comprehensive study of the SnRK gene family in Phaseolus vulgaris is not available. Symbiotic associations of P. vulgaris with Rhizobium and/or mycorrhizae are crucial for the growth and productivity of the crop. In the present study, we identified PvSnRK genes and analysed their expression in response to the presence of the symbiont. A total of 42 PvSnRK genes were identified in P. vulgaris and annotated by comparing their sequence homology to Arabidopsis SnRK genes. Phylogenetic analysis classified the three sub-families into individual clades, and PvSnRK3 was subdivided into two groups. Chromosome localization analysis showed an uneven distribution of PvSnRK genes on 10 of the 11 chromosomes. Gene structural analysis revealed great variation in intron number in the PvSnRK3 sub-family, and motif composition is specific and highly conserved in each sub-family of PvSnRKs. Analysis of cis-acting elements suggested that PvSnRK genes respond to hormones, symbiosis and other abiotic stresses. Furthermore, expression data from databases and transcriptomic analyses revealed differential expression patterns for PvSnRK genes under symbiotic conditions. Finally, an in situ gene interaction network of the PvSnRK gene family with symbiosis-related genes showed direct and indirect interactions. Taken together, the present study contributes fundamental information for a better understanding of the role of the PvSnRK gene family not only in symbiosis but also in other biotic and abiotic interactions in P. vulgaris.

Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation.

Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N2, and a major example relies on the high contribution associated with the soybean (Glycine max), contrasting with the low rates reported with the common bean (Phaseolus vulgaris) crop worldwide. Understanding these differences represents a major challenge that can help to design strategies to increase the contribution of BNF, and next-generation sequencing (NGS) analyses of the nodule and root microbiomes may bring new insights to explain differential symbiotic performances. In this study, three treatments evaluated in non-sterile soil conditions were investigated in both legumes: (i) non-inoculated control; (ii) inoculated with host-compatible rhizobia; and (iii) co-inoculated with host-compatible rhizobia and Azospirillum brasilense. In the more efficient and specific symbiosis with soybean, Bradyrhizobium presented a high abundance in nodules, with further increases with inoculation. Contrarily, the abundance of the main Rhizobium symbiont was lower in common bean nodules and did not increase with inoculation, which may explain the often-reported lack of response of this legume to inoculation with elite strains. Co-inoculation with Azospirillum decreased the abundance of the host-compatible rhizobia in nodules, probably because of competitiveness among the species at the rhizosphere, but increased in root microbiomes. The results showed that several other bacteria compose the nodule microbiomes of both legumes, including nitrogen-fixing, growth-promoters, and biocontrol agents, whose contribution to plant growth deserves further investigation. Several genera of bacteria were detected in root microbiomes, and this microbial community might contribute to plant growth through a variety of microbial processes. However, massive inoculation with elite strains should be better investigated, as it may affect the root microbiome, verified by both relative abundance and diversity indices, that might impact the contribution of microbial processes to plant growth.

The AbcCl1 transporter of Colletotrichum lindemuthianum acts as a virulence factor involved in fungal detoxification during common bean (Phaseolus vulgaris) infection.

Anthracnose, caused by Colletotrichum lindemuthianum, is a disease affecting the common bean plant, Phaseolus vulgaris. To establish infection, the phytopathogen must survive the toxic compounds (phytoanticipins and phytoalexins) that are produced by the plant as a defense mechanism. To study the detoxification and efflux mechanisms in C. lindemuthianum, the abcCl1 gene, which encodes an ABC transporter, was analyzed. The abcCl1 gene (4558 pb) was predicted to encode a 1450-amino acid protein. Structural analysis of 11 genome sequences from Colletotrichum spp. showed that the number of ABC transporters varied from 34 to 64. AbcCl1 was classified in the ABC-G family of transporters, and it appears to be orthologs to ABC1 from Magnaporthe grisea and FcABC1 from Fusarium culmorum, which are involved in pleiotropic drug resistance. A abcT3 (ΔabcCl1) strain showed reduction on aggressivity when inoculated on bean leaves that presented diminishing anthracnose symptoms, which suggests the important role of AbcCl1 as a virulence factor and in fungal resistance to host compounds. The expression of abcCl1 increased in response to different toxic compounds, such as eugenol, hygromycin, and pisatin phytoalexin. Together, these results suggest that AbcCl1 is involved in fungal resistance to the toxic compounds produced by plants or antagonistic microorganisms.

Visualization of the Crossroads between a Nascent Infection Thread and the First Cell Division Event in Phaseolus vulgaris Nodulation.

The development of a symbiotic nitrogen-fixing nodule in legumes involves infection and organogenesis. Infection begins when rhizobia enter a root hair through an inward structure, the infection thread (IT), which guides the bacteria towards the cortical tissue. Concurrently, organogenesis takes place by inducing cortical cell division (CCD) at the infection site. Genetic analysis showed that both events are well-coordinated; however, the dynamics connecting them remain to be elucidated. To visualize the crossroads between IT and CCD, we benefited from the fact that, in Phaseolus vulgaris nodulation, where the first division occurs in subepidermal cortical cells located underneath the infection site, we traced a Rhizobium etli strain expressing DsRed, the plant cytokinesis marker YFP-PvKNOLLE, a nuclear stain and cell wall auto-fluorescence. We found that the IT exits the root hair to penetrate an underlying subepidermal cortical (S-E) cell when it is concluding cytokinesis.

Evaluation of the incidence of endophytic fungi in leaves, stems and roots of bean plants in the State of Paraná / Avaliação da incidência de fungos endofíticos em folhas, caules e raízes de plantas de feijão no Estado do Paraná

The present study aimed to isolate endophilic fungi from plant tissues (leaves, stems and roots) of beans, in addition to identifying them at the genus level. The experiment was conducted at IDR-Londrina. Bean samples were collected at the Londrina Research Station and at UENP-Bandeirantes. The leaves, stems and roots were separated; fragments of 5 mm diameter were cut and disinfested. They were later transferred to BDA culture medium. The plates were incubated at room temperature for seven days for growth of the microorganisms present. The presence and absence, colonization rate (TC) for each tissue and gender identification of fungi were evaluated. The experiment was conducted in a completely randomized design, with five replications. Forty-eight endophilic isolates were found, 13 in root, 17 in stem and 18 in leaf. CT ranged from 17-100% (leaf), 17-83% (stem) and 16-100% (root). The genus Alternaria sp. and Cladosporium sp. have greater specificity with the leaf and stem, Penicillium sp. root and stem. The genera Fusarium sp. and Aspergillus sp. are found in all organs, Curvularia sp., Nigrospora sp. and Thichoderma sp. demonstrated leaf specificity, Macrophomina sp. the root, and Colletotrichum sp. to the stem. Thus, the identified fungi present potential for future studies in their application in the biocontrol of various plant diseases.

O presente estudo teve como objetivo realizar o isolamento de fungos endofíticos dos tecidos vegetais (folhas, caules e raízes) de feijão, além de identifica-los a nível de gênero. O experimento foi conduzido no IDR-Londrina. Amostras de feijão foram coletadas na Estação de Pesquisa de Londrina e na UENP-Bandeirantes. Foram separadas as folhas, caules e raízes, cortados fragmentos de 5 mm diâmetro e desinfestados. Posteriormente foram transferidos para meio de cultura BDA. As placas foram incubadas à temperatura ambiente por sete dias, para crescimento dos microrganismos presentes. Foram avaliados a presença e ausência, taxa de colonização (TC) para cada tecido e identificação a nível de gênero dos fungos. O experimento foi conduzido em delineamento inteiramente casualizado, com cinco repetições. Encontrou-se 48 isolados endofíticos, sendo 13 em raiz, 17 em caule e 18 em folha. A TC variou de 17-100% (folha), de 17-83% (caule) e 16-100% (raiz). O gênero Alternaria sp. e Cladosporium sp. apresentam especificidade maior com a folha e caule, o Penicillium sp. com raiz e caule. Os gêneros Fusarium sp. e Aspergillus sp. são encontrados em todos os órgãos, Curvularia sp., Nigrospora sp. e Thichoderma sp. demonstraram especificidade em folha, Macrophomina sp. a raiz, e Colletotrichum sp. ao caule. Dessa forma, os fungos identificados apresentam-se com potencial para futuros estudos em sua aplicação no biocontrole de diversas doenças de plantas.

Nodulation competitiveness and diversification of symbiosis genes in common beans from the American centers of domestication.

Phaseolus vulgaris (common bean), having a proposed Mexican origin within the Americas, comprises three centers of diversification: Mesoamerica, the southern Andes, and the Amotape-Huancabamba Depression in Peru-Ecuador. Rhizobium etli is the predominant rhizobium found symbiotically associated with beans in the Americasalthough closely related Rhizobium phylotypes have also been detected. To investigate if symbiosis between bean varieties and rhizobia evolved affinity, firstly nodulation competitiveness was studied after inoculation with a mixture of sympatric and allopatric rhizobial strains isolated from the respective geographical regions. Rhizobia strains harboring nodC types α and [Formula: see text], which were found predominant in Mexico and Ecuador, were comparable in nodule occupancy at 50% of each in beans from the Mesoamerican and Andean gene pools, but it is one of those two nodC types which clearly predominated in Ecuadorian-Peruvian beans as well as in Andean beans nodC type [Formula: see text] predominated the sympatric nodC type δ. The results indicated that those beans from Ecuador-Peru and Andean region, respectively exhibited no affinity for nodulation by the sympatric rhizobial lineages that were found to be predominant in bean nodules formed in those respective areas. Unlike the strains isolated from Ecuador, Rhizobium etli isolated from Mexico as well from the southern Andes was highly competitive for nodulation in beans from Ecuador-Peru, and quite similarly competitive in Mesoamerican and Andean beans. Finally, five gene products associated with symbiosis were examined to analyze variations that could be correlated with nodulation competitiveness. A small GTPase RabA2, transcriptional factors NIN and ASTRAY, and nodulation factor receptors NFR1 and NFR5- indicated high conservation but NIN, NFR1 and NFR5 of beans representative of the Ecuador-Peru genetic pool clustered separated from the Mesoamerican and Andean showing diversification and possible different interaction. These results indicated that both host and bacterial genetics are important for mutual affinity, and that symbiosis is another trait of legumes that could be sensitive to evolutionary influences and local adaptation.

Metallothionein1A Regulates Rhizobial Infection and Nodulation in Phaseolus vulgaris.

Metallothioneins (MTs) constitute a heterogeneous family of ubiquitous metal ion-binding proteins. In plants, MTs participate in the regulation of cell growth and proliferation, protection against heavy metal stress, oxidative stress responses, and responses to pathogen attack. Despite their wide variety of functions, the role of MTs in symbiotic associations, specifically nodule-fabacean symbiosis, is poorly understood. Here, we analyzed the role of the PvMT1A gene in Phaseolus vulgaris-Rhizobium tropici symbiosis using bioinformatics and reverse genetics approaches. Using in silico analysis, we identified six genes encoding MTs in P. vulgaris, which were clustered into three of the four classes described in plants. PvMT1A transcript levels were significantly higher in roots inoculated with R. tropici at 7 and 30 days post inoculation (dpi) than in non-inoculated roots. Functional analysis showed that downregulating PvMT1A by RNA interference (RNAi) reduced the number of infection events at 7 and 10 dpi and the number of nodules at 14 and 21 dpi. In addition, nodule development was negatively affected in PvMT1A:RNAi transgenic roots, and these nodules displayed a reduced nitrogen fixation rate at 21 dpi. These results strongly suggest that PvMT1A plays an important role in the infection process and nodule development in P. vulgaris during rhizobial symbiosis.

Biological contamination of the common bean (Phaseolus vulgaris L.) and its impact on food safety.

The occurrence of biological contaminants in common beans is a challenge for food safety, as they can affect the bean at different points in the production chain. Their presence can result in damage to the health of consumers through their direct toxic effect or by promoting nutritional deficiencies, in addition to decreasing the crop yield that has an economic impact. In this article, the information available in the literature on the occurrence of biological contaminants in the common bean (Phaseolus vulgaris L.) was organized to identify the main risks to food safety due to biological contamination. Research showed that many studies investigated the effects of microbial contaminants during the farming and harvested of beans and that some strategies have been used to avoid losses. The presence of toxigenic fungi and some mycotoxins have also been reported, indicating that common beans may carry thermostable toxic residues, directly impacting human health. Further studies are needed to identify the role of microorganisms in determining the quality of common beans and to estimate their risks to food safety. HighlightsBeans can be contaminated by biological agents.Plants infected with parasites may be highly susceptible to other contaminants.Micotoxicologic contamination is less prevalent in beans than other grains.There are strategies to decrease the risk of bacterial contamination in beans.

Evidence of post-formed structures during systemic Curtobacterium flaccumfaciens pv. flaccumfaciens infection in resistant Phaseolus vulgaris genotypes / Evidência de estruturas pós-formadas na infecção sistêmica de Curtobacterium flaccumfaciens pv. flaccumfaciens em genótipos resistentes de Phaseolus vulgaris L

Bacterial wilt of the common bean caused by Curtobacterium flaccumfacienspv. flaccumfaciensresults in economic losses. The aim of this study was to analyze the colonization of C. flaccumfaciens pv. flaccumfaciens in resistant, moderately resistant, and susceptible genotypes of common bean plants. The genotypes OuroBranco and IPA 9 (resistant), Diacol Calima (moderately resistant), and CNFRS 11997 and CNFP 10429 (susceptible) were inoculated in the epicotyl, with 100 µL of bacterial suspension of the BRM 14933(Cff25). Disease severity was evaluated 21 days after inoculation (DAI), on a scale from 1 to 9. Plant samples were prepared for scanning electron microscopy analyses. Ouro Branco and IPA 9 (resistant) plants exhibited low colonization, the formation of filaments surrounding bacterial cells and vestures more developed in the pit the xylem vessels. Diacol Calima (moderately resistant) plants presented lower levels of colonization and filament formation than that of resistant cultivars. CNFC 10429 and CNFRS 11997 (susceptible) showed high levels of colonization in the xylem and vessel obstruction, preventing water and nutrient flow, which explains the symptoms of wilt and plant death. Thus, resistance to C. flaccumfacienspv. flaccumfacienscan be explained by plant's capacity to limit pathogen propagation as a post-formed defense mechanismin this pathosystem.(AU)

Curtobacterium flaccumfaciens pv. flaccumfaciensé causadora da murcha-de-curtobacterium, responsável por perdas econômicas.O objetivo deste estudo foi analisara colonização de C. flaccumfaciens pv. flaccumfaciensem genótipos de feijoeiro comumresistente, moderamente resistente e suscetível. Ouro Branco e IPA 9 (resistente), Diacol Calima (moderadamente resistente), CNFRS 11997 e CNFP 10429 (suscetíveis) foram inoculados,no epicótilo,com 100 µL de suspensão bacteriana do isolado BRM 14933(Cff25). A severidade da doença foi avaliada 21 dias após a inoculação, utilizando a escala de 1 a 9. As amostras para MEV foram desidratadas em série alcoólica, secas em ponto crítico com dióxido de carbono (CO2), banhadas em ouro e analisadas em microscópio eletrônico de varredura. As plantas de Ouro Branco e IPA 9 (resistentes) exibiram baixa colonização, formação de filamentos envolvendo células bacterianas e guarnições mais desenvolvidas nas pontoaçõesdos vasos do xilema. Diacol Calima (moderadamente resistente) apresentou menor colonização e formação de filamentos do que as cultivares resistentes. Os genótipos CNFC 10429 e CNFRS 11997 (suscetíveis) mostraram grande colonização no xilema, com vasos obstruídos, impedindo o fluxo de água e nutrientes, explicando os sintomas de murcha e morte da planta. Portanto, a resistência à C. flaccumfacienspv. flaccumfacienspode ser explicada pela capacidade da planta em limitar a multiplicação do patógeno como um mecanismo de defesa celular, sugerindo que este é um dos fatores de resistência estrutural pós-formado que ocorre nesse patossistema.(AU)

An NADPH oxidase regulates carbon metabolism and the cell cycle during root nodule symbiosis in common bean (Phaseolus vulgaris).

BACKGROUND: Rhizobium-legume symbiosis is a specific, coordinated interaction that results in the formation of a root nodule, where biological nitrogen fixation occurs. NADPH oxidases, or Respiratory Burst Oxidase Homologs (RBOHs) in plants, are enzymes that generate superoxide (O2 •-). Superoxide produces other reactive oxygen species (ROS); these ROS regulate different stages of mutualistic interactions. For example, changes in ROS levels are thought to induce ROS scavenging, cell wall remodeling, and changes in phytohormone homeostasis during symbiotic interactions. In common bean (Phaseolus vulgaris), PvRbohB plays a key role in the early stages of nodulation. RESULTS: In this study, to explore the role of PvRbohB in root nodule symbiosis, we analyzed transcriptomic data from the roots of common bean under control conditions (transgenic roots without construction) and roots with downregulated expression of PvRbohB (by RNA interference) non-inoculated and inoculated with R. tropici. Our results suggest that ROS produced by PvRBOHB play a central role in infection thread formation and nodule organogenesis through crosstalk with flavonoids, carbon metabolism, cell cycle regulation, and the plant hormones auxin and cytokinin during the early stages of this process. CONCLUSIONS: Our findings provide important insight into the multiple roles of ROS in regulating rhizobia-legume symbiosis.

Genetic Diversity and Characterization of Symbiotic Bacteria Isolated from Endemic Phaseolus Cultivars Located in Contrasting Agroecosystems in Venezuela.

Phaseolus vulgaris is a grain cultivated in vast areas of different countries. It is an excellent alternative to the other legumes in the Venezuelan diet and is of great agronomic interest due to its resistance to soil acidity, drought, and high temperatures. Phaseolus establishes symbiosis primarily with Rhizobium and Ensifer species in most countries, and this rhizobia-legume interaction has been studied in Asia, Africa, and the Americas. However, there is currently no evidence to show that rhizobia nodulate the endemic cultivars of P. vulgaris in Venezuela. Therefore, we herein investigated the phylogenetic diversity of plant growth-promoting and N2-fixing nodulating bacteria isolated from the root nodules of P. vulgaris cultivars in a different agroecosystem in Venezuela. In comparisons with other countries, higher diversity was found in isolates from P. vulgaris nodules, ranging from α- and ß-proteobacteria. Some isolates belonging to several new phylogenetic lineages within Bradyrhizobium, Ensifer, and Mesorhizobium species were also specifically isolated at some topographical regions. Additionally, some isolates exhibited tolerance to high temperature, acidity, alkaline pH, salinity stress, and high Al levels; some of these characteristics may be related to the origin of the isolates. Some isolates showed high tolerance to Al toxicity as well as strong plant growth-promoting and antifungal activities, thereby providing a promising agricultural resource for inoculating crops.

Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.

Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14 locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14 locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.

Application of Azospirillum on seeds and leaves, associated with Rhizobium inoculation, increases growth and yield of common bean.

Association of rhizobia with other plant growth-promoting bacteria (PGPB), such as Azospirillum, have the potential to increase crop yields. This work aimed to assess how Rhizobium tropici and Azospirillum brasilense alone or in combination, affect the growth and yields of common bean grains (Phaseolus vulgaris L.). In a field experiment, R. tropici and A. brasilense were inoculated on seeds, alone or in combination, associated or not with foliar spraying of A. brasilense. Shoot biomass, nitrogen accumulation, thousand-grain weight, and grain yield were evaluated. Application of A. brasilense, on seed or by foliar spraying, and seed inoculation of R. tropici, had an additive effect, increasing biomass and accumulated nitrogen, thousand-grain weight, and grain yield.

Validation of an in vitro system to trigger changes in the gene expression of effectors of Sclerotinia sclerotiorum.

AIMS: Sclerotinia sclerotiorum, the causal agent of white mold, can infect several host species, including economically important crops. In this study, we propose and validate a new in vitro system able to mimic the conditions of interaction with the host and promote the induction of S. sclerotiorum effectors. METHODS AND RESULTS: For culture media production, we selected three plant species, common bean (Phaseolus vulgaris L, cv. Requinte.), maize (Zea mays, cv. BRS1030) and beggarticks (Bidens pilosa). To validate this system as an in vitro inducer of effectors, the qRT-PCR technique was used to investigate the expression profile of some S. sclerotiorum effector genes in each growth medium at different times after inoculation. CONCLUSION: The results obtained in this study provide a validation of a new method to study S. sclerotiorum during mimetic interaction with different hosts. Although leaf extract does not fully represent the plant environment, the presence of plant components in the culture medium seems to induce effector genes, mimicking in planta conditions. The use of MEVM is simpler than in planta growth, bypasses problems such as the amount of mycelium produced, as well as contamination of host cells during transcriptomic and proteomic analyses. SIGNIFICANCE AND IMPACT OF THE STUDY: We have devised MEVM media as a model mimicking the interaction of S. sclerotiorum and its hosts and used it to evaluate in vitro expression of effectors normally expressed only in planta.

Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean.

KEY MESSAGE: Linkage and genome-wide association analyses using high-throughput SNP genotyping revealed different loci controlling resistance to different isolates of race 65 of Colletotrichum lindemuthianum in common bean. Development of varieties with durable resistance to anthracnose is a major challenge in common bean breeding programs because of the extensive virulence diversity of Colletotrichum lindemuthianum fungus. We used linkage and genome-wide association analyses to tap the genomic regions associated with resistance to different isolates of race 65. Linkage mapping was done using an F2 population derived from the cross between the Mesoamerican common beans BRS Estilo x Ouro Vermelho, inoculated with two different isolates of race 65. Association genetics relied on a diversity common bean panel containing 189 common bean accessions inoculated with five different isolates of race 65 as an attempt to validate the linkage analysis findings and, eventually, identify other genomic regions associated with resistance to race 65. The F2 population and diversity panel were genotyped with the BARCBean6K_3 Illumina BeadChip containing 5398 SNP markers. Both linkage and genome-wide association analyses identified different loci controlling resistance to different isolates of race 65 on linkage group Pv04. Genome-wide association analysis also detected loci on Pv05, Pv10 and Pv11 associated with resistance to race 65. These findings indicate that resistance to race 65 can be overcome by the virulence diversity among different isolates of the same race and could lead to the loss of resistance after cultivar release. We identified 25 resistant common bean cultivars to all five isolates of race 65 in the diversity panel. The accessions should be useful to develop cultivars combining different resistance genes that favor durable resistance to anthracnose in common bean.

Diagrammatic scales for the estimation of black node disease severity in common bean / Escalas diagramáticas para a estimativa da gravidade da doença do nó negro no feijão comum

The objective of this study was to design two diagrammatic scales for the evaluation of black node disease (Stagonosporopsis hortensis and Boeremia spp.) in common bean (Phaseolus vulgaris L.). The developed scales corresponded to logarithmic intervals (SADL) of seven levels and equal intervals (SADE) of nine levels. These scales were compared to the scale developed by the International Center for Tropical Agriculture (CIAT), which corresponds to a descriptive scale (NoSAD). In the scale validation the accuracy, precision, and concordance of repeatability were determined using Lins concordance correlation coefficient, whereas inter-rater reproducibility was determined by the overall concordance correlation coefficient (OCCC). It was observed that with the use of the proposed scales, reproducibility and repeatability were significantly improved for inexperienced raters, and reproducibility was improved in the case of experienced raters. Thus, the designed standard area diagrams with equal and logarithmic intervals are a useful tool for estimating severity under field and experimental conditions as part of the study of this patho-system.(AU)

O objetivo deste estudo foi delinear duas escalas diagramáticas para avaliação da doença do nó preto (Stagonosporopsis hortensis e Boeremia spp.) em feijoeiro (Phaseolus vulgaris L.). As escalas desenvolvidas corresponderam a intervalos logarítmicos (SADL) de sete níveis e intervalos iguais (SADE) de nove níveis. Essas escalas foram comparadas com a escala desenvolvida pelo Centro Internacional de Agricultura Tropical (CIAT), que corresponde a uma escala descritiva (NoSAD). Na validação da escala, a exatidão, precisão e concordância da repetibilidade foram determinadas usando o coeficiente de correlação de concordância de Lin, enquanto a reprodutibilidade entre avaliadores foi determinada pelo coeficiente de correlação de concordância geral (OCCC). Observou-se que, com o uso das escalas propostas, a reprodutibilidade e a repetibilidade foram significativamente melhoradas para os avaliadores inexperientes, e a reprodutibilidade foi melhorada no caso dos avaliadores experientes. Assim, as escalas diagramáticas projetadas são uma ferramenta útil para estimar a severidade em condições experimentais e de campo como parte do estudo desse sistema patológico.(AU)