Exploring novel resistance sources for rust (Uromyces appendiculatus) in common bean using AMMI analysis

Rust, caused by Uromyces appendiculatus (Pers.) Unger, is among the most devastating diseases of the common bean (Phaseolus vulgaris L.) worldwide. The pathogen is highly genetically variable, causing severe epidemics under favourable weather conditions. The objectives of this study were to determine the distribution of bean rust in major production areas in Kenya and identify potential sources of resistance for breeding. A field survey was conducted in five counties targeting smallholder common bean farmers in western and central Kenya, where data on the incidence and severity of bean rust and crop management practices by farmers were recorded. Additionally, seeds of the evaluated genotypes were collected from farms visited for further testing. A total of 77 common bean genotypes were subjected to natural infection under field conditions and inoculated with races 29–1, 29–3, 61–1, and 63–1 of rust under greenhouse conditions at the University of Embu. The gene pool affiliation of the genotypes was determined through the phaseolin protein marker analysis. Rust incidence and severity data were subjected to an analysis of variance using GenStat statistical software. The results showed that bean rust occurred in all counties although there were significant differences ( P < 0.001 ) in incidence and severity among the surveyed localities. Based on a 1–9 severity rating scale, Bungoma County recorded the highest mean severity of 3.99 and an incidence of 71%. Cultivar grown, use of fungicides, management of residues, and crop spacing had a significant effect on bean rust severity. Under field and greenhouse conditions, the genotypes revealed high variations in response to rust, with 71% of the genotypes being susceptible under greenhouse inoculations. Enclave, MU#13, UN2-Darkgreen, UN6-Nakholo, Kat X56, and KMR-11 genotypes were identified as resistant and can be used as prospective parents in common bean improvement programs in Kenya. This study revealed high occurrence and distribution of common bean rust and thus provides critical baseline information for common bean rust management in Kenya.

Bean rust caused by Uromyces appendiculatus Pers., is one of the major foliar diseases in bean (Phaseolus vulgaris L.) worldwide, which leads to considerable crop loss. Selected fluorescent rhizobacteria were screened for their ability to trigger induced systemic resistance (ISR) against rust in beans under greenhouse and field conditions. Rhizobacteria, applied as seed treatments, were compared to untreated seeds (control) for the suppression of rust. Because of rhizobacteria and the pathogen were spatially separated the phenomenon has to be attributed to ISR. Only three isolates out of four root colonizers namely Pseudomonas fluorescens WM35, Pseudomonas aureofaciens WM09 and Pseudomonas putida WM06 significantly protected bean leaves in detached leaf assays, indicating that apart from the root colonization some other criteria may play a role in triggering ISR by rhizobacteria. Moreover, Pseudomonas aeruginosa 7NSK2 and SA44, soil application of salicylic acid, previously reported ISR inducers in bean, also significantly reduced disease development in greenhouse pot experiments. Under field conditions, WM35, WM09 and WM06 significantly induced ISR against bean rust up to 30 days after seeding (DAS). However, only P. fluorescens WM35 and P. putida WM06 were able to protect bean plants from rust infection throughout the experiment. Therefore, this study clearly demonstrated the ability of rhizobacteria to suppress bean rust under field conditions.

Bean rust (Uromyces appendiculatus (Pers.:Pers.) Unger var. appendiculatus) is one of the most devastating and variable pathogens of common bean (Phaseolus vulgaris L.) worldwide that can cause total crop loss. Characterization of bean rust races can help in screening resistant materials during gene pyramiding. The aims of the present research were first, to characterize bean rust isolates collected from snap bean growing areas in Kenya. Secondly, to identify which of the available rust resistance genes in common bean differentials are most effective to control rust in those areas. Snap bean leaf tissues with rust pustules were collected from different farms in eight locations in central and western Kenya during the years 2010 and 2011. Forty seven single pustule isolates were obtained and inoculated on 12 bean rust differential cultivars. For consistent results, the inoculation was repeated twice. The new international classification system and the binary nomenclature grouped the 47 single pustule isolates of U. appendiculatus into 9 different races, most of this affected the Andean gene pool. Hierarchical cluster analysis grouped the races into two major clusters depending on the virulence of the races on the host differential cultivars. The most resistant genes for pyramiding in Kenya were identified as Ur-5, Ur-11 and Ur-CNC. An important output of this study was the identification of races with potential use during gene pyramiding process. Key words: Uromyces appendiculatus, snap bean, races, genes, characterization.

Common bean rust (Uromyces appendiculatus) is an important disease affecting common bean (Phaseolus vulgaris L.) production in the world. In Ethiopia, this is the most destructive disease constraining common bean production. Field experiments were carried out at Hirna Research Sub-Station of Haramaya University in the 2010 main cropping season to elucidate reaction of released common bean varieties to rust infection and to study the effect of integrated use of host resistance and fungicide foliar sprays on incidence of the disease and its control. For the evaluation of common bean varieties to rust disease the experiment was laid out in randomized complete block design with three replications and 15 varieties and the experiment was laid out as a randomized complete block design in factorial arrangement with three replications for the management part. In the fungicide spray, three contact (i.e., Chlorothalonil, Mancozeb and Copper hydroxide) and one systemic (Triadimefon) fungicides were tested on a susceptible (Mexican-142) and a moderately resistant (Awash-1) varieties. The research results obtained indicated that the evaluated common bean varieties varied significantly in severity, area under disease progress curve, disease progress rate and grain yield. Three reaction groups of common bean varieties were identified, viz. susceptible, moderately resistant and resistant. The resistant varieties produced the highest grain yield. At Hirna the varieties, Kufanzik, Haramaya, Melkadima, Gofta, Chore and Awash Melka were found to be resistant to the disease. These varieties were also high yielders. However, in case seeds of resistant varieties are inadequate to cover the major growing areas, farmers can use the moderately resistant varieties with fungicide sprays wherever the disease is a pervasive and pressing problem. In the management study, lower rust incidence, severity, area under progress curve and slower disease progress rate occurred on the moderately resistant variety sprayed with Triadimefon than on the susceptible variety with Triadimefon and/or with other fungicides (Mancozeb, Copper hydroxide and Chlorothalonil). The integrated use of moderately resistant variety (Awash-1) with Triadimefon proved to be the best management option producing the highest (2306.25 kg ha-1) grain yield. Triadimefon foliar spray reduced relative grain yield loss by 10.84% on the moderately resistant variety Awash-1 compared to the susceptible variety Mexican-142. In conclusion, integrated use of Awash-1 with Triadimefon spray was found to be the most effective bean rust management option.

Common bean (Phaseolus vulgaris) is one of the legume crops most consumed worldwide and bean rust is one of the most severe foliar biotrophic fungal diseases impacting its production. In this work, we searched for new sources of rust resistance (Uromyces appendiculatus) in a representative collection of the Portuguese germplasm, known to have accessions with an admixed genetic background between Mesoamerican and Andean gene pools. We identified six accessions with incomplete hypersensitive resistance and 20 partially resistant accessions of Andean, Mesoamerican, and admixed origin. We detected 11 disease severity-associated single-nucleotide polymorphisms (SNPs) using a genome-wide association approach. Six of the associations were related to partial (incomplete non-hypersensitive) resistance and five to incomplete hypersensitive resistance, and the proportion of variance explained by each association varied from 4.7 to 25.2%. Bean rust severity values ranged from 0.2 to 49.1% and all the infection types were identified, reflecting the diversity of resistance mechanisms deployed by the Portuguese germplasm.The associations with U. appendiculatus partial resistance were located in chromosome Pv08, and with incomplete hypersensitive resistance in chromosomes Pv06, Pv07, and Pv08, suggesting an oligogenic inheritance of both types of resistance. A resolution to the gene level was achieved for eight of the associations. The candidate genes proposed included several resistance-associated enzymes, namely β-amylase 7, acyl-CoA thioesterase, protein kinase, and aspartyl protease. Both SNPs and candidate genes here identified constitute promising genomics targets to develop functional molecular tools to support bean rust resistance precision breeding.

As biorationals, plant oils offer numerous advantages such as being natural products, with low ecotoxicological side effects, and high biodegradability. In particular, drying glyceride plant oils, which are rich in unsaturated fatty acids, might be promising candidates for a more sustainable approach in the discussion about plant protection and the environment. Based on this, we tested the protective and curative efficacy of an oil-in-water-emulsion preparation using drying plant oils (linseed oil, tung oil) and a semi-drying plant oil (rapeseed oil) separately and in different mixtures. Plant oils were tested in greenhouse experiments (in vivo) on green beans (Phaseolus vulgaris L.) against bean rust (Uromyces appendiculatus). We observed that a 2% oil concentration showed no or very low phytotoxic effects on green beans. Both tested drying oils showed a protective control ranging from 53–100% for linseed oil and 32–100% for tung oil. Longer time intervals of 6 days before inoculation (6dbi) were less effective than shorter intervals of 2dbi. Curative efficacies were lower with a maximum of 51% for both oils when applied 4 days past inoculation (4dpi) with the fungus. Furthermore, the results showed no systemic effects. These results underline the potential of drying plant oils as biorationals in sustainable plant protection strategies.

Uganda is the second largest producer of dry beans (Phaseolus vulgaris L.) in Africa, but common bean rust caused by Uromyces appendiculatus (Pers. Unger), is negatively impacting the production of the crop. There is little information on the occurrence and identity of the rust pathotypes present in the country. Consequently, a field survey was carried out during the 2015 second planting season in fifteen districts, representing the areas of high beans production in Uganda. High common bean rust incidence and severity were observed in the low altitudes and the South-Western Highlands of Uganda. Wakiso and Hoima districts had the highest rust disease incidence 72 and 76% respectively and severity rates of 6 and 5.5, respectively. Rust disease incidence was uniformly high on commercial genotypes and landraces. Similarly, high rust disease incidence and severity were observed in the bean-maize–groundnut cropping system. Twenty-three single rust isolates were collected in Uganda and inoculated on 11 bean rust differentials and Ouro Negro (Ur-14) genotypes. Six rust pathotypes were identified and these included 2-0, 4-0, 50-0, 5-1, 4-33 and 63-19. Five of the pathotypes were of Andean origin and only pathotype 4-33 was of Mesoamerican origin. The rust pathotype 63-19 showed similar pathogenic characteristics with the Puerto Rico rust race 19-63. This study provides critical baseline information to integrate breeding and crop protection in the efforts to develop an overall strategy for the management of common beans in Uganda. Key words: Phaseolus vulgaris, Uromyces appendiculatus, rust differentials, co-evolution, disease severity.

Race-specific resistance to the bean rust pathogen (Uromyces appendiculatus) is provided by a number of loci in common bean (Phaseolus vulgaris). The Ur-3 locus controls hypersensitive resistance (HR) to 44 of the 89 races curated in the United States. To better understand resistance mediated by this locus, we developed new genetic material for analysis. We developed a population of mutagenized seed of cv. Sierra (genotype = Ur-3 ur-4 ur-6) that was screened with a bean rust race that is normally incompatible (HR response) on Ur-3 genotypes. We discovered two mutants of common bean, crg and ur3-delta3, in which uredinia formed on leaves (a compatible interaction) following infection. The F1 generation from a cross of these two mutants expressed the HR response, and the F2 generation segregated in a ratio of 9:7 (HR/uredinia formation). Therefore, the two genes are unlinked. Further genetic analysis determined that the mutation in ur3-delta3 was in the Ur-3 locus, and the mutation in crg was in a newly discovered gene given the symbol Crg (Complements resistance gene). Each mutation was inherited in a recessive manner. Unlike ur3-delta3, crg expressed reduced compatibility to bean rust races 49 and 47 that are normally fully compatible on genotypes, such as Sierra, that are homozygous recessive at the Ur-4 and Ur-6 loci. This suggests a gene mutated in crg is normally a positive compatibility factor for the bean-bean rust interaction. Polymerase chain reaction analysis of crg with primers to common bean resistance gene analogs (RGA) that contain a nucleotide-binding site sequence similar to those found in a number of plant disease resistance genes revealed that crg is missing the SB1 RGA, but not the linked SB3 and SB5 RGAs. Genetic analyses revealed that Crg cosegregates with the SB1 RGA. These results demonstrate that Crg is located near a RGA cluster in the common bean genome.

Bean rust caused by Uromyces appendiculatus (Pers.) Unger is an important disease in common bean (Phaseolus vulgaris L.) worldwide. To our knowledge this is the first report of a new race of U. appendiculatus (19-63) in Puerto Rico and in the western hemisphere. Accepted for publication 4 February 2009. Published 25 March 2009.

Benzo‐(1,2,3)‐thiadiazole‐7‐carbothioic acid S‐methyl ester (BTH), trade name Bion®, was used to induce resistance in bean cultivars Borlotto Nano Lingua di Fuoco (BLF), Borlotto Taylor, Cannellino, Cannellino Montalbano, Saxa and Top Crop, against rust caused by Uromyces appendiculatus. A single 0.3 mm BTH spray 7 days before inoculation was sufficient to fully control the disease in all the examined cultivars. As regards the more susceptible BLF, either a single treatment 14 days before inoculation, or three applications on the third, fifth and seventh day before inoculation, were equally effective to prevent infection. Histochemical and cytochemical investigations showed that BTH causes hydrogen peroxide (H2O2) accumulation in the treated tissues. H2O2 deposits were localized in situ for the first time in the apoplast of the leaf epidermis. No cell death was detected at BTH concentrations below the phytotoxicity threshold, suggesting that acquired resistance against bean rust is mainly related to the enhanced activity of anionic peroxidases, promoted by H2O2 accumulation, thereby leading to cell wall strengthening. This hypothesis is also supported by the long induction phase required to establish complete resistance.

Common bean (Phaseolus vulgaris L.) is important legume crop world-wide and in Ethiopia for its multipurpose uses. Common bean rust, is the most destructive fungal disease that severely reduces bean yield. For years, rust appeared in a farmer's field in Southern Ethiopia; however, the disease's significance remains unclear. The research aimed to ascertain the distribution and intensity of common bean rust, as well as elucidate the association of biophysical parameters. The field survey was conducted in southern Ethiopia in 2022. Ninety percent of the 78 commonbean fields were affected by common bean rust. Mareko, Meskan, Duguna Fango, Damot Woide, and Demba Gofa had 100% of the fields affected, and Boricha had 90%. Damot Woide and Lanfuro had the highest and lowest mean rust incidence rates, respectively, 59.2% and 22.5%. Duguna Fango had the highest rust severity (35.5%), while Lanfuro had the lowest (13.5%). In the research areas, the biophysical factors, either alone or in combination, have a significant impact on the intensity of common bean rust. The current investigation verified the distributionand the association biophysical factors with common bean rust. In addition, the survey of the disease and the identification of factors should continue over time and space.

Bean rust, caused by Uromyces appendiculatus, is a major disease of common bean (Phaseolus vulgaris). The objective was to identify RAPD markers linked to the gene (Ur-7) for specific resistance to rust race 59 using bulked segregant analysis in an F2 segregating population from the common bean cross GN1140 (resistant to rust) × Nebraska #1 (susceptible to rust). A single dominant gene controlling specific resistance to race 59 was found in the F2 and was confirmed in the F3. Seven RAPD markers were detected in a coupling-phase linkage with the Ur-7 gene. Coupling-phase RAPD markers OAA11.500, OAD12.550, and OAF17.900 with no recombination to the Ur-7 gene were found. Three RAPD markers were identified in a repulsion-phase linkage with the Ur-7 gene among the three markers at a distance of 8.2 cM. This is the first report on RAPD markers linked to the Ur-7 gene in common bean. The RAPD markers linked to the gene for specific rust resistance of Middle American origin detected here, along with other independent rust resistance genes from other germplasm, could be used to pyramid multiple genes into a bean cultivar for more-durable rust resistance.

The common bean (Phaseolus vulgaris L.) is the most important legume crop directly used for human consumption worldwide. Bean rust, caused by Uromyces appendiculatus, is a devastating disease and usually causes severe loss of seed yield and pod quality. Deployment of resistant cultivars is the best strategy to combat this disease. However, despite being the largest snap bean-producing country, the genetic basis research of rust resistance has largely lagged in China. In this study, an RIL population and a diversity panel were evaluated for rust resistance against a purified rust isolate Cua-LS using a detached leaf assay. Deploying a QTL-Seq analysis in the RIL population, a 1.81 Mb interval on chromosome 4, a 2.73 Mb interval on chromosome 5 and a 1.26 Mb interval on chromosome 6 were identified as major QTLs for rust resistance, designated as Qur-1, Qur-2 and Qur-3, respectively. Through a GWAS diversity panel, 64 significant SNPs associated with rust resistance were detected, distributed in all 11 chromosomes and explaining 19–49% of the phenotypic variation. Synteny analysis showed that Qur-2 was validated in GWAS, but the rust QTL/SNPs detected in our study were different from the known genes, except Ur-11. A total of 114 candidate genes, including the typical NBS-LRR genes, protein kinase superfamily proteins and ABC transporter family proteins, were identified and proposed as the likely candidates. The identified 17 resistant accessions will enrich the resistant germplasm resources, and the detected QTLs/SNPs will facilitate the molecular breeding of rust resistance in the common bean.

Bean rust, caused by Uromyces appendiculatus, is a devastating disease of common bean (Phaseolus vulgaris) in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome other rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker-assisted selection produce false results. Here, we describe the fine mapping of the Ur-3 locus for the development of highly accurate markers linked to Ur-3. An F2 population from the cross Pinto 114 (susceptible) × Aurora (resistant with Ur-3) was evaluated for its reaction to four different races of U. appendiculatus. A bulked segregant analysis using the SNP chip BARCBEAN6K_3 placed the approximate location of Ur-3 in the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean varieties positioned Ur-3 in a 46.5 kb genomic region from 46.96 to 47.01 Mb on Pv11. We discovered in this region the SS68 KASP marker that was tightly linked to Ur-3. Validation of SS68 on a panel of 130 diverse common bean cultivars containing all known rust resistance genes revealed that SS68 was highly accurate and produced no false results. The SS68 marker will be of great value in pyramiding Ur-3 with other rust resistance genes. It will also significantly reduce time and labor associated with the current phenotypic detection of Ur-3. This is the first utilization of fine mapping to discover markers linked to rust resistance in common bean.

Common bean is an economically, nutritionally, and socially important crop. It is grown in distinct regions and different seasons around the world by subsistence level farmers with low-technology input as well as by farmers that use high input technologies. One important factor that can limit the bean growing and drastically affect grain yields is the high number of destructive pathogens that attack and cause serious damage to the crop. Among them is bean rust, incited by the fungus Uromyces appendiculatus. This disease is distributed throughout the world, but it effectively causes major production problems in humid tropical and subtropical regions. In Brazil, rust causes major losses in south, southeast, and central regions of the country. Bean rust control by resistant cultivars is an easy and economical strategy to be used in association to other rust management practices. Pyramiding of different race-specific resistance genes in association with other genes conferring adult plant resistance, slow rusting, and reduced pustule size can prolong the lifespan of a common bean cultivar by creating a more durable resistance complex against the rust pathogen. This review manuscript presents an overview on bean rust and reports some breeding efforts aiming to develop rust resistant cultivars in Brazil.