Breeding Common Bean for Resistance to Common Blight: A Review

A dTALE approach demonstrates that induction of common bean OVATE Family Protein 7 promotes resistance to common bacterial blight

Common bacterial blight (CBB) is a devastating seed-transmitted disease of common bean (Phaseolus vulgaris L.), caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans. The genes responsible for CBB resistance are largely unknown. Moreover, the lack of a reproducible and universal transformation protocol limits the study of genetic traits in common bean. We produced X. phaseoli pv. phaseoli strains expressing artificially designed transcription-activator like effectors (dTALEs) to target 14 candidate genes for resistance to CBB based on previous transcriptomic data. In planta assays in a susceptible common bean genotype showed that induction of PvOFP7, PvAP2-ERF71, or PvExpansinA17 expression by dTALEs resulted in CBB symptom reduction. After PvOFP7 induction, in planta bacterial growth was reduced at early colonization stages, and RNA-seq analysis revealed up-regulation of cell wall formation and primary metabolism, together with major down-regulation of heat shock proteins. Our results demonstrated that PvOFP7 contributes to CBB resistance, and underlined the usefulness of dTALEs for functional validation of genes whose induction impacts Xanthomonas-plant interactions.

Transcriptomic dataset of Phaseolus vulgaris leaves in response to the inoculation of pathogenic Xanthomonas citri pv. fuscans and its type III secretion system-defective mutant hrcV

Xanthomonas citri pv. fuscans (Xcf) and Xanthomonas phaseoli pv. phaseoli (Xpp) are responsible for the Common Bacterial Blight (CBB), a major common bean (Phaseolus vulgaris) disease. The pathogenicity of Xcf and Xpp is known to be dependent upon a functional Type III Secretion System (T3SS) allowing the injection of numerous bacterial Type III Effectors (T3Es) into plant cells. T3Es have been described as able to disrupt plant defence and manipulate plant metabolism. In this work we described the transcriptomic response of one susceptible (Flavert) and one resistant (Vezer) cultivars of P. vulgaris to the inoculation of the virulent strain Xcf CFBP4885 or its avirulent T3SS-defective hrcV mutant (CFBP13802). Leaves of both bean cultivars were infiltrated with water or bacterial suspensions. Inoculated leaves were sampled at 24 or 48 h post inoculation (hpi). The experiment was independently repeated three times for total RNA extraction and sequencing analysis. Library construction and total RNA sequencing were performed with BGISEQ-500 at Beijing Genomics Institute (BGI, Hong-Kong), generating an average of 24M of paired-end reads of 100bp per sample. FastQC was used to check reads quality. Mapping analyses were made using a quasi-mapping alignment from Salmon (version 1.2.1) against the Phaseolus vulgaris reference genome (version 2.1), revealing the expression profiles of 36,978 transcripts in leaf tissues. Fastq raw data and count files from 36 samples are available in the Gene Expression Omnibus (GEO) repository of the National Center for Biotechnology Information (NCBI) under the accession number GSE271236. This dataset is a valuable resource to investigate the role of T3Es in subverting the cellular functions of bean.

GWAS of resistance to three bacterial diseases in the Andean common bean diversity panel

Bacterial brown spot (BBS) caused by Pseudomonas syringae pv. syringae (Pss), common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli (Xap) and Xanthomonas fuscans subsp. fuscans (Xff), and halo bacterial blight (HBB), caused by Pseudomonas syringae pv. phaseolicola (Psph), are major bacterial diseases that severely affect common bean yields and global food security. Andean-origin dry beans, representing large-seeded market classes, are particularly susceptible. Using 140,325 SNPs, a multi-locus GWAS was conducted on subsets of the Andean diversity panel (ADP) phenotyped for BBS in South Africa, CBB in Puerto Rico, South Africa, and Zambia, and HBB in South Africa, through natural infection, artificial inoculation, or both. Twenty-four QTL associated with resistance were identified: nine for BBS, eight for CBB, and seven for HBB. Four QTL intervals on Pv01, Pv03, Pv05, and Pv08 overlapped with BBS and HBB resistance. A genomic interval on Pv01, near the fin gene, which determines growth habit, was linked to resistance to all three pathogens. Different QTLs were detected for BBS and CBB resistance when phenotyped under natural infection versus artificial inoculation. These results underscore the importance of combining phenotyping methods in multi-GWAS to capture the full genetic spectrum. Previously recognized CBB resistance QTL SAP6 and SU91 and HBB resistance QTL HB4.2, and HB5.1, were observed. Other common (MAF >0.25) and rare (MAF <0.05) resistance QTL were also detected. Overall, these findings enhance the understanding and utilization of bacterial resistance present in ADP for the development of common beans with improved resistance.

Improving Common Bacterial Blight Phenotyping by Using Rub Inoculation and Machine Learning: Cheaper, Better, Faster, Stronger

Accurate assessment of plant symptoms plays a key role for measuring the impact of pathogens during plant-pathogen interaction. Common bacterial blight caused by Xanthomonas phaseoli pv. phaseoli and X. citri pv. fuscans is a major threat to common bean. The pathogenicity of these bacteria is variable among strains and depends mainly on a type III secretion system and associated type III effectors such as transcription activator-like effectors. Because the impact of a single gene is often small and difficult to detect, a discriminating methodology is required to distinguish the slight phenotype changes induced during the progression of the disease. Here, we compared two different inoculation and symptom assessment methods for their ability to distinguish two tal mutants from their corresponding wild-type strains. Interestingly, rub inoculation of the first leaves combined with symptom assessment by machine learning-based imaging allowed significant distinction between wild-type and mutant strains. By contrast, dip inoculation of first-trifoliate leaves combined with chlorophyll fluorescence imaging did not differentiate the strains. Furthermore, the new method developed here led to the miniaturization of pathogenicity tests and significant time savings.

Regulatory Mechanisms of the Resistance to Common Bacterial Blight Revealed by Transcriptomic Analysis in Common Bean (Phaseolus vulgaris L.)

Common bean blight (CBB), primarily caused by Xanthomonas axonopodis pv. phaseoli (Xap), is one of the most destructive diseases of common bean (Phaseolus vulgaris L.). The tepary bean genotype PI 319443 displays high resistance to Xap, and the common bean genotypes HR45 and Bilu display high resistance and susceptibility to Xap, respectively. To identify candidate genes related to Xap resistance, transcriptomic analysis was performed to compare gene expression levels with Xap inoculation at 0, 24, and 48 h post inoculation (hpi) among the three genotypes. A total of 1,146,009,876 high-quality clean reads were obtained. Differentially expressed gene (DEG) analysis showed that 1,688 DEGs responded to pathogen infection in the three genotypes. Weighted gene coexpression network analysis (WGCNA) was also performed to identify three modules highly correlated with Xap resistance, in which 334 DEGs were likely involved in Xap resistance. By combining differential expression analysis and WGCNA, 139 DEGs were identified as core resistance-responsive genes, including 18 genes encoding resistance (R) proteins, 19 genes belonging to transcription factor families, 63 genes encoding proteins with oxidoreductase activity, and 33 plant hormone signal transduction-related genes, which play important roles in the resistance to pathogen infection. The expression patterns of 20 DEGs were determined by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-seq results.

Common bacterial blight of bean: a model of seed transmission and pathological convergence

BACKGROUND

Xanthomonas citri pv. fuscans (Xcf) and Xanthomonas phaseoli pv. phaseoli (Xpp) are the causal agents of common bacterial blight of bean (CBB), an important disease worldwide that remains difficult to control. These pathogens belong to distinct species within the Xanthomonas genus and have undergone a dynamic evolutionary history including the horizontal transfer of genes encoding factors probably involved in adaptation to and pathogenicity on common bean. Seed transmission is a key point of the CBB disease cycle, favouring both vertical transmission of the pathogen and worldwide distribution of the disease through global seed trade.

TAXONOMY

Kingdom: Bacteria; phylum: Proteobacteria; class: Gammaproteobacteria; order: Lysobacterales (also known as Xanthomonadales); family: Lysobacteraceae (also known as Xanthomonadaceae); genus: Xanthomonas; species: X. citri pv. fuscans and X. phaseoli pv. phaseoli (Xcf-Xpp).

HOST RANGE

The main host of Xcf-Xpp is the common bean (Phaseolus vulgaris). Lima bean (Phaseolus lunatus) and members of the Vigna genus (Vigna aconitifolia, Vigna angularis, Vigna mungo, Vigna radiata, and Vigna umbellata) are also natural hosts of Xcf-Xpp. Natural occurrence of Xcf-Xpp has been reported for a handful of other legumes such as Calopogonium sp., Pueraria sp., pea (Pisum sativum), Lablab purpureus, Macroptilium lathyroides, and Strophostyles helvola. There are conflicting reports concerning the natural occurrence of CBB agents on tepary bean (Phaseolus acutifolius) and cowpea (Vigna unguiculata subsp. unguiculata).

SYMPTOMS

CBB symptoms occur on all aerial parts of beans, that is, seedlings, leaves, stems, pods, and seeds. Symptoms initially appear as water-soaked spots evolving into necrosis on leaves, pustules on pods, and cankers on twigs. In severe infections, defoliation and wilting may occur.

DISTRIBUTION

CBB is distributed worldwide, meaning that it is frequently encountered in most places where bean is cultivated in the Americas, Asia, Africa, and Oceania, except for arid tropical areas. Xcf-Xpp are regulated nonquarantine pathogens in Europe and are listed in the A2 list by the European and Mediterranean Plant Protection Organization (EPPO).

GENOME

The genome consists of a single circular chromosome plus one to four extrachromosomal plasmids of various sizes, for a total mean size of 5.27 Mb with 64.7% GC content and an average predicted number of 4,181 coding sequences.

DISEASE CONTROL

Management of CBB is based on integrated approaches that comprise measures aimed at avoiding Xcf-Xpp introduction through infected seeds, cultural practices to limit Xcf-Xpp survival between host crops, whenever possible the use of tolerant or resistant bean genotypes, and chemical treatments, mainly restricted to copper compounds. The use of pathogen-free seeds is essential in an effective management strategy and requires appropriate sampling, detection, and identification methods. USEFUL WEBSITES: https://gd.eppo.int/taxon/XANTPH, https://gd.eppo.int/taxon/XANTFF, and http://www.cost.eu/COST_Actions/ca/CA16107.

The Induction of the Isoflavone Biosynthesis Pathway Is Associated with Resistance to Common Bacterial Blight in Phaseolus vulgaris L

Xanthomonas axonopodis infects common bean (Phaseolus vulgaris L.) causing the disease common bacterial blight (CBB). The aim of this study was to investigate the molecular and metabolic mechanisms underlying CBB resistance in P. vulgaris. Trifoliate leaves of plants of a CBB-resistant P. vulgaris recombinant inbred line (RIL) and a CBB-susceptible RIL were inoculated with X. axonopodis or water (mock treatment). Leaves sampled at defined intervals over a 48-h post-inoculation (PI) period were monitored for alterations in global transcript profiles. A total of 800 genes were differentially expressed between pathogen and mock treatments across both RILs; approximately half were differentially expressed in the CBB-resistant RIL at 48 h PI. Notably, there was a 4- to 32-fold increased transcript abundance for isoflavone biosynthesis genes, including several isoflavone synthases, isoflavone 2'-hydroxylases and isoflavone reductases. Ultra-high performance liquid chromatography-tandem mass spectrometry assessed leaf metabolite levels as a function of the PI period. The concentrations of the isoflavones daidzein and genistein and related metabolites coumestrol and phaseollinisoflavan were increased in CBB-resistant RIL plant leaves after exposure to the pathogen. Isoflavone pathway transcripts and metabolite profiles were unaffected in the CBB-susceptible RIL. Thus, induction of the isoflavone pathway is associated with CBB-resistance in P. vulgaris.

Sources of Resistance to Common Bacterial Blight and Charcoal Rot Disease for the Production of Mesoamerican Common Beans in the Southern United States

The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) to evaluate field-level resistance from the various commercial classes and subgroups represented in the Mesoamerican gene pool as sources for breeding beans for the region and (2) to evaluate genome-wide marker × trait associations (GWAS) using genetic markers for the genotypes. A total of 300 genotypes from the Mesoamerican Diversity Panel (MDP) were evaluated for CBB and CR in field experiments for three years. CBB resistance was also tested with a field isolate in controlled greenhouse conditions. The analysis of variance revealed the presence of variability in the MDP for the evaluated traits. We also identified adapted common bean genotypes that could be used directly in Southeastern production or that could be good parents in breeding programs for CBB and CR resistance. The GWAS detected 14 significant Single-Nucleotide Polymorphism (SNP) markers associated with CBB resistance distributed on five chromosomes, namely Pv02, Pv04, Pv08, Pv10, and Pv11, but no loci for resistance to CR. A total of 89 candidate genes were identified in close vicinity (±100 kb) to the significant CBB markers, some of which could be directly or indirectly involved in plant defense to diseases. These results provide a basis to further understand the complex inheritance of CBB resistance in Mesoamerican common beans and show that this biotic stress is unrelated to CR resistance, which was evident during a drought period. Genotypes with good yield potential for the Southeastern U.S. growing conditions were found with resistant to infection by the two diseases, as well as adaptation to the hot and humid conditions punctuated by droughts found in this region.

Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

BACKGROUND

Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major production constraint for common bean, a situation that will be aggravated with current climate change scenarios. In this context, new tools designed to understand the genetic basis governing the phenotypic responses to abiotic stress are required to improve transfer of desirable traits into cultivated beans.

RESULTS

A multiparent advanced generation intercross (MAGIC) population of common bean was generated from eight Mesoamerican breeding lines representing the phenotypic and genotypic diversity of the CIAT Mesoamerican breeding program. This population was assessed under drought conditions in two field trials for yield, 100 seed weight, iron and zinc accumulation, phenology and pod harvest index. Transgressive segregation was observed for most of these traits. Yield was positively correlated with yield components and pod harvest index (PHI), and negative correlations were found with phenology traits and micromineral contents. Founder haplotypes in the population were identified using Genotyping by Sequencing (GBS). No major population structure was observed in the population. Whole Genome Sequencing (WGS) data from the founder lines was used to impute genotyping data for GWAS. Genetic mapping was carried out with two methods, using association mapping with GWAS, and linkage mapping with haplotype-based interval screening. Thirteen high confidence QTL were identified using both methods and several QTL hotspots were found controlling multiple traits. A major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified. Further hotspots affecting several traits were observed on chromosomes Pv03 and Pv08. A major QTL for seed Fe content was contributed by MIB778, the founder line with highest micromineral accumulation. Based on imputed WGS data, candidate genes are reported for the identified major QTL, and sequence changes were identified that could cause the phenotypic variation.

CONCLUSIONS

This work demonstrates the importance of this common bean MAGIC population for genetic mapping of agronomic traits, to identify trait associations for molecular breeding tool design and as a new genetic resource for the bean research community.

Screening Andean Diversity Panel Dry Bean Lines for Resistance to Bacterial Brown Spot Disease Under Field Conditions in South Africa

Bacterial brown spot (BBS) disease caused by Pseudomonas syringae pv. syringae is an important disease of dry bean (Phaseolus vulgaris L.), with grain yield losses of 55% reported in South Africa. This study aimed to identify BBS disease-resistant genotypes from 415 Andean Diversity Panel (ADP) dry bean lines and 5 check cultivars under field conditions across three sites in South Africa: Warden and Middelburg under natural infestation and Potchefstroom under artificial inoculation. Plants at Potchefstroom were inoculated with P. syringae pv. syringae using three isolates at 21, 28, and 36 days after planting, and disease scoring was done at 7, 14, and 21 days after inoculation following a modified 1 to 9 International Centre for Tropical Agriculture (CIAT) scale. The BBS severity percentage and the area under the disease progress curve (AUDPC) were applied to quantify the reaction of bean genotypes to BBS disease. The study identified 17.2% of evaluated germplasm as resistant and 45.3% as moderately resistant. Genotypes ADP-0592, ADP-0790, ADP-0120, and ADP-0008 were selected for both resistance and high seed yield across the three environments. Genotypes ADP-0546, ADP-0630, ADP-0120, and ADP-0279 were selected for both high yield and resistance at Warden, whereas ADP-0038, ADP-0721, and ADP-0790 were selected for both traits at Middelburg, and lastly, ADP-0120 and ADP-0079 were selected for both traits at Potchefstroom. The best genotypes selected for both high yield and BBS resistance had grain yield >1.45 t ha^-1 across sites and >1.85 t ha^-1 at individual sites, and they out yielded the best-performing check cultivar (1.13 t ha^-1) and the grand mean yield (0.87 t ha^-1) across sites. The AUDPC had a strong negative correlation (r = -0.55, P < 0.001) with grain yield at Potchefstroom. Medium-seeded genotypes showed a lower AUDPC than the large-seeded genotypes, and indeterminate genotypes showed a lower AUDPC than determinate genotypes. The genotypes selected for resistance and yield can be utilized in future dry bean improvement efforts for the South African bean market.

Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis

BACKGROUND

Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown.

RESULTS

We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification.

CONCLUSIONS

This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.

Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis

Background

Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown.

Results

We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification.

Conclusions

This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.

Sources, Spectrum, Genetics, and Inheritance of Phaseolus vulgaris Resistance Against Xanthomonas citri pv. fuscans

Common bean (Phaseolus vulgaris) is one of the most consumed agricultural products in the world. Its production is affected by common bacterial blight (CBB) caused by Xanthomonas citri pv. fuscans and X. phaseoli pv. phaseoli. In this work, we investigated the spectrum, genetics, and inheritance of common bean resistance to X. citri pv. fuscans. Inoculation of nine selected cultivars with an X. citri pv. fuscans strain showed that BRS Radiante and IAPAR 16 were resistant. These two cultivars were also resistant to six X. phaseoli pv. phaseoli strains of different geographic origins, demonstrating their broad-spectrum resistances. BRS Radiante sustained smaller X. citri pv. fuscans populations than two susceptible cultivars. Stomatal densities of IAPAR 16 and BRS Radiante were significantly higher than or not different from susceptible cultivars. BRS Radiante showed the lowest general combining ability values and the combination BRS Radiante × Carioca MG the lowest specific combining ability (SCA) values, revealing the capacity of BRS Radiante to increase resistance to X. citri pv. fuscans. Positive and negative parental SCA values indicated dominant and recessive genes involved in X. citri pv. fuscans resistance. Resistance of the BRS Radiante × Carioca MG cross segregated in a 9:7 ratio in the F₂ population, indicating that it is governed by two complementary dominant genes. Maximum likelihood analysis showed that the resistance of BRS Radiante to X. citri pv. fuscans is conferred by a gene of major effect with contribution of additional polygenes. This study contributes with important knowledge on the resistance against CBB in Brazilian common bean cultivars as well as with molecular tools for confirmation of common bean hybrids.

Imidazolium salts as alternative compounds to control diseases caused by plant pathogenic bacteria

AIMS

To evaluate the inhibitory effect of five structurally different imidazolium salts on the in vitro growth of plant pathogenic bacteria that belong to divergent taxonomic genera as well as their ability to reduce the severity of common bacterial blight of common bean caused by Xanthomonas axonopodis pv. phaseoli and bacterial speck of tomato caused by Pseudomonas syringae pv. tomato.

METHODS AND RESULTS

Growth inhibition of Xanthomonas, Pseudomonas, Erwinia, Pectobacterium and Dickeya strains by imidazolium salts was assessed in vitro by radial diffusion on agar medium and by ressazurin reduction in liquid medium. The reduction of common bacterial blight and bacterial speck symptoms and the area under de disease progress curves were determined by spraying two selected imidazolium salts on healthy plants 48 h prior to inoculation with virulent strains of the bacterial pathogens. All imidazolium salts inhibited the growth of all plant pathogenic bacteria when tested by radial diffusion on agar medium. The strength of inhibition differed among imidazolium salts when tested on the same bacterial strain and among bacterial strains when tested with the same imidazolium salt. In liquid medium, most imidazolium salts presented the same minimum inhibitory concentration (MIC) and minimum bactericidal concentration values (200 µmol l^-1 ), the most notable exception of which was the MIC (at least 1000 µmol l^-1 ) for the dicationic MImC₁₀ MImBr₂ . The imidazolium salts C₁₆ MImBr and C₁₆ MImCl caused significant reductions in the severity of common bacterial blight symptoms when compared with nontreated plants.

CONCLUSION

Imidazolium salts inhibit the in vitro growth of plant pathogenic bacteria and reduce plant disease symptoms to levels comparable to an authorized commercial antibiotic product.

SIGNIFICANCE AND IMPACT OF THE STUDY

New compounds exhibiting broad-spectrum antibacterial activity with potential use in agriculture were identified.