Complete and Circularized Genome Sequences of 17 Xanthomonas Strains Responsible for Common Bacterial Blight of Bean

We report the complete and circularized genome sequences of 17 strains of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli, which cause common bacterial blight of bean. These new assemblies combining PacBio and short-read sequencing methods provide high-quality material for studying the evolution of these plant pathogens.

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 Xanthomonas citri pv. fuscans (Xpp-Xcf) 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 (TALEs). 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.

Association of common bacterial blight (Xanthomonas axonopodis pv. phaseoli) epidemics with agro ecological factors in Southwestern Ethiopia

Common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli, is an economically important disease of common bean and causes significant yield losses in Ethiopia. A field survey was conducted to understand the spatial distribution, relative importance and association of common bacterial blight epidemics with agro-ecological factors in low and mid-land areas of Southwestern, Ethiopia, during the 2018-19 cropping season. A total 85 bean fields were assessed in four common bean growing districts. High diseases incidence and severity was recorded at Debub Ari (77.6 and 52.7%, respectively) while the lowest was from Male (38.5 and 28.0%, respectively). The associations between disease parameters and agro-ecological factors were analyzed using multiple logistic regression models. Agronomic practices including NPS fertilization, preceding crop, weed management and plant population had highly significant (P<0.0001) association with both disease incidence and severity. Also, altitude, seed source and cropping system significantly (P<0.05) influenced disease severity while cropping pattern showed significant (P<0.05) association with disease incidence in the reduced model. Higher mean disease severity (≥40%) had high probability of association with district, absence of NPS fertilization, poor weed management practice, and preceding crops, than their counter parts. Adequate NPS fertilization increases growth performance of the crop in turn decreases disease intensity, weed serve as alternate host for incoming inoculum and previous crops were source for inocula as well as crop rotation used as reduce inoculum load. Therefore, the present study showed that the disease is a major production constraint of common bean, and suggested proper nutrient and weed management practices, and crop rotation to reduce common bacterial blight in the study areas. Int. J. Agril. Res. Innov. Tech. 11(1): 74-83, June 2021

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.

Using Breeding Populations With a Dual Purpose: Cultivar Development and Gene Mapping—A Case Study Using Resistance to Common Bacterial Blight in Dry Bean (Phaseolus vulgaris L.)

Dry bean (Phaseolus vulgaris L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli. A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 41,998 single-nucleotide polymorphisms (SNPs) and 30,285 SNPs were used in GWAS for the Middle American and Andean gene pools, respectively. One region near the distal end of Pv10 near the SAP6 molecular marker from the Andean gene pool explained 26.7–36.4% of the resistance variation. Three to seven regions from the Middle American gene pool contributed to 25.8–27.7% of the resistance, with the most significant peak also near the SAP6 marker. Six of the eight total regions associated with CBB resistance are likely the physical locations of quantitative trait loci identified from previous genetic studies. The two new locations associated with CBB resistance are located at Pv10:22.91–23.36 and Pv11:52.4. A lipoxgenase-1 ortholog on Pv10 emerged as a candidate gene for CBB resistance. The state of one SNP on Pv07 was associated with susceptibility. Its subsequent use in MAB would reduce the current number of lines in preliminary and advanced field yield trial by up to 14% and eliminate only susceptible genotypes. These results provide a foundational SNP data set, improve our understanding of CBB resistance in dry bean, and impact resource allocation within breeding programs as breeding populations may be used for dual purposes: cultivar development as well as genetic studies.