Finding resistance genes of common bean to common bacterial blight

Common bean is an important source of protein, vitamins, minerals and fibre for human consumption, especially for the African and Latin American populations.  According to the Food and Agriculture Organization (FAO), growers around the world provide ca. 28.3 million tons of beans annually. However, the common bean, like many other crops, is negatively impacted by diseases of different aetiologies that compromise its production.

The main bacterial disease that negatively impacts common bean plants is common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans. These Gram-negative bacteria penetrate the plant mainly through natural openings and colonize the internal tissue, causing symptoms that initiate as water-soaked lesions, which develop into necrotic spots surrounded by chlorotic haloes that may coalesce and compromise a larger portion of the leaves, leading to defoliation. The bacteria can also affect the stems, petioles and pods, reaching the seeds and compromising their quality. Within the plant tissue, the bacteria secrete an arsenal of virulence weapons whose main functions are to suppress the plant immune system and to contribute to the development of disease symptoms. Yield losses caused by CBB can reach up to 45% in susceptible cultivars and under favourable environmental conditions.

In many crop plants, cytoplasmic or membrane-anchored proteins, coded by single resistant genes, can recognize some of those virulence factors (so-called avirulence proteins) eliciting a strong resistance response that halts pathogen infection. Hence, in those crops, some varieties are fully resistant (or immune) while others are susceptible to the pathogen. Nonetheless, that kind of complete resistance has not been demonstrated for CBB. Instead, the common bean cultivars exhibit different levels of resistance, implying that several genes may be conferring the resistant phenotype. Knowing which genes are involved in the resistant response is not only important for advancing our scientific knowledge, but also, for developing novel alternatives to control the CBB disease.

The Laboratory of Molecular Phytobacteriology at Universidade Federal de Viçosa in Brazil, led by Prof. Jorge Luis Badel, is conducting experiments aimed at uncovering the genes involved in the incomplete resistance of common bean to CBB. In a recent study published in Plant Pathology, the researchers sprayed inoculated plants of a genetically diverse panel of common bean cultivars with a X. phaseoli pv. phaseoli suspension (mimicking the natural infection) and rated the disease symptoms at several days after inoculation. These experiments allowed them to identify six varieties that exhibit high levels of resistance to the bacterial strain inoculated and that could be useful in the development of varieties with more desirable agronomic traits.

In order to identify common bean genes putatively associated with resistance to CBB, the authors conducted a genome-wide association study (GWAS) employing single-nucleotide polymorphisms (SNPs). The GWAS aimed to identify SNPs associated with resistance by detecting differences in allele frequencies between individuals that exhibit contrasting phenotypes, taking into consideration linkage disequilibrium and population structure. Using that approach, the researchers identified five SNPs within different common bean genes that code for biochemical functions that had not been previously implicated in plant resistance to bacterial pathogens. These genes could be used in future studies to unveil the molecular mechanisms underlying the quantitative resistance of common bean to CBB and as molecular markers in the selection of plant resistant genotypes.

Figure 3. Manhattan plot depicting the distribution of single-nucleotide polymorphisms (SNPs) along the 11 common bean chromosomes and their probability (-log₁₀ (p)) of association with resistance to common bacterial blight (CBB). Colours indicate the location of SNPs in different chromosomes. SNPs above the horizontal red line are significantly associated with resistance, according to two genome-wide association study (GWAS) methods: squares, Fixed and Random Model Circulating Probability Unification (FarmCPU); circles, Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK).

TITLE IMAGE: Contrasting phenotypes of common bean cultivars in response to inoculation with Xanthomonas phaseoli pv. phaseoli. Left panel, highly resistant cultivar; right panel, highly susceptible cultivar.