Genome-wide association study (GWAS) of Phaseolus vulgaris resistance to Xanthomonas citri pv. fuscans

Abstract

Common bean is one of the main legumes used for food worldwide. Among the main limitations for its production is common bacterial blight (CBB) caused by Xanthomonas citri pv. fuscans (Xcf). The most desirable method to control the disease is the use of plant genetic resistance, but resistance against Xcf has not been sufficiently investigated. Genetic studies have shown that resistance to CBB is of quantitative type, but no gene associated with resistance has been identified. Here, we aimed to determine the resistance to CBB of 103 Mesoamerican common bean cultivars by evaluating disease severity and the area under the disease progress curve (AUDPC) after inoculation with a Xcf strain. In addition, 80 of the evaluated cultivars were used to investigate the association of single nucleotide polymorphisms (SNPs) with the resistance phenotype in a genome-wide association study (GWAS). Twenty-nine cultivars were classified as highly resistant, 15 of which are shown to be resistant to CBB for the first time in this work. A positive correlation between AUDPC and disease severity was observed. The 10 SNPs with the highest −log10(p) values in the GWAS are located on bean chromosomes Pv01, Pv03, Pv06, Pv07, Pv08, Pv09, Pv10, and Pv11 within or near genes predicted to code for biochemical functions such as serine/threonine-protein kinase, glutamine synthase, lectin domain protein, MADS-domain transcription factor, and pentatricopeptide repeat protein, previously associated with immunity. This work identifies common bean germplasm resistant to Xcf, molecular markers for germplasm selection, and genes potentially involved in the resistance response.