Soybean bacterial pustule is caused by the gram‐negative bacterium Xanthonomas citri pv. glycines. The identification of sources of resistance for use in molecular breeding is a challenge due to the existence of complex interactions between pathogenic strains and soybean cultivars. This study aimed to evaluate the reaction of 118 soybean cultivars to inoculation with strains 2440P and 2447 of X. citri pv. glycines and to identify molecular markers associated with the resistance. The genome‐wide association study approach was used to identify association between the phenotype and the single nucleotide polymorphisms (SNP) markers. The positions of significant SNPs were mapped to the soybean Williams 82 genome, and protein‐coding genes near them were identified. One and 116 cultivars were resistant to strains 2440P and 2447, respectively. Eleven SNPs were significantly associated with resistance to strain 2440P and five to 2447. Two significant SNPs are predicted to result in amino acid changes in benzyl alcohol O‐benzoyltransferase‐like and MAIN‐LIKE 1‐like proteins, which after confirmation, could be used in marker‐assisted selection in order to increase the frequency of resistant alleles in new cultivars.

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