Sequence analysis of cytochrome b gene in Vietnamese isolates of Hemileia vastatrix, the causal agent of coffee leaf rust, in relation to potential QoI fungicide resistance

Coffee leaf rust, caused by Hemileia vastatrix, is a devastating fungal disease threat to coffee production and the economy globally. Spraying fungicides including quinone outside inhibitors (QoIs) can effectively extinguish a disease outbreak quickly. However, mutations in the cytochrome b (CYTB) gene associated with QoI resistance have been reported in rust fungi and many other pathogens. In the Asian soybean rust fungus, Phakopsora pachyrhizi, a nucleotide mutation in the first exon of the CYTB gene, leading to the amino acid substitution F129L, is responsible for QoI resistance. Together with the F129L, amino acid substitutions at positions 137 and 143 are linked with moderate or high resistance to QoIs, respectively, in other pathogens. As an important obligate parasitic fungus causing disease to major and valuable tropical plant, therefore, it is important to develop molecular methods to detect resistance development in this pathogen H. vastatrix. Difference from the soybean rust fungus, codon 129 is located in exon 2 of the CYTB gene of this fungus, while exon 3 harbors codons 137 and 143. In this study, three PCR primer pairs were designed to amplify exons 2, 3, and 4 of the H. vastatrix CYTB gene and used for 40 isolates from Vietnam, the second-largest coffee producer worldwide. The following sequencing results showed that Vietnamese isolates did not harbor F129L and G143A mutations in exons 2 and 3 of the CYTB gene. The three primer pairs used in this study can be applied for live or dried mycelia to detect potential resistance to QoI fungicides in H. vastatrix in the future.