In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach

• Published in: PloS one 2020-07, Vol.15 (7), p.e0222747-e0222747
• Main Authors: Barka, Geleta Dugassa, Caixeta, Eveline Teixeira, Ferreira, Sávio Siqueira, Zambolim, Laércio, Sahu, Binod Bihari
• Format: Article
• Language: English
• Subjects: Analogs; Binding sites; Biology and Life Sciences; Breeding; Cloning; Coffee; Coffee rust disease; Comparative analysis; Computer and Information Sciences; Cultivars; Deoxyribonucleic acid; Disease resistance; Disease resistance (Plants); DNA; Function analysis; Functional analysis; Genes; Genetic aspects; Genetic engineering; Genomes; Kinases; Leaf rust; Pathogens; Phenotypes; Physiology; Proteins; Research and Analysis Methods; Risk factors; Signal transduction; Structure-function relationships; Tomatoes; Virulence
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0222747

Physiology-based differentiation of S.sub.H genes and Hemileia vastatrix races is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (S.sub.H 1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any S.sub.H related candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other S.sub.H genes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the S.sub.H genes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.