Characterization and functional validation of a genomic region involved in resistance to rust race II in Coffea arabica

Coffee leaf rust (CLR) is one of the most economically important diseases affecting Coffea arabica production, having a significant economic impact. Among the main goals of coffee breeding programs is the development of cultivars resistant to this disease. A source of resistance genes is Híbrido de Timor (HdT), a spontaneous hybrid originated from the cross between C. arabica and C. canephora. Previously, in a transcriptome study, the Ca TDF77 NBS-LRR gene from HdT involved in resistance to CLR was identified. Hence, our aim was to characterize the genomic region surrounding the Ca TDF77 NBS-LRR gene in Coffea spp. Furthermore, we aimed to analyze the transcriptional profile of this gene, in the C. arabica cultivar IAPAR 59, which is originated from HdT introgression and is resistant to CLR race II. The outcome delineated the gene’s localization on chromosome 11 (canephora subgenome) of C. arabica, spotlighting intragenic polymorphisms between HdT and Arabica coffee susceptible to CLR race II. The genomic region surrounding the gene in Coffea spp. revealed a tandem structure and transposable elements. Notably, within IAPAR 59, the gene exhibited significant upregulation at 24 and 72 h post CLR infection, contrasting starkly with the susceptible genotype. This observation validates its role in fortifying the defense mechanism of this particular cultivar. This study enriches our understanding of the evolutionary dynamics of Coffea spp. genomes and also provides genomic resources instrumental in devising biotechnological strategies for resistance to CLR.