Genome-wide association study for resistance to pv. in .

Bacteria halo blight (BHB), a coffee plant disease caused by pv. , has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of , we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C Ethiopian accessions from a historical FAO collection, 11 C cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to (Chr_0_434_435) and genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a susceptible cultivar and in a cultivar with quantitative resistance, when infected with pv. . However, peaks of upregulation were observed in a cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in . In addition, the findings contribute to increasing understanding of the domestication history.