The chloroplast nuclear-encoded thioredoxin-like protein HCF164 is predicted to be associated with Coffea SH9 resistance factor against Hemileia vastatrix

To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, the whole genome of 42 coffee genotypes was sequenced and de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid Híbrido de Timor (HDT). Individual reads were aligned on the C. arabica reference to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled to discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (inherited from C. canephora ). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. This is the first time that specific DNA variants allow discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.