Chloroplast Genome Sequence Variations and Development of Polymorphic Markers in Coffea arabica

Coffee is a popular beverage in the world and a valuable agricultural export commodity for several developing countries. Coffea arabica is one of the widely cultivated species and is believed to have originated from Ethiopia. Currently, a large number of C. arabica accessions are conserved ex situ in field gene banks in Ethiopia. However, there is no useful molecular barcoding to identify the conserved accessions, which presents a challenge to sustainable utilization of this economic species. To identify polymorphic chloroplast markers for the use in various studies, the complete chloroplast genome sequences of 24 C. arabica accessions were assembled and screened for variable regions in this study. The total length of the individual chloroplast genome sequence varied from 155,059 to 155,192 bp. Genome annotation revealed a total of 114 unique genes, consisting of 80 protein-coding, 30 tRNA, and four rRNA genes in all the 24 genomes. Twenty-four polymorphic regions were identified and developed. Most (71%) of the variable regions were found in non-coding sequence, and 54% of the variations detected are single base pairs. Three non-synonymous SNPs were found in accD, rpoA, and ycf1 genes. The markers developed were able to cluster the majority of the coffee accessions according to their geographical regions of collection. Five out of 24 newly developed markers were validated by assessing the diversity levels that were assessed in five original regions. The southwest region displayed the highest genetic diversity (HE = 0.224; I = 0.370) and might become a potential coffee genetic resource bank. Overall, the polymorphic markers developed and validated in this study could be a useful genomic resource for molecular breeding, identification, and biogeography studies of this commercially important crop.