Whole-genome resequencing of 93 coffee accessions unveils diversity and genetic relationship of three important Coffea species

Three Coffea species, C. arabica, C. canephora and C. excelsa compose majority of global coffee production. However, they feature differentiated morphological traits and require distinct agro-climatic conditions. Understanding their genetic diversity and divergence at genome-wide level is important to genetic improvement of coffee. Here in this study, we sequenced the genomes of 93 accessions encompassing the three Coffea species by Illumina with average depth of 16.6 and mapped to the C. canephora reference genome. Based on stringent SNP markers, we found the allotetraploid Coffea arabica exhibit the greatest nucleotide diversity owing to high heterozygosity of polyploids, following by C. excelsa and C. canephora. Population divergence based on FST, population stratification, principal component analysis and phylogenetic tree support strong divergence among the three species, while Coffea arabica and its parental species C. canephora exhibit much closer genetic relationship. Scanning of genomic islands contributing to species divergence identified strong genetic divergence on many functional genes. These genes including functions in response to diseases and pests, which are likely under selection after split of C. arabica and C. canephora, and might be applied in future genetic improvement of C. arabica. Overall, our whole genome-resequencing study not only uncovers the genetic basis of the three most important Coffea species, but also contributes important resource for future molecular breeding of coffee.