The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Abstract

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Reticulate Evolution: Detection and Utility in the Phylogenomics Era

“…Allopolyploidy has been observed in numerous plants, fungi, and a few vertebrates (Ozkan et al 2001;Session et al 2016;Edger et al 2019;Steenwyk et al 2020a;Chen et al 2022;Session and Rokhsar 2023). Genome evolution in allopolyploids can be rapid-marked by pronounced loss of genetic material (Ozkan et al 2001)-or relatively stable, resulting in retention of both parental genomes (Steenwyk et al 2020a(Steenwyk et al , 2023bSalojärvi et al 2024). In either case, introgression/hybridization results in novel combinations of genes and genetic backgrounds that can, in turn, lead to distinct phenotypic profiles (Steenwyk et al 2020a;Bautista et al 2021).…”