Prospects for improvement of coffee quality and stress resilience using genomic and genetic resources

Coffee is one of the most widely traded and highly valuable commodities, known for its pleasant flavor, unique aroma, and caffeine's stimulatory effect. Beyond their sensory perceptions, coffee beans are rich in several bioactive compounds and biomolecules beneficial to human health. Only two species, Coffea arabica and Coffea canephora, account for nearly all the world's coffee production, owing to their high quality and commercial value. Despite low variability and narrow genetic diversity, coffee plant genomic resources are underrepresented. Recent advancements in high-throughput sequencing technologies and reduced costs have enabled the development of various crop genomic resources, including coffee. In this review, we systematically cataloged the genetic and genomic resources available to the coffee research community, including reference genomes, DNA polymorphisms, transcriptomes, and non-coding regulatory transcripts. Furthermore, we highlighted promising candidate genes that may have functional roles in improving coffee quality, yield, and stress resilience. These resources provide an excellent knowledge base for studying genetic factors influencing coffee quality and agronomic traits, and for developing new breeding and CRISPR-based biotechnological strategies for coffee improvement.