Molecular marker applications and functional genomics of drought tolerance in Coffea canephora: a comprehensive review.

Genetic diversity and resilience to climate change form the basic building blocks of sustainable coffee production, especially under increasing climatic variability conditions and intensifying biotic as well as abiotic stresses. Coffee supports the livelihood of nearly 25 million people worldwide and contributes about 2-3% of global agricultural trade, making the stability of its production important for both economic and social systems. Yet coffee cultivation is increasingly challenged by erratic rainfall and prolonged droughts, placing global production and farmer livelihoods at risk. Within this context, Coffea canephora (robusta) stands out as a critical genetic resource for climate-resilient breeding due to its broader genetic base and greater inherent tolerance compared to C. arabica. Over the past three decades, a wide range of molecular marker systems, from early RFLPs and RAPDs to advanced SNP genotyping and high-throughput sequencing platforms, have been employed to investigate genetic diversity, population structure, and adaptive traits in C. canephora. At the same time, transcriptomic, proteomic, and metabolomic studies have begun to reveal the molecular mechanisms underlying drought tolerance. Collectively, these approaches have provided insights into osmotic adjustment, antioxidant defense, hormone signaling, and stress-responsive regulatory networks. Nevertheless, significant challenges remain, including the reliance on a narrow set of genotypes, the scarcity of integrated multi-omics frameworks, and limited translation of molecular discoveries into breeder-friendly tools. This review synthesizes historical and recent advances in molecular diversity and functional genomics of C. canephora, discusses the limitations that restrict their deployment in breeding programs, and emphasizes their importance for the development of climate-resilient cultivars.