Adaptive genetic variation for climate-resilient breeding in cacao (Theobroma cacao L.)

Breeding abiotic stress tolerance in tropical perennial crops is essential as weather conditions are becoming more erratic due to climate change. Cacao is a very valuable global commodity cultivated in West Africa, Asia, and Latin America but its production is vulnerable due to persistent diseases and reduced water availability for farming. Cacao wild populations as a result of continued exposition to different soil and climate conditions in Amazonia offer valuable adaptive genetic variation for breeding abiotic stress tolerance. We conducted a genetic-environmental association (GEA) analysis using 157 georeferenced cacao genotypes representing different geographic locations and forest habitats. We also used local environmental information, including 20 climatic and 15 soil variables associated with germplasm collection sites in Amazonia, as well as genotypic data from 42 single-nucleotide polymorphism (SNP) markers. The GEA analysis identified genotype associations with environmental variables suggesting adaptation to seasonal droughts and high temperatures, and to low-fertility soils in Southwestern and Eastern Amazon. This study represents progress in characterizing cacao germplasm and improves our understanding of the adaptive genetic variation available in diverse cacao populations and its optimal utilization for breeding climate resilient and abiotic stress tolerant cacao varieties.