Adaptive potential of Coffea canephora from Uganda in response to climate change

Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long-lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy-one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB-like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate-associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed.

Automated summary

Understanding vulnerabilities of plant populations to climate change can help protect their biodiversity and identify potential parents for breeding programs. In this study, we used landscape genomics to assess the potential adaptations of Coffea canephora trees to future climate conditions. By sequencing candidate genes related to key metabolic and defense pathways, we identified 71 single nucleotide polymorphisms (SNPs) associated with bioclimatic variables. These climate-associated SNPs were linked to important candidate genes controlling plant responses to abiotic stresses and caffeine biosynthesis. Using these genetic markers, we estimated the genetic offsets and found significant levels of genetic differentiation between present and future populations. The findings suggest that populations in certain regions of Uganda have lower genetic offsets and may be more resilient to climate change. The implications of these findings for ex situ conservation strategies are discussed.