Tracing Coffea canephora genetic diversity from the wild African population to cultivated germplasm in Vietnam and its suitability to future climate

Abstract

Robusta coffee is produced from Coffea canephora species of the Rubiaceae flowering-plant family. The genetic diversity of wild C. canephora is structured across its natural distribution in inter-tropical Africa. These different genetic groups differ in their adaptation to various environments. Only a limited portion of its wild genetic diversity has been selected and for cultivation in other parts of the world since the 1900s. Vietnam has been the largest global Robusta producer since the 2000s, but is now facing a risk of losing coffee yield loss due to climate change. To propose strategies of adaptation to climate change for Vietnamese C. canephora, it is crucial to understand the part of genetic diversity contributing to the cultivated germplasm, and assess the suitability of all the wild genetic sources to the current and future local environment. Using population genetic analyses with a reference set of native African accessions, we identified that a genetic group originating from the Congo basin was the main contributor to the Vietnamese accessions. We developed an approach for chromosome painting detect the distribution of wild ancestry-of-origin segments in cultivated Robusta genomes. We then revealled multiple hybrids of two or three groups with complex genome-wide admixture patterns. Finally, we estimated genomic suitability of wild African accessions to the current and future climate in Vietnam, based on relationships between genetic variants and climatic variables. Our predictions highlighted that the best suitable material comes from a genetic group in Gabon and Angola, which is currently only present in few hybrids in the Vietnamese varieties. The mismatch between the genetic origins of cultivated accessions and the predicted suitable genetic sources would offer useful information for establishing C. canephora coffee improvement and conservation plans in Vietnam.