Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world

The reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.

Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo

BACKGROUND AND AIMS

Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridization with their nearby cultivated crops. This might be a particular problem for wild coffee species, which often occur near coffee cultivation areas. Here, we briefly review the evidence for wild Coffea arabica (cultivated as Arabica coffee) and Coffea canephora (cultivated as Robusta coffee) and then focused on C. canephora in the Yangambi region in the Democratic Republic of the Congo. There, we examined the geographical distribution of cultivated C. canephora and the incidence of hybridization between cultivated and wild individuals within the rainforest.

METHODS

We collected 71 C. canephora individuals from home gardens and 12 C. canephora individuals from the tropical rainforest in the Yangambi region and genotyped them using genotyping-by-sequencing (GBS). We compared the fingerprints with existing GBS data from 388 C. canephora individuals from natural tropical rainforests and the INERA Coffee Collection, a Robusta coffee field gene bank and the most probable source of cultivated genotypes in the area. We then established robust diagnostic fingerprints that genetically differentiate cultivated from wild coffee, identified cultivated-wild hybrids and mapped their geographical position in the rainforest.

KEY RESULTS

We identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where cultivated C. canephora in home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests.

CONCLUSIONS

The cultivation of C. canephora in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high genetic similarity between the cultivated and wild gene pool, together with the relatively low incidence of hybridization, our results indicate that the overall impact in terms of risk of introgression remains limited so far.

A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm

In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid species Coffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species, Coffea canephora, presumably as a consequence of introgressions deriving from the so-called Timor hybrid. It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges. These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.