Data from: Genetic variation and risks of introgression in the wild Coffea arabica gene pool in south-western Ethiopian montane rainforests

The montane rainforests of SW Ethiopia are the primary centre of diversity
of Coffea arabica and the origin of all Arabica coffee cultivated
worldwide. This wild gene pool is potentially threatened by forest
fragmentation and degradation, and by introgressive hybridization with
locally improved coffee varieties. We genotyped 703 coffee shrubs from
unmanaged and managed coffee populations, using 24 microsatellite loci.
Additionally, we genotyped 90 individuals representing 23 Ethiopian
cultivars resistant to coffee berry disease (CBD). We determined
population genetic diversity, genetic structure, and admixture of cultivar
alleles in the in situ gene pool. We found strong genetic differentiation
between managed and unmanaged coffee populations, but without significant
differences in within-population genetic diversity. The widespread
planting of coffee seedlings including CBD-resistant cultivars most likely
offsets losses of genetic variation attributable to genetic drift and
inbreeding. Mixing cultivars with original coffee genotypes, however,
leaves ample opportunity for hybridization and replacement of the original
coffee gene pool, which already shows signs of admixture. In situ
conservation of the wild gene pool of C. arabica must therefore focus on
limiting coffee production in the remaining wild populations, as
intensification threatens the genetic integrity of the gene pool by
exposing wild genotypes to cultivars.