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

Abstract

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.

Keywords: Afromontane rainforest; admixture; coffee; crop wild relative; ecosystem services; genetic erosion.

Figure 1

Afromontane rainforests in Southwest-Ethiopia and sampled Coffea arabica populations: forest coffee (closed circles) and semi-forest coffee (open circles). Insets show detail of the forest coffee (A) and of the semi-forest coffee landscape (B). Satellite imagery © 2012 DigitalGlobe, GeoEye and Cnes/Spot Image, via Google Earth.

Figure 2

Principal coordinates (PCo) plot based on Φ_PT calculated with 24 SSR markers for Coffea arabica, demonstrating population genetic differentiation between forest coffee (closed circles) and semi-forest coffee systems (open circles).

Figure 3

Population structure of Coffea arabica based on structure analysis of 24 SSR markers for forest coffee (N = 383, six populations), semi-forest coffee (N = 320, five populations) and cultivar (N = 90) samples for K = 2 clusters (Fig. S1). Individuals are represented by columns, with colours showing the average proportion (R = 5 runs) of their genome assigned to the different clusters, demonstrating the prevalence of a genotype associated to the coffee berry disease (CBD)-resistant gene pool in the semi-forest coffee (SFC) populations.

Figure 4

Maximum likelihood hybrid index estimates h for 320 Coffea arabica individuals from five semi-forest coffee populations and for 233 Coffea arabica individuals from four forest coffee populations in SW Ethiopia. The h index or admixture coefficient, based on frequencies for 159 alleles, a parental population of N = 150 wild individuals (from populations A10 and Q3) and a parental population of N = 90 specimens from 23 coffee berry disease (CBD)-resistant varieties, gives the fraction of the genome shared with the cultivated varieties for each individual.