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.埃塞俄比亚西南部的山地雨林是小粒咖啡（Coffea arabica）的核心多样性起源中心，亦是全球所有栽培小粒咖啡的发源地。该野生基因库正面临森林破碎化与退化的潜在威胁，同时还存在与当地改良咖啡品种发生渐渗杂交（introgressive hybridization）的风险。本研究利用24个微卫星位点（microsatellite loci），对来自未管理自然种群与人工管理种群的703株咖啡灌木开展了基因分型。此外，我们还对代表23个抗咖啡浆果病（coffee berry disease, CBD）埃塞俄比亚栽培品种的90个个体进行了基因分型。我们分析了种群遗传多样性、遗传结构，以及栽培品种等位基因在原位基因库中的渗入情况。研究发现，人工管理与自然未管理的咖啡种群间存在显著遗传分化，但两类种群的内部遗传多样性并无显著差异。大规模种植包含抗CBD品种在内的咖啡种苗，大概率抵消了遗传漂变（genetic drift）与近交（inbreeding）所导致的遗传变异流失。然而，将栽培品种与原始咖啡基因型混合种植，会为杂交事件以及原始咖啡基因库的替代提供充足契机，目前该基因库已显现出基因混合的迹象。因此，对小粒咖啡野生基因库的原位保护（in situ conservation），必须将重点放在限制剩余野生种群分布区内的咖啡生产活动上——因为种植集约化会使野生基因型暴露于栽培品种之下，进而威胁该基因库的遗传完整性。