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

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.学界普遍认为，遗传变异可降低植物种群的病害发生水平。然而，作物物种在育种过程中因针对特定性状的选择而逐步丧失遗传变异，从而提升了其对病原物等生物胁迫的易感风险。本研究探究了埃塞俄比亚西南部阿拉比卡咖啡（Arabica coffee）种植位点的遗传变异与四种主要真菌病害发病率的关联关系。我们沿着管理强度梯度选取了60个种植位点，覆盖从近乎野生到集约化管理的咖啡林分。针对每个位点的16株咖啡灌木的混池叶片样本，我们采用混池测序分型（pool-GBS）技术进行测序分型，以此评估各位点间的遗传组成变异（多变量分析：参考等位基因频率）与遗传多样性（单变量分析：平均期望杂合度）。研究结果显示，遗传组成呈现出清晰的空间分布模式，且管理强度越低的位点，其遗传多样性越高。四种真菌病害的发病率与咖啡林分的遗传组成存在关联，但这种关联因病害种类不同而各有特异性。相比之下，遗传多样性仅与咖啡浆果病的位点内变异存在关联，却与四种病害在各位点的平均发病率均无关联。鉴于真菌病害是阿拉比卡咖啡原生分布区内的主要生产挑战，本研究发现咖啡种植位点的遗传组成会影响主要真菌病害的发生，这一结果可作为研究咖啡抗病性分子机制的基础参考数据。总而言之，本研究表明，在探究病害发生水平变异的遗传基础时，需同时考量宿主的遗传组成与遗传多样性。