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.