Genetic Composition Is Associated with Arabica Coffee Biochemical Composition and Quality in Southwestern Ethiopia

Globally, coffee ranks among the most widely marketed commodities after oil. Since genotype strongly influences green coffee bean biochemical composition and quality, understanding this relationship is crucial. We studied the associations between genetic composition and biochemical, physical, and cup quality attributes across 54 sampling sites in Southwestern Ethiopia. Leaf samples collected in 2017 from 16 coffee trees at each site were pooled for genotyping-by-sequencing (GBS), while coffee berries from the same coffee trees were collected in 2022 for quality assessment. Redundancy analysis (RDA) assessed associations between Hellinger-transformed reference allele frequencies and eleven quality attributes. Similarly, linear mixed-effects models evaluated genetic cluster, elevation, and management effects. The primary RDA (45 sites, 487 variants) revealed a significant overall association (p = 0.0225), but modest adjusted explained variation (adjusted R2 = 0.0716). Chlorogenic acids exhibited a nominally significant cluster effect (p = 0.0374), without significant Tukey-adjusted pairwise differences. Cluster 3 exhibited higher flavor, acidity, aftertaste, body, overall preference, and specialty total scores than Cluster 2 (Tukey-adjusted p < 0.05). However, only acidity remained significant after false discovery rate adjustment across the 13 quality attributes. Site-level sensitivity analyses retained nominally significant overall cluster effects for acidity and overall preference, whereas the other sensory and composite attributes showed less consistent support. Elevation was positively associated with hundred-bean mass (0.474 g per 100 m; p < 0.001), and management category showed no significant associations. These findings indicate a modest association between genetic composition and coffee quality, with acidity showing the most consistent cluster-related evidence and highlighting the importance of considering environmental conditions.