Integration of Proteomics and Phenomics to Reveal Molecular Differences in High and Low Semen Quality in Donkeys

, p < 0.05). Proteomic analysis identified 6 differentially abundant proteins in seminal plasma (SPINKL, HSP-1, GBA2) and sperm (PAFAH1B1, SSMEM1, SPINK2), whose abundances showed potential associations with semen-quality traits and reproductive-organ biometry. The Spearman rank correlation analysis showed that GBA2 abundance was positively correlated with PM (ρ = 0.886), MMP (ρ = 0.943), TC (ρ = 0.986), CSACE (ρ = 1.000) and LASC (ρ = 0.829), and negatively correlated with PSA (ρ = -0.829), CA (ρ = -0.941) and ROS (ρ = -0.886). The other five proteins were positively correlated with PM (ρ > 0.829), while HSP-1, SPINKL, SSMEM1 and SPINK2 were also positively correlated with TC (ρ > 0.812). These findings suggest that semen-quality variation in donkeys is associated with differences in testicular and accessory sex gland biometry, and the 6 identified proteins are potentially associated with semen-quality variation and require further biological validation using targeted proteomics and antibody-based assays in independent populations.