We identified four important KEGG enrichment pathways and 10 candidate genes that are closely associated with milk yield in East Frisian sheep: beta-Alanine metabolism (SMOX, HIBCH), pathways in cancer (GLI2, AR, TXNRD3, TRAF3, FGF16), non-homologous end-joining (MRE11), Epstein-Barr virus infection (TRAF3, PSMD13, SIN3A). Here, FGF16 is linked to cancer.