Selective sweep and mammary transcriptomics identify breed-specific lactation drivers in East Friesian dairy sheep

East Friesian sheep (EFR) are one of the world's highest-performing sheep breeds for milk production. Whole-genome resequencing data from 35 EFR sheep were combined with published whole-genome data from 45 additional sheep. Population genetic analysis revealed that EFR sheep are genetically distinct from other breeds, with evidence of ancestral gene flow from other sheep lineages. Genome-wide selective sweep identified strong selection signals on chromosome 2, including extended haplotypes overlapping with QTL associated with milk protein content. Notably, missense mutations in the COL3A1 and COL5A2 genes-linked to mammary gland development-were detected within these regions. Based on these findings, molecular markers for lactation performance were derived and applied to EFR sheep selection. To further investigate lactation-related genes, we performed transcriptome sequencing of mammary gland tissue from lactating and dry crossbred dairy sheep (EFR male × Hu female). Differential expression analysis identified 2,178 significantly differentially expressed genes (DEGs), including the COL3A1 gene, which was significantly downregulated. Integrating genomic and transcriptomic data, we confirmed COL3A1 as a candidate gene influencing milk production traits. Notably, the COL3A1 locus (g.130226140G>A) showed a significant association with milk yield in 1,019 EFR×Hu crossbred sheep. The GG genotype exhibited the highest milk yield, significantly outperforming AG (Δ = 11 kg, P < 0.05). These findings provide novel insights into the genetic basis of milk production in dairy sheep and offer valuable markers for breeding programs aimed at enhancing lactation performance.