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.