Chromosome-level dairy goat genome reveals the regulatory landscape of lactation

Goat milk is rich in various nutrients that are beneficial for human health. However, the genomic evolution and genetic basis underlying the nutritional value and unique flavor formation in dairy goats remain poorly understood. In the present study, we generate a chromosome-level genome assembly for dairy goats comprising 2.63 Gb with a contig N50 of 43 Mb and a scaffold N50 of 101 Mb. Genome quality comparisons revealed that the dairy goat genome has higher integrity and continuity than the published goat and sheep genomes. The identification of genes under positive selection in dairy goats highlights potential candidates to explain their high milk production. Comparative genomic analysis elucidates the adaptive evolutionary mechanisms of dairy goats such as strong disease resistance, broad adaptability, and unique milk flavor. Moreover, we demonstrate the conservation of the lactation gene network and identify new potential regulators associated with lipid metabolism. Additionally, we establish the regulatory landscape of lactation for the first time in dairy goats, revealing its unique gene regulatory characteristics. Hence, our study not only provides the first chromosome-level reference genome for dairy goat, but also offers potential research directions for dairy production and genetic improvement.