The Bovine Lactation Genome: Insights into the Evolution of Mammalian Milk

Background: The newly assembled Bos taurus genome sequence enables the linkage of bovine milkand lactation data with other mammalian genomes.Results: Using publicly available milk proteome data and mammary expressed sequence tags, 197milk protein genes and over 6,000 mammary genes were identified in the bovine genome.Intersection of these genes with 238 milk production quantitative trait loci curated from theliterature decreased the search space for milk trait effectors by more than an order of magnitude.Genome location analysis revealed a tendency for milk protein genes to be clustered with othermammary genes. Using the genomes of a monotreme (platypus), a marsupial (opossum), and fiveplacental mammals (bovine, human, dog, mice, rat), gene loss and duplication, phylogeny, sequenceconservation, and evolution were examined. Compared with other genes in the bovine genome,milk and mammary genes are: more likely to be present in all mammals; more likely to be duplicatedin therians; more highly conserved across Mammalia; and evolving more slowly along the bovine lineage. The most divergent proteins in milk were associated with nutritional and immunologicalcomponents of milk, whereas highly conserved proteins were associated with secretory processes.Conclusions: Although both copy number and sequence variation contribute to the diversity ofmilk protein composition across species, our results suggest that this diversity is primarily due toother mechanisms. Our findings support the essentiality of milk to the survival of mammalianneonates and the establishment of milk secretory mechanisms more than 160 million years ago.