title: The bovine lactation genome: insights into the evolution of mammalian milk.
abstract: BACKGROUND
  The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes.
  
  
  RESULTS
  Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk 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 the literature 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 other mammary genes. Using the genomes of a monotreme (platypus), a marsupial (opossum), and five placental mammals (bovine, human, dog, mice, rat), gene loss and duplication, phylogeny, sequence conservation, 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 duplicated in 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 immunological components of milk, whereas highly conserved proteins were associated with secretory processes.
  
  
  CONCLUSIONS
  Although both copy number and sequence variation contribute to the diversity of milk protein composition across species, our results suggest that this diversity is primarily due to other mechanisms. Our findings support the essentiality of milk to the survival of mammalian neonates and the establishment of milk secretory mechanisms more than 160 million years ago.
authors.affiliation: Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA. dglemay@ucdavis.edu
authors.forename: Danielle G
authors.initials: DG
authors.lastname: Lemay
authors.forename: David J
authors.initials: DJ
authors.lastname: Lynn
authors.forename: William F
authors.initials: WF
authors.lastname: Martin
authors.forename: Margaret C
authors.initials: MC
authors.lastname: Neville
authors.forename: Theresa M
authors.initials: TM
authors.lastname: Casey
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Rincon
authors.forename: Evgenia V
authors.initials: EV
authors.lastname: Kriventseva
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Barris
authors.forename: Angie S
authors.initials: AS
authors.lastname: Hinrichs
authors.forename: Adrian J
authors.initials: AJ
authors.lastname: Molenaar
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Pollard
authors.forename: Nauman J
authors.initials: NJ
authors.lastname: Maqbool
authors.forename: Kuljeet
authors.initials: K
authors.lastname: Singh
authors.forename: Regan
authors.initials: R
authors.lastname: Murney
authors.forename: Evgeny M
authors.initials: EM
authors.lastname: Zdobnov
authors.forename: Ross L
authors.initials: RL
authors.lastname: Tellam
authors.forename: Juan F
authors.initials: JF
authors.lastname: Medrano
authors.forename: J Bruce
authors.initials: JB
authors.lastname: German
authors.forename: Monique
authors.initials: M
authors.lastname: Rijnkels
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping; D033481:Chromosomes, Mammalian / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005260:Female; D016678:Genome / Q000235:genetics*; D006801:Humans; D007774:Lactation / Q000235:genetics*; D008322:Mammals / Q000145:classification / Q000235:genetics; D008321:Mammary Glands, Animal / Q000378:metabolism; D008892:Milk / Q000737:chemistry; D008894:Milk Proteins / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D040641:Quantitative Trait Loci / Q000235:genetics
chemical_list: D008894:Milk Proteins