Journal
GENOME BIOLOGY
Volume 10, Issue 4, Pages -Publisher
BMC
DOI: 10.1186/gb-2009-10-4-r43
Keywords
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Funding
- International Milk Genomics Consortium
- NIEHS Superfund [P42 ES04699]
- CHARGE study [P01 ES11269]
- USDA Agricultural Research Service [6250-51000-048]
- NIH [PO1-HD38129]
- Foundation for Research Science and Technology from the New Zealand Government
- California Dairy Research Foundation [05 MEJ-01-NH]
- National Human Genome Research Institute [2 P41 HG002371-06]
- Genome Canada and Genome BC through the Pathogenomics of Innate Immunity
- Michael Smith Foundation for Health Research
- Swiss National Science Foundation [3100A0-112588]
- Australia's Cooperative Research Centre for Innovative Dairy Products and the Gardiner Foundation
- EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT [P01HD038129] Funding Source: NIH RePORTER
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [P41HG002371] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES [P42ES004699, P01ES011269] Funding Source: NIH RePORTER
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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.
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