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This article is part of a series on Bovine: the companion papers for the publication of the bovine genome sequence.

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The bovine lactation genome: insights into the evolution of mammalian milk

Danielle G Lemay1 email, David J Lynn2 email, William F Martin1 email, Margaret C Neville3 email, Theresa M Casey4 email, Gonzalo Rincon5 email, Evgenia V Kriventseva6 email, Wesley C Barris7 email, Angie S Hinrichs8 email, Adrian J Molenaar9 email, Katherine S Pollard10 email, Nauman J Maqbool11 email, Kuljeet Singh9 email, Regan Murney9 email, Evgeny M Zdobnov12,13,14 email, Ross L Tellam7 email, Juan F Medrano5 email, J Bruce German1,15 email and Monique Rijnkels16 email

1  Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA

2  Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, BC, V5A 1S6, Canada

3  Department of Physiology and Biophysics, University of Colorado Denver, Anschutz Medical Center, E. 19th Ave, Aurora CO 80045, USA

4  Department of Animal Science, Michigan State University, East Lansing, MI 48824-1225, USA

5  Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA

6  Department of Structural Biology and Bioinformatics, University of Geneva Medical School, rue Michel-Servet, 1211 Geneva, Switzerland

7  CSIRO Livestock Industries, Queensland Bioscience Precinct, Carmody Road, St Lucia, Queensland 4067, Australia

8  Center for Biomolecular Science and Engineering, University of California Santa Cruz, High St, Santa Cruz, CA 95064, USA

9  Dairy Science and Technology, AgResearch, Ruakura Research Centre, East Street, Hamilton, 3240, New Zealand

10  Division of Biostatistics and Gladstone Institutes, University of California San Francisco, Owens St, San Francisco, CA 94158, USA

11  Bioinformatics, Mathematics and Statistics, AgResearch, Invermay Agricultural Centre, Puddle Alley, Mosgiel 9053, New Zealand

12  Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet, 1211 Geneva, Switzerland

13  Swiss Institute of Bioinformatics, rue Michel-Servet, 1211 Geneva, Switzerland

14  Imperial College London, South Kensington Campus, London, SW7 2AZ, UK

15  Nestlé Research Centre, Vers-chez-les-Blanc CH-1000, Lausanne 26, Switzerland

16  Department of Pediatrics, Children's Nutrition Research Center, Baylor College of Medicine, Bates Street, Houston TX 77030, USA

author email corresponding author email

Genome Biology 2009, 10:R43doi:10.1186/gb-2009-10-4-r43

Published: 24 April 2009

Subject areas: Development, Evolution, Physiology

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.

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