The Tools: Databases, Genomics Tools & Models – Status Structure and Accessibility

Genomics involves the large scale identification of organisms’ genes and their function, and the variation that exists between individuals. This has become possible in the last decade due to significant technical advances in biotechnology that lead to the mapping and sequencing of mammalian genomes (structural genomics) and to the characterization of patterns of gene expression (functional genomics).  The bioinformatics’ cataloging of genomic data in organized databases and the tools to understand this information has become essential. Specialized databases are being created to centralize access to genomic information for products like milk (“milkER” informatics resource, http://www.milker.org.uk). As sequencing has proceeded, the identification of structural variation has made possible the genetic mapping of complex traits and the identification of responsible candidate genes in domestic animals.  Osteopontin (OPN or SPP1) is one of these genes in bovine chromosome 6, which codes for a secreted glycoprotein that is functionally important in milk.

One important realization from having the complete genomic sequence of organisms was the remarkable similarities that exist in the structure, chromosomal organization and function of genes. These similarities have made comparative genomic approaches a primary tool for functional annotation and identification of genes. One interesting example of this organization is the conserved chromosomal synteny that exists of genes coding for proteins associated with mineralized tissue (teeth and bones) and calcium phosphate stabilization in body fluids (milk and saliva) on human chromosome 4, chromosome 14 in rat, 5 in mouse, 6 in cattle and sheep, 8 in pig, and 13 in dog. 

Patterns of gene expression are important to understand the function of genes. In relation to milk components, we have developed a useful approach to examine gene expression patterns in epithelial cells isolated from milk that correlates well with gene expression patterns in the mammary gland tissue. Comparing patterns of gene expression together with comparative sequence analysis is facilitating functional annotation of genes and their regulatory sequences.