Bovine lactation genome data description

A brief description of each data type with links to tables is provided below.

Please review the publication for more complete descriptions.

Milk Protein Gene Set

Amino acid sequences from two proteomic studies (Reinhardt et al, Smolenski et al) and those that were annotated as part of the bovine genome project were aligned against the bovine genome assembly 3.1 using BLAT. The best scoring hits were manually reviewed to identify these milk protein genes.  Click here for a table with embedded links to the milk protein genes, their locations, and their orthologs.

Mammary Gene Sets

Genes expressed in the bovine mammary gland during virgin, pregnancy, lactation, involution, and mastitis conditions were identified by aligning ESTs from the AgResearch/Genesis and ViaLactia Biosciences EST libraries to consensus gene models in the bovine genome assembly 3.1. Click here for a file that describes EST libraries that were surveyed for this study, the number of ESTs in each library, a description of the physiological state of the animal and tissue used to derive the library, and, if the library was excluded from this study, the reason for exclusion.  Click on the following links for tables of these gene sets and accompanying annotations:

Virgin Mammary Gene Set

Pregnancy Mammary Gene Set

Lactation Mammary Gene Set

Involution Mammary Gene Set

Mastitis Mammary Gene Set

Milk trait QTLs

QTL for five milk traits –milk yield, protein yield, fat yield, protein percentage, and fat percentage–were identified in the bovine genome assembly 3.1 based on markers reported in 59 literature references:  Milk Trait QTL Table

Milk trait candidate genes

Milk trait candidate genes were identified by intersecting the milk and mammary gene sets with the milk trait QTLs.  This Excel file lists candidate genes with one spreadsheet per milk trait:  Milk Trait Candidate Gene Tables

Mammary gene neighborhoods (genomic clusters)

Genomic intervals of 500KB or larger which contain more milk or mammary genes than would be expected by chance were identified in the bovine genome assembly 3.1. This Excel file contains separate spreadsheets for genomic neighborhoods identified using each mammary gene set:  Mammary Gene Neighborhood Table

Mammalian orthologs of bovine milk and mammary gene sets

As part of the bovine genome project, consensus gene models (GLEAN models) were identified on a genome-wide basis and whole genome orthology detection was automated.  We identified the subset of these gene models that corresponded to the milk and mammary gene sets to derive human, mouse, rat, dog, oppossum, and platypus orthologs of bovine milk and mammary genes.  Orthologs of milk protein genes were additionally manually curated if there was a unique duplication identified in the bovine genome or if the ortholog was missing in one or more of the placental mammal genomes (i.e. human, mouse, rat, or dog).

While the single best human and mouse orthologs of the bovine genes are given in the milk and mammary gene set tables above, this file additionally lists orthologs for the other species as well as all paralogs: Milk and Mammary Gene Ortholog List