Abstract
A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3′UTRs of candidate genes.
Highlights
Association and quantitative trait locus (QTL) studies in large farm animals are typically performed in outbred populations, making the identification of robust QTL and candidate genes difficult and less reliable due to the variation of genetic background and population-specific interactions between loci
Candidate loci were collected considering seven different research approaches: (i) gene knockouts and transgenes in mice that result in specific phenotypes associated with mammary gland; (ii) cattle QTL for milk production and mastitis traits; (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production or mastitis in cattle; (iv) genes with expression profiles associated with milk production or mastitis in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants; (vi) micro RNAs (miRNAs) expressed in bovine mammary gland; (vii) epigenetically regulated cattle genes associated with mammary gland function
We reviewed the literature published up to December 2008 searching for the relevant publications through PubMed and Web of Science using key phrases: genetics, gene candidates, mammary gland, miRNA, mastitis, milk, epigenetics, methylation, QTL, SNP, association
Summary
Association and quantitative trait locus (QTL) studies in large farm animals are typically performed in outbred populations, making the identification of robust QTL and candidate genes difficult and less reliable due to the variation of genetic background and population-specific interactions between loci. This situation differs very much from the situation in model and laboratory animal species, where. A fair amount of genetic research related to lactation and udder health has already been performed due to its economic importance for milk production and manufacturing. Ron et al (2007) utilized murine gene expression data from multiple analyses combined with bovine QTL mapping data to identify candidate genes for QTL for milk production traits in dairy cattle
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