Combining gene expression data with SNP association studies to identify genes effecting bovine milk production traits

It has been argued that microarray technology is becoming somewhat obsolete and being superseded by the more recent methodologies of next generation sequencing (in particular RNA-seq). However, there are still many instances where the use of microarrays is preferable. When transcript profiling in model organisms with well-annotated genomes, microarrays have the advantage of having low-cost, short turn-around time, quantitative accuracy, robust sample processing and well-established analysis-pipelines. In this study, we aim to identify genes critical for bovine milk production by examining a series of cDNA microarray experiments conducted in a collaboration between AgResearch (New Zealand) and the Department of Primary Industries (DPI) Victoria. The experiments performed involved investigating changes in bovine mammary gene expression under a number of experimental conditions (both in vivo and in vitro) and are briefly outlined below:
• In vivo bromocriptine-mediated prolactin loss
• In vitro bovine mammary epithelial cells in response to prolactin and extracellular matrix
• Extended lactation program in cows examining difference between:
– Early and late lactation
– Persistent and non-persistent dairy cows
– Cows in extended lactation with low, medium or high nutritional status
• Genetic merit experiment comparing cows of high and low genetic merit under normal conditions, when fasted for 36 hrs and when on 50% rations for 7 days
• Time since milking: 6hrs, 12hrs, 18hrs and 36hrs post milking in cows
These experiments were analysed and Expressed Sequence Tags (ESTs) displaying significant (p<0.05) differential regulation of 2-fold or greater were identified and annotated. Gene Ontology terms and pathways linked significantly to these EST lists were used to generate a biological profile of the mammary gland under each condition. In addition, EST lists were compared between experiments and ESTs displaying differential regulation under multiple conditions were identified. Single Nucleotide Polymorphisms (SNPs) falling within corresponding genes or 50/500 kb on either side of each gene were identified. These SNPs had previously been tested for an association with bovine milk production traits in genotyping experiments using an 800k (Illumina) SNP-chip. It was found that a number of the candidate genes contained SNPs that were significantly associated with bovine milk production and/or milk composition traits. These results are discussed and potential roles in milk production hypothesised.

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