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Gene expression profiling in caprine milk somatic and white blood cells upon intramammary challenge with Staphylococcus aureus

ABSTRACT: In dairy ruminants transcriptome profiling has enabled the identification of genes, pathways and regulatory networks activated in mammary tissues during experimental infection by various pathogens, including E. coli, S. aureus and S. uberis. Information in goats are still low and many host-pathogen interaction mechanisms have to be explained. The objectives of the present study were (1) to identify the network of genes that becomes activated in caprine blood and milk somatic cells in early response towards a S. aureus challenge in order to better understand the local and sistemic response and (2) to search any difference in this immune response by using two animal groups belonging to a caprine reference family established based on founders with adverse SCC breeding values.

ORGANISM(S): Capra hircus Bos taurus

PROVIDER: GSE33894 | GEO | 2011/11/23

SECONDARY ACCESSION(S): PRJNA148333

REPOSITORIES: GEO

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Project description:Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip. The analysis used a polygenic model where the dropping criteria was the Call Rate ≥ 0.95. The initial dataset was composed of ~ 60,000 rows of SNPs, 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50KBeadchip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provide precision breeding methods will thereby increase breeding value. Specific aims: 1) Improve on contributions to the phenotype repository, the Council on Dairy Cattle Breeding (CDCB) for milk quality traits that are economically important for goat production while developing a corresponding DNA repository for each of the animals with significant genotype-phenotype associations. 2) Develop genomic prediction tools and provide data for a better database for tools to predict phenotypic traits by initially using the high density Goat50KSNP BeadChip for the selection of more specific SNPs associated with select signatures (genes) for phenotypic traits in American Alpine goats. 3) To establish whether a low number of goat subjects (< 300 goats) will provide statistically significant (p < 0.05) predictive capabilities for desired breeding traits in American Alpine dairy goats.

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Gene expression profiling in caprine milk somatic and white blood cells upon intramammary challenge with Staphylococcus aureus

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