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Comparing gene expression profiles in the mammary glands of high- and low-milk-yield Holstein Friesian cows

ABSTRACT: Analysis of key genes and gene networks determining milk productivity of the dairy HF cows

ORGANISM(S): Bos taurus

PROVIDER: GSE33680 | GEO | 2011/11/16

SECONDARY ACCESSION(S): PRJNA148301

REPOSITORIES: GEO

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Comparing gene expression profiles in the mammary glands of high- and low-milk-yield Holstein Friesian cows

Project description:Analysis of key genes and gene networks determining milk productivity of the dairy HF cows Transcriptomes were compared of in the mammary glands of the healthy lactating Holstein Friesian cows of the high- (average 11097 kg milk/lactation) and low- (average 6956 kg milk/lactation) milk yield.

2011-11-16 | E-GEOD-33680 | biostudies-arrayexpress

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Expression data from uterine endometrial tissues of Holstein-Friesian cows on days 14-16 after calving

Project description:Most dairy cows suffer uterine microbial contamination postpartum. Persistent endometritis often develops, associated with reduced fertility. We used a model of differential feeding and milking regimes to produce cows in differing negative energy balance (NEB) status in early lactation. We used Affymetrix GeneChipÒ Bovine Genome Array to investigate the global gene expression underlying negative energy balance and to identify the significantly differentially expressed genes during this process.

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Expression data from uterine endometrial tissues of Holstein-Friesian cows on days 14-16 after calving

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Exome of Holstein Friesian Cows

Project description:Despite the large amounts of transcriptome data generated for many non-model organisms, there has been a much lesser uptake of individual genomic sequencing for detecting SNPs and determining haplotypes in these species. Transcriptome data represents a source of variant information, specifically for coding DNA, however there is little information on the accuracy, coverage and limitations of using transcriptomic data for the identification of single nucleotide polymorphisms (SNPs) in non-model organisms. To investigate this, we generated the first whole exome design for bovine using the Roche Nimblegen Developer system (Roche, USA) and used it to sequence and call SNPs from a lactating dairy cow model with genetically divergent fertility phenotypes (Fert+, n=8; Fert-, n=8). We compared these results to SNPs called from liver and muscle transcriptomes from the same animals. Our exome demonstrated 99.1% coverage of the target design of 56.7MB, whereas the transcriptomes only covered 60 and 54.5% of 44.2 and 42.8MB in liver and muscle respectively. We found that specificity of SNP detection in the transcriptome data is ~75% following basic hard-filtering, but could be increased marginally to ~80% by increasing the minimum threshold of reads covering a SNP, and number of samples in which it was found. Functional annotation of non-synonymous SNPs specific to both the high and low fertility phenotype identified immune response-related genes, supporting previous work that identified this process as key to the phenotype.

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Stranded Total RNA-seq of liver biopsy collected from Holstein Friesian cows that were defined from cluster analysis as being metabolically "balanced", "imbalanced" or "other

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2021-07-09 | E-MTAB-9348 | biostudies-arrayexpress

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Stranded Total RNA-seq of whole blood cells collected from Holstein Friesian cows that were defined from cluster analysis as being metabolically "balanced", "imbalanced" or "other

2021-07-09 | E-MTAB-9347 | biostudies-arrayexpress

Bos taurus breed:Holstein Friesian

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Transcriptomic Regulations of Heat Stress Response in the liver of Lactating Dairy Cows

Project description:Heat stress (HS) has become a major challenge in the dairy industry around the world. Although numerous measures have been taken to alleviate the HS impact on milk production, the cellular level response to HS remains unclear in dairy cows. The objective of this study was to dissect functional alterations based on transcriptomic dynamics in the liver of cows under HS. Dairy cows exposed to HS exhibited both decreased feed intake and milk yield. Through liver transcriptomic analysis, differentially expressed genes were identified among three experimental conditions, including heat stress (HS), pair-fed (PF), and thermoneutral (TN) groups. We observed the upregulation of protein folding and inflammation-related genes in the HS group, while the mitochondrial genes were downregulated. Gene functional enrichment also revealed that mitochondria function and oxidative phosphorylation were dysregulated under HS. The liver transcriptome analysis generated a comprehensive gene expression regulation network upon HS in lactating dairy cows. Overall, this study provides novel insights into molecular and metabolic changes of cows conditioned under HS. Our results could facilitate the development of efficient biomarkers to mitigate the negative effect of HS on dairy cow health and productivity.

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