Abstract
BackgroundThe objective of this research was to investigate the variation of gene expression in the blood transcriptome profile of Chinese Holstein cows associated to the milk yield traits.ResultsWe used RNA-seq to generate the bovine transcriptome from the blood of 23 lactating Chinese Holstein cows with extremely high and low milk yield. A total of 100 differentially expressed genes (DEGs) (p < 0.05, FDR < 0.05) were revealed between the high and low groups. Gene ontology (GO) analysis demonstrated that the 100 DEGs were enriched in specific biological processes with regard to defense response, immune response, inflammatory response, icosanoid metabolic process, and fatty acid metabolic process (p < 0.05). The KEGG pathway analysis with 100 DEGs revealed that the most statistically-significant metabolic pathway was related with Toll-like receptor signaling pathway (p < 0.05). The expression level of four selected DEGs was analyzed by qRT-PCR, and the results indicated that the expression patterns were consistent with the deep sequencing results by RNA-Seq. Furthermore, alternative splicing analysis of 100 DEGs demonstrated that there were different splicing pattern between high and low yielders. The alternative 3’ splicing site was the major splicing pattern detected in high yielders. However, in low yielders the major type was exon skipping.ConclusionThis study provides a non-invasive method to identify the DEGs in cattle blood using RNA-seq for milk yield. The revealed 100 DEGs between Holstein cows with extremely high and low milk yield, and immunological pathway are likely involved in milk yield trait. Finally, this study allowed us to explore associations between immune traits and production traits related to milk production.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2901-1) contains supplementary material, which is available to authorized users.
Highlights
The objective of this research was to investigate the variation of gene expression in the blood transcriptome profile of Chinese Holstein cows associated to the milk yield traits
differentially expressed gene (DEG) and splice events between high and low yielders To provide a better understanding of the biological mechanism of milk yield, it is essential to identify the DEGs between high and low milk yield cows
All the DEGs were located in chromosomes randomly, but there were no DEGs identified in chromosome 14, 20, 27, and 28
Summary
The objective of this research was to investigate the variation of gene expression in the blood transcriptome profile of Chinese Holstein cows associated to the milk yield traits. Milk yield and milk composition of lactating cows are the most important economic traits in dairy cattle. Cui et al collected mammary gland samples from four lactating cows after slaughter. They used RNA-seq to generate the bovine mammary transcriptome with high and low milk fat and protein percentage [11]. There are still limitations in analysis of milk performance traits using bovine mammary tissue, such as sampling difficultly, high cost of sampling and tremendous damage to the lactating cows, which resulted in small sample size
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