title: Whole blood transcriptional profiling comparison between different milk yield of Chinese Holstein cows using RNA-seq data.
abstract: 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.
  
  
  
  We 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.
  
  
  
  This 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.
authors.affiliation: College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Bai
authors.affiliation: College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.|Institute of ATCG Nei Mongol Bio-Information, Hohhot, 010020, China.
authors.forename: Zhuqing
authors.initials: Z
authors.lastname: Zheng
authors.affiliation: College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.|Institute of ATCG Nei Mongol Bio-Information, Hohhot, 010020, China.|Nei Mongol BioNew Technology Co.Ltd, Hohhot, 010018, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.affiliation: College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.|Institute of ATCG Nei Mongol Bio-Information, Hohhot, 010020, China.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Ji
authors.affiliation: Department of Biology, Indiana State University, Terre Haute, IN, 47809, U.S.A.. Yongsheng.Bai@indstate.edu.
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Bai
authors.affiliation: College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China. atcgnmbi@aliyun.com.|Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. atcgnmbi@aliyun.com.
authors.forename: Wenguang
authors.initials: W
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D002417:Cattle; D005091:Exons; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D007774:Lactation / Q000235:genetics*; D050356:Lipid Metabolism / Q000235:genetics; D008892:Milk; D020641:Polymorphism, Single Nucleotide; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*
keywords: Dairy cattle; Differentially expressed genes; Immune response; Milk yield; Whole blood