title: Transcriptional profiling of mammary gland in Holstein cows with extremely different milk protein and fat percentage using RNA sequencing.
abstract: BACKGROUND
  Recently, RNA sequencing (RNA-seq) has rapidly emerged as a major transcriptome profiling system. Elucidation of the bovine mammary gland transcriptome by RNA-seq is essential for identifying candidate genes that contribute to milk composition traits in dairy cattle.
  
  
  RESULTS
  We used massive, parallel, high-throughput, RNA-seq to generate the bovine transcriptome from the mammary glands of four lactating Holstein cows with extremely high and low phenotypic values of milk protein and fat percentage. In total, we obtained 48,967,376-75,572,578 uniquely mapped reads that covered 82.25% of the current annotated transcripts, which represented 15549 mRNA transcripts, across all the four mammary gland samples. Among them, 31 differentially expressed genes (p < 0.05, false discovery rate q < 0.05) between the high and low groups of cows were revealed. Gene ontology and pathway analysis demonstrated that the 31 differently expressed genes were enriched in specific biological processes with regard to protein metabolism, fat metabolism, and mammary gland development (p < 0.05). Integrated analysis of differential gene expression, previously reported quantitative trait loci, and genome-wide association studies indicated that TRIB3, SAA (SAA1, SAA3, and M-SAA3.2), VEGFA, PTHLH, and RPL23A were the most promising candidate genes affecting milk protein and fat percentage.
  
  
  CONCLUSIONS
  This study investigated the complexity of the mammary gland transcriptome in dairy cattle using RNA-seq. Integrated analysis of differential gene expression and the reported quantitative trait loci and genome-wide association study data permitted the identification of candidate key genes for milk composition traits.
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Cui
authors.forename: Yali
authors.initials: Y
authors.lastname: Hou
authors.forename: Shaohua
authors.initials: S
authors.lastname: Yang
authors.forename: Yan
authors.initials: Y
authors.lastname: Xie
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhang
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.forename: Xuemei
authors.initials: X
authors.lastname: Lu
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
authors.affiliation: Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. sundx@cau.edu.cn.
authors.forename: Dongxiao
authors.initials: D
authors.lastname: Sun
mesh_terms: D000818:Animals; D002417:Cattle; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D050356:Lipid Metabolism / Q000235:genetics; D008321:Mammary Glands, Animal / Q000378:metabolism*; D008892:Milk / Q000378:metabolism*; D008894:Milk Proteins / Q000378:metabolism*; D044162:Parathyroid Hormone-Related Protein / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D017346:Protein Serine-Threonine Kinases / Q000037:antagonists & inhibitors / Q000235:genetics; D040641:Quantitative Trait Loci; D012269:Ribosomal Proteins / Q000235:genetics; D017423:Sequence Analysis, RNA; D000685:Serum Amyloid A Protein / Q000235:genetics; D059467:Transcriptome; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics
chemical_list: D008894:Milk Proteins; D044162:Parathyroid Hormone-Related Protein; D012269:Ribosomal Proteins; D000685:Serum Amyloid A Protein; D042461:Vascular Endothelial Growth Factor A; D017346:Protein Serine-Threonine Kinases