1. Detection of tissue- and sex-specific gene expression
in Bos taurus using high depth RNA sequencing
Thomas Lopdell, Matt Littlejohn
Livestock Improvement Corporation, Hamilton, New Zealand

2. Introduction
LIC is using RNA-Seq to help identify genes and variants underlying major dairy traits
Two tissues examined so far:
29 lactating mammary samples
8 pituitary samples
Pituitary samples include three males and five females

3. Methods Truseq reads sequenced using Illumina HiSeq
Mapped to UMD3.1 bovine genome using Tophat2
Transcripts assembled using Cufflinks and Cuffmerge
DESeq used to find genes differentially- expressed by sex

4. Mammary Sample Results
Caseins (CSN1S1, CSN1S2, CSN2, CSN3)
Beta-lactoglobulin (LGB)
45S rRNA

5. Pituitary Sample Results
Growth Hormone 1 (GH1)
45S rRNA
Prolactin (PRL)

6. Differentially-Expressed Genes
136 genes in pituitary tissue
Four of the five most significant are Y-linked
Other is XIST

7. Conclusions
Specialised tissues can produce large numbers of transcripts from small numbers of genes, affecting the sensitivity to detect less abundant transcripts.
It appears to be possible to determine sex from RNA-Seq data. Validation with more male animals is required.