Detection of tissue- and sex-specific gene expression

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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

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

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

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

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

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

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.