The Sheep Gene Expression Atlas Project

Sheep are central to livestock production and of high socioeconomic importance across the globe. Improvements in productivity have, however, been relatively limited and there are numerous opportunities for genetic improvement.  We aim to produce a high-resolution atlas of gene expression from a comprehensive set of sheep tissues and cell types. The atlas will provide insight into gene, cell and tissue function with the goal of improving functional annotation of the sheep reference genome (currently, Oar v3.1).

Approximately 80 tissues and 5 cell types were collected from each of six adult (Scottish Blackface x Texel) sheep. Stranded Illumina TruSeq libraries were generated for RNASeq at high depth (>100 million reads) for a subset of 10 key tissues, for each individual, and at medium depth (>25 million reads) for the remainder. The Illumina platform was also used to sequence the genomes of the six adult sheep at 10X coverage. In addition, samples were collected from juveniles, fetuses and blastocysts. We are currently analysing the RNASeq and genomic data.

One initial priority is to compare the expression patterns from the RNASeq data with SNPs identified in the genome sequence data for evidence of allelic expression imbalance. The sequence data, which will be deposited in the public domain sequence repositories, will be a valuable resource for the international Functional Annotation of Animal Genomes (FAANG) initiative. The expression atlas will be a key foundation for sheep research, including studies with potential to inform future improvements in productivity, efficiency and health in sheep and other ruminants.