Gene expression analysis can aid in prioritising regions or classes of variants for genomic prediction and they increase our understanding of quantitative traits. The number of reads from RNA sequencing that align to a gene can be used to quantify gene expression. We sampled liver and muscle tissues of 150 lambs at slaughter. Their dams had been managed to high, medium, and low body condition scores (BCS) during mid-to-late pregnancy and the lambs were fed three different finishing diets. Differential expression of genes (DEG) was investigated contrasting tissue, BCS, lamb diets, other treatment differences, as well as high and low lamb carcass eye muscle width (CEMW). A large number of DEG were identified between tissues, but only the low versus high BCS comparison resulted in DEG for treatments. DEG were also found when we contrasted high and low CEMW. A strong trend toward down regulation was observed in all tests, except in BCS where all DEG were overexpressed in fatter ewes.
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