GSE119563
A transcriptome analyses of Longissimus dorsi muscle in Nguni cattle finished on different feedlot diets
Background: The Nguni is an indigenous Bos taurus Sanga breed which is primarily used in extensive commercial and communal farming systems in South Africa. The Nguni is a small framed early maturing breed not preferred for finishing under feedlot systems, as the large framed later maturing types are favoured for high lean meat yield. In this study we aim to investigate differentially expressed genes in Longissimus dorsi muscle of Nguni cattle fed diets differing in energy levels finished under commercial feedlot conditions. Results: Twenty Nguni and twenty Bonsmara were fed either a low (10.9 MJ ME/kg) or a high (12.00 MJ ME/kg) energy diet for 120 days. At slaughter, muscle samples were taken for RNA extraction and RNA-sequencing. A total of 2214 differentially expressed genes (DEG) were observed between the two breeds regardless of diet. For the low energy diets, 2244 DEG in the Nguni and the Bonsmara were significantly expressed, while a higher number of were differentially expression between the Nguni and Bonsmara on high energy diet (3154 DEG). A difference of 288 DEG were identified between the Nguni fed on the low and high energy diets.  Most of the fat deposition genes were upregulated in the Bonsmara (ASIP, OXT, SNAI3, FOX01, PPARGC1A), with lower levels in the Nguni. Conclusion: Clear breed differences were found for the number and level of gene expression, while a larger variation in DEG were observed between the two diets within in the Bonsmara breed. Overall design: The effect of 2 diets (high or low energy) on two breeds