Transcriptomics profiling reveals candidate genes to improve feed efficiency in dairy cattle

Feed is the largest variable cost in milk production industries, thus improving feed efficiency (FE) will give better use of resources. To identify and select animals with high FE, it might be helpful to understand the biological mechanisms and the role of gene expression patterns across the whole genome (transcriptomics). In the present study, RNA sequencing data was used to detect differentially expressed (DE) genes in Danish Holstein and Jersey dairy cows having either a high or low FE (assessed as residual feed intake (RFI). Functional analysis was performed on these genes to identify molecular pathways involved in FE. Ten Jersey and nine Holstein cows were used in the experiment and divided into two RFI groups depending on their calculated RFI. The two RFI groups received a Control (C) and High Concentrate (HC) diet containing 68:32 and 39:61 ratio of forage:concentrate, respectively. This enabled us to compare the interaction between RFI status and diet. The mRNA samples extracted from liver biopsies were paired end sequenced. The RNA-Seq gene expression data was then analyzed using a statistical-bioinformatics pipeline to identify DE genes and perform functional enrichment. We compared gene expressions of the RFI groups, and identified 70 and 19 DE genes in Holstein and Jersey, respectively. An interaction term (RFI x diet) detected two significantly DE genes in Jersey cows. The functional enrichment analysis of the DE genes showed involvement in pathways that might regulate RFI, such as primary immunodeficiency, retinol metabolism, starch and sucrose metabolism, arachidonic acid metabolism and cytochrome P450 drug metabolism. In conclusion, the transcriptomics approach was effective in identifying DE genes and understanding their biological functions. These findings could contribute to the development of biomarkers for RFI and to improving augmented genomic selection procedures that make use of functional information.