GSE64289
RNA-seq analysis of differential gene expression in muscle from Holstein Friesian bulls undergoing diet restriction and compensatory growth
The objective of this study was to examine changes in muscle gene expression of growing bulls during a period of dietary energy restriction followed by a period of subsequent realimentation and compensatory growth. Purebred Holstein Friesian bulls (n=20) were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=10) followed by ad libitum access to feed for a further 55 days or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=10).  The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependnet on each treatment group. Muscle biopsies were collected at 2 time points (end of the differential feeding in Period 1 (d 120) and during the realimentation phase in Period 2 (d 15 of re-alimentation). RNA was extracted and muscle gene expression was examined using RNAseq technology and bioinformatic analysis. During the differential feeding period, over-represented pathways including fatty acid beta oxidaiton, oxidative phosphorylation and TCA cyclewere identified, which indicate utilisation of lipid sotes for energy utilisaiton and also alterations in energy produciton during dietary restriciton in muscle. During the realimentation period, pathways involved in energy produciton were over-represented, with the direction of fold changes opposite to that of these pathways in Period 1. additionally, a number of genes involved in cell division and cellular proliferation were up-regulated during compensatory growth in re-alimentation, thereby promoting accelerated cell growth and proliferation in muscle tissue of animals experiencing compensatory growth. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction. Overall design: 40 muscle RNA samples were analysed in total. 10 samples were from muscle biopsies collected at the end of a period of dietary restriction (d 120) and 10 samples were from muscle biopsis collected during the initial stages of compensatory growth (d 15 of re-alimentation). In addition,  RNA was also anlaysed from 10 samples collected from animals fed a libitum at each of these two timepoints.