Abstract
BackgroundWe contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis of FE.ResultsApplication of a virtual muscle model to gene expression data pointed to a coordinated reduction in slow twitch muscle isoforms of the contractile apparatus (MYH15, TPM3, MYOZ2, TNNI1, MYL2, MYOM3, CSRP3, TNNT2), consistent with diminishment in associated slow machinery (myoglobin and phospholamban) in the high FE animals. These data are in line with the repeated transition from red slow to white fast muscle fibres observed in agricultural species selected on mass and FE. Surprisingly, we found that the expression of 699 genes encoding the broiler mitoproteome is modestly–but significantly–biased towards the high FE group, suggesting a slightly elevated mitochondrial content. This is contrary to expectation based on the slow muscle isoform data and theoretical physiological capacity arguments. Reassuringly, the extreme 40 most DE genes can successfully cluster the 12 individuals into the appropriate FE treatment group. Functional groups contained in this DE gene list include metabolic proteins (including opposing patterns of CA3 and CA4), mitochondrial proteins (CKMT1A), oxidative status (SEPP1, HIG2A) and cholesterol homeostasis (APOA1, INSIG1). We applied a differential network method (Regulatory Impact Factors) whose aim is to use patterns of differential co-expression to detect regulatory molecules transcriptionally rewired between the groups. This analysis clearly points to alterations in progesterone signalling (via the receptor PGR) as the major driver. We show the progesterone receptor localises to the mitochondria in a quail muscle cell line.ConclusionsProgesterone is sometimes used in the cattle industry in exogenous hormone mixes that lead to a ~20% increase in FE. Because the progesterone receptor can localise to avian mitochondria, our data continue to point to muscle mitochondrial metabolism as an important component of the phenotypic expression of variation in broiler FE.
Highlights
We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis of FE
Phenotypic Impact Factor (PIF) We computed a modified differential expression (DE) called PIF (DE multiplied by abundance) which we have found to have a number of appealing characteristics, both numerical and biological
804 million 100 bp sequences were obtained with an average of 67 million reads per sample and 80% of the reads were mapped to the G. gallus reference genome assembly
Summary
We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis of FE. Bottje et al BMC Systems Biology (2017) 11:29 gain [2] This makes broilers valuable as biological models for understanding the mechanistic basis of feed efficiency. Along with other avian meat producing species, cf turkeys, pheasants, partridge, grouse and quails, chickens are members of the Phasianidae taxonomic clade, the largest branch of the Galliformes. The members of this group tend to be sedentary, resident ground-dwelling birds that use short, burst flights to escape predators [3, 4]. This behaviour explains the functionally unusual breast muscle metabolism of the ancestral birds such as the Red Junglefowl (Gallus gallus) progenitor of modern domestic chickens, which is dominated by explosive, fast twitch contractile isoforms and a relatively low oxidative capacity metabolism
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