Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers

Abstract

Development of management paradigms that enhance the rate of gain and qualitative characteristics of beef carcass development has the potential to impact production and nutrient use efficiency but also mitigate losses to the environment. We used eight Black Angus beef steers (272.5 ± 17.6 kg initial body wt) fed a forage-based pelleted diet alone ( n = 4) or supplemented with sodium propionate included ( n = 4) for 42 days. High-quality RNA was extracted from the longissimus lumborum and subjected to transcriptome sequencing using RNA-seq technology. Trimmed reads were aligned to the bovine reference genome (Btau4.0, release 63) and uniquely mapped reads from control and propionate treatment groups were subject to further analysis using edgeR. Candidates were filtered to account for multiple testing and differentially expressed genes (153 at a false discovery rate of <5%) were analyzed using Gene Ontology (GO) analysis (GOseq) to select terms where enrichment had occurred. Significant GO terms included regulation of cholesterol transport, regulation of sterol transport, and cellular modified amino acid metabolic process. Furthermore, the top four identified gene networks included lipid metabolism, small molecule biochemistry, carbohydrate metabolism, and molecular transport-related categories. Notably, changes in lipid metabolism specific genes reflect both increased oxidative and lipid synthetic capacities. Metabolism-related gene changes are reflective of expected enhancements in lean tissue accretion patterns exhibited in steers where high ruminal propionate relative to other short chain fatty acids is observed. Propionate feeding induced increased N retention in rapidly growing Angus cattle, and the observed alterations in LL tissue lipid metabolism-related gene networks are consistent with enhanced cell formation and function (protein synthesis, and lipogenic vs. lipolytic activities).

A genomewide association mapping study using ultrasound‐scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

“…In the second region, two SNPs are located in the ARF-GAP3 gene (ADP-ribosylation factor GTPase activating protein 3), rs135897211 in intron 7 and rs137777225 in exon 7. Additionally, close to this region, the MGST1, CLEC1A and C12orf5 genes were upregulated in longissimus lumborum of Angus cattle according to the transcriptomics analysis (Baldwin et al 2012). Our results provide additional evidence that candidate genes that affect muscle tissue are in this genomic region.…”

“…Additionally, close to this region, the MGST1, CLEC1A and C12orf5 genes were upregulated in longissimus lumborum of Angus cattle according to the transcriptomics analysis (Baldwin et al . ). Our results provide additional evidence that candidate genes that affect muscle tissue are in this genomic region.…”

Comparative muscle transcriptome associated with carcass traits of Nellore cattle

“…Besides these, many studies have used RNA Sequencing (RNA-Seq) to unravel complex traits in production animals. This high-throughput technology has been successfully employed in beef cattle for traits such as muscle development, intramuscular fat, and fatty acid profile, with interesting results of the phenotypic differences within and between populations [13–20]. …”

Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism

“…These can detect not only mRNA from highly expressed genes but also from less abundant genes [70, 71, 99]. In fact, RNA-Seq has several advantages over DNA microarrays including the detection of single nucleotide polymorphisms (SNP), alternative splice variants, and RNA editing [102]. These approaches have the ability to unravel genomic information at systems level in contrast to the reductionist paradigm.…”