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Bos taurus

ABSTRACT: RNA-seq analysis of differential gene expression in muscle from angus beef steers undergoing diet restriction and compensatory growth

PROVIDER: PRJNA210308 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR924500_1.fastq.gz	Fastqsanger.gz
	SRR924500_2.fastq.gz	Fastqsanger.gz
	SRR924501_1.fastq.gz	Fastqsanger.gz
	SRR924501_2.fastq.gz	Fastqsanger.gz
	SRR924502_1.fastq.gz	Fastqsanger.gz

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Project description:The objective of this study was to examine changes in muscle gene expression of growing steers during a period of dietary energy restriction followed by a period of realimentation. Crossbred Aberdeen Angus x Holstein Friesian (n = 24) steers were assigned to one of two feeding treatments. Over a 99 d period, 1 group (n=12) was offered a high energy control diet consisting of concentrates ad libitum and 7 kg of grass silage per head daily. The second group (n=12) was offered an energy restricted diet consisting of grass silage ad libitum plus 0.5 kg of concentrate per head per day. From the end of the differential feeding period (99 d), both groups of animals were offered a total mixed ration (grass silage:concentrate ratio of 80:20). This period, which lasted 200 d, was known as the realimentation period. All animals were slaughtered on d 299 of the study. Muscle biopsies were collected at 2 time points (end of the differential feeding period (d 99) and during the realimentation period (d131). RNA was extracted and muscle gene expression was examined using RNA-seq technology and bioinformatic analysis. During the differential feeding period, 17 over-represented pathways were identified, including the peroxisome proliferator activated receptor signalling, glycolysis/ gluconeogenesis and metabolic pathways controlling the metabolism of lipids and lipoproteins which indicate reduced energy intake and fat tissue accumulation occurring in muscle tissue during the restriction phase. During the realimentation period, 164 differentially expressed genes were annotated to 9 over-represented pathways including starch and sucrose metabolism, carbohydrate digestion and absorption and TGF-β signalling pathway. It is hypothesised that the signalling effects of the TGF-β pathway were reduced 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. 24 muscle RNA samples were analysed in total. 6 samples were from muscle biopsies collected at the end of a period of dietary restriction (d99) and 6 samples were from muscle biopsies collected at the peak of compensatory growth (d131). In addition, RNA was also analysed from 6 samples collected from animals fed ad libitum at each of these two timepoints.

Project description:Beef represents a major diet component and source of protein in many countries. With an increment demand for beef, the industry is currently undergoing changes towards natural produced beef. Consumers not only concern about product quality, but also for the well-being of animals. Therefore, the consumption of grass-fed meat is continuously growing. However, the nutritional true differences between feeding systems are still unclear. The aim of this study was to examine latissimus dorsi muscle quality and animal welfare by transcriptome and metabolome profiles, and to identify biological pathways related to the differences between grass- and grain-fed Angus steers. By RNA-Seq analysis of latissimus dorsi muscle, we have recognized 241 differentially expressed genes (FDR < 0.1). The metabolome examination of muscle and blood revealed 163 and 179 altered compounds in each tissue (P-value < 0.05), respectively. Accordingly, alterations in glucose metabolism, divergences in free fatty acids and carnitine conjugated lipid levels, and altered Î²-oxidation, have been observed. In summary, this study demonstrates a unique transcriptomic and metabolic signature in the muscle of grain and grass finished cattle. Results support the accumulation of anti-inflammatory n3 polyunsaturated fatty acids in grass finished cattle, while higher levels of n6 PUFAs in grain finished animals may promote inflammation and oxidative stress. Furthermore, grass-fed animals produce tender beef with lower total fat and higher omega3/omega6 ratio than grain fed animals, which could potentially benefit consumer health. Finally, blood cortisol levels strongly indicate that grass fed animals experience less stress than the grass fed individuals The steers came from a closed Wye Angus herd with very similar genetics. The grass-fed group was comprised of steers that received alfalfa and orchard grass hay, clover and orchard grass pasture, or orchard grass and alfalfa pasture. The grass-fed individuals consumed grazed alfalfa upon availability and bales during winter and were not exposed to any corn, any form of grain or feed by-products. The alfalfa and grass hay were harvested from land that has had minimal fertilizer and no application of pesticides or inorganic chemicals. The control group was fed a conventional diet consisting of corn silage, soybean, shelled corn and minerals. The pastures were managed as organic landsâwithout fertilizers, pesticides or any chemical additives. At the slaughter plant, 10 ml whole blood sample from the jugular vein was collected in EDTA tubes and directly storage at -80Â°C. Then, a small piece of longissimus dorsi muscle was obtained from each hot carcass at the level of the 12th intercostal space and immediately frozen in dry ice for posterior analysis.

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Bos taurus

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