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Identification of key pathways associated with residual feed intake of beef cattle

ABSTRACT: Identification of key pathways associated with residual feed intake of beef cattle

PROVIDER: PRJNA813568 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18258981_1.fastq.gz	Fastqsanger.gz
	SRR18258981_2.fastq.gz	Fastqsanger.gz
	SRR18258982_1.fastq.gz	Fastqsanger.gz
	SRR18258982_2.fastq.gz	Fastqsanger.gz
	SRR18258984_1.fastq.gz	Fastqsanger.gz

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Identification of key pathways associated with residual feed intake of beef cattle

Project description:The biological mechanisms associated with the residual feed intake in ruminants have been harnessed immensely via transcriptome analysis of liver and ruminal epithelium, however, this concept has not been fully explored using whole blood. We applied whole blood transcriptome analysis and gene set enrichment analysis to identify key pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261.3 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, weekly whole blood samples were collected three times from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.

2022-04-07 | GSE198068 | GEO

Transcriptome Profiling of the Rumen Epithelial Tissues of Beef Cattle Differing in Residual Feed Intake

Project description:We functionally analyzed the rumen epithelial transcriptomes from low- and high- feed efficient beef steers to identify differences that might contribute to variation in feed efficiency.

2017-01-01 | GSE76501 | GEO

Gene Expression Profiling of Hormonal Regulation Related to the Residual Feed Intake of Holstein Cattle

Project description:An accumulation of over a decade of research in cattle has shown that genetic selection for decreased residual feed intake (RFI), defined as the difference between an animal’s actual feed intake and its expected feed intake, is a viable option for improving feed efficiency and reducing the feed requirements of herds, thereby improving the profitability of cattle producers. Hormonal regulation is one of the most important factors in feed intake. To determine the relationship between hormones and feed efficiency, we performed gene expression profiling of hormonal regulation in whole blood of Chinese Holstein cattle with low and high RFI coefficients. 857 differential expression genes (from 24683 genes) were found. Among these, 415 genes were up-regulated and 442 genes were down-regulated in the low RFI group. The gene ontology (GO) search revealed 6 significant terms and 64 genes associated with hormonal regulation, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) selected the adipocytokine signaling pathway, insulin signaling pathway. In conclusion, the study indicated that the molecular expression of genes associated with hormonal regulation differs in dairy cows, depending on their RFI coefficients, and that these differences may be related to the molecular regulation of the leptin-NPY and insulin signaling pathways.

2015-03-24 | GSE67176 | GEO

Differential gene expression in the liver among crossbred beef steers with divergent gain and feed intake phenotypes

Project description:Steer liver transcriptome Evaluation of the naturally occurring transcriptome variation in liver among beef steers with divergent gain and feed intake phenotypes.

2016-03-31 | GSE75700 | GEO

Differential gene expression in the spleen among crossbred beef steers with divergent gain and feed intake phenotypes.

Project description:Steer spleen transcriptome Evaluation of the naturally occurring transcriptome variation in the spleen among beef steers with divergent gain and feed intake phenotypes.

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Differential gene expression in the mesenteric fat among crossbred beef steers with divergent gain and feed intake phenotypes

Project description:Steer mesenteric fat transcriptome. Evaluation of the naturally occurring transcriptome variation in mesenteric fat among beef steers with divergent gain and feed intake phenotypes.

2015-11-30 | GSE73699 | GEO

Characterization and profiling of liver microRNAs in cattle divergently selected for residual feed intake by RNA-sequencing

Project description:MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle Results: Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs (miRBase v.19). Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378 and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (version 19). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle Conclusions: Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying residual feed intake in bovine

2015-11-27 | GSE63691 | GEO

Differential gene expression in the duodenum, jejunum, and ileum among crossbred beef steers with divergent gain and feed intake phenotypes.

Project description:Steer small intestine transcriptome Evaluation of the naturally occurring transcriptome variation among beef steers with divergent gain and feed intake phenotypes.

2015-09-19 | GSE73159 | GEO

miRNA data for residual feed intake

Project description:An integrative transcriptome analysis indicates regulatory networks for residual feed intake in Nelore cattle

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Transcriptome analysis of mRNA expression in skeletal muscle of Yorkshire pigs with differential residual feed intake

Project description:Feed accounts for more than 60% of the costs for pig production, and FE can be measured as residual feed intake (RFI). In this study, we compared the transcriptome difference of longissimus dorsi muscles of Yorkshire pigs with high RFI (RFI_H) and low RFI (RFI_L) using Solexa mRNA sequencing.

2015-05-31 | E-MTAB-2946 | biostudies-arrayexpress

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