Dataset Information

RNA-Seq Meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers.

ABSTRACT: BACKGROUND:Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed intake and gain across a large segment of the cattle industry. Transcriptomic studies often suffer from issues with reproducibility and cross-validation. One way to improve reproducibility is by integrating multiple datasets via meta-analysis. RNA sequencing (RNA-Seq) was performed on longissimus dorsi muscle from 80 steers (5 cohorts, each with 16 animals) selected from the outside fringe of a bivariate gain and feed intake distribution to understand the genes and pathways involved in feed efficiency. In each cohort, 16 steers were selected from one of four gain and feed intake phenotypes (n?=?4 per phenotype) in a 2?×?2 factorial arrangement with gain and feed intake as main effect variables. Each cohort was analyzed as a single experiment using a generalized linear model and results from the 5 cohort analyses were combined in a meta-analysis to identify differentially expressed genes (DEG) across the cohorts. RESULTS:A total of 51 genes were differentially expressed for the main effect of gain, 109 genes for the intake main effect, and 11 genes for the gain x intake interaction (Pcorrected?

SUBMITTER: Keel BN

PROVIDER: S-EPMC5987596 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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RNA-Seq Meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers.

Keel Brittney N BN Zarek Christina M CM Keele John W JW Kuehn Larry A LA Snelling Warren M WM Oliver William T WT Freetly Harvey C HC Lindholm-Perry Amanda K AK

BMC genomics 20180604 1

<h4>Background</h4>Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed intake and gain across a large segment of the cattle industry. Transcriptomic studies often suffer from issues with reproducibility and cross-validation. One way to improve reproducibility is by integrating multiple datasets via meta-analysis. RNA sequencing (RNA-Seq) was ...[more]

PMID: 29866053

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Project description:We applied ruminal and plasma metabolomics and ruminal 16S rRNA gene sequencing to determine the metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers. A group of 108 crossbred growing beef steers (average BW = 282.87 ± 30 kg) were fed a forage-based diet for a period of 56 d in a confinement dry lot equipped with GrowSafe intake nodes to determine their residual body weight gain (RADG) phenotype. After RADG identification, blood and rumen fluid samples were collected from beef steers with the highest RADG (most efficient; n = 16; 0.76 kg/d) and lowest RADG (least efficient; n = 16; -0.65 kg/d). Quantitative untargeted metabolome analysis of the plasma and rumen fluid samples were conducted using chemical isotope labelling/liquid chromatography-mass spectrometry. Differentially abundant metabolites in each of the plasma and rumen fluid samples between the two groups of beef steers were determined using a false discovery rate (FDR)-adjusted P-values ≤ 0.05 and area under the curve (AUC) > 0.80. Rumen and plasma metabolic pathways that were differentially enriched or depleted (P ≤ 0.05) in beef steers with positive RADG compared to those with negative RADG were determined by the quantitative pathway enrichment analysis. A total of 1,629 metabolites were detected and identified in the plasma of the beef steers; eight metabolites including alanyl-phenylalanine, 8-hydroxyguanosine, and slaframine were differentially abundant (FDR ≤ 0.05; AUC > 0.80) in beef steers with divergent RADG; five metabolic pathways including steroid hormone biosynthesis, thiamine metabolism, propanoate metabolism, pentose phosphate pathway, and butanoate metabolism were enriched (P ≤ 0.05) in beef steers with positive RADG, relative to negative RADG steers. A total of 1,908 metabolites were detected and identified in the rumen of the beef steers; results of the pathway enrichment analysis of all the metabolites revealed no metabolic pathways in the rumen were altered (P > 0.05). The rumen fluid samples were also analyzed using 16S rRNA gene sequencing to assess the bacterial community composition. We compared the rumen bacterial community composition at the genus level using a linear discriminant analysis effect size (LEfSe) to identify the differentially abundant taxa between the two groups of beef steers. The LEfSe results showed greater relative abundance of Bacteroidetes_vadinHA17 and Anaerovibrio in steers with positive RADG compared to the negative RADG group, while steers in the negative RADG group had greater relative abundance of Candidatus_Amoebophilus, Clostridium_sensu_stricto_1, Pseudomonas, Empedobacter, Enterobacter, and Klebsiella compared to the positive RADG group. Our results demonstrate that beef steers with positive or negative RADG exhibit differences in plasma metabolic profiles and some ruminal bacterial taxa which probably explain their divergent feed efficiency phenotypes.

Project description:Single-pass corn stover harvest is a method whereby combine harvester tailings consisting of cob, stalk, leaf, husk, and tassel fractions are collected and baled without coming into contact with soil. The objective was to feed beef steers diets that included a roughage component consisting of harvested corn residue in chopped form from conventional corn stover bales (CST) or single-pass bales (SPB) to assess intake selectivity of corn stover fractions and estimate net energy values of these corn stovers. Whole plant corn silage served as the control roughage in the control diet (CSIL). Steers (n = 90, 5 pens per treatment) were fed during Grow (84 d) and Finish (66 d) trials. Steers sorted through corn stover during both trials and consumed 52.5% of corn stover offered and 40% of cob offered. Intake of SPB cob was 2.6-fold and 3.3-fold greater than CST cob intake (P < 0.01) in Grow and Finish trials, respectively, indicating that when more cob was available, cattle consumed more. During the Grow trial, stover intake tended (P = 0.07) to be lower for SPB and diet dry matter intake (DMI) was less (P ≤ 0.05) for SPB, which may be due to the elevated cob intake by SPB steers. Across treatments, stover DMI was similar in the Grow (1.10 kg per steer per d) and Finish (1.11 kg per steer per d) trials. The proportion (65%) of Fines (<8 mm) consumed from the Grow diet (40% neutral detergent fiber, aNDF) was greater than the Finish diet (25% aNDF; 18% to 31%) and gleaning of concentrate feeds from orts seemed to be more extensive in the Grow diet. Steers consuming Finish diets containing SPB and CST had DMI that were 17% and 18%, respectively, greater (P ≤ 0.05) than CSIL, an indication of compensatory intake. The physical effectiveness factors for stovers fed in the Grow and Finish diets were 0.85 and 0.95, respectively. Estimates for net energy maintenance and net energy gain (NEg), respectively, using National Research Council methods from 2001 were as follows for consumed stovers: SPB (1.09 and 0.54 Mcal/kg) and CST (0.98 and 0.44 Mcal/kg) in the Grow trial, and SPB (0.96 and 0.42 Mcal/kg) and CST (0.95 and 0.40 Mcal/kg) in the Finish trial. Although SPB and CST differ in botanical fraction composition and net intakes of botanical fractions, their energetic contributions to steer performance were very similar. Steers fed the Finish diet (1.25 Mcal performance-adjusted NEg per kg) selected stover botanical components to achieve a diet composition of 25% aNDF.

Dataset Information

RNA-Seq Meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers.

Publications

RNA-Seq Meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers.

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