Dataset Information

The effect of breed and diet type on the global transcriptome of hepatic tissue in beef cattle divergent for feed efficiency.

ABSTRACT: BACKGROUND:Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar production levels but decreased feed intake, while also emitting less methane. RFI is difficult and expensive to measure and is not widely adopted in beef production systems. However, development of DNA-based biomarkers for RFI may facilitate its adoption in genomic-assisted breeding programmes. Cattle have been shown to re-rank in terms of RFI across diets and age, while also RFI varies by breed. Therefore, we used RNA-Seq technology to investigate the hepatic transcriptome of RFI-divergent Charolais (CH) and Holstein-Friesian (HF) steers across three dietary phases to identify genes and biological pathways associated with RFI regardless of diet or breed. RESULTS:Residual feed intake was measured during a high-concentrate phase, a zero-grazed grass phase and a final high-concentrate phase. In total, 322 and 33 differentially expressed genes (DEGs) were identified across all diets for CH and HF steers, respectively. Three genes, GADD45G, HP and MID1IP1, were differentially expressed in CH when both the high-concentrate zero-grazed grass diet were offered. Two canonical pathways were enriched across all diets for CH steers. These canonical pathways were related to immune function. CONCLUSIONS:The absence of common differentially expressed genes across all dietary phases and breeds in this study supports previous reports of the re-ranking of animals in terms of RFI when offered differing diets over their lifetime. However, we have identified biological processes such as the immune response and lipid metabolism as potentially associated with RFI divergence emphasising the previously reported roles of these biological processes with respect to RFI.

SUBMITTER: Higgins MG

PROVIDER: S-EPMC6593537 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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The effect of breed and diet type on the global transcriptome of hepatic tissue in beef cattle divergent for feed efficiency.

Higgins Marc G MG Kenny David A DA Fitzsimons Claire C Blackshields Gordon G Coyle Séan S McKenna Clare C McGee Mark M Morris Derek W DW Waters Sinéad M SM

BMC genomics 20190626 1

<h4>Background</h4>Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar production levels but decreased feed intake, while also emitting less methane. RFI is difficult and expensive to measure and is not widely adopted in beef production systems. However, development of DNA-based biomarkers for RFI may facilitate its adoption in genomic-assisted ...[more]

PMID: 31242854

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Project description:Exploring the compositional characteristics of rumen eukaryotic community can expand our understanding of their role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen eukaryotic community (protozoa and fungi) in beef cattle (n = 48) of three breeds [Angus (AN), Charolais (CH), and Kinsella Composite (KC)] and with divergent residual feed intake (RFI). The composition of active rumen eukaryotic microbiota was evaluated based on enriched 18S rRNAs from the metatranscriptomic datasets. At the phylum level, a total of four protozoal taxa (Ciliophora, Parabasalia, unclassified SAR, and unclassified Alveolata), six fungal taxa (Neocallimastigomycota, Basidiomycota, unclassified Fungi, Mucoromycota, Ascomycota, and Chytridiomycota), and one sister group of kingdom Fungi (unclassified Opisthokonta) were detected with relative abundances higher than 0.01% and in at least 50% of animals within each breed. Among these, Ciliophora, Parabasalia, unclassified Opisthokonta, and Neocallimastigomycota were the top four active eukaryotic phyla. At the genus level, a total of 8 ciliated protozoa, 5 flagellated protozoa, 5 anaerobic fungi, and 10 aerobic fungi taxa were detected, with unclassified Trichostomatia, Tetratrichomonas, unclassified Neocallimastigaceae, and Pleurotus being the most predominant taxa of ciliated protozoa, flagellated protozoa, anaerobic fungi, and aerobic fungi, respectively. Differential abundance analysis revealed that breed had a significant effect on the phylogenetic lineages of rumen eukaryotes, and seven fungal taxa were more abundant (linear discriminant analysis score > 2 with P < 0.05) in the rumen of KC steers than in the rumen of AN and CH steers. Although principal coordinate analysis (PCoA) revealed that the ruminal active eukaryotic profiles were not distinguishable between high- and low-RFI groups, the diversity indices, including Faith's phylogenetic diversity (PD), observed operational taxonomic units (OTUs), and Shannon index of rumen eukaryotes were higher in low-RFI steers than those in high-RFI steers. Meanwhile, the abundance of genus Entodinium and the kingdom Fungi was higher in low-RFI steers than that in high-RFI steers. This information on active rumen eukaryotic microbiota and identified differential abundance of taxa between high- and low-RFI animals suggests the possibility of improving feed efficiency through altering rumen eukaryotic microbiota.

Dataset Information

The effect of breed and diet type on the global transcriptome of hepatic tissue in beef cattle divergent for feed efficiency.

Publications

The effect of breed and diet type on the global transcriptome of hepatic tissue in beef cattle divergent for feed efficiency.

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