RNA-Seq transcriptome analysis of breast muscle in Pekin ducks supplemented with the dietary probiotic Clostridium butyricum

Abstract

Background: Increased attention is being paid to breast muscle yield and meat quality in the duck breeding industry. Our previous report has demonstrated that dietary Clostridium butyricum (C. butyricum) can improve meat quality of Pekin ducks. However, the potential biological processes and molecular mechanisms that are modulated by dietary C. butyricum in the breast muscle of Pekin ducks remain unknown.

Results: Supplementation with C. butyricum increased growth performance and meat yield. Therefore, we utilized de novo assembly methods to analyze the RNA-Seq transcriptome profiles in breast muscle to explore the differentially expressed genes between C. butyricum-treated and control Pekin ducks. A total of 1119 differentially expressed candidate genes were found of which 403 genes were significantly up-regulated and 716 genes were significantly down-regulated significantly. qRT-PCR analysis was used to confirm the accuracy of the of RNA-Seq results. GO annotations revealed potential genes, processes and pathways that may participate in meat quality and muscle development. KEGG pathway analysis showed that the differentially expressed genes participated in numerous pathways related to muscle development, including ECM-receptor interaction, the MAPK signaling pathway and the TNF signaling pathway.

Conclusions: This study suggests that long-time dietary supplementation with C. butyricum can modulate muscle development and meat quality via altering the expression patterns of genes involved in crucial metabolic pathways. The findings presented here provide unique insights into the molecular mechanisms of muscle development in Pekin ducks in response to dietary C. butyricum.

Keywords: Breast muscle; C. Butyricum; De novo assembly; Pekin duck; RNA-Seq.

Fig. 1

Annotation of genes using Gene ontology in breast muscle of Pekin duck. The number of genes for each GO annotation is exhibited in right axis, and the proportion of genes for each GO annotation is listed in left axis

Fig. 2

KEGG pathway classified annotation of genes in breast muscle of Pekin duck. a Metabolism; b Genetic Information Processing; c Environmental Information Processing; d Cellular Processes; e Organismal Systems

Fig. 3

COG function classification of genes in breast muscle of Pekin duck

Fig. 4

Cluster analysis of DEGs in breast muscle between control group (A1, A2, and A3) and treatment group (B1, B2, and B3). Values of log₁₀FPKM were conducted at normalized transformation before clustering. Red indicates high expressed genes, and green indicates low expressed genes. Each column represented a sample, and each row represented a gene. The left was the tree diagram of gene clustering, and the right was the name of each gene. The closer the two gene branches were, the closer their expression level was. The upper part was the tree diagram of sample clustering, and the bottom was the name of each sample. The closer the two sample branches were to each other, the closer the expression pattern of all genes in the two samples was and the closer the change trend of gene expression quantity was

Fig. 5

a The numbers of differentially expressed genes (DEGs; up/down-regulated) in breast muscle between control group and treatment group. b Volcano plot of global DEGs in breast muscle between control group and treatment group. Red dots (Up) represent significantly up-regulated genes (P < 0.05, fold change ≥2); Yellow dots (Up) represent extremely significantly up-regulated genes (P < 0.01, fold change ≥2); Mazarine dots (Down) represent significantly down-regulated genes (P < 0.05, fold change ≤0.5); Wathet dots (Down) represent extremely significantly down-regulated genes (P < 0.01, fold change ≤0.5); black dots (nosig) represent insignificantly differential expressed genes

Fig. 6

Gene ontology (GO) annotation of DEGs between control and treatment group. * means GO categories with significant enrichment

Fig. 7

KEGG Pathway analysis of DEGs between control group and treatment group. * means KEGG pathway with significant enrichment

Fig. 8

Expression levels of selected DEGs quantified by quantitative reverse transcription-PCR (qRT-PCR). GAPDH was used as an internal control, and data are presented as fold change (N = 6 per group)