Identification of differentially expressed genes in breast muscle and skin fat of postnatal Pekin duck

Abstract

Lean-type Pekin duck is a commercial breed that has been obtained through long-term selection. Investigation of the differentially expressed genes in breast muscle and skin fat at different developmental stages will contribute to a comprehensive understanding of the potential mechanisms underlying the lean-type Pekin duck phenotype. In the present study, RNA-seq was performed on breast muscle and skin fat at 2-, 4- and 6-weeks of age. More than 89% of the annotated duck genes were covered by our RNA-seq dataset. Thousands of differentially expressed genes, including many important genes involved in the regulation of muscle development and fat deposition, were detected through comparison of the expression levels in the muscle and skin fat of the same time point, or the same tissue at different time points. KEGG pathway analysis showed that the differentially expressed genes clustered significantly in many muscle development and fat deposition related pathways such as MAPK signaling pathway, PPAR signaling pathway, Calcium signaling pathway, Fat digestion and absorption, and TGF-beta signaling pathway. The results presented here could provide a basis for further investigation of the mechanisms involved in muscle development and fat deposition in Pekin duck.

Figure 1. Random distribution of reads across genes.

Note: Figure 1A–1G represent the reads across genes from the total RNA-seq dataset (All), reads from the skin fat sample at 2-, 4- and 6-weeks of age (F2, F4 and F6); reads from the breast muscle sample at 2-, 4- and 6-weeks of age (M2, M4 and M6) respectively,

Figure 2. Coverage statistics of annotated duck genes by the current RNA-seq data.

Note: Figure 2A-2G represent percent of each gene covered by the total RNA-seq dataset coverage (All), the skin fat samples at 2-, 4- and 6-weeks of age (F2, F4 and F6), and the breast muscle samples at 2-, 4- and 6-weeks of age (M2, M4 and M6) respectively.

Figure 3. Validation of genetic variation among individuals.

Note: The validation of genetic variation among individuals was performed by comparing of the relative expression of ten randomly selected genes within each tissue type and time point using qRT-PCR.

Figure 4. Validation of the accuracy of RNA-seq data.

Note: The validation of the accuracy of RNA-seq data was carried out by comparing of RPKM and the relative expression of five randomly selected genes using qRT-PCR for each tissue and time point.

Figure 5. Differentially expressed genes between each sample pair.

Note: The number of differentially expressed genes found in each sample pair, expressed as the number of up-regulated and down-regulated genes. The first sample in each comparison is considered the control sample. For example, in the F2-VS-F4 comparison, 341 genes are up-regulated in F4 compared to F2.

Figure 6. Validation of expression levels of important genes involved in muscle development and fat deposition.

Note: The validation of important genes was performed by comparing of RPKM and relative expression using qRT- PCR for each tissue and time point.