Comparative Transcriptome Profiling of Ileal and Cecal Tissues Between Pekin Ducks and Shaoxing Ducks

Abstract

Background: Pekin ducks are well-known meat-type ducks, whereas Shaoxing ducks are bred for their egg-laying abilities. Growth and development of poultry species is well studied; however, very little is known regarding differences in intestinal gene expression between Pekin and Shaoxing ducks. Methods: To investigate intestinal differences between Pekin and Shaoxing ducks, we conducted transcriptome analysis on ileal and cecal tissues from five 42-day-old ducks per breed, raised under identical housing and feeding conditions to minimize environmental influences. Results: The results showed that a total of 379 differentially expressed genes (DEGs) with p < 0.05 and |log₂FoldChange| > 1 were identified in the ileum when Pekin ducks were compared to Shaoxing ducks, among which 158 were upregulated and 221 were downregulated. Compared to Shaoxing ducks, a total of 367 DEGs with p < 0.05 and |log₂FoldChange| > 1 were identified in the ceca of Pekin ducks, among which 204 were upregulated and 163 were downregulated. Among these DEGs, nine genes were reported to be associated with growth and metabolism, namely, P2RX6, KCNJ6, CASQ2, EHHADH, ACSBG1, ELOVL4, AIF1L, VILL, and FABP1. Functional enrichment analyses using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases indicated that the DEGs were significantly involved in pathways such as calcium signaling, unsaturated fatty acid biosynthesis, fatty acid degradation, and tryptophan metabolism. Conclusions: In conclusion, our study identified transcriptome differences in the intestines of meat-type and laying-type ducks, offering insights into the genetic basis of their growth and metabolic differences. Future studies should validate key genes and explore environmental influences on gene expression.

Keywords: cecum; duck; ileum; transcriptome.

Figure 1

(A) Volcanic plots of total ileal gene expression in Pekin ducks and Shaoxing ducks. (B) Volcanic plots of total cecal gene expression in Pekin ducks and Shaoxing ducks. The x-axis indicates the log₂ (fold change) value of gene expression, while the y-axis represents −log₁₀(p-value) (where the p-value in the figure represents the p-value; p < 0.5 means −log₁₀(p-value) > 1.0. Red dots indicate upregulated DEGs, green dots represent downregulated DEGs, and grey dots denote non-differentially expressed genes. (C) A bar chart showing the DEGs in the ileum and cecum of Pekin ducks and Shaoxing ducks, with red bars indicating upregulated genes and blue bars indicating downregulated genes. (D) Ileal and cecal tissue expression profiles of 616 DEGs in the SX vs. BJ group. The color scale in the heatmap represents the log₁₀-transformed, FPKM-normalized expression values. Each horizontal bar corresponds to a gene, while each vertical column represents a sample, as indicated by the sample names. Red denotes upregulated genes, and blue signifies downregulated genes.

Figure 2

The bar chart of the top 20 GO terms enriched in DEGs. (A) The top 20 GO terms enriched in differentially expressed genes between Shaoxing ducks and Pekin ducks’ ileum. (B) The top 20 GO terms enriched in differentially expressed genes between Shaoxing ducks and Pekin ducks’ ceca.

Figure 3

Top 20 KEGG pathways enriched with differentially expressed genes in the ileum and cecum between Shaoxing ducks and Pekin ducks. (A) Top 20 enriched KEGG pathways of DEGs identified in the ileum. (B) Top 20 enriched KEGG pathways of DEGs identified in the ceca. In the dot plot, the size of each dot reflects the number of genes involved in the corresponding pathway, and the color gradient represents the q-value of the enrichment.

Figure 4

qPCR validation of DEGs in the ileum and cecum of Pekin and Shaoxing ducks. “*” indicates a significant difference (p < 0.05); “**” denotes a highly significant difference (p < 0.01). SH: ileum of Shaoxing duck; BH: ileum of Pekin duck; SM: cecum of Shaoxing duck; BM: cecum of Pekin duck.