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. 2024 Jan 29;15(2):181.
doi: 10.3390/genes15020181.

Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks

Yuguang Chang  1 , Rongbing Guo  2 , Tao Zeng  1 , Hanxue Sun  1 , Yong Tian  1 , Xue Han  3 , Yongqing Cao  1 , Ligen Xu  1 , Mingcai Duan  1 , Lizhi Lu  1 , Li Chen  1
Affiliations

Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks

Yuguang Chang et al. Genes (Basel). .

Abstract

The egg-laying performance of Shan Ma ducks (Anas Platyrhynchos) is a crucial economic trait. Nevertheless, limited research has been conducted on the egg-laying performance of this species. We examined routine blood indicators and observed higher levels of metabolic and immune-related factors in the high-egg-production group compared with the low-egg-production group. Furthermore, we explored the ovarian transcriptome of both high- and low-egg-production groups of Shan Ma ducks using Illumina NovaSeq 6000 sequencing. A total of 1357 differentially expressed genes (DEGs) were identified, with 686 down-regulated and 671 up-regulated in the high-egg-production (HEP) ducks and low-egg-production (LEP) ducks. Several genes involved in the regulation of ovarian development, including neuropeptide Y (NPY), cell cycle protein-dependent kinase 1 (CDK1), and transcription factor 1 (E2F1), exhibited significant differential expressions at varying stages of egg production. Pathway functional analysis revealed that the DEGs were primarily associated with the steroid biosynthesis pathway, and the neuroactive ligand-receptor interaction pathway exhibited higher activity in the HEP group compared to the LEP group. This study offers valuable information about and novel insights into high egg production.

Keywords: RNA-seq; duck; egg production; ovary.

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Conflict of interest statement

The authors declare that this research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

Figures

Figure 1
Figure 1
Ovarian gene expression differed between the HEP and LEP groups. (A) Principal component analysis graph. Each point in the diagram represents a sample, and the position of the sample in space is determined by the differences in expression of the genes contained within it. (B) Volcano plots of differential gene expression. Each point in the graph represents a specific gene or transcript, with red points indicating significantly up-regulated genes, blue points indicating significantly down-regulated genes, and black points indicating non-significantly different genes. (C) Heat map of DEGs. The color represents the level of expression: the redder the color, the higher the gene expression. The heat map in the analysis results is a plot of the top 100 genes with the smallest p-values for display.
Figure 2
Figure 2
Functional annotations of differentially expressed genes in HEP and LEP groups. (A) Histogram of differential gene GO enrichment. The horizontal coordinate is the number of genes, and the vertical coordinate is the enrichment of genes in GO. (B) Scatter plot of KEGG enrichment for differentially expressed genes. The top 30 enrichment classifications of the KEGG pathway of the DEGs are listed in the figure. The horizontal axis indicates the enrichment factor, and the vertical axis indicates the name of the pathway. The point size indicates the number of enriched DEGs in the pathway, and the point color corresponds to a different range of p-values.
Figure 3
Figure 3
Protein–protein interaction (PPI) network for the cutoff differentially expressed genes (DEGs) based on the KEGG pathway. A total of 170 nodes and 450 edges were identified. The line color indicates the type of interaction evidence.
Figure 4
Figure 4
The three protein–protein interaction (PPI) hub network modules. The three significant modules, including (A) module 1 (MCODE score = 3.3), (B) module 2 (score = 10), and (C) module 3 (score = 3.7), were constructed from the PPI network of differentially expressed genes using MCODE. The seed node of each module was shaped, as highlighted by the red gene symbols.
Figure 5
Figure 5
Comparative analysis of qRT-PCR versus RNA-seq. Selected DEGs were validated by qRT-PCR for comparison.
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