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. 2022 Nov 17;8(11):e11644.
doi: 10.1016/j.heliyon.2022.e11644. eCollection 2022 Nov.

Genome-wide DNA methylation differences between conservation and breeding populations of Shaoxing ducks

Ligen Xu  1   2 , Zhenzhen Shi  1   3 , Haiying Li  3 , Jun He  2 , Bindan Chen  4 , Zeng Tao  1 , Yong Tian  1 , Li Chen  1 , Guoqin Li  1 , Zhengrong Tao  1 , Tiantian Gu  1 , Wenwu Xu  1 , Lizhi Lu  1
Affiliations

Genome-wide DNA methylation differences between conservation and breeding populations of Shaoxing ducks

Ligen Xu et al. Heliyon. .

Abstract

The genome-wide DNA methylation assay was used to analyze the difference in methylation between the breeding and conservation populations of Shaoxing ducks. The methylation level of the breeding population was higher than that of the two conservation populations, and the proportion of CG methylation sites was the largest in the three populations, most of the methylation sites were located in the exon region. There were 1247 different methylation regions in the two populations (group A and B), and 927 different methylation regions in the two groups (group A and group C). The differential methylation regions of the three groups were evenly distributed in the gene and intergene regions. GO and KEGG enrichment analysis showed that the differentially expressed genes in the A and B groups were mainly involved in synaptic and cell connections and the signaling pathways were significantly enriched in cAMP and oxytocin signaling pathways. The results showed that the group C was significantly enriched in eight signaling pathways, including the cAMP signaling pathway and long-term enhancement, compared to the group A. There were thirty-five differentially methylated genes, including CACNA1C, GRIA1, GRIA2, GABBR2, PDE10A, BRAF, GRM5, CPEB3, FMn2, GABRB2, PTK2, and CNTN1. These genes were involved in the development and ovulation of ovaries and follicles and were closely related to the excellent production performance of the breeding population. In addition, ATP2B1, ATP2B2, and other genes related to eggshell quality were identified, which can be used as molecular markers to improve eggshell quality in the future.

Keywords: Breeding population; Conservation populations; DNA methylation; Methylated genes; Shaoxing ducks.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Distribution of methylation levels 1 K upstream and downstream of the gene. The red denotes group A, blue is group B, and green is group C, the vertical axis represents the methylation level and the horizontal axis represents different gene regions.
Figure 2
Figure 2
Distribution of methylation levels of groups A, B, and C on chromosomes. The three methylation types are CG, CHG and CHH.
Figure 3
Figure 3
Sequence feature maps. CHG is on the left, CHH is on the right. A, T, C, and G are different bases.
Figure 4
Figure 4
GO enrichment of differentially methylated genes (group B vs. A). The larger the circle, the larger the number of differentially enriched genes for this function. The color spectrum from blue to red represents the uncorrected P-value.
Figure 5
Figure 5
GO enrichment of differentially methylated genes (group C vs. A).
Figure 6
Figure 6
KEGG enrichment of differentially methylated genes (group B vs. A).
Figure 7
Figure 7
KEGG enrichment of differentially methylated genes (group C vs. A).
See this image and copyright information in PMC

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