鸡繁殖性能近交衰退相关CpG岛差异甲基化基因的筛选

doi:10.11843/j.issn.0366-6964.2021.04.010

Abstract

Abstract: Inbreeding depression of chicken reproduction is one of major concerns during preserving local chicken genetic resources. This study aimed to investigate the role of genome-wide CpG island (CGI) DNA methylation in inbreeding depression of chicken reproduction. Three healthy hens were selected from the strongly and weakly inbred chicken groups respectively, that is, two groups were set in the experiment with 3 replicates in each group. Whole-genome bisulfite sequencing (WGBS) technology was used to detect and analyze genome-wide methylation differences in gonad axis tissues (including ovary and hypothalamus) between the two groups, and to identify the differentially methylated regions (DMRs). Functional annotation and enrichment analysis of genes with DMRs in their CpG islands were performed. The results showed that no significant differences were found at the methylation levels of ovary and hypothalamus genome between the strongly and weakly inbred chickens (P>0.05). However, 5 948 and 4 593 DMRs were identified between the two groups in hypothalamus and ovary, respectively, of which 1 798 and 995 DMRs were located in CpG islands of the genome. These DMRs were annotated to 1 020 and 552 genes, respectively. In hypothalamus, the genes with DMRs in CpG islands were significantly enriched in GO terms related to reproduction(P<0.05), such as signal transduction, nervous system development, reproductive system development and oocyte maturation regulation. And a total of 19 KEGG pathways were significantly enriched(P<0.05), including TGF-beta signaling pathway, Hepatitis B, fatty acid metabolism and insulin signaling pathways, etc. In ovary, the differentially methylated genes were significantly enriched in 12 pathways(P<0.05), such as chronic myeloid leukemia, influenza A, arginine and proline metabolism and focal adhesion, etc. Particularly, several pathways associated with oocyte development and sex hormone secretion were also enriched, for example, progesterone mediated oocyte maturation, oocyte meiosis, GnRH signaling pathway and estrogen signaling pathways, etc, which included a total of 10 genes, such as CDC27, ADCY8 and AKT3, etc. Thus, a large number of differentially methylated regions were detected between the strongly and weakly inbred Langshan chickens, and a number of differentially methylated genes were found to be related to reproductive traits. It is inferred that the DNA methylation in CpG islands of these genes may play important roles in regulation of inbreeding depression of reproduction in Langshan chicken. The study results will provide a basis for further research on the regulation mechanism of inbreeding depression of chicken reproduction, and will supply a reference for conservation of species resource and future poultry breeding.

Key words: Langshan chicken, DNA methylation, reproduction, inbreeding depression, differentially methylated region

CLC Number:

S831.2

XUE Qian, LI Guohui, YIN Jianmei, ZHANG Huiyong, ZHOU Chenghao, ZHU Yunfen, XING Weijie, SU Yijun, ZOU Jianmin, HAN Wei. Screening of Genes with Differential Methylated CpG Island Related to Inbreeding Depression of Chicken Reproduction[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(4): 943-953.

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Screening of Genes with Differential Methylated CpG Island Related to Inbreeding Depression of Chicken Reproduction

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