Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle

BMC Genomics

Hans D. Daetwyler¹  Amanda J. Chamberlain¹  Ying Yu²  Shuli Liu²  Shengli Zhang²  Li Ma³  Daniel J.A. Santos³  Ruidong Xiang⁴  Yang Zhou⁵  John B. Cole⁶  George E. Liu⁶  Cong-jun Li⁶  Lingzhao Fang⁶ 

[1] Agriculture Victoria, AgriBio, Centre for AgriBiosciences;College of Animal Science and Technology, China Agricultural University;Department of Animal and Avian Sciences, University of Maryland;Faculty of Veterinary & Agricultural Science, The University of Melbourne;Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University;USDA-ARS, Animal Genomics and Improvement Laboratory;

关键词: Sperm DNA methylation;    Methylation haplotype blocks;    Variably methylated regions;    Reproduction traits;    Cattle;   

DOI  :  10.1186/s12864-019-6228-6

来源: DOAJ

【 摘 要 】

Abstract Background DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. Results Based on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486 × coverage), we obtained 31,272 methylation haplotype blocks (MHBs). Among them, we defined conserved methylated regions (CMRs), variably methylated regions (VMRs) and highly variably methylated regions (HVMRs) among individuals, and showed that HVMRs might play roles in transcriptional regulation and function in complex traits variation and adaptive evolution by integrating evidence from traditional and molecular quantitative trait loci (QTL), and selection signatures. Using a weighted correlation network analysis (WGCNA), we also detected a co-regulated module of HVMRs that was significantly associated with reproduction traits, and enriched for glycosyltransferase genes, which play critical roles in spermatogenesis and fertilization. Additionally, we identified 46 VMRs significantly associated with reproduction traits, nine of which were regulated by cis-SNPs, implying the possible intrinsic relationships among genomic variations, DNA methylation, and phenotypes. These significant VMRs were co-localized (± 10 kb) with genes related to sperm motility and reproduction, including ZFP36L1, CRISP2 and HGF. We provided further evidence that rs109326022 within a predominant QTL on BTA18 might influence the reproduction traits through regulating the methylation level of nearby genes JOSD2 and ASPDH in sperm. Conclusion In summary, our results demonstrated associations of sperm DNA methylation with reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for cattle.

【 授权许可】

Unknown