Genome-wide analysis of DNA Methylation profiles on sheep ovaries associated with prolificacy using whole-genome Bisulfite sequencing
Yanli Zhang,
Fengzhe Li,
Xu Feng,
Hua Yang,
Aoxiang Zhu,
Jing Pang,
Le Han,
Tingting Zhang,
Xiaolei Yao,
Feng Wang
Affiliations
Yanli Zhang
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Fengzhe Li
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Xu Feng
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Hua Yang
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Aoxiang Zhu
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Jing Pang
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Le Han
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Tingting Zhang
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Xiaolei Yao
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Feng Wang
Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University
Abstract Background Ovulation rate and litter size are important reproductive traits in sheep with high economic value. Recent work has revealed a potential link between DNA methylation and prolificacy. However, a genome-wide study that sought to identify potential DNA methylation sites involved in sheep prolificacy indicated that it is still unknown. Here, we aimed to investigate the genome-wide DNA methylation profiles of Hu sheep ovaries by comparing a high-prolificacy group (HP, litter size of three for at least 2 consecutive lambings) and low prolificacy group (LP, litter size of one for at least 2 consecutive lambings) using deep whole-genome bisulfite sequencing (WGBS). Results First, our results demonstrated lower expression levels of DNA methyltransferase (DNMT) genes in the ovaries of the HP group than that in the ovaries of the LP group. Both groups showed similar proportions of methylation at CpG sites but different proportions at non-CpG sites. Subsequently, we identified 70,899 differential methylated regions (DMRs) of CG, 16 DMRs of CHG, 356 DMRs of CHH and 12,832 DMR-related genes(DMGs). Gene Ontology (GO) analyses revealed that some DMGs were involved in regulating female gonad development and ovarian follicle development. Finally, we found that 10 DMGs, including BMP7, BMPR1B, CTNNB1, FST, FSHR, LHCGR, TGFB2 and TGFB3, are more likely to be involved in prolificacy of Hu sheep, as assessed by correlation analysis and listed in detail. Conclusions This study revealed the global DNA methylation pattern of sheep ovaries associated with high and low prolificacy groups, which may contribute to a better understanding of the epigenetic regulation of sheep reproductive capacity.
