https://orcid.org/0000-0001-8667-6682
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ABSTRACT
The current decline in dairy cattle fertility has resulted in significant financial losses for dairy farmers. In the past, most efforts to improve dairy cattle fertility have been focused on either management or genetics, while epigenetics have received less attention. In this study, 12 bulls were selected from a provided 100 bull list and studied (High daughter fertility = 6, Low daughter fertility = 6) for Enzymatic methylation sequencing in the Illumina HiSeq platform according to the Canadian daughter fertility index (DFI), sires with high and low daughter fertility have average DFI of 92 and 112.6, respectively. And the bull list provided shows a mean DFI of 103.4. 252 CpGs with methylation differences greater than 20% (q < 0.01) were identified, as well as the top 10 promising DMRs with a 15% methylation difference (q < 1.1e−26). Interestingly, the DMCs and DMRs were found to be distributed more on the X chromosome than on the autosome, and they were covered by gene clusters linked to germ cell formation and development. In conclusion, these findings could enhance our ability to make informed decisions when deciding on superior bulls and advance our understanding of paternal epigenetic inheritance.
Abbreviations
| AI | = | (Artificial Insemination) |
| CDN | = | (Canadian dairy network) |
| DMCs | = | (Differentially methylated cytosines) |
| DMRs | = | (Differentially methylated regions) |
| DMGs | = | (Differentially methylated genes) |
| DFI | = | (Daughter fertility index) |
| DNA | = | (Deoxyribonucleic acid) |
| DAVID (Database for Annotation | = | (Visualization, and Integrated Discovery) |
| IPA | = | (Ingenuity pathway analysis) |
| WGBS | = | (Whole genome bisulphite sequencing) |
| NRR | = | (Non-return rate) |
| GO | = | (Gene ontology) |
| KEGG | = | (Kyoto Encyclopedia of Genes and Genomes) |
| NRR | = | (Non-Return rate) |
| QTLs | = | (Quantitative trait locus) |
| SNP | = | (Single-nucleotide Polymorphism) |
| SPATA1 | = | (Spermatogenesis Associated 1) |
| SPATA6L | = | (Spermatogenesis Associated 6 Like) |
| SPATA22 | = | (Spermatogenesis Associated 22) |
| APOBECA | = | (Apolipoprotein B mRNA-editing) |
| SncRNA | = | (Small non-coding RNA) |
| LOC786530 | = | (Spermatogenesis associated 1 pseudogene) |
| TESK1 | = | (Testis associated actin remodelling kinase 1) |
| RPL10L | = | (Ribosomal protein L10 like) |
| HSPA2 | = | (Heat shock protein family A (Hsp70) member 2) |
| PARM1 | = | (Prostate androgen-regulated mucin-like protein 1) |
| UTR | = | (Untranslated regions) |
| ADCY9 | = | (Adenylate cyclase 9) |
| PDGFRA | = | (Platelet derived growth factor receptor alpha) |
| NMT1 | = | (N-myristoyltransferase 1) |
| EXT1 | = | (Exostosin glycosyltransferase 1) |
| FZD3 | = | (Frizzled class receptor 3) |
| TBX2 | = | (T-box transcription factor 2) |
| IPA | = | (Ingenuity pathway analysis) |
| KCNQ1 | = | (Potassium Voltage-Gated Channel Subfamily Q Member 1) |
| SNRPN | = | (Small Nuclear Ribonucleoprotein Polypeptide N) |
| TBX5 | = | (T-box transcription factor 5) |
| GPC3 | = | (Glypican 3) |
| OXTR | = | (Oxytocin receptor) |
Availability of data and materials
Whole-genome methylation sequencing data were deposited in NCBI’s Gene Expression Omnibus (GEO) and are accessible through the GEO series accession number: GSE211926.
Acknowledgments
This work was supported by SEMEX Alliance (Guelph, ON, Canada) and the CHINA SCHOLARSHIP COUNCIL. The authors thank SEMEX for the donation of the experimental materials and the use of their private database. The authors would also like to thank Patrick Blondin and collaborators from Boviteq (Saint-Hyacinthe, QC, Canada) for the original data collection, Julien Prunier and Eric Fournier for the bioinformatic analysis, Dominic Gagné for technical support, and Sylvie Bilodeau-Goeseels for proofreading the manuscript.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Supplementary material
Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592294.2023.2280889