Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits

References

• Manirakiza J, Hatungumukama G, Thévenon S, et al. Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands. Anim Genet. 2017;48(5):544–12.
   PubMed Web of Science ®Google Scholar
• Rodrigues RT, Chizzotti ML, Vital CE, et al. Differences in beef quality between Angus (Bos Taurus Taurus) and Nellore (Bos Taurus indicus) cattle through a Proteomic and phosphoproteomic approach. PLoS One. 2017;12:e0170294.
   PubMed Web of Science ®Google Scholar
• Utsunomiya YT, Milanesi M, Fortes MRS, et al. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet. 2019;50:557–568.
   PubMed Web of Science ®Google Scholar
• Verdugo MP, Mullin VE, Scheu A, et al. Ancient cattle genomics, origins, and rapid turnover in the fertile crescent. Science. 2019;365:173–176.
   PubMed Web of Science ®Google Scholar
• Bolormaa S, Pryce JE, Kemper KE, et al. Detection of quantitative trait loci in Bos indicus and Bos Taurus cattle using genome-wide association studies. 9114088. 2013;45:43.
   Google Scholar
• O’Brien AM P, Mészáros G, Utsunomiya YT, et al. Linkage disequilibrium levels in Bos indicus and Bos Taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. Livest Sci. 2014;166:121.
   Web of Science ®Google Scholar
• Hu Y, Xia H, Li M, et al. Comparative analyses of copy number variations between Bos Taurus and Bos indicus. BMC Genomics. 2020;21:682.
   PubMed Web of Science ®Google Scholar
• Barbato M, Hailer F, Upadhyay M, et al. Adaptive introgression from indicine cattle into white cattle breeds from Central Italy. Sci Rep. 2020;10:1279.
   PubMed Web of Science ®Google Scholar
• Angers B, Perez M, Menicucci T, et al. Sources of epigenetic variation and their applications in natural populations. Evol Appl. 2020;13:1262–1278.
   PubMed Web of Science ®Google Scholar
• Biwer C, Kawam B, Chapelle V, et al. The role of stochasticity in the origin of epigenetic variation in animal populations. Integr Comp Biol. 2020;60(6):1544–1557.
   PubMed Web of Science ®Google Scholar
• Vogt G. Epigenetic variation in animal populations: sources, extent, phenotypic implications, and ecological and evolutionary relevance. J Biosci. 2021;46:24.
   PubMed Web of Science ®Google Scholar
• Larson G, Fuller DQ. The evolution of animal domestication. Annu. Rev. Ecol. Evol. Syst. 2014;45:115–136.
   Web of Science ®Google Scholar
• Janowitz Koch I, Clark MM, Thompson MJ, et al. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol. 2016;25:1838–1855.
   PubMed Web of Science ®Google Scholar
• Hu J, Barrett RDH. Epigenetics in natural animal populations. J Evol Biol. 2017;30:1612–1632.
   PubMed Web of Science ®Google Scholar
• Ibeagha-Awemu EM, Zhao X. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet. 2015;6:302.
   PubMed Web of Science ®Google Scholar
• Triantaphyllopoulos KA, Ikonomopoulos I, Bannister AJ. Epigenetics and inheritance of phenotype variation in livestock. Epigenetics Chromatin. 2016;9:31.
   PubMed Web of Science ®Google Scholar
• Braunschweig M, Jagannathan V, Gutzwiller A, et al. Investigations on transgenerational epigenetic response down the male line in F2 pigs. PLoS One. 2012;7:e30583.
   PubMed Web of Science ®Google Scholar
• Braz CU, Taylor T, Namous H, et al. Paternal diet induces transgenerational epigenetic inheritance of DNA methylation signatures and phenotypes in sheep model. PNAS Nexus. 2022;1:40.
   Google Scholar
• Del Corvo M, Lazzari B, Capra E, et al. Methylome patterns of cattle adaptation to heat stress. Front Genet. 2021;12:633132.
   PubMed Web of Science ®Google Scholar
• Ponsuksili S, Trakooljul N, Basavaraj S, et al. Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs. BMC Genomics. 2019;20:492.
   PubMed Web of Science ®Google Scholar
• Peel MC, Finlayson BL, McMahon TA. Updated world map of the Köppen-Geiger climate classification. Hydrol. Earth Syst. Sci. 2007;11:1633–1644.
   Web of Science ®Google Scholar
• Alvares CA, Stape JL, Sentelhas PC, et al. Koppen’s climate classification map for Brazil. Meteorologische Zeitschrift. 2013;22:711–728.
   Web of Science ®Google Scholar
• Mallona I, Díez-Villanueva A. Peinado MA.Methylation plotter: a web tool for dynamic visualization of DNA methylation data.source code . Biol Med. 2014;9:11.
   Google Scholar
• Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760.
   PubMed Web of Science ®Google Scholar
• Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012.
   Google Scholar
• Ewels PA, Peltzer A, Fillinger S, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38:276–278.
   PubMed Web of Science ®Google Scholar
• Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32:292–294.
   PubMed Web of Science ®Google Scholar
• Bindea G, Mlecnik B, Hackl H, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25:1091–1093.
   PubMed Web of Science ®Google Scholar
• Achilli A, Bonfiglio S, Olivieri A, et al. The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS One. 2009;4:e5753.
   PubMed Web of Science ®Google Scholar
• Sevane N, Martínez R, Bruford MW. Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors. Anim Genet. 2019;50:15–26.
   PubMed Web of Science ®Google Scholar
• Yuan XL, Zhang Z, Pan RY, et al. Performances of different fragment sizes for reduced representation bisulfite sequencing in pigs. Biol Proced Online. 2017;19:5.
   PubMed Web of Science ®Google Scholar
• Costes V, Chaulot-Talmon A, Sellem E, et al. Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records. Clin Epigenetics. 2022;14:54.
   PubMed Web of Science ®Google Scholar
• Yan J, Zierath JR, Barrès R. Evidence for non-CpG methylation in mammals. Exp Cell Res. 2011;317:2555–2561.
   PubMed Web of Science ®Google Scholar
• Heyn H, Moran S, Hernando-Herraez I, et al. DNA methylation contributes to natural human variation. Genome Res. 2013 Sep;23:1363–1372.
   PubMed Web of Science ®Google Scholar
• Zhi D, Aslibekyan S, Irvin MR, et al. SNPs located at CpG sites modulate genome-epigenome interaction. Epigenetics. 2013;8:802–806.
   PubMed Web of Science ®Google Scholar
• Herman JJ, Spencer HG, Donohue K, et al. How stable ‘should’ epigenetic modifications be? Insights from adaptive plasticity and bet hedging. Evolution. 2013;68:632–643.
   PubMed Web of Science ®Google Scholar
• Grossniklaus U, Kelly WG, Ferguson-Smith AC, et al. Transgenerational epigenetic inheritance: how important is it? Nat Rev Genet. 2013;14:228–235.
   PubMed Web of Science ®Google Scholar
• Fanti L, Piacentini L, Cappucci U, et al. Canalization by Selection of de Novo Induced Mutations. Genetics. 2017;206:1995–2006.
   PubMed Web of Science ®Google Scholar
• Alvarado S, Rajakumar R, Abouheif E, et al. Epigenetic variation in the Egfr gene generates quantitative variation in a complex trait in ants. Nat Commun. 2015;6:6513.
   PubMed Web of Science ®Google Scholar
• Lindner M, Laine VN, Verhagen I, et al. Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird. Mol.Ecol. 2021;30:3645–3659.
   PubMed Web of Science ®Google Scholar
• Heckwolf MJ, Meyer BS, Hasler R, et al. Two different epigenetic information channels in wild three spined sticklebacks are involved in salinity adaptation. Sci Adv. 2020;6:eaaz1138.
   PubMed Web of Science ®Google Scholar
• Gore AV, Tomins KA, Iben J, et al. An epigenetic mechanism for cavefish eye degeneration. Nat Ecol Evol. 2018;2:1155–1160.
   PubMed Web of Science ®Google Scholar
• Candini O, Spano C, Murgia A, et al. Mesenchymal progenitors aging highlights a miR-196 switch targeting HOXB7 as master regulator of proliferation and osteogenesis. Stem Cells. 2015;33:939–950.
   PubMed Web of Science ®Google Scholar
• Brancaccio A, Minichiello A, Grachtchouk M, et al. Requirement of the forkhead gene Foxe1, a target of sonic hedgehog signaling, in hair follicle morphogenesis. Hum Mol Genet. 2004;13:2595–2606.
   PubMed Web of Science ®Google Scholar
• Thompson CA, DeLaForest A, Battle MA. Patterning the gastrointestinal epithelium to confer regional-specific functions. Dev Biol. 2018;435:97–108.
   PubMed Web of Science ®Google Scholar
• Han X, Yoshizaki K, Miyazaki K, et al. The transcription factor NKX2-3 mediates p21 expression and ectodysplasin-A signaling in the enamel knot for cusp formation in tooth development. J Biol Chem. 2018;293:14572–14584.
   PubMed Web of Science ®Google Scholar
• Wang M, Bissonnette N, Dudemaine PL, et al. Whole genome DNA methylation variations in mammary gland tissues from holstein cattle producing milk with various fat and protein contents. Genes (Basel). 2021;12:1727.
   PubMed Web of Science ®Google Scholar
• Kim ET, Joo SS, Kim DH, et al. Common and differential dynamics of the function of peripheral blood mononuclear cells between holstein and jersey cows in heat-stress environment. Animals (Basel). 2020;11:19.
   PubMedGoogle Scholar