Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs

References

• Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D. 2015. Genomation: a toolkit to summarize, annotate and visualize genomic intervals. Bioinformatics. 31(7):1127–1129. doi: 10.1093/bioinformatics/btu775.
   PubMed Web of Science ®Google Scholar
• Battram T, Gaunt TR, Relton CL, Timpson NJ, Hemani G. 2022. A comparison of the genes and genesets identified by GWAS and EWAS of fifteen complex traits. Nat Commun. 13(1):7816. doi: 10.1038/s41467-022-35037-3.
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi: 10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Cameron ND, Enser M, Nute GR, Whittington FM, Penman JC, Fisken AC, Perry AM, Wood JD. 2000. Genotype with nutrition interaction on fatty acid composition of intramuscular fat and the relationship with flavour of pig meat. Meat Sci. 55(2):187–195. doi: 10.1016/s0309-1740(99)00142-4.
   PubMed Web of Science ®Google Scholar
• DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 43(5):491–498. doi: 10.1038/ng.806.
   PubMed Web of Science ®Google Scholar
• Gomez-Alonso MDC, Kretschmer A, Wilson R, Pfeiffer L, Karhunen V, Seppälä I, Zhang W, Mittelstraß K, Wahl S, Matias-Garcia PR, et al. 2021. DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures. Clin Epigenetics. 13(1):7. doi: 10.1186/s13148-020-00957-8.
   PubMed Web of Science ®Google Scholar
• Gong J, Wan H, Mei S, Ruan H, Zhang Z, Liu C, Guo AY, Diao L, Miao X, Han L. 2019. Pancan-meQTL: a database to systematically evaluate the effects of genetic variants on methylation in human cancer. Nucleic Acids Res. 47(D1):D1066–d1072. doi: 10.1093/nar/gky814.
   PubMed Web of Science ®Google Scholar
• Grundberg E, Meduri E, Sandling JK, Hedman AK, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, et al. 2013. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet. 93(5):876–890. doi: 10.1016/j.ajhg.2013.10.004.
   PubMed Web of Science ®Google Scholar
• Guo T, Ren J, Yang K, Ma J, Zhang Z, Huang L. 2009. Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2 population. Anim Genet. 40(2):185–191. doi: 10.1111/j.1365-2052.2008.01819.x.
   PubMed Web of Science ®Google Scholar
• Hao Z, Lv D, Ge Y, Shi J, Weijers D, Yu G, Chen J. 2020. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Comput Sci. 6:e251. doi: 10.7717/peerj-cs.251.
   PubMedGoogle Scholar
• He Z, Zhang R, Jiang F, Zhang H, Zhao A, Xu B, Jin L, Wang T, Jia W, Jia W, et al. 2018. FADS1-FADS2 genetic polymorphisms are associated with fatty acid metabolism through changes in DNA methylation and gene expression. Clin Epigenetics. 10(1):113. doi: 10.1186/s13148-018-0545-5.
   PubMedGoogle Scholar
• Huan T, Joehanes R, Song C, Peng F, Guo Y, Mendelson M, Yao C, Liu C, Ma J, Richard M, et al. 2019. Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease. Nat Commun. 10(1):4267. doi: 10.1038/s41467-019-12228-z.
   PubMedGoogle Scholar
• Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, Alexsson A, Nordmark G, Eloranta ML, Rantapää-Dahlqvist S, Bengtsson AA, Jönsen A, Padyukov L, et al. 2018. DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus. Ann Rheum Dis. 77(5):736–743. doi: 10.1136/annrheumdis-2017-212379.
   PubMed Web of Science ®Google Scholar
• Kremmyda LS, Tvrzicka E, Stankova B, Zak A. 2011. Fatty acids as biocompounds: their role in human metabolism, health and disease: a review. part 2: fatty acid physiological roles and applications in human health and disease. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 155(3):195–218. doi: 10.5507/bp.2011.052.
   PubMed Web of Science ®Google Scholar
• Krueger F, Andrews SR 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics (Oxford, England) 27:1571–1572.doi:10.1093/bioinformatics/btr167.
   PubMed Web of Science ®Google Scholar
• Lin D, Chen J, Perrone-Bizzozero N, Bustillo JR, Du Y, Calhoun VD, Liu J. 2018. Characterization of cross-tissue genetic-epigenetic effects and their patterns in schizophrenia. Genome Med. 10(1):13. doi: 10.1186/s13073-018-0519-4.
   PubMed Web of Science ®Google Scholar
• Luo J, Shen L, Gan M, Jiang A, Chen L, Ma J, Jin L, Liu Y, Tang G, Jiang Y, et al. 2021. Profiling of skeletal muscle tissue for long non-coding RNAs related to muscle metabolism in the QingYu pig at the growth inflection point. Anim Biosci. 34(8):1309–1320. doi: 10.5713/ajas.20.0429.
   PubMedGoogle Scholar
• Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, et al. 2019. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One. 14(9):e0222329. doi: 10.1371/journal.pone.0222329.
   PubMed Web of Science ®Google Scholar
• Muñoz M, Rodríguez MC, Alves E, Folch JM, Ibañez-Escriche N, Silió L, Fernández AI. 2013. Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics. 14(1):845. doi: 10.1186/1471-2164-14-845.
   PubMedGoogle Scholar
• Nii M, Hayashi T, Tani F, Niki A, Mori N, Fujishima‐Kanaya N, Komatsu M, Aikawa K, Awata T, Mikawa S. 2006. Quantitative trait loci mapping for fatty acid composition traits in perirenal and back fat using a Japanese wild boar × Large White intercross. Anim Genet. 37(4):342–347. doi: 10.1111/j.1365-2052.2006.01485.x.
   PubMed Web of Science ®Google Scholar
• Orozco LD, Rubbi L, Martin LJ, Fang F, Hormozdiari F, Che N, Smith AD, Lusis AJ, Pellegrini M. 2014. Intergenerational genomic DNA methylation patterns in mouse hybrid strains. Genome Biol. 15(5):R68. doi: 10.1186/gb-2014-15-5-r68.
   PubMed Web of Science ®Google Scholar
• Qin YM, Hu CY, Pang Y, Kastaniotis AJ, Hiltunen JK, Zhu YX. 2007. Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis. Plant Cell. 19(11):3692–3704. doi: 10.1105/tpc.107.054437.
   PubMed Web of Science ®Google Scholar
• Ros-Freixedes R, Gol S, Pena RN, Tor M, Ibáñez-Escriche N, Dekkers JC, Estany J. 2016. Genome-wide association study singles out SCD and LEPR as the two main loci influencing intramuscular fat content and fatty acid composition in Duroc pigs. PLoS One. 11(3):e0152496. doi: 10.1371/journal.pone.0152496.
   PubMed Web of Science ®Google Scholar
• Sato S, Uemoto Y, Kikuchi T, Egawa S, Kohira K, Saito T, Sakuma H, Miyashita S, Arata S, Suzuki K. 2017. Genome-wide association studies reveal additional related loci for fatty acid composition in a Duroc pig multigenerational population. Anim Sci J. 88(10):1482–1490. doi: 10.1111/asj.12793.
   PubMed Web of Science ®Google Scholar
• Schulz H, Ruppert AK, Herms S, Wolf C, Mirza-Schreiber N, Stegle O, Czamara D, Forstner AJ, Sivalingam S, Schoch S, et al. 2017. Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus. Nat Commun. 8(1):1511. doi: 10.1038/s41467-017-01818-4.
   PubMedGoogle Scholar
• Shoemaker R, Deng J, Wang W, Zhang K. 2010. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res. 20(7):883–889. doi: 10.1101/gr.104695.109.
   PubMed Web of Science ®Google Scholar
• Triantaphyllopoulos KA, Ikonomopoulos I, Bannister AJ. 2016. Epigenetics and inheritance of phenotype variation in livestock. Epigen Chrom. 9:31. doi: 10.1186/s13072-016-0081-5.
   PubMed Web of Science ®Google Scholar
• Turner SDJB. 2014. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots.
   Google Scholar
• Tvrzicka E, Kremmyda LS, Stankova B, Zak A. 2011. Fatty acids as biocompounds: their role in human metabolism, health and disease–a review. Part 1: classification, dietary sources and biological functions. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 155(2):117–130. doi: 10.5507/bp.2011.038.
   PubMed Web of Science ®Google Scholar
• Verma M. 2012. Epigenome-Wide Association Studies (EWAS) in Cancer. Curr Genomics. 13(4):308–313. doi: 10.2174/138920212800793294.
   PubMed Web of Science ®Google Scholar
• Viterbo VS, Lopez BIM, Kang H, Kim H, Song CW, Seo KS. 2018. Genome wide association study of fatty acid composition in Duroc swine. Asian-Australas J Anim Sci. 31(8):1127–1133. doi: 10.5713/ajas.17.0779.
   PubMed Web of Science ®Google Scholar
• Wang M, Ibeagha-Awemu EM. 2020. Impacts of epigenetic processes on the health and productivity of livestock. Front Genet. 11:613636. doi: 10.3389/fgene.2020.613636.
   PubMed Web of Science ®Google Scholar
• Wood JD, Enser M, Fisher AV, Nute GR, Sheard PR, Richardson RI, Hughes SI, Whittington FM. 2008. Fat deposition, fatty acid composition and meat quality: a review. Meat Sci. 78(4):343–358. doi: 10.1016/j.meatsci.2007.07.019.
   PubMed Web of Science ®Google Scholar
• Wood JD, Richardson RI, Nute GR, Fisher AV, Campo MM, Kasapidou E, Sheard PR, Enser M. 2004. Effects of fatty acids on meat quality: a review. Meat Sci. 66(1):21–32. doi: 10.1016/S0309-1740(03)00022-6.
   PubMed Web of Science ®Google Scholar
• Xu CJ, Söderhäll C, Bustamante M, Baïz N, Gruzieva O, Gehring U, Mason D, Chatzi L, Basterrechea M, Llop S, et al. 2018. DNA methylation in childhood asthma: an epigenome-wide meta-analysis. Lancet Respir Med. 6(5):379–388. doi: 10.1016/S2213-2600(18)30052-3.
   PubMed Web of Science ®Google Scholar
• Zhang W, Zhang J, Cui L, Ma J, Chen C, Ai H, Xie X, Li L, Xiao S, Huang L, et al. 2016. Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations. Genet Sel Evol. 48:5. doi: 10.1186/s12711-016-0184-2.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang J, Gong H, Cui L, Zhang W, Ma J, Chen C, Ai H, Xiao S, Huang L, et al. 2019. Genetic correlation of fatty acid composition with growth, carcass, fat deposition and meat quality traits based on GWAS data in six pig populations. Meat Sci. 150:47–55. doi: 10.1016/j.meatsci.2018.12.008.
   PubMed Web of Science ®Google Scholar
• Zhi D, Aslibekyan S, Irvin MR, Claas SA, Borecki IB, Ordovas JM, Absher DM, Arnett DK. 2013. SNPs located at CpG sites modulate genome-epigenome interaction. Epigenetics. 8(8):802–806. doi: 10.4161/epi.25501.
   PubMed Web of Science ®Google Scholar