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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #370227

Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

Title: Developmental and allele-specific methylation patterns in fetal liver of pigs derived from White Composite x Meishan reciprocal crosses

item CORBETT, RYAN - Michigan State University
item LIU, HAIBO - Iowa State University
item Nonneman, Danny - Dan
item Smith, Timothy - Tim
item RANEY, NANCY - Michigan State University
item TUGGLE, CHRIS - Iowa State University
item ERNST, CATHY - Michigan State University

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/15/2019
Publication Date: 1/15/2020
Citation: Corbett, R.J., Liu, H., Nonneman, D., Smith, T.P.L., Raney, N.E., Tuggle, C.K., Ernst, C.W. 2020. Developmental and allele-specific methylation patterns in fetal liver of pigs derived from White Composite x Meishan reciprocal crosses [abstract]. In proceedings: Plant and Animal Genome Conference, San Diego, CA, 11-15 Jan 2020. W034. Available:

Interpretive Summary:

Technical Abstract: The liver is a major metabolic organ that influences numerous economically important phenotypes in swine. However developmental and allele-specific gene regulation, including that governed by DNA methylation, are understudied in pig liver. We performed whole-genome bisulfite sequencing (WGBS) of pig fetal liver collected from White Composite and Meishan reciprocal crosses at 30 and 70 days of gestation (dg;N=8,2/stage/cross) in order to assess stage- and allele-specific methylation (ASM). WGBS read alignment and extraction of CpG methylation rates were performed using Bismark, and differential methylation analyses were performed using methylKit. We also performed allele-specific mapping of reads and ASM analyses, using SNPs identified from whole-genome sequencing data. Global CpG methylation rates ranged from 59.5-63.6% and were significantly higher in 70dg samples (p=0.01). We identified 24,601 differentially methylated regions (DMRs; difference>10%, FDR<1e-5) between stages, 91% of which were hypermethylated at 70dg. DMRs were enriched in gene promoters; 1956 promoter-hypermethylated genes (70dg vs. 30dg) were enriched for GO terms related to early development, while 676 promoter-hypomethylated genes were enriched for lipid and glucose metabolism terms, suggesting decreased and increased transcription of genes involved in these processes, respectively. 529 regions exhibited ASM between White and Meishan alleles, and these were enriched in genes associated with lipid metabolism. Lastly, 430 regions exhibited ASM between maternal and paternal alleles, including regions in the IGF2 and IGF2R gene clusters that are known to exhibit genomic imprinting. This work provides novel insight into epigenetic regulation during pig liver development and has identified genomic regions subject to breed- and parent-specific regulation.