biostudies-literatureUnknown15(1)Quan JHybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificitNature communications5587https://www.ebi.ac.uk/biostudies/studies/S-EPMC11222378biostudies-literatureMulti-omic characterization of allele-specific regulatory variation in hybrid pigs.PMC11222378Wu JDeng SLiu LZhang JDong LQuan JYe YCai GZhan YQiu YLiu YWu ZYao ZLiu ZDing RWang SWang XZhou FZheng EGu TYang JChen QZhou SYang MXu CZhuang ZMeng FLi XHuang SYang YLi ZLi SZhang ZLin DZhang YHuang WTan SGao XLin MMa FXu ZRuan DYe JfalseMulti-omic characterization of allele-specific regulatory variation in hybrid pigs.Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificit2024-01-01T00:00:00Z2024 Jul2025-04-04T12:54:04.715Z2025-04-04T12:54:04.715ZS-EPMC112223783896107610.1038/s41467-024-49923-5