文献类型： 外文期刊

作者： Quan, Jianping ¹ ; Yang, Ming ⁵ ; Wang, Xingwang ¹ ; Cai, Gengyuan ¹ ; Ding, Rongrong ¹ ; Zhuang, Zhanwei ¹ ; Zhou, Shenping ¹ ; Tan, Suxu ² ; Ruan, Donglin ¹ ; Wu, Jiajin ¹ ; Zheng, Enqin ¹ ; Zhang, Zebin ¹ ; Liu, Langqing ¹ ; Meng, Fanming ¹ ; Wu, Jie ¹ ; Xu, Cineng ¹ ; Qiu, Yibin ¹ ; Wang, Shiyuan ¹ ; Lin, Meng ¹ ; Li, Shaoyun ¹ ; Ye, Yong ¹ ; Zhou, Fuchen ¹ ; Lin, Danyang ¹ ; Li, Xuehua ¹ ; Deng, Shaoxiong ¹ ; Zhang, Yuling ¹ ; Yao, Zekai ¹ ; Gao, Xin ⁵ ; Yang, Yingshan ¹ ; Liu, Yiyi ¹ ; Zhan, Yuexin ¹ ; Liu, Zhihong ⁵ ; Zhang, Jiaming ¹ ; Ma, Fucai ¹ ; Yang, Jifei ¹ ; Chen, Qiaoer ¹ ; Yang, Jisheng ¹ ; Ye, Jian ⁴ ; Dong, Linsong ⁴ ; Gu, Ting ¹ ; Huang, Sixiu ¹ ; Xu, Zheng ¹ ; Li, Zicong ¹ ; Yang, Jie ¹ ; Huang, Wen ² ; Wu, Zhenfang ¹ ;

作者机构： 1.South China Agr Univ, Coll Anim Sci, Natl Engn Res Ctr Breeding Swine Ind, State Key Lab Swine & Poultry Breeding Ind, Guangzhou, Guangdong, Peoples R China

2.Michigan State Univ, Dept Anim Sci, E Lansing, MI 48824 USA

3.South China Agr Univ, State Reg Livestock & Poultry Genebank, Guangdong Genebank Livestock & Poultry, Guangzhou, Guangdong, Peoples R China

4.Guangdong Zhongxin Breeding Technol Co Ltd, Guangzhou, Guangdong, Peoples R China

5.Zhongkai Univ Agr & Engn, Coll Anim Sci & Technol, Guangzhou, Guangdong, Peoples R China

6.Yunfu Subctr, Guangdong Lab Lingnan Modern Agr, Yunfu, Guangdong, Peoples R China

7.South China Agr Univ, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou, Guangdong, Peoples R China

8.Guangdong Acad Agr Sci, Inst Anim Sci, Guangdong Key Lab Anim Breeding & Nutr, Guangzhou, Guangdong, Peoples R China

期刊名称：NATURE COMMUNICATIONS （ 影响因子：14.7； 五年影响因子：16.1 ）

ISSN：

年卷期： 2024 年 15 卷 1 期

页码：

收录情况： SCI

摘要： 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 specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs. Here, the authors use multi-omic data to reveal how genetic and epigenetic variation affects gene expression in two pig breeds. The findings highlight strong tissue-specific regulation and identify genes with allele-specific expression.