Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs
文献类型： 外文期刊
作者： Yin, Hongwei 1 ; Yang, Liu 1 ; Zhao, Qianyi 1 ; Yao, Wenye 1 ; Teng, Jinyan 4 ; Gao, Yahui 4 ; Xu, Zhiting 4 ; Lin, Qing 4 ; Diao, Shuqi 4 ; Liu, Xiaohong 6 ; Zhao, Fuping 7 ; Zhou, Zhongyin 8 ; Wang, Qishan 9 ; Li, Jiaqi 4 ; Zhang, Zhe 4 ; Zhou, Huaijun 5 ; Groenen, Martien A. M. 3 ; Madsen, Ole 3 ; Bai, Lijing 1 ; Guan, Dailu 5 ; Fang, Lingzhao 2 ; Li, Kui 1 ;
作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,CAAS,Key Lab Live, Bldg A,Room 311,Buxin Rd, Shenzhen 518124, Peoples R China
2.Aarhus Univ, Ctr Quantitat Genet & Genom QGG, Aarhus, Denmark
3.Wageningen Univ & Res, Anim Breeding & Genom, NL-6708 PB Wageningen, Netherlands
4.South China Agr Univ SCAU, Coll Anim Sci, Natl Engn Res Ctr Breeding Swine Ind, State Key Lab Swine & Poultry Breeding Ind,Guangdo, Guangzhou, Peoples R China
5.Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA
6.Sun Yat Sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangzhou, Peoples R China
7.Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China
8.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming, Peoples R China
9.Zhejiang Univ, Coll Anim Sci, Dept Anim Sci, Hangzhou, Peoples R China
关键词： Genomic variants; Gene expression and splicing; Complex traits; Non-coding regions; Epigenome
期刊名称：BMC BIOLOGY （ 影响因子：4.5； 五年影响因子：5.4 ）
ISSN：
年卷期： 2025 年 23 卷 1 期
页码：
收录情况： SCI
摘要： BackgroundInvestigating the functional impact of genomic variants is essential to uncover the molecular mechanisms behind complex traits. This study compiled a comprehensive dataset of 1,817 whole-genome sequences from diverse pig breeds and populations, capturing the global pig genetic diversity.ResultsOur analyses first revealed 27,167 loss-of-function variants (LoFs), the majority of which also influenced gene expression and splicing, and enriched in genomic regions associated with complex traits in pigs. We further genome-wide annotated non-coding variants, and then focused on these resided in 5 ' untranslated region (5 ' UTR). Although they had lower deleterious impact on protein sequence compared to coding variants, they enriched in promoters and exhibited functional consequences on gene expression and splicing and finally complex traits. We employed the Basenji deep learning model and ATAC-seq to predict the impact of these SNPs on chromatin accessibility in 13 pig tissues. SNPs with higher predicted scores demonstrated stronger effects on gene expression/splicing and complex traits-particularly average backfat thickness-compared to variants with lower scores.ConclusionsIn summary, our study provides a comprehensive catalog of genomic variants in both protein-coding and non-coding regions, and elucidated their functional consequences on epigenome, transcriptome, and complex traits in pigs.
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