Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs
Hongwei Yin,
Liu Yang,
Qianyi Zhao,
Wenye Yao,
Jinyan Teng,
Yahui Gao,
Zhiting Xu,
Qing Lin,
Shuqi Diao,
Xiaohong Liu,
Fuping Zhao,
Zhongyin Zhou,
Qishan Wang,
Jiaqi Li,
Zhe Zhang,
Huaijun Zhou,
Martien A. M. Groenen,
Ole Madsen,
Lijing Bai,
Dailu Guan,
Lingzhao Fang,
Kui Li
Affiliations
Hongwei Yin
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS
Liu Yang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS
Qianyi Zhao
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS
Wenye Yao
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS
Jinyan Teng
State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU)
Yahui Gao
State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU)
Zhiting Xu
State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU)
Qing Lin
State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU)
Shuqi Diao
State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU)
Xiaohong Liu
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University
Fuping Zhao
Institute of Animal Science, Chinese Academy of Agricultural Sciences
Zhongyin Zhou
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Qishan Wang
Department of Animal Science, College of Animal Sciences, Zhejiang University
Jiaqi Li
State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU)
Zhe Zhang
State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU)
Huaijun Zhou
Department of Animal Science, University of California
Martien A. M. Groenen
Animal Breeding and Genomics, Wageningen University and Research
Ole Madsen
Animal Breeding and Genomics, Wageningen University and Research
Lijing Bai
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS
Dailu Guan
Department of Animal Science, University of California
Lingzhao Fang
Center for Quantitative Genetics and Genomics (QGG), Aarhus University
Kui Li
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS
Abstract Background Investigating 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. Results Our 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. Conclusions In 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.
