数字农科院2.0

Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs

文献类型： 外文期刊

作者： 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

作者机构：

关键词： Complex traits;Epigenome;Gene expression and splicing;Genomic variants;Non-coding regions

期刊名称： BMC Biology

ISSN： 1741-7007

年卷期： 2025 年 23 卷 1 期

页码：

收录情况： SCIE（2025版）

摘要： 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.

分类号：

  • 相关文献

[1]Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. He, Guangming,Li, Jigang,He, Hang,Yang, Mei,Deng, Xing Wang,Chen, Beibei,Li, Xueyong,Li, Jigang,Deng, Xing Wang,Chen, Beibei,Wang, Xuncheng,Li, Xueyong,Lu, Lu,Wang, Xiping,Qi, Yijun. 2013

[2]Editorial: Evolution of crop genomes and epigenomes. Hai Du,Wei Hu,Viktor Demko,梁哲. 2022

[3]Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses. Xuelei Lin,Yongxin Xu,Dongzhi Wang,Yiman Yang,Xiaoyu Zhang,Xiaomin Bie,Lixuan Gui,Zhongxu Chen,Yiliang Ding,Long Mao,Xueyong Zhang,Fei Lu,Xiansheng Zhang,Cristobal Uauy,Xiangdong Fu,Jun Xiao. 2024

[4]Epigenomic identification of vernalization cis-regulatory elements in winter wheat. Yanhong Liu,Pan Liu,Lifeng Gao,Yushan Li,Xueni Ren,Jizeng Jia,Lei Wang,Xu Zheng,Yiping Tong,Hongcui Pei,Zefu Lu. 2024

[5]Dissection Of Complicate Genetic Architecture A.nd Breeding Perspective Of C ottonseed Traits By Genome-Wide Association Study. Xia, Qiuju,Xiang, Haitao,Ma, Jun,Xu, Haiming,Du, Xiongming,Sun, Gaofei,Jia, Yinhua,Pan, Zhaoe,He, Shoupu,Quan, Zhiwu,Shi, Weijun,Jenkins, Johnie N.,Du, Xiongming,Sun, Junling,Zhu, Jun,Zhang, Gengyun,Xiao, Songhua,Pang, Baoyin,Liu, Jianguang,Lou, Xiangyang,Gong, Wenfang,Wang, Liru,Liu, Shouye. 2018

[6]Simultaneous improvement and genetic dissection of grain yield and its related traits in a backbone parent of hybrid rice (Oryza sativa L.) using selective introgression. Zhang, Hongjun,Wang, Hui,Qian, Yiliang,Shi, Yingyao,Zhu, Linghua,Gao, Yongming,Li, Zhikang,Qian, Yiliang,Shi, Yingyao,Xia, Jiafa,Li, Zefu,Ali, Jauhar.

[7]A new approach to dissecting complex traits by combining quantitative trait transcript (QTT) mapping and diallel cross analysis. Yang DaiGang;YE ChengYin,Ma XiongFeng,ZHU ZhiHong,ZHOU XiaoJian,WANG HaiFeng,MENG QingQin,PEI XiaoYu,YU ShuXun,ZHU Jun. 2012

[8]Galbase: a comprehensive repository for integrating chicken multi-omics data. Fu, Weiwei,Wang, Rui,Xu, Naiyi,Wang, Jinxin,Li, Ran,Asadollahpour Nanaei, Hojjat,Nie, Qinghua,Zhao, Xin,Han, Jianlin,Yang, Ning,Jiang, Yu. 2022

[9]Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication. 郑晓明,,逄洪波,,刘莎,,王君瑞,,乔卫华,,杨庆文. 2019

[10]Complex genetic architecture underlying the plasticity of maize agronomic traits. Jin, Minliang,Liu, Haijun,Liu, Xiangguo,Guo, Tingting,Guo, Jia,Yin, Yuejia,Ji, Yan,Li, Zhenxian,Zhang, Jinhong,Wang, Xiaqing,Qiao, Feng,Xiao, Yingjie,Zan, Yanjun,Yan, Jianbing. 2023

[11]Editorial: Multi-omics strategies to analyze complex agronomic traits in plants. Lin Chen,Guo Fei Tan. 2023

[12]Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs. Zhiting Xu,Qing Lin,Xiaodian Cai,Zhanming Zhong,Jinyan Teng,Bingjie Li,Haonan Zeng,Yahui Gao,Zexi Cai,Xiaoqing Wang,Liangyu Shi,Xue Wang,Yi Wang,Zipeng Zhang,Yu Lin,Shuli Liu,Hongwei Yin,Zhonghao Bai,Chen Wei,Jun Zhou,Wenjing Zhang,Xiaoke Zhang,Shaolei Shi,Jun Wu,Shuqi Diao,Yuqiang Liu,Xiangchun Pan,Xueyan Feng,Ruiqi Liu,Zhanqin Su,Chengjie Chang,Qianghui Zhu,Yuwei Wu,Zhongyin Zhou,Lijing Bai,Kui Li,Qishan Wang,Yuchun Pan,Zhong Xu,Xianwen Peng,Shuqi Mei,Delin Mo,Xiaohong Liu,Hao Zhang,Xiaolong Yuan,Yang Liu,George E. Liu,Guosheng Su,Goutam Sahana,Mogens Sandø Lund,Li Ma,Ruidong Xiang,Xia Shen,Pinghua Li,Ruihua Huang,Maria Ballester,Daniel Crespo-Piazuelo,Marcel Amills,Alex Clop,Peter Karlskov-Mortensen,Merete Fredholm,Guoqing Tang,Mingzhou Li,Xuewei Li,Xiangdong Ding,Jiaqi Li,Yaosheng Chen,Qin Zhang,Yunxiang Zhao,Fuping Zhao,Lingzhao Fang,Zhe Zhang. 2025

作者其他论文 更多>>