Evidence map›Paper›PMID 40598185›Full record

ArticleBMC biology2025

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 and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Hongwei YinShenzhen 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, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China.
Liu YangShenzhen 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, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China.
Qianyi ZhaoShenzhen 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, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China.
Wenye YaoShenzhen 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, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China.
Jinyan TengState 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), Guangzhou, China.
Yahui GaoState 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), Guangzhou, China.
Zhiting XuState 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), Guangzhou, China.
Qing LinState 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), Guangzhou, China.
Shuqi DiaoState 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), Guangzhou, China.
Xiaohong LiuState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
Fuping ZhaoInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Zhongyin ZhouState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Qishan WangDepartment of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Jiaqi LiState 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), Guangzhou, China.
Zhe ZhangState 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), Guangzhou, China.
Huaijun ZhouDepartment of Animal Science, University of California, Davis, CA, 95616, USA.
Martien A M GroenenAnimal Breeding and Genomics, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands.
Ole MadsenAnimal Breeding and Genomics, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands.
Lijing BaiShenzhen 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, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China. bailijing@caas.cn.
Dailu GuanDepartment of Animal Science, University of California, Davis, CA, 95616, USA. dguan@ucdavis.edu.
Lingzhao FangCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.
Kui LiShenzhen 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, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China. likui@caas.cn.

Funding

China Scholarship Council 202003250046National Key R&D Program of China 2021YFD301201National Key Research and Developmental Program of China 2021YFF1000600National Natural Science Foundation of China 31972539National Natural Science Foundation of Guangxi province 2024GXNSFAAO10105Outstanding Talents Training Fund in Shenzhen 32140102Science and Technology Program of Shenzhen CJGJZD20210408092402006Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District PT20170201Shenzhen Outstanding Talents Training Fund 202102STI 2030-Major Projects 2022ZD04017
6 · The paper itself

Abstract

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.

Indexed as

EpigenomicsGenetic VariationGenomeSus scrofaAnimalsMolecular Sequence AnnotationPolymorphism, Single NucleotideSwineComplex traitsEpigenomeGene expression and splicingGenomic variantsNon-coding regions

Identifiers

PMID40598185
PMCPMC12220224

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.