{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T19:19:30Z","timestamp":1791487170603,"version":"4.3.4"},"reference-count":0,"publisher":"Cold Spring Harbor Laboratory","funder":[{"name":"National Key Research and Development Program of China","award":["2023YFD1300200"],"award-info":[{"award-number":["2023YFD1300200"]}]},{"name":"Guangdong Provincial Special Project on Seed Industry Revitalization","award":["2025-XPY-01-002"],"award-info":[{"award-number":["2025-XPY-01-002"]}]},{"name":"Key Technologies Research and Development Program of Guangdong Province","award":["2022B0202090002"],"award-info":[{"award-number":["2022B0202090002"]}]},{"name":"Local Innovative and Research Teams Project of Guangdong Province","award":["2019BTO2N630"],"award-info":[{"award-number":["2019BTO2N630"]}]},{"DOI":"10.13039\/501100001809","name":"Young Scientists Fund of the National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32502859"],"award-info":[{"award-number":["32502859"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"South China Agricultural University discipline construction and development project","award":["2023B10564001"],"award-info":[{"award-number":["2023B10564001"]}],"id":[{"id":"https:\/\/ror.org\/05v9jqt67","id-type":"ROR","asserted-by":"crossref"}]},{"name":"South China Agricultural University discipline construction and development project","award":["2023B10564003"],"award-info":[{"award-number":["2023B10564003"]}],"id":[{"id":"https:\/\/ror.org\/05v9jqt67","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genome Res."],"accepted":{"date-parts":[[2026,9,9]]},"abstract":"<jats:p>Pigs are one of the most important livestock species worldwide. Although multiple high-quality reference genomes exist, reliance on a single linear reference limits the detection of structural variants (SVs) and the characterization of population-specific genetic diversity. To address this limitation, we developed SwinePan, a comprehensive and integrated multiomic database for pigs built on a graph-based pangenome framework. SwinePan incorporates a variome derived from the graph-based pangenome, covering 2598 individuals across 35 breeds, including 185,759 SVs, 117 million SNPs, and 6.8 million indels. The database also integrates transcriptomic data from liver, loin muscle, abdominal fat, and backfat, along with more than 150,000 phenotypic records. The online toolkit deployed in SwinePan enables genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and colocalization, whereas interactive modules visualize population structure and multiomic associations, streamlining candidate gene and variant exploration. Additionally, two proof-of-concept analyses demonstrate how SwinePan pinpoints trait-associated loci and deciphers their potential regulatory mechanisms.<\/jats:p>","DOI":"10.1101\/gr.281750.125","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T19:40:19Z","timestamp":1789587619000},"source":"Crossref","is-referenced-by-count":0,"title":["SwinePan for pig graph-based pangenome and multiomics data mining"],"prefix":"10.1101","author":[{"given":"Meng","family":"Lin","sequence":"first","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"National and Regional Livestock and Poultry Gene Bank, Guangdong Gene Bank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Langqing","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"National and Regional Livestock and Poultry Gene Bank, Guangdong Gene Bank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gengyuan","family":"Cai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"National and Regional Livestock and Poultry Gene Bank, Guangdong Gene Bank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong 527300, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sixiu","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"National and Regional Livestock and Poultry Gene Bank, Guangdong Gene Bank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yibin","family":"Qiu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zekai","family":"Yao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoxiong","family":"Deng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research 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of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuchen","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajin","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong 527300, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zebin","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enqin","family":"Zheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong 510642, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7031-2160","authenticated-orcid":false,"given":"Jie","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"National and Regional Livestock and Poultry Gene Bank, Guangdong Gene Bank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong 510642, China;"},{"name":"Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong 510642, 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