PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

Haonan Zeng; Wenjing Zhang; Qing Lin; Yahui Gao; Jinyan Teng; Zhiting Xu; Xiaodian Cai; Zhanming Zhong; Jun Wu; Yuqiang Liu; Shuqi Diao; Chen Wei; Wentao Gong; Xiangchun Pan; Zedong Li; Xiaoyu Huang; Xifan Chen; Jinshi Du; Fuping Zhao; Yunxiang Zhao; Maria Ballester; Daniel Crespo-Piazuelo; Marcel Amills; Alex Clop; Peter Karlskov-Mortensen; Merete Fredholm; Pinghua Li; Ruihua Huang; Guoqing Tang; Mingzhou Li; Xiaohong Liu; Yaosheng Chen; Qin Zhang; Jiaqi Li; Xiaolong Yuan; Xiangdong Ding; Lingzhao Fang; Zhe Zhang; PigGTEx Consortium

doi:10.1093/nar/gkad1080

PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

Haonan Zeng, Wenjing Zhang, Qing Lin, Yahui Gao, Jinyan Teng, Zhiting Xu, Xiaodian Cai, Zhanming Zhong, Jun Wu, Yuqiang Liu, Shuqi Diao, Chen Wei, Wentao Gong, Xiangchun Pan, Zedong Li, Xiaoyu Huang, Xifan Chen, Jinshi Du, Fuping Zhao, Yunxiang ZhaoMaria Ballester, Daniel Crespo-Piazuelo, Marcel Amills, Alex Clop, Peter Karlskov-Mortensen, Merete Fredholm, Pinghua Li, Ruihua Huang, Guoqing Tang, Mingzhou Li, Xiaohong Liu, Yaosheng Chen, Qin Zhang, Jiaqi Li, Xiaolong Yuan, Xiangdong Ding^*, Lingzhao Fang^*, Zhe Zhang^*, PigGTEx Consortium

^*Corresponding author af dette arbejde

Center for Kvantitativ Genetik og Genomforskning, Aarhus

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

12 Citationer (Scopus)

Abstract

To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http:////pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.

Originalsprog	Engelsk
Tidsskrift	Nucleic Acids Research
Vol/bind	52
Nummer	D1
Sider (fra-til)	D980-D989
Antal sider	10
ISSN	0305-1048
DOI	https://doi.org/10.1093/nar/gkad1080
Status	Udgivet - jan. 2024

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10.1093/nar/gkad1080Licens: CC BY-NC

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Zeng, H., Zhang, W., Lin, Q., Gao, Y., Teng, J., Xu, Z., Cai, X., Zhong, Z., Wu, J., Liu, Y., Diao, S., Wei, C., Gong, W., Pan, X., Li, Z., Huang, X., Chen, X., Du, J., Zhao, F., ... PigGTEx Consortium (2024). PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs. Nucleic Acids Research, 52(D1), D980-D989. https://doi.org/10.1093/nar/gkad1080

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title = "PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs",

abstract = "To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http:////pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.",

keywords = "Animals, Databases, Genetic, Genome-Wide Association Study, Genotype, Multifactorial Inheritance, Multiomics, Phenotype, Swine/genetics",

author = "Haonan Zeng and Wenjing Zhang and Qing Lin and Yahui Gao and Jinyan Teng and Zhiting Xu and Xiaodian Cai and Zhanming Zhong and Jun Wu and Yuqiang Liu and Shuqi Diao and Chen Wei and Wentao Gong and Xiangchun Pan and Zedong Li and Xiaoyu Huang and Xifan Chen and Jinshi Du and Fuping Zhao and Yunxiang Zhao and Maria Ballester and Daniel Crespo-Piazuelo and Marcel Amills and Alex Clop and Peter Karlskov-Mortensen and Merete Fredholm and Pinghua Li and Ruihua Huang and Guoqing Tang and Mingzhou Li and Xiaohong Liu and Yaosheng Chen and Qin Zhang and Jiaqi Li and Xiaolong Yuan and Xiangdong Ding and Lingzhao Fang and Zhe Zhang and {PigGTEx Consortium}",

year = "2024",

month = jan,

doi = "10.1093/nar/gkad1080",

language = "English",

volume = "52",

pages = "D980--D989",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

Zeng, H, Zhang, W, Lin, Q, Gao, Y, Teng, J, Xu, Z, Cai, X, Zhong, Z, Wu, J, Liu, Y, Diao, S, Wei, C, Gong, W, Pan, X, Li, Z, Huang, X, Chen, X, Du, J, Zhao, F, Zhao, Y, Ballester, M, Crespo-Piazuelo, D, Amills, M, Clop, A, Karlskov-Mortensen, P, Fredholm, M, Li, P, Huang, R, Tang, G, Li, M, Liu, X, Chen, Y, Zhang, Q, Li, J, Yuan, X, Ding, X, Fang, L, Zhang, Z & PigGTEx Consortium 2024, 'PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs', Nucleic Acids Research, bind 52, nr. D1, s. D980-D989. https://doi.org/10.1093/nar/gkad1080

TY - JOUR

T1 - PigBiobank

T2 - a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

AU - Zeng, Haonan

AU - Zhang, Wenjing

AU - Lin, Qing

AU - Gao, Yahui

AU - Teng, Jinyan

AU - Xu, Zhiting

AU - Cai, Xiaodian

AU - Zhong, Zhanming

AU - Wu, Jun

AU - Liu, Yuqiang

AU - Diao, Shuqi

AU - Wei, Chen

AU - Gong, Wentao

AU - Pan, Xiangchun

AU - Li, Zedong

AU - Huang, Xiaoyu

AU - Chen, Xifan

AU - Du, Jinshi

AU - Zhao, Fuping

AU - Zhao, Yunxiang

AU - Ballester, Maria

AU - Crespo-Piazuelo, Daniel

AU - Amills, Marcel

AU - Clop, Alex

AU - Karlskov-Mortensen, Peter

AU - Fredholm, Merete

AU - Li, Pinghua

AU - Huang, Ruihua

AU - Tang, Guoqing

AU - Li, Mingzhou

AU - Liu, Xiaohong

AU - Chen, Yaosheng

AU - Zhang, Qin

AU - Li, Jiaqi

AU - Yuan, Xiaolong

AU - Ding, Xiangdong

AU - Fang, Lingzhao

AU - Zhang, Zhe

AU - PigGTEx Consortium

PY - 2024/1

Y1 - 2024/1

N2 - To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http:////pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.

AB - To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http:////pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.

KW - Animals

KW - Databases, Genetic

KW - Genome-Wide Association Study

KW - Genotype

KW - Multifactorial Inheritance

KW - Multiomics

KW - Phenotype

KW - Swine/genetics

UR - http://www.scopus.com/inward/record.url?scp=85181760510&partnerID=8YFLogxK

U2 - 10.1093/nar/gkad1080

DO - 10.1093/nar/gkad1080

M3 - Journal article

C2 - 37956339

SN - 0305-1048

VL - 52

SP - D980-D989

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

Abstract

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