Unravelling regulatory variants affecting gene expression in four porcine tissues

M. Gòdia; M.F.L. Derks; B. Harlizius; O. Madsen; M.A.M. Groenen

doi:10.3920/978-90-8686-940-4_558

Unravelling regulatory variants affecting gene expression in four porcine tissues

M. Gòdia, M.F.L. Derks, B. Harlizius, O. Madsen, M.A.M. Groenen

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

Abstract

The aim of this work was to identify functional variants potentially associated to complex phenotypes, to improve genomic selection. In this study, we combined genomics, transcriptomics and epigenomics data. First, we genotyped 100 pigs with the high-density genotyping array (with 660K markers). Then, we generated RNA-seq data on these animals in 4 biologically divergent tissues: liver, spleen, lung and muscle. We performed an expression GWAS (eGWAS) resulting in the identification of over 150,000 significant associations in each of the tissues. We were able to detect over 1,300 genes that showed a significant eGWAS associations. We also found an enrichment of eGWAS hits within regulatory elements such as enhancers and promoters, which indicates their pivotal role as drivers of phenotypic variation and thus are of highly relevance towards understanding the genetics of complex traits.

Original language	English
Title of host publication	Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)
Subtitle of host publication	Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges
Editors	R.F. Veerkamp, Y. de Haas
Place of Publication	Wageningen
Publisher	Wageningen Academic Publishers
Pages	2313-2316
ISBN (Electronic)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_558
Publication status	Published - 2022
Event	World Congress on Genetics Applied to Livestock Production: WCGALP 2022 - Rotterdam, Netherlands Duration: 3 Jul 2022 → 8 Jul 2022

Conference

Conference	World Congress on Genetics Applied to Livestock Production: WCGALP 2022
Country/Territory	Netherlands
City	Rotterdam
Period	3/07/22 → 8/07/22

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10.3920/978-90-8686-940-4_558Licence: CC BY

https://edepot.wur.nl/588203Licence: CC BY

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Gòdia, M., Derks, M. F. L., Harlizius, B., Madsen, O., & Groenen, M. A. M. (2022). Unravelling regulatory variants affecting gene expression in four porcine tissues. In R. F. Veerkamp, & Y. de Haas (Eds.), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges (pp. 2313-2316). Article 558 Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-940-4_558

Gòdia, M. ; Derks, M.F.L. ; Harlizius, B. et al. / Unravelling regulatory variants affecting gene expression in four porcine tissues. Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. editor / R.F. Veerkamp ; Y. de Haas. Wageningen : Wageningen Academic Publishers, 2022. pp. 2313-2316

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abstract = "The aim of this work was to identify functional variants potentially associated to complex phenotypes, to improve genomic selection. In this study, we combined genomics, transcriptomics and epigenomics data. First, we genotyped 100 pigs with the high-density genotyping array (with 660K markers). Then, we generated RNA-seq data on these animals in 4 biologically divergent tissues: liver, spleen, lung and muscle. We performed an expression GWAS (eGWAS) resulting in the identification of over 150,000 significant associations in each of the tissues. We were able to detect over 1,300 genes that showed a significant eGWAS associations. We also found an enrichment of eGWAS hits within regulatory elements such as enhancers and promoters, which indicates their pivotal role as drivers of phenotypic variation and thus are of highly relevance towards understanding the genetics of complex traits.",

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booktitle = "Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)",

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Gòdia, M , Derks, MFL, Harlizius, B, Madsen, O & Groenen, MAM 2022, Unravelling regulatory variants affecting gene expression in four porcine tissues. in RF Veerkamp & Y de Haas (eds), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges., 558, Wageningen Academic Publishers, Wageningen, pp. 2313-2316, World Congress on Genetics Applied to Livestock Production: WCGALP 2022, Rotterdam, Netherlands, 3/07/22. https://doi.org/10.3920/978-90-8686-940-4_558

Unravelling regulatory variants affecting gene expression in four porcine tissues. / Gòdia, M.; Derks, M.F.L.; Harlizius, B. et al.
Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. ed. / R.F. Veerkamp; Y. de Haas. Wageningen: Wageningen Academic Publishers, 2022. p. 2313-2316 558.

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

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Gòdia M , Derks MFL, Harlizius B, Madsen O , Groenen MAM. Unravelling regulatory variants affecting gene expression in four porcine tissues. In Veerkamp RF, de Haas Y, editors, Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. Wageningen: Wageningen Academic Publishers. 2022. p. 2313-2316. 558 doi: 10.3920/978-90-8686-940-4_558

Unravelling regulatory variants affecting gene expression in four porcine tissues

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