Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle

Abstract Understanding genotype-by-environment interactions (G × E) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortm...

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Autores principales:	Camila U. Braz, Troy N. Rowan, Robert D. Schnabel, Jared E. Decker
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4cc7e0a66b394fe6b975ef62db6ca75d
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spelling	oai:doaj.org-article:4cc7e0a66b394fe6b975ef62db6ca75d2021-12-02T17:12:25ZGenome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle10.1038/s41598-021-92455-x2045-2322https://doaj.org/article/4cc7e0a66b394fe6b975ef62db6ca75d2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92455-xhttps://doaj.org/toc/2045-2322Abstract Understanding genotype-by-environment interactions (G × E) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortment of environmental variables and searching for SNPs controlling phenotypic variance (vQTL) using a large beef cattle dataset. We showed that G × E contribute 10.1%, 3.8%, and 2.8% of the phenotypic variance of birth weight, weaning weight, and yearling weight, respectively. G × E genome-wide association analysis (GWAA) detected a large number of G × E loci affecting growth traits, which the traditional GWAA did not detect, showing that functional loci may have non-additive genetic effects regardless of differences in genotypic means. Further, variance-heterogeneity GWAA detected loci enriched with G × E effects without requiring prior knowledge of the interacting environmental factors. Functional annotation and pathway analysis of G × E genes revealed biological mechanisms by which cattle respond to changes in their environment, such as neurotransmitter activity, hypoxia-induced processes, keratinization, hormone, thermogenic and immune pathways. We unraveled the relevance and complexity of the genetic basis of G × E underlying growth traits, providing new insights into how different environmental conditions interact with specific genes influencing adaptation and productivity in beef cattle and potentially across mammals.Camila U. BrazTroy N. RowanRobert D. SchnabelJared E. DeckerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Camila U. Braz Troy N. Rowan Robert D. Schnabel Jared E. Decker Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
description	Abstract Understanding genotype-by-environment interactions (G × E) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortment of environmental variables and searching for SNPs controlling phenotypic variance (vQTL) using a large beef cattle dataset. We showed that G × E contribute 10.1%, 3.8%, and 2.8% of the phenotypic variance of birth weight, weaning weight, and yearling weight, respectively. G × E genome-wide association analysis (GWAA) detected a large number of G × E loci affecting growth traits, which the traditional GWAA did not detect, showing that functional loci may have non-additive genetic effects regardless of differences in genotypic means. Further, variance-heterogeneity GWAA detected loci enriched with G × E effects without requiring prior knowledge of the interacting environmental factors. Functional annotation and pathway analysis of G × E genes revealed biological mechanisms by which cattle respond to changes in their environment, such as neurotransmitter activity, hypoxia-induced processes, keratinization, hormone, thermogenic and immune pathways. We unraveled the relevance and complexity of the genetic basis of G × E underlying growth traits, providing new insights into how different environmental conditions interact with specific genes influencing adaptation and productivity in beef cattle and potentially across mammals.
format	article
author	Camila U. Braz Troy N. Rowan Robert D. Schnabel Jared E. Decker
author_facet	Camila U. Braz Troy N. Rowan Robert D. Schnabel Jared E. Decker
author_sort	Camila U. Braz
title	Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
title_short	Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
title_full	Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
title_fullStr	Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
title_full_unstemmed	Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
title_sort	genome-wide association analyses identify genotype-by-environment interactions of growth traits in simmental cattle
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4cc7e0a66b394fe6b975ef62db6ca75d
work_keys_str_mv	AT camilaubraz genomewideassociationanalysesidentifygenotypebyenvironmentinteractionsofgrowthtraitsinsimmentalcattle AT troynrowan genomewideassociationanalysesidentifygenotypebyenvironmentinteractionsofgrowthtraitsinsimmentalcattle AT robertdschnabel genomewideassociationanalysesidentifygenotypebyenvironmentinteractionsofgrowthtraitsinsimmentalcattle AT jarededecker genomewideassociationanalysesidentifygenotypebyenvironmentinteractionsofgrowthtraitsinsimmentalcattle
_version_	1718381375761940480

Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle

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