Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)

Abstract Most of the knowledge about genetic variants at the sequence level in cattle is for Bos primigenius taurus populations. Here, we presented a complete genomic characterization of 52 Nellore (Bos primigenius indicus) bulls, revealing specific zebu DNA variants with putative impact in tropical...

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Autores principales:	Gerardo Alves Fernandes Júnior, Henrique Nunes de Oliveira, Roberto Carvalheiro, Diercles Francisco Cardoso, Larissa Fernanda Simielli Fonseca, Ricardo Vieira Ventura, Lucia Galvão de Albuquerque
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/648a63d9507c49a9bb43f0b78f4cdd67
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spelling	oai:doaj.org-article:648a63d9507c49a9bb43f0b78f4cdd672021-12-02T17:52:42ZWhole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)10.1038/s41598-020-66272-72045-2322https://doaj.org/article/648a63d9507c49a9bb43f0b78f4cdd672020-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-66272-7https://doaj.org/toc/2045-2322Abstract Most of the knowledge about genetic variants at the sequence level in cattle is for Bos primigenius taurus populations. Here, we presented a complete genomic characterization of 52 Nellore (Bos primigenius indicus) bulls, revealing specific zebu DNA variants with putative impact in tropical adaptation and productive traits. Single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) mutations were identified using the newest bovine reference genome ARS_UCD1.2, and variant functional consequences were predicted using the Ensembl VEP software. A total of 35,753,707 SNPs and 4,492,636 INDELs were detected and annotated to their functional effects. We identified 400 genes that comprised both, a SNP and an INDEL, of high functional impact on proteins (i.e. variants that cause protein truncation, loss of function or triggering nonsense-mediated decay). Among these, we highlight the following genes: BoLA, associated with cattle immune response to infections and reproduction aspects; HSPA8, DNAJC27, and DNAJC28, involved with thermoregulatory protective mechanisms in mammals; and many olfactory signaling pathway related genes that are important genetic factors in the evolution of mammalian species. All these functional aspects are directly related to cattle adaptability to tropical environments.Gerardo Alves Fernandes JúniorHenrique Nunes de OliveiraRoberto CarvalheiroDiercles Francisco CardosoLarissa Fernanda Simielli FonsecaRicardo Vieira VenturaLucia Galvão de AlbuquerqueNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-7 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gerardo Alves Fernandes Júnior Henrique Nunes de Oliveira Roberto Carvalheiro Diercles Francisco Cardoso Larissa Fernanda Simielli Fonseca Ricardo Vieira Ventura Lucia Galvão de Albuquerque Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)
description	Abstract Most of the knowledge about genetic variants at the sequence level in cattle is for Bos primigenius taurus populations. Here, we presented a complete genomic characterization of 52 Nellore (Bos primigenius indicus) bulls, revealing specific zebu DNA variants with putative impact in tropical adaptation and productive traits. Single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) mutations were identified using the newest bovine reference genome ARS_UCD1.2, and variant functional consequences were predicted using the Ensembl VEP software. A total of 35,753,707 SNPs and 4,492,636 INDELs were detected and annotated to their functional effects. We identified 400 genes that comprised both, a SNP and an INDEL, of high functional impact on proteins (i.e. variants that cause protein truncation, loss of function or triggering nonsense-mediated decay). Among these, we highlight the following genes: BoLA, associated with cattle immune response to infections and reproduction aspects; HSPA8, DNAJC27, and DNAJC28, involved with thermoregulatory protective mechanisms in mammals; and many olfactory signaling pathway related genes that are important genetic factors in the evolution of mammalian species. All these functional aspects are directly related to cattle adaptability to tropical environments.
format	article
author	Gerardo Alves Fernandes Júnior Henrique Nunes de Oliveira Roberto Carvalheiro Diercles Francisco Cardoso Larissa Fernanda Simielli Fonseca Ricardo Vieira Ventura Lucia Galvão de Albuquerque
author_facet	Gerardo Alves Fernandes Júnior Henrique Nunes de Oliveira Roberto Carvalheiro Diercles Francisco Cardoso Larissa Fernanda Simielli Fonseca Ricardo Vieira Ventura Lucia Galvão de Albuquerque
author_sort	Gerardo Alves Fernandes Júnior
title	Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)
title_short	Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)
title_full	Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)
title_fullStr	Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)
title_full_unstemmed	Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)
title_sort	whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in nellore (bos primigenius indicus)
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/648a63d9507c49a9bb43f0b78f4cdd67
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Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)

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