Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula

Abstract The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia...

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Autores principales:	Dora Henriques, Andreas Wallberg, Julio Chávez-Galarza, J. Spencer Johnston, Matthew T. Webster, M. Alice Pinto
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0cf4d6c749ee4647906230e2ab84df8b
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spelling	oai:doaj.org-article:0cf4d6c749ee4647906230e2ab84df8b2021-12-02T15:08:16ZWhole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula10.1038/s41598-018-29469-52045-2322https://doaj.org/article/0cf4d6c749ee4647906230e2ab84df8b2018-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-29469-5https://doaj.org/toc/2045-2322Abstract The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.Dora HenriquesAndreas WallbergJulio Chávez-GalarzaJ. Spencer JohnstonMatthew T. WebsterM. Alice PintoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-14 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dora Henriques Andreas Wallberg Julio Chávez-Galarza J. Spencer Johnston Matthew T. Webster M. Alice Pinto Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
description	Abstract The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.
format	article
author	Dora Henriques Andreas Wallberg Julio Chávez-Galarza J. Spencer Johnston Matthew T. Webster M. Alice Pinto
author_facet	Dora Henriques Andreas Wallberg Julio Chávez-Galarza J. Spencer Johnston Matthew T. Webster M. Alice Pinto
author_sort	Dora Henriques
title	Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
title_short	Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
title_full	Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
title_fullStr	Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
title_full_unstemmed	Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
title_sort	whole genome snp-associated signatures of local adaptation in honeybees of the iberian peninsula
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/0cf4d6c749ee4647906230e2ab84df8b
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Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula

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