Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
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.
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Subjects: | Honeybee, Apis mellifera L., Iberian Peninsula, Genome SNP-associated, Genes, Otras ciencias agrícolas, |
Online Access: | http://repositorio.inia.gob.pe/handle/20.500.12955/1223 |
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dig-inia-pe-20.500.12955-12232022-11-21T20:26:24Z Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula Henriques, Dora Wallberg, Andreas Chávez Galarza, Julio César Johnston, J. Spencer Webster, Matthew Pinto, María Alice Honeybee Apis mellifera L. Iberian Peninsula Genome SNP-associated Genes Otras ciencias agrícolas 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. 2018-07-24 info:eu-repo/semantics/article http://repositorio.inia.gob.pe/handle/20.500.12955/1223 eng Scientific Reports (2018) 8:11145 https://doi.org/10.1038/s41598-018-29469-5 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Nature Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
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Honeybee Apis mellifera L. Iberian Peninsula Genome SNP-associated Genes Otras ciencias agrícolas Honeybee Apis mellifera L. Iberian Peninsula Genome SNP-associated Genes Otras ciencias agrícolas |
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Honeybee Apis mellifera L. Iberian Peninsula Genome SNP-associated Genes Otras ciencias agrícolas Honeybee Apis mellifera L. Iberian Peninsula Genome SNP-associated Genes Otras ciencias agrícolas Henriques, Dora Wallberg, Andreas Chávez Galarza, Julio César Johnston, J. Spencer Webster, Matthew Pinto, María Alice Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula |
description |
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 |
info:eu-repo/semantics/article |
topic_facet |
Honeybee Apis mellifera L. Iberian Peninsula Genome SNP-associated Genes Otras ciencias agrícolas |
author |
Henriques, Dora Wallberg, Andreas Chávez Galarza, Julio César Johnston, J. Spencer Webster, Matthew Pinto, María Alice |
author_facet |
Henriques, Dora Wallberg, Andreas Chávez Galarza, Julio César Johnston, J. Spencer Webster, Matthew Pinto, María Alice |
author_sort |
Henriques, Dora |
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 |
Springer Nature |
url |
http://repositorio.inia.gob.pe/handle/20.500.12955/1223 |
work_keys_str_mv |
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