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...
| Autores principales: | , , , , , |
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| Formato: | info:eu-repo/semantics/article |
| Lenguaje: | Inglés |
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Springer Nature
2021
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| Materias: | |
| Acceso en línea: | https://repositorio.inia.gob.pe/handle/20.500.12955/1223 https://doi.org/10.1038/s41598-018-29469-5 |
| _version_ | 1855028488791130112 |
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| author | Henriques, Dora Wallberg, Andreas Chávez Galarza, Julio César Johnston, J. Spencer Webster, Matthew Pinto, María Alice |
| author_browse | Chávez Galarza, Julio César Henriques, Dora Johnston, J. Spencer Pinto, María Alice Wallberg, Andreas Webster, Matthew |
| author_facet | Henriques, Dora Wallberg, Andreas Chávez Galarza, Julio César Johnston, J. Spencer Webster, Matthew Pinto, María Alice |
| author_sort | Henriques, Dora |
| collection | Repositorio INIA |
| 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 |
| id | INIA1223 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | INIA12232022-11-21T20:26:24Z 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. Abstract. Introduction. Results. Discussion. Methods. References 2021-01-12T15:19:15Z 2021-01-12T15:19:15Z 2018-07-24 info:eu-repo/semantics/article Henriques, D., Wallberg, A., Chávez-Galarza, J. et al. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 8, 11145 (2018). doi: 10.1038/s41598-018-29469-5 https://repositorio.inia.gob.pe/handle/20.500.12955/1223 Scientific Reports https://doi.org/10.1038/s41598-018-29469-5 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 application/pdf Península Ibérica Springer Nature Reino Unido Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | 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 |
| title | 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_short | 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 |
| topic | Honeybee Apis mellifera L. Iberian Peninsula Genome SNP-associated Genes Otras ciencias agrícolas |
| url | https://repositorio.inia.gob.pe/handle/20.500.12955/1223 https://doi.org/10.1038/s41598-018-29469-5 |
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