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Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones

2022Journal article Open access
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dc.contributor.authorWragg, David
dc.contributor.authorEynard, Sonia E.
dc.contributor.authorBasso, Benjamin
dc.contributor.authorCanale‐Tabet, Kamila
dc.contributor.authorLabarthe, Emmanuelle
dc.contributor.authorBouchez, Olivier
dc.contributor.authorBienefeld, Kaspar
dc.contributor.authorBieńkowska, Małgorzata
dc.contributor.authorCosta, Cecilia
dc.contributor.authorGregorc, Aleš
dc.contributor.authorKryger, Per
dc.contributor.authorParejo, Melanie
dc.contributor.authorPinto, M. Alice
dc.contributor.authorBidanel, Jean‐Pierre
dc.contributor.authorServin, Bertrand
dc.contributor.authorLe Conte, Yves
dc.contributor.authorVignal, Alain
dc.date.accessioned2023-01-13T11:40:32Z
dc.date.available2023-01-13T11:40:32Z
dc.date.issued2022
dc.description.abstractHoney bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environ-ment and mate naturally with queens from the local subspecies. The resulting ad-mixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to sub-species, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP- chip or by low- pass sequencing, or (iii) selecting SNPs compatible with the re-quirements of genotyping chips.pt_PT
dc.description.sponsorshipThis work was performed in collaboration with the GeT platform, Toulouse (France), a partner of the National Infrastructure France Génomique, thanks to support by the Commissariat aux Grands Invetissements (ANR-10- INBS-0009). Bioinformatics analyses were performed on the GenoToul Bioinfo computer cluster. This work was funded by a grant from the INRA Département de Génétique Animale (INRA Animal Genetics division) and by the SeqApiPop pro-gramme, funded by the FranceAgriMer grant 14-21- AT. We thank John Kefuss for helpful discussions. We thank Andrew Abrahams for providing honey bee samples from Colonsay (Scotland), the Association Conservatoire de l'Abeille Noire Bretonne (ACANB) for samples from Ouessant (France), CETA de Savoie for sample from Savoie, ADAPI for samples from Porquerolles and all beekeepers and bee breeders who kindly participated in this study by providing sam-ples from their colonies.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationWragg, David; Eynard, Sonia E.; Basso, Benjamin; Canale‐Tabet, Kamila; Labarthe, Emmanuelle; Bouchez, Olivier; Bienefeld, Kaspar; Bieńkowska, Małgorzata; Costa, Cecilia; Gregorc, Aleš; Kryger, Per; Parejo, Melanie; Pinto, M. Alice; Bidanel, Jean‐Pierre; Servin, Bertrand; Le Conte, Yves; Vignal, Alain (2022). Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones. Molecular Ecology Resources. ISSN 1755-098X. 22:8, p. 3068-3086pt_PT
dc.identifier.doi10.1111/1755-0998.13665pt_PT
dc.identifier.eissn1755-0998
dc.identifier.issn1755-098X
dc.identifier.urihttp://hdl.handle.net/10198/26491
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherWileypt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectGenomept_PT
dc.subjectHaplotypept_PT
dc.subjectHoney beept_PT
dc.subjectPopulation geneticspt_PT
dc.subjectSNPpt_PT
dc.titleComplex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid dronespt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage3086pt_PT
oaire.citation.issue8pt_PT
oaire.citation.startPage3068pt_PT
oaire.citation.titleMolecular Ecology Resourcespt_PT
oaire.citation.volume22pt_PT
person.familyNamePinto
person.givenNameM. Alice
person.identifier.ciencia-idF814-A1D0-8318
person.identifier.orcid0000-0001-9663-8399
person.identifier.scopus-author-id8085507800
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication0667fe04-7078-483d-9198-56d167b19bc5
relation.isAuthorOfPublication.latestForDiscovery0667fe04-7078-483d-9198-56d167b19bc5

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