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Wragg D, Eynard SE, Basso B, Canale‐Tabet K, Labarthe E, Bouchez O, Bienefeld K, Bieńkowska M, Costa C, Gregorc A, Kryger P, Parejo M, Pinto MA, Bidanel J, Servin B, Le Conte Y, Vignal A. Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones. Mol Ecol Resour 2022; 22:3068-3086. [PMID: 35689802 PMCID: PMC9796960 DOI: 10.1111/1755-0998.13665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 01/07/2023]
Abstract
Honey 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 environment and mate naturally with queens from the local subspecies. The resulting admixture 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 subspecies, 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 requirements of genotyping chips.
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Affiliation(s)
- David Wragg
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance,Roslin InstituteUniversity of EdinburghMidlothianUK
| | - Sonia E. Eynard
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance
| | - Benjamin Basso
- Institut de l'abeille (ITSAP), UMT PrADEAvignonFrance,INRAE, UR 406 Abeilles et Environment, UMT PrADEAvignonFrance
| | | | | | | | | | | | - Cecilia Costa
- CREA Research Centre for Agriculture and EnvironmentBolognaItaly
| | - Aleš Gregorc
- Faculty of Agriculture and Life SciencesUniversity of MariborPivolaSlovenia
| | - Per Kryger
- Department of Agroecology, Science and TechnologyAarhus UniversitySlagelseDenmark
| | - Melanie Parejo
- Agroscope, Swiss Bee Research CentreBernSwitzerland,Applied Genomics and Bioinformatics, Department of Genetics, Physical Anthropology and Animal PhysiologyUniversity of the Basque CountryLeioaSpain
| | - M. Alice Pinto
- Centro de Investigação de Montanha (CIMO)Instituto Politécnico de BragançaBragançaPortugal
| | | | - Bertrand Servin
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance
| | - Yves Le Conte
- INRAE, UR 406 Abeilles et Environment, UMT PrADEAvignonFrance
| | - Alain Vignal
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance
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Paolillo G, De Iorio MG, Filipe JFS, Riva F, Stella A, Gandini G, Pagnacco G, Lazzari B, Minozzi G. Analysis of Complementary Sex-Determiner (csd) Allele Diversity in Different Honeybee Subspecies from Italy Based on NGS Data. Genes (Basel) 2022; 13:genes13060991. [PMID: 35741752 PMCID: PMC9222915 DOI: 10.3390/genes13060991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/21/2022] [Accepted: 05/28/2022] [Indexed: 02/05/2023] Open
Abstract
Sexual regulation in Apis mellifera is controlled by the complementary sex-determiner (csd) gene: females (queens and workers) are heterozygous at this locus and males (drones) are hemizygous. When homozygous diploid drones develop, they are eaten by worker bees. High csd allelic diversity in honeybee populations is a priority for colony survival. The focus of this study is to investigate csd variability in the genomic sequence of the hypervariable region (HVR) of the csd gene in honeybee subspecies sampled in Italy. During the summer of 2017 and 2018, worker bees belonging to 125 colonies were sampled. The honeybees belonged to seven different A. mellifera subspecies: A. m. ligustica, A. m. sicula, A. m cecropia, A. m. carnica, A. m. mellifera, Buckfast and hybrid Carnica. Illumina genomic resequencing of all samples was performed and used for the characterization of global variability among colonies. In this work, a pipeline using existing resequencing data to explore the csd gene allelic variants present in the subspecies collection, based on de novo assembly of sequences falling within the HVR region, is described. On the whole, 138 allelic sequences were successfully reconstructed. Among these, 88 different alleles were identified, 68 of which match with csd alleles present in the NCBI GenBank database.
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Affiliation(s)
- Gianluigi Paolillo
- Dipartimento di Medicina Veterinaria (DIMEVET), University of Milan, 26900 Lodi, Italy; (G.P.); (M.G.D.I.); (J.F.S.F.); (F.R.); (G.G.)
| | - Maria Grazia De Iorio
- Dipartimento di Medicina Veterinaria (DIMEVET), University of Milan, 26900 Lodi, Italy; (G.P.); (M.G.D.I.); (J.F.S.F.); (F.R.); (G.G.)
| | - Joel F. Soares Filipe
- Dipartimento di Medicina Veterinaria (DIMEVET), University of Milan, 26900 Lodi, Italy; (G.P.); (M.G.D.I.); (J.F.S.F.); (F.R.); (G.G.)
| | - Federica Riva
- Dipartimento di Medicina Veterinaria (DIMEVET), University of Milan, 26900 Lodi, Italy; (G.P.); (M.G.D.I.); (J.F.S.F.); (F.R.); (G.G.)
| | | | - Gustavo Gandini
- Dipartimento di Medicina Veterinaria (DIMEVET), University of Milan, 26900 Lodi, Italy; (G.P.); (M.G.D.I.); (J.F.S.F.); (F.R.); (G.G.)
| | | | - Barbara Lazzari
- IBBA-CNR, 20133 Milano, Italy; (A.S.); (G.P.)
- Correspondence: (B.L.); (G.M.)
| | - Giulietta Minozzi
- Dipartimento di Medicina Veterinaria (DIMEVET), University of Milan, 26900 Lodi, Italy; (G.P.); (M.G.D.I.); (J.F.S.F.); (F.R.); (G.G.)
- Correspondence: (B.L.); (G.M.)
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Ma C, Hu R, Costa C, Li J. Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica). Front Genet 2022; 13:835967. [PMID: 35222549 PMCID: PMC8864236 DOI: 10.3389/fgene.2022.835967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) are involved in cellular energy metabolism and have been shown to undergo adaptive evolution in organisms with increased energy-consuming activities. The genetically selected high royal jelly-producing bees (RJBs, Apis mellifera ligustica) in China can produce 10 times more royal jelly, a highly nutritional and functional food, relative to unselected Italian bees (ITBs). To test for potential adaptive evolution of RJB mitochondrial genes, we sequenced mitogenomes from 100 RJBs and 30 ITBs. Haplotype network and phylogenetic analysis indicate that RJBs and ITBs are not reciprocally monophyletic but mainly divided into the RJB- and ITB-dominant sublineages. The RJB-dominant sublineage proportion is 6-fold higher in RJBs (84/100) than in ITBs (4/30), which is mainly attributable to genetic drift rather than positive selection. The RJB-dominant sublineage exhibits a low genetic diversity due to purifying selection. Moreover, mitogenome abundance is not significantly different between RJBs and ITBs, thereby rejecting the association between mitogenome copy number and royal jelly-producing performance. Our findings demonstrate low genetic diversity levels of RJB mitogenomes and reveal genetic drift and purifying selection as potential forces driving RJB mitogenome evolution.
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Affiliation(s)
- Chuan Ma
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruoyang Hu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cecilia Costa
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | - Jianke Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Jianke Li,
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