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Lefebre R, Broeckx BJG, De Smet L, Peelman L, de Graaf DC. Population-wide modelling reveals prospects of marker-assisted selection for parasitic mite resistance in honey bees. Sci Rep 2024; 14:7866. [PMID: 38570723 PMCID: PMC10991324 DOI: 10.1038/s41598-024-58596-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/01/2024] [Indexed: 04/05/2024] Open
Abstract
In 2019, a joint eight-variant model was published in which eight single nucleotide polymorphisms (SNPs) in seven Apis mellifera genes were associated with Varroa destructor drone brood resistance (DBR, i.e. mite non-reproduction in drone brood). As this model was derived from only one Darwinian Black Bee Box colony, it could not directly be applied on a population-overarching scale in the northern part of Belgium (Flanders), where beekeepers prefer the carnica subspecies. To determine whether these eight SNPs remained associated with the DBR trait on a Flemish colony-broad scope, we performed population-wide modelling through sampling of various A. mellifera carnica colonies, DBR scoring of Varroa-infested drone brood and variant genotyping. Novel eight-variant modelling was performed and the classification performance of the eight SNPs was evaluated. Besides, we built a reduced three-variant model retaining only three genetic variants and found that this model classified 76% of the phenotyped drones correctly. To examine the spread of beneficial alleles and predict the DBR probability distribution in Flanders, we determined the allelic frequencies of the three variants in 292 A. mellifera carnica queens. As such, this research reveals prospects of marker-assisted selection for Varroa drone brood resistance in honeybees.
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Affiliation(s)
- Regis Lefebre
- Laboratory of Molecular Entomology and Bee Pathology (L-MEB), Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
| | - Bart J G Broeckx
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Lina De Smet
- Laboratory of Molecular Entomology and Bee Pathology (L-MEB), Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Luc Peelman
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology (L-MEB), Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
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2
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Du M, Bernstein R, Hoppe A. Comparison of pooled semen insemination and single colony insemination as sustainable honeybee breeding strategies. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231556. [PMID: 38298391 PMCID: PMC10827426 DOI: 10.1098/rsos.231556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024]
Abstract
Instrumental insemination of honeybees allows for two opposing breeding strategies. In single colony insemination (SCI), all drones to inseminate a queen are taken from one colony. In pooled semen insemination (PSI), sperm of many genetically diverse drones is mixed and queens are fertilized from the resulting drone pool. While SCI allows for maximum pedigree control, proponents of PSI claim to reduce inbreeding and maintain genetic variance. Using stochastic simulation studies, we compared genetic progress and inbreeding rates in small honeybee populations under SCI and PSI. Four different selection criteria were covered: estimated breeding values (EBV), phenotypes, true breeding values (TBV) and random selection. Under EBV-based truncation selection, SCI yielded 9.0% to 44.4% higher genetic gain than PSI, but had vastly increased inbreeding rates. Under phenotypical or TBV selection, the gap between SCI and PSI in terms of genetic progress narrowed. Throughout, PSI yielded lower inbreeding rates than SCI, but the differences were only substantial under EBV truncation selection. As a result, PSI did not appear as a viable breeding strategy owing to its incompatibility with modern methods of genetic evaluation. Instead, SCI is to be preferred but instead of strict truncation selection, strategies to avoid inbreeding need to be installed.
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Affiliation(s)
- Manuel Du
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Strasse 32, 16540 Hohen Neuendorf, Germany
| | - Richard Bernstein
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Strasse 32, 16540 Hohen Neuendorf, Germany
| | - Andreas Hoppe
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Strasse 32, 16540 Hohen Neuendorf, Germany
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3
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Willcox BK, Potts SG, Brown MJF, Alix A, Al Naggar Y, Chauzat MP, Costa C, Gekière A, Hartfield C, Hatjina F, Knapp JL, Martínez-López V, Maus C, Metodiev T, Nazzi F, Osterman J, Raimets R, Strobl V, Van Oystaeyen A, Wintermantel D, Yovcheva N, Senapathi D. Emerging threats and opportunities to managed bee species in European agricultural systems: a horizon scan. Sci Rep 2023; 13:18099. [PMID: 37872212 PMCID: PMC10593766 DOI: 10.1038/s41598-023-45279-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023] Open
Abstract
Managed bee species provide essential pollination services that contribute to food security worldwide. However, managed bees face a diverse array of threats and anticipating these, and potential opportunities to reduce risks, is essential for the sustainable management of pollination services. We conducted a horizon scanning exercise with 20 experts from across Europe to identify emerging threats and opportunities for managed bees in European agricultural systems. An initial 63 issues were identified, and this was shortlisted to 21 issues through the horizon scanning process. These ranged from local landscape-level management to geopolitical issues on a continental and global scale across seven broad themes-Pesticides & pollutants, Technology, Management practices, Predators & parasites, Environmental stressors, Crop modification, and Political & trade influences. While we conducted this horizon scan within a European context, the opportunities and threats identified will likely be relevant to other regions. A renewed research and policy focus, especially on the highest-ranking issues, is required to maximise the value of these opportunities and mitigate threats to maintain sustainable and healthy managed bee pollinators within agricultural systems.
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Affiliation(s)
- Bryony K Willcox
- Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK.
| | - Simon G Potts
- Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
| | - Mark J F Brown
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Anne Alix
- Corteva Agriscience, Regulatory and Stewardship Europe, Middle East and Africa, Abingdon, UK
| | - Yahya Al Naggar
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
- Zoology Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, 61413, Abha, Saudi Arabia
| | - Marie-Pierre Chauzat
- ANSES, Sophia Antipolis Laboratory, Unit of Honey Bee Pathology, 06902, Sophia Antipolis, France
| | - Cecilia Costa
- CREA Research Centre for Agriculture and Environment, 40128, Bologna, Italy
| | - Antoine Gekière
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Chris Hartfield
- National Farmers' Union, Agriculture House, Stoneleigh Park, Stoneleigh, Warwickshire, CV8 2TZ, UK
| | - Fani Hatjina
- Department of Apiculture, Institute of Animal Science, ELGO 'DIMITRA', 63200, Nea Moudania, Greece
| | - Jessica L Knapp
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
- Department of Biology, Lund University, Lund, Sweden
| | - Vicente Martínez-López
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100, Murcia, Spain
| | | | | | - Francesco Nazzi
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Julia Osterman
- Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Str. 4, 79106, Freiburg, Germany
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Risto Raimets
- Department of Plant Protection, Estonian University of Life Sciences, 51014, Tartu, Estonia
| | - Verena Strobl
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Dimitry Wintermantel
- Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Str. 4, 79106, Freiburg, Germany
| | | | - Deepa Senapathi
- Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
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4
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Parejo M, Talenti A, Richardson M, Vignal A, Barnett M, Wragg D. AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap. Sci Data 2023; 10:198. [PMID: 37037860 PMCID: PMC10086014 DOI: 10.1038/s41597-023-02097-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen's alleles and none from the many drones she mated with. Thus the ordered combination or 'phase' of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.
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Affiliation(s)
- M Parejo
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - A Talenti
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - M Richardson
- University of Edinburgh, King's Buildings Campus, Edinburgh, UK
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK
| | - A Vignal
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet Tolosan, France
| | - M Barnett
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK
| | - D Wragg
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK.
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK.
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5
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First large-scale genomic prediction in the honey bee. Heredity (Edinb) 2023; 130:320-328. [PMID: 36878945 PMCID: PMC10163272 DOI: 10.1038/s41437-023-00606-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Genomic selection has increased genetic gain in several livestock species, but due to the complicated genetics and reproduction biology not yet in honey bees. Recently, 2970 queens were genotyped to gather a reference population. For the application of genomic selection in honey bees, this study analyzes the accuracy and bias of pedigree-based and genomic breeding values for honey yield, three workability traits, and two traits for resistance against the parasite Varroa destructor. For breeding value estimation, we use a honey bee-specific model with maternal and direct effects, to account for the contributions of the workers and the queen of a colony to the phenotypes. We conducted a validation for the last generation and a five-fold cross-validation. In the validation for the last generation, the accuracy of pedigree-based estimated breeding values was 0.12 for honey yield, and ranged from 0.42 to 0.61 for the workability traits. The inclusion of genomic marker data improved these accuracies to 0.23 for honey yield, and a range from 0.44 to 0.65 for the workability traits. The inclusion of genomic data did not improve the accuracy of the disease-related traits. Traits with high heritability for maternal effects compared to the heritability for direct effects showed the most promising results. For all traits except the Varroa resistance traits, the bias with genomic methods was on a similar level compared to the bias with pedigree-based BLUP. The results show that genomic selection can successfully be applied to honey bees.
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6
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Moškrič A, Pavlin A, Mole K, Marinč A, Bubnič J, Opara A, Kovačić M, Puškadija Z, Uzunov A, Andonov S, Dahle B, Prešern J. Cutting corners: The impact of storage and DNA extraction on quality and quantity of DNA in honeybee ( Apis mellifera) spermatheca. Front Physiol 2023; 14:1139269. [PMID: 36935742 PMCID: PMC10020693 DOI: 10.3389/fphys.2023.1139269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The purpose of our study was to investigate methods of short-term storage that allow preservation, transport and retrieval of genetic information contained in honeybee queen's spermatheca. Genotyping of the honeybee colony requires well ahead planned sample collection, depending on the type of data to be acquired. Sampling and genotyping of spermatheca's content instead of individual offspring is timesaving, allowing answers to the questions related to patriline composition immediately after mating. Such procedure is also cheaper and less error prone. For preservation either Allprotect Tissue Reagent (Qiagen) or absolute ethanol were used. Conditions during transportation were simulated by keeping samples 6-8 days at room temperature. Six different storing conditions of spermathecas were tested, complemented with two DNA extraction methods. We have analysed the concentration of DNA, RNA, and proteins in DNA extracts. We also analysed how strongly the DNA is subjected to fragmentation (through amplification of genetic markers ANT2 and tRNAleu-COX2) and whether the quality of the extracted DNA is suitable for microsatellite (MS) analysis. Then, we tested the usage of spermatheca as a source of patriline composition in an experiment with three instrumentally inseminated virgin queens and performed MS analysis of the extracted DNA from each spermatheca, as well as queens' and drones' tissue. Our results show that median DNA concentration from spermathecas excised prior the storage, regardless of the storing condition and DNA extraction method, were generally lower than median DNA concentration obtained from spermathecas dissected from the whole queens after the storage. Despite the differences in DNA yield from the samples subjected to different storing conditions there was no significant effect of storage method or the DNA extraction method on the amplification success, although fewer samples stored in EtOH amplified successfully in comparison to ATR storing reagent. However, we recommend EtOH as a storing reagent due to its availability, low price, simplicity in usage in the field and in the laboratory, and capability of good preservation of the samples for DNA analysis during transport at room temperature.
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Affiliation(s)
- Ajda Moškrič
- Department of Animal Production, Agricultural Institute of Slovenia, Ljubljana, Slovenia
- *Correspondence: Ajda Moškrič,
| | - Anja Pavlin
- Department of Animal Production, Agricultural Institute of Slovenia, Ljubljana, Slovenia
- Department of Biology, Biotechnical faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katarina Mole
- Department of Animal Production, Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Andraž Marinč
- Department of Animal Production, Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Jernej Bubnič
- Department of Animal Production, Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Andreja Opara
- Department of Animal Production, Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Marin Kovačić
- Faculty of Agrobiotechnical Sciences Osijek, University of J.J. Strossmayer, Osijek, Croatia
- Centre for Applied Life Sciences Healthy Food Chain Ltd., Osijek, Croatia
| | - Zlatko Puškadija
- Faculty of Agrobiotechnical Sciences Osijek, University of J.J. Strossmayer, Osijek, Croatia
- Centre for Applied Life Sciences Healthy Food Chain Ltd., Osijek, Croatia
| | - Aleksandar Uzunov
- Faculty of Agricultural Sciences and Food, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
- Company for Applied Research and Permanent Education in Agriculture, Skopje, Macedonia
| | - Sreten Andonov
- Department of Animal Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bjørn Dahle
- Norwegian Beekeepers Association, Kløfta, Norway
| | - Janez Prešern
- Department of Animal Production, Agricultural Institute of Slovenia, Ljubljana, Slovenia
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7
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Bovo S, Utzeri VJ, Ribani A, Taurisano V, Schiavo G, Fontanesi L. A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA. Sci Rep 2022; 12:19541. [PMID: 36379985 PMCID: PMC9666642 DOI: 10.1038/s41598-022-24101-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Awareness has been raised over the last years on the genetic integrity of autochthonous honey bee subspecies. Genomic tools available in Apis mellifera can make it possible to measure this information by targeting individual honey bee DNA. Honey contains DNA traces from all organisms that contributed or were involved in its production steps, including the honey bees of the colony. In this study, we designed and tested a genotyping by sequencing (GBS) assay to analyse single nucleotide polymorphisms (SNPs) of A. mellifera nuclear genome using environmental DNA extracted from honey. A total of 121 SNPs (97 SNPs informative for honey bee subspecies identification and 24 SNPs associated with relevant traits of the colonies) were used in the assay to genotype honey DNA, which derives from thousands of honey bees. Results were integrated with information derived from previous studies and whole genome resequencing datasets. This GBS method is highly reliable in estimating honey bee SNP allele frequencies of the whole colony from which the honey derived. This assay can be used to identify the honey bee subspecies of the colony that produced the honey and, in turn, to authenticate the entomological origin of the honey.
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Affiliation(s)
- Samuele Bovo
- grid.6292.f0000 0004 1757 1758Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Valerio Joe Utzeri
- grid.6292.f0000 0004 1757 1758Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- grid.6292.f0000 0004 1757 1758Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Valeria Taurisano
- grid.6292.f0000 0004 1757 1758Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- grid.6292.f0000 0004 1757 1758Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- grid.6292.f0000 0004 1757 1758Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
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8
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Eynard SE, Vignal A, Basso B, Canale‐Tabet K, Le Conte Y, Decourtye A, Genestout L, Labarthe E, Mondet F, Servin B. Reconstructing queen genotypes by pool sequencing colonies in eusocial insects: Statistical Methods and their application to honeybee. Mol Ecol Resour 2022; 22:3035-3048. [PMID: 35816386 PMCID: PMC9796407 DOI: 10.1111/1755-0998.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 01/01/2023]
Abstract
Eusocial insects are crucial to many ecosystems, and particularly the honeybee (Apis mellifera). One approach to facilitate their study in molecular genetics, is to consider whole-colony genotyping by combining DNA of multiple individuals in a single pool sequencing experiment. Cheap and fast, this technique comes with the drawback of producing data requiring dedicated methods to be fully exploited. Despite this limitation, pool sequencing data have been shown to be informative and cost-effective when working on random mating populations. Here, we present new statistical methods for exploiting pool sequencing of eusocial colonies in order to reconstruct the genotypes of the queen of such colony. This leverages the possibility to monitor genetic diversity, perform genomic-based studies or implement selective breeding. Using simulations and honeybee real data, we show that the new methods allow for a fast and accurate estimation of the queen's genetic ancestry, with correlations of about 0.9 to that obtained from individual genotyping. Also, it allows for an accurate reconstruction of the queen genotypes, with about 2% genotyping error. We further validate these inferences using experimental data on colonies with both pool sequencing and individual genotyping of drones. In brief, in this study we present statistical models to accurately estimate the genetic ancestry and reconstruct the genotypes of the queen from pool sequencing data from workers of an eusocial colony. Such information allows to exploit pool sequencing for traditional population genetics analyses, association studies and for selective breeding. While validated in Apis mellifera, these methods are applicable to other eusocial hymenopterans.
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Affiliation(s)
- Sonia E. Eynard
- GenPhySE, INRAE, INP, ENVTUniversité de ToulouseCastanet‐TolosanFrance,LABOGENA DNAJouy‐en‐JosasFrance
| | - Alain Vignal
- GenPhySE, INRAE, INP, ENVTUniversité de ToulouseCastanet‐TolosanFrance
| | - Benjamin Basso
- Abeilles et EnvironnementINRAEAvignonFrance,ITSAPAvignonFrance
| | | | | | | | | | | | | | - Bertrand Servin
- GenPhySE, INRAE, INP, ENVTUniversité de ToulouseCastanet‐TolosanFrance
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9
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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] [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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10
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Du M, Bernstein R, Hoppe A, Bienefeld K. Influence of model selection and data structure on the estimation of genetic parameters in honeybee populations. G3 (BETHESDA, MD.) 2022; 12:6500294. [PMID: 35100384 PMCID: PMC8824827 DOI: 10.1093/g3journal/jkab450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/22/2021] [Indexed: 11/12/2022]
Abstract
Estimating genetic parameters of quantitative traits is a prerequisite for animal breeding. In honeybees, the genetic variance separates into queen and worker effects. However, under data paucity, parameter estimations that account for this peculiarity often yield implausible results. Consequently, simplified models that attribute all genetic contributions to either the queen (queen model) or the workers (worker model) are often used to estimate variance components in honeybees. However, the causes for estimations with the complete model (colony model) to fail and the consequences of simplified models for variance estimates are little understood. We newly developed the necessary theory to compare parameter estimates that were achieved by the colony model with those of the queen and worker models. Furthermore, we performed computer simulations to quantify the influence of model choice, estimation algorithm, true genetic parameters, rates of controlled mating, apiary sizes, and phenotype data completeness on the success of genetic parameter estimations. We found that successful estimations with the colony model were only possible if at least some of the queens mated controlled on mating stations. In that case, estimates were largely unbiased if more than 20% of the colonies had phenotype records. The simplified queen and worker models proved more stable and yielded plausible parameter estimates for almost all settings. Results obtained from these models were unbiased when mating was uncontrolled, but with controlled mating, the simplified models consistently overestimated heritabilities. This study elucidates the requirements for variance component estimation in honeybees and provides the theoretical groundwork for simplified honeybee models.
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Affiliation(s)
- Manuel Du
- Breeding and Behavior, Institute for Bee Research Hohen Neuendorf, 16540 Hohen Neuendorf, Germany
| | - Richard Bernstein
- Breeding and Behavior, Institute for Bee Research Hohen Neuendorf, 16540 Hohen Neuendorf, Germany
| | - Andreas Hoppe
- Breeding and Behavior, Institute for Bee Research Hohen Neuendorf, 16540 Hohen Neuendorf, Germany
| | - Kaspar Bienefeld
- Breeding and Behavior, Institute for Bee Research Hohen Neuendorf, 16540 Hohen Neuendorf, Germany
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11
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Bernstein R, Du M, Hoppe A, Bienefeld K. Simulation studies to optimize genomic selection in honey bees. Genet Sel Evol 2021; 53:64. [PMID: 34325663 PMCID: PMC8323320 DOI: 10.1186/s12711-021-00654-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Background With the completion of a single nucleotide polymorphism (SNP) chip for honey bees, the technical basis of genomic selection is laid. However, for its application in practice, methods to estimate genomic breeding values need to be adapted to the specificities of the genetics and breeding infrastructure of this species. Drone-producing queens (DPQ) are used for mating control, and usually, they head non-phenotyped colonies that will be placed on mating stations. Breeding queens (BQ) head colonies that are intended to be phenotyped and used to produce new queens. Our aim was to evaluate different breeding program designs for the initiation of genomic selection in honey bees. Methods Stochastic simulations were conducted to evaluate the quality of the estimated breeding values. We developed a variation of the genomic relationship matrix to include genotypes of DPQ and tested different sizes of the reference population. The results were used to estimate genetic gain in the initial selection cycle of a genomic breeding program. This program was run over six years, and different numbers of genotyped queens per year were considered. Resources could be allocated to increase the reference population, or to perform genomic preselection of BQ and/or DPQ. Results Including the genotypes of 5000 phenotyped BQ increased the accuracy of predictions of breeding values by up to 173%, depending on the size of the reference population and the trait considered. To initiate a breeding program, genotyping a minimum number of 1000 queens per year is required. In this case, genetic gain was highest when genomic preselection of DPQ was coupled with the genotyping of 10–20% of the phenotyped BQ. For maximum genetic gain per used genotype, more than 2500 genotyped queens per year and preselection of all BQ and DPQ are required. Conclusions This study shows that the first priority in a breeding program is to genotype phenotyped BQ to obtain a sufficiently large reference population, which allows successful genomic preselection of queens. To maximize genetic gain, DPQ should be preselected, and their genotypes included in the genomic relationship matrix. We suggest, that the developed methods for genomic prediction are suitable for implementation in genomic honey bee breeding programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00654-x.
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Affiliation(s)
- Richard Bernstein
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany. .,Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, 10099, Berlin, Germany.
| | - Manuel Du
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany
| | - Andreas Hoppe
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany
| | - Kaspar Bienefeld
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany.,Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, 10099, Berlin, Germany
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12
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Henriques D, Lopes AR, Chejanovsky N, Dalmon A, Higes M, Jabal-Uriel C, Le Conte Y, Reyes-Carreño M, Soroker V, Martín-Hernández R, Pinto MA. A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.). Sci Rep 2021; 11:15317. [PMID: 34321557 PMCID: PMC8319136 DOI: 10.1038/s41598-021-94833-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
With a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3' and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.
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Affiliation(s)
- Dora Henriques
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Ana R Lopes
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Nor Chejanovsky
- Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
| | - Anne Dalmon
- INRAE, Unité Abeilles et Environnement, Avignon, France
| | - Mariano Higes
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
| | - Clara Jabal-Uriel
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
| | - Yves Le Conte
- INRAE, Unité Abeilles et Environnement, Avignon, France
| | | | - Victoria Soroker
- Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
| | - Raquel Martín-Hernández
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología (INCRECYT-FEDER), Fundación Parque Científico y Tecnológico de Castilla-La Mancha, 02006, Albacete, Spain
| | - M Alice Pinto
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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13
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Utzeri VJ, Ribani A, Taurisano V, Banqué CHI, Fontanesi L. Distribution of the Main Apis mellifera Mitochondrial DNA Lineages in Italy Assessed Using an Environmental DNA Approach. INSECTS 2021; 12:insects12070620. [PMID: 34357280 PMCID: PMC8304627 DOI: 10.3390/insects12070620] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/31/2022]
Abstract
Growing interest has been emerging on the need to monitor the genetic integrity of the European Apis mellifera subspecies that could be threatened by the human-mediated dispersion of non-native populations and lines. Mitochondrial DNA (mtDNA) lineages can provide useful information for this purpose. In this study, we took advantage of the environmental DNA (eDNA) contained in the honey, which can be analyzed to detect the main groups of mitotypes of the honey bees that produced it. In this study, we applied this eDNA to produce a distribution map all over the Italian peninsula and the two major islands (Sicily and Sardinia) of the following three honey bee mtDNA lineages: A, C and M. A total of 607 georeferenced honey samples, produced in all Italian regions, was analyzed to detect these lineages. The A lineage was widespread in Sicily, as expected, considering that A. m. siciliana carries the African lineage. Surprisingly, this lineage was also reported in about 14% of all other samples produced in almost all continental regions, and in Sardinia. The applied method obtained an updated distribution map of honey bee mtDNA lineages that could be useful to design policies for the conservation of Italian honey bee genetic resources.
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14
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Guichard M, Dainat B, Eynard S, Vignal A, Servin B, Neuditschko M. Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole-genome sequences. Anim Genet 2021; 52:472-481. [PMID: 33970494 PMCID: PMC8360191 DOI: 10.1111/age.13070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2021] [Indexed: 01/05/2023]
Abstract
The identification of quantitative trait loci (QTL) through genome-wide association studies (GWAS) is a powerful method for unravelling the genetic background of selected traits and improving early-stage predictions. In honey bees (Apis mellifera), past genetic analyses have particularly focused on individual queens and workers. In this study, we used pooled whole-genome sequences to ascertain the genetic variation of the entire colony. In total, we sampled 216 Apis mellifera mellifera and 28 Apis mellifera carnica colonies. Different experts subjectively assessed the gentleness and calmness of the colonies using a standardised protocol. Conducting a GWAS for calmness on 211 purebred A. m. mellifera colonies, we identified three QTL, on chromosomes 8, 6, and 12. The two first QTL correspond to LOC409692 gene, coding for a disintegrin and metalloproteinase domain-containing protein 10, and to Abscam gene, coding for a Dscam family member Abscam protein, respectively. The last gene has been reported to be involved in the domestication of A. mellifera. The third QTL is located 13 kb upstream of LOC102655631, coding for a trehalose transporter. For gentleness, two QTL were identified on chromosomes 4 and 3. They are located within gene LOC413669, coding for a lap4 protein, and gene LOC413416, coding for a bicaudal C homolog 1-B protein, respectively. The identified positional candidate genes of both traits mainly affect the olfaction and nervous system of honey bees. Further research is needed to confirm the results and to better understand the genetic and phenotypic basis of calmness and gentleness.
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Affiliation(s)
- M Guichard
- Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, Bern, 3003, Switzerland.,Agroscope, Animal GenoPhenomics, Rte de la Tioleyre 4, Posieux, 1725, Switzerland
| | - B Dainat
- Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, Bern, 3003, Switzerland
| | - S Eynard
- GenPhySE, INRA, INPT, INPENVT, Université de Toulouse, Castanet-Tolosan, 31320, France.,UMT PrADE, Protection des Abeilles Dans l'Environnement, Avignon, 84914, France
| | - A Vignal
- GenPhySE, INRA, INPT, INPENVT, Université de Toulouse, Castanet-Tolosan, 31320, France.,UMT PrADE, Protection des Abeilles Dans l'Environnement, Avignon, 84914, France
| | - B Servin
- GenPhySE, INRA, INPT, INPENVT, Université de Toulouse, Castanet-Tolosan, 31320, France.,UMT PrADE, Protection des Abeilles Dans l'Environnement, Avignon, 84914, France
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- Domaine de Vilvert, Bat 224, CS80009, Jouy-en-Josas CEDEX, 78353, France
| | - M Neuditschko
- Agroscope, Animal GenoPhenomics, Rte de la Tioleyre 4, Posieux, 1725, Switzerland
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15
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Non-Destructive Genotyping of Honeybee Queens to Support Selection and Breeding. INSECTS 2020; 11:insects11120896. [PMID: 33371316 PMCID: PMC7767382 DOI: 10.3390/insects11120896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 11/16/2022]
Abstract
In traditional bee breeding, the honeybee queen is chosen for breeding based on the performance of the colony produced by its mother. However, we cannot be entirely certain that a specific queen will produce offspring with desirable traits until we observe the young queen's new colony. Collecting the queen's genetic material enables quick and reliable determination of the relevant information. We sampled exuviae, feces, and wingtips for DNA extraction to avoid fatally injuring the queen when using tissue samples. Quantity and purity of extracted DNA were measured. Two mitochondrial markers were used to determine the lineage affiliation and exclude possible contamination of DNA extracts with non-honeybee DNA. dCAPS (derived Cleaved Amplified Polymorphic Sequences) markers allowed detection of single nucleotide polymorphisms (SNPs) in nuclear DNA regions presumably associated with Varroa sensitive hygiene and set the example of successful development of genotyping protocol from non-destructive DNA sources. One of the logical future steps in honeybee breeding is introducing genomic selection and non-destructive sampling methods of genetic material may be the prerequisite for successful genotyping. Our results demonstrate that the extraction of DNA from feces and exuviae can be introduced into practice. The advantage of these two sources over wingtips is reducing the time window for processing the samples, thus enabling genotyping directly after the queen's emergence.
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16
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Le Conte Y, Meixner MD, Brandt A, Carreck NL, Costa C, Mondet F, Büchler R. Geographical Distribution and Selection of European Honey Bees Resistant to Varroa destructor. INSECTS 2020; 11:E873. [PMID: 33302465 PMCID: PMC7764010 DOI: 10.3390/insects11120873] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 01/12/2023]
Abstract
Developing resistance to the varroa mite in honey bees is a major goal for apicultural science and practice, the development of selection strategies and the availability of resistant stock. Here we present an extended literature review and survey of resistant populations and selection programs in the EU and elsewhere, including expert interviews. We illustrate the practical experiences of scientists, beekeepers, and breeders in search of resistant bees. We describe numerous resistant populations surviving without acaricide treatments, most of which developed under natural infestation pressure. Their common characteristics: reduced brood development; limited mite population growth; and low mite reproduction, may cause conflict with the interests of commercial beekeeping. Since environmental factors affect varroa mite resistance, particular honey bee strains must be evaluated under different local conditions and colony management. The resistance traits of grooming, hygienic behavior and mite reproduction, together with simple testing of mite population development and colony survival, are significant in recent selection programs. Advanced breeding techniques and genetic and physiological selection tools will be essential in the future. Despite huge demand, there is no well-established market for resistant stock in Europe. Moreover, reliable experience or experimental evidence regarding the resistance of stocks under different environmental and management conditions is still lacking.
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Affiliation(s)
- Yves Le Conte
- INRAE, Abeilles et Environnement, 84914 Avignon, France;
| | - Marina D. Meixner
- Landesbetrieb Landwirtschaft Hessen, Bee Institute, Erlenstrasse 9, 35274 Kirchhain, Germany; (M.D.M.); (A.B.); (R.B.)
| | - Annely Brandt
- Landesbetrieb Landwirtschaft Hessen, Bee Institute, Erlenstrasse 9, 35274 Kirchhain, Germany; (M.D.M.); (A.B.); (R.B.)
| | - Norman L. Carreck
- Carreck Consultancy Ltd., Woodside Cottage, Dragons Lane, Shipley RH13 8GD, West Sussex, UK;
- Laboratory of Apiculture and Social Insects, University of Sussex, Falmer, Brighton BN1 9QG, East Sussex, UK
| | - Cecilia Costa
- CREA Research Centre for Agriculture and Environment, via di Saliceto 80, 40128 Bologna, Italy;
| | - Fanny Mondet
- INRAE, Abeilles et Environnement, 84914 Avignon, France;
| | - Ralph Büchler
- Landesbetrieb Landwirtschaft Hessen, Bee Institute, Erlenstrasse 9, 35274 Kirchhain, Germany; (M.D.M.); (A.B.); (R.B.)
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17
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Substantial Genetic Progress in the International Apis mellifera carnica Population Since the Implementation of Genetic Evaluation. INSECTS 2020; 11:insects11110768. [PMID: 33171738 PMCID: PMC7694995 DOI: 10.3390/insects11110768] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary The Apis mellifera carnica subspecies of the honeybee is known for its gentleness and good honey yield. In the early 20th century, systematic breeding efforts began. Breeding progress was slow before the introduction of modern techniques of genetic evaluation in the mid 1990s. Here, the results of the official breeding value estimation in BeeBreed.eu are analyzed. From about 2000 onward, breeding progress accelerated. The result is a considerable gain in honey yield and desirable properties without increased inbreeding coefficients. The success of A. m. carnica breeding shows the potential of genetic evaluation. Abstract The Apis mellifera carnica subspecies of the honeybee has long been praised for its gentleness and good honey yield before systematic breeding efforts began in the early 20th century. However, before the introduction of modern techniques of genetic evaluation (best linear unbiased prediction, BLUP) and a computerized data management in the mid 1990s, genetic progress was slow. Here, the results of the official breeding value estimation in BeeBreed.eu are analyzed to characterize breeding progress and inbreeding. From about the year 2000 onward, the genetic progression accelerated and resulted in a considerable gain in honey yield and desirable properties without increased inbreeding coefficients. The prognostic quality of breeding values is demonstrated by a retrospective analysis. The success of A. m. carnica breeding shows the potential of BLUP-based breeding values and serves as an example for a large-scale breeding program.
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Plate M, Bernstein R, Hoppe A, Bienefeld K. Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies. INSECTS 2020; 11:insects11070404. [PMID: 32629773 PMCID: PMC7412524 DOI: 10.3390/insects11070404] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/12/2020] [Accepted: 06/25/2020] [Indexed: 11/16/2022]
Abstract
Modern breeding structures are emerging for European honeybee populations. However, while genetic evaluations of honeybees are becoming increasingly well understood, little is known about how selection decisions shape the populations' genetic structures. We performed simulations evaluating 100 different selection schemes, defined by selection rates for dams and sires, in populations of 200, 500, or 1000 colonies per year and considering four different quantitative traits, reflecting different genetic parameters and numbers of influential loci. Focusing on sustainability, we evaluated genetic progress over 100 years and related it to inbreeding developments. While all populations allowed for sustainable breeding with generational inbreeding rates below 1% per generation, optimal selection rates differed and sustainable selection was harder to achieve in smaller populations and for stronger negative correlations of maternal and direct effects in the selection trait. In small populations, a third or a fourth of all candidate queens should be selected as dams, whereas this number declined to a sixth for larger population sizes. Furthermore, our simulations indicated that, particularly in small populations, as many sires as possible should be provided. We conclude that carefully applied breeding provides good prospects for currently endangered honeybee subspecies, since sustainable genetic progress improves their attractiveness to beekeepers.
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Affiliation(s)
- Manuel Plate
- Institute for Bee Research, Friedrich-Engels Str. 32, 16540 Hohen Neuendorf, Germany; (R.B.); (A.H.); (K.B.)
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, 10099 Berlin, Germany
- Correspondence:
| | - Richard Bernstein
- Institute for Bee Research, Friedrich-Engels Str. 32, 16540 Hohen Neuendorf, Germany; (R.B.); (A.H.); (K.B.)
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Andreas Hoppe
- Institute for Bee Research, Friedrich-Engels Str. 32, 16540 Hohen Neuendorf, Germany; (R.B.); (A.H.); (K.B.)
| | - Kaspar Bienefeld
- Institute for Bee Research, Friedrich-Engels Str. 32, 16540 Hohen Neuendorf, Germany; (R.B.); (A.H.); (K.B.)
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, 10099 Berlin, Germany
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