617. Inferring whole-genome tree sequences and population and demographic parameters of the Western honeybee

Obšteter, Jana; Marinč, Andraž; Prešern, Janez; Wragg, David

doi:10.3920/978-90-8686-940-4_617

Cited by 3 publications

(2 citation statements)

References 11 publications

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“…Population Structure For each colony, we ran the model presented in Eynard, Vignal, et al 2022 to estimate the genetic background on 48,589 SNPs selected so that they differentiate the three main genetic background of honey bees in Europe (Dogantzis et al 2021;Wragg et al 2022;Obšteter et al 2022): the C lineage comprising the lowly differentiated Apis mellifera ligustica and Apis mellifera carnica, the M lineage of Western Europe Apis mellifera mellifera and the O lineage of Eastern Europe/ South-Western Asia Apis mellifera caucasia. Specifically, the SNPs were chosen based on the following criteria: (i) there is a maximum of two polymorphic sites within a 100 base pair window, (ii) only one representative marker per linkage disequilibrium block with 𝑟 2 higher than 0.8, (iii) the variance between allele frequencies in the three main European genetic background is higher than zero, to allow for population identification and…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

“…Population Structure For each colony, we ran the model presented in Eynard et al (2022) [30] to estimate the genetic background on 48,589 SNPs selected so that they differentiate the three main genetic background of honey bees in Europe [80,39,81]): the C lineage comprising the lowly differentiated Apis mellifera ligustica and Apis mellifera carnica, the M lineage of Western Europe Apis mellifera mellifera and the O lineage of Eastern Europe/ South-Western Asia Apis mellifera caucasia. Specifically, the SNPs were chosen based on the following criteria:…”

Section: Snp Genotypingmentioning

confidence: 99%

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Sequence-based genome-wide association studies reveal the polygenic architecture ofVarroa destructorresistance in Western honey beesApis mellifera

Eynard,

Mondet,

Basso

et al. 2024

Preprint

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Honey bees,Apis mellifera, have experienced the full impacts of globalisation, including the recent invasion by the parasiteVarroa destructor, hereafter called varroa. This deadly mite has rapidly become one of the main causes of colony losses worldwide, with a huge economic impact on beekeeping. Despite the lethal effects of varroa, some colonies survive infestation. In such colonies, honey bees are able to develop defence strategies that limit mite spread and confer colony resistance to varroa. In some populations, resistance traits were found to be sufficiently heritable to offer sustainable opportunities to fight varroa infestations through selective breeding of naturally resistant honey bees. Recent advances in genomics allow for the development of new tools to assess the importance of genetic mechanisms involved in varroa resistance. Here we report on the largest genome-wide association study performed on honey bees to understand the genetic basis of multiple phenotypes linked to varroa resistance inApis mellifera. Genome wide association studies for varroa resistance traits were performed on whole genome sequencing of more than 1,500 colonies belonging to three different genetic backgrounds and combined in a meta-analysis. Results show that varroa resistance is largely polygenic in nature, involving many genes with small effects. Still, a total of 60 genetic markers were identified as having a significant impact on varroa resistance in at least one of the honey bee populations tested. These associations pinpoint several regions of the honey bee genome that are linked with varroa resistance phenotypes and increase our understanding of the mechanisms underlying honey bee resistance to its main parasite. Our results will also support the building of strategies for genomic selection in honey bee breeding.

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Section: Whole Genome Sequencingmentioning

confidence: 99%

Section: Snp Genotypingmentioning

confidence: 99%

Sequence-based genome-wide association studies reveal the polygenic architecture ofVarroa destructorresistance in Western honey beesApis mellifera

Eynard,

Mondet,

Basso

et al. 2024

Preprint

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SIMplyBee: R package for simulating honeybee populations and breeding programs

Obšteter

Strachan

Bubnič

et al. 2022

Preprint

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Background The Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testing of breeding programs and methods, yet no existing simulator allows for a detailed simulation of honeybee populations. Here we describe SIMplyBee, a holistic simulator of honeybee populations and breeding programs. SIMplyBee is an R package and hence freely available for installation from CRAN \url{http://cran.r-project.org/package=SIMplyBee}. Implementation SIMplyBee builds upon the stochastic simulator AlphaSimR that simulates individuals with their corresponding genomes and quantitative genetic values. To enable a honeybee specific simulation, we extended AlphaSimR by developing classes for global simulation parameters, \texttt{SimParamBee}, for a honeybee colony, \texttt{Colony}, and multiple colonies, \texttt{MultiColony}. We also developed functions to address major specificities of the honeybees: honeybee genome, haplo-diploid inheritance, social organisation, complementary sex determination, polyandry, colony events, and quantitative genetics of honeybees. Results We describe and show implementation regarding simulating a honeybee genome, creating a honeybee colony and its members, haplodiploid inheritance and complementary sex determination, colony events, creating and managing multiple colonies at once, and obtaining genomic data and honeybee quantitative genetics. Further documentation at \url{http://SIMplyBee.info} provides details on these operations and describes additional operations related to genomics, quantitative genetics, and other functionality. Discussion SIMplyBee is a holistic simulator of honeybee populations and breeding programs that simulates individual honeybees with their genomes, colonies with colony events, and individual- and colony-level quantitative values. SIMplyBee provides a research platform for testing breeding and conservation strategies and their effect on future genetic gain and variability. Future development of SIMplyBee will focus on improving the simulation of honeybee genomes, optimizing the performance of the simulator, and including spatial awareness to crossing functions and phenotype simulation. We welcome the honeybee genetics and breeding community to join us in the future development of SIMplyBee.

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SIMplyBee: an R package to simulate honeybee populations and breeding programs

et al. 2023

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Background The Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testing of breeding programs and methods, yet no existing simulator allows for a detailed simulation of honeybee populations. Here we describe SIMplyBee, a holistic simulator of honeybee populations and breeding programs. SIMplyBee is an R package and hence freely available for installation from CRAN http://cran.r-project.org/package=SIMplyBee. Implementation SIMplyBee builds upon the stochastic simulator AlphaSimR that simulates individuals with their corresponding genomes and quantitative genetic values. To enable honeybee-specific simulations, we extended AlphaSimR by developing classes for global simulation parameters, , for a honeybee colony, , and multiple colonies, . We also developed functions to address major honeybee specificities: honeybee genome, haplodiploid inheritance, social organisation, complementary sex determination, polyandry, colony events, and quantitative genetics at the individual- and colony-levels. Results We describe its implementation for simulating a honeybee genome, creating a honeybee colony and its members, addressing haplodiploid inheritance and complementary sex determination, simulating colony events, creating and managing multiple colonies at the same time, and obtaining genomic data and honeybee quantitative genetics. Further documentation, available at http://www.SIMplyBee.info, provides details on these operations and describes additional operations related to genomics, quantitative genetics, and other functionalities. Discussion SIMplyBee is a holistic simulator of honeybee populations and breeding programs. It simulates individual honeybees with their genomes, colonies with colony events, and individual- and colony-level genetic and breeding values. Regarding the latter, SIMplyBee takes a user-defined function to combine individual- into colony-level values and hence allows for modeling any type of interaction within a colony. SIMplyBee provides a research platform for testing breeding and conservation strategies and their effect on future genetic gain and genetic variability. Future developments of SIMplyBee will focus on improving the simulation of honeybee genomes, optimizing the simulator’s performance, and including spatial awareness in mating functions and phenotype simulation. We invite the honeybee genetics and breeding community to join us in the future development of SIMplyBee.

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617. Inferring whole-genome tree sequences and population and demographic parameters of the Western honeybee

Cited by 3 publications

References 11 publications

Sequence-based genome-wide association studies reveal the polygenic architecture ofVarroa destructorresistance in Western honey beesApis mellifera

Sequence-based genome-wide association studies reveal the polygenic architecture ofVarroa destructorresistance in Western honey beesApis mellifera

SIMplyBee: R package for simulating honeybee populations and breeding programs

SIMplyBee: an R package to simulate honeybee populations and breeding programs

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