Periodic Reporting for period 2 - BEE NATURAL (A sustainable future for honeybees by unravelling the mechanisms of natural disease resistance)
Periodo di rendicontazione: 2022-09-01 al 2024-02-29
The ectoparasitic mite, Varroa destructor, together with its associated honeybee viruses that it vectors, in particular Deformed wing virus (DWV), remains unarguably the leading cause of honeybee colony mortality world-wide and the main cause of the near complete eradication of wild honeybees in Europe and North America. In almost all parts of the world, survival of managed honeybee colonies is completely dependent on control treatments applied by beekeepers, to reduce mite levels in the colony and thus avoid the establishment of a virus epidemic. Without treatment, colonies commonly die within 1-2 years. These treatments are chemical based and therefore are harmful to bees, leave residues in hive products, and are increasingly ineffective as the mite develops resistance.
The natural host of varroa mites, the Asian hive bee (Apis cerana), rarely experiences damage by the mite since a stable host-parasite relationship has been established over a long evolutionary scale. Such a relationship is clearly missing with the new host, the Western honeybee (Apis mellifera). In the 1970s and 1980s, the mite made a host jump to the Western honeybee and has since then successfully spread throughout the world, only leaving Australia and a few isolated locations mite-free. At present, treatments are necessary for honeybee colony survival, but with the unwanted side-effect that they also remove the selective pressure necessary to establish a stable host-parasite relationship. Hence, the current rationale for beekeeping to treat and remove the parasite both hampers the evolution of resistance and obstructs fundamental research on natural selection host‒parasite coevolution in this new host‒parasite system, which is now only possible in a few rare honeybee populations surviving long-term without varroa control. These honeybee populations offer exclusive insight into the natural adaptive capacity of honeybees, yet little is understood about their mechanisms of resistance or tolerance.
The goal of BEE NATURAL is to comprehensively describe resistant and tolerant phenotypes in rare and valuable naturally adapted varroa-resistant honeybee population existing in Gotland, Sweden, Avignon France and Oslo, Norway, in order to deeper our fundamental understanding of host-parasite interaction and to identify candidate genes for marker assisted selection. Genomic regions or target genes associated with resistant and tolerant traits will be identified through the efforts of the BEE NATURAL project, using Next Generation Sequencing (NGS) technologies such as RNA-seq and whole genome sequencing (WGS), providing valuable information that can be applied towards developing marker-assisted selection: a powerful new approach for disease resistant breeding that can facilitate major advances in breeding efforts and genetic stock improvement.This will be achieved through a set of complementary approaches presented in four work plans (WP).
WP1 – Reveal the phenotypic and genetic mechanisms of naturally adapted mite resistance by identifying host chemical signals that inhibit the reproduction of mites and identify host genomic regions or causative genes associated with this adaptation through a transcriptomic analysis.
WP2 – Characterise the molecular adaptations of naturally adapted tolerance and resistance to virus infections by analysing the transcriptome of both the host and viruses in laboratory virus inoculation time course experiments.
WP3 – Identify potential virus adaptations over 20 years of natural selection by analysing historical host samples from the long-term surviving, mite-resistant honeybee population on Gotland, Sweden.
WP4 – Identify genomic regions and causative genes associated with disease resistance to develop marker-assisted selection by performing a Genome-wide association study using whole genome sequencing (WGS) of honeybee DNA from samples provided by a network of volunteer beekeepers recruited to facilitate large-scale phenotyping and sampling in different geographical environments.
The knowledge gained from this project can be used to improve honeybee health through disease resistance/tolerance breeding and remove the dependency on chemical treatments currently necessarily used in beekeeping today to reduce virus epidemics. This will lead to improved sustainability of pollination services provided by honeybees for both crop production and wild plant biodiversity. Therefore, the project is in-line with the European sustainable development goals for zero hunger, good health and well-being and life on land.
The natural host of varroa mites, the Asian hive bee (Apis cerana), rarely experiences damage by the mite since a stable host-parasite relationship has been established over a long evolutionary scale. Such a relationship is clearly missing with the new host, the Western honeybee (Apis mellifera). In the 1970s and 1980s, the mite made a host jump to the Western honeybee and has since then successfully spread throughout the world, only leaving Australia and a few isolated locations mite-free. At present, treatments are necessary for honeybee colony survival, but with the unwanted side-effect that they also remove the selective pressure necessary to establish a stable host-parasite relationship. Hence, the current rationale for beekeeping to treat and remove the parasite both hampers the evolution of resistance and obstructs fundamental research on natural selection host‒parasite coevolution in this new host‒parasite system, which is now only possible in a few rare honeybee populations surviving long-term without varroa control. These honeybee populations offer exclusive insight into the natural adaptive capacity of honeybees, yet little is understood about their mechanisms of resistance or tolerance.
The goal of BEE NATURAL is to comprehensively describe resistant and tolerant phenotypes in rare and valuable naturally adapted varroa-resistant honeybee population existing in Gotland, Sweden, Avignon France and Oslo, Norway, in order to deeper our fundamental understanding of host-parasite interaction and to identify candidate genes for marker assisted selection. Genomic regions or target genes associated with resistant and tolerant traits will be identified through the efforts of the BEE NATURAL project, using Next Generation Sequencing (NGS) technologies such as RNA-seq and whole genome sequencing (WGS), providing valuable information that can be applied towards developing marker-assisted selection: a powerful new approach for disease resistant breeding that can facilitate major advances in breeding efforts and genetic stock improvement.This will be achieved through a set of complementary approaches presented in four work plans (WP).
WP1 – Reveal the phenotypic and genetic mechanisms of naturally adapted mite resistance by identifying host chemical signals that inhibit the reproduction of mites and identify host genomic regions or causative genes associated with this adaptation through a transcriptomic analysis.
WP2 – Characterise the molecular adaptations of naturally adapted tolerance and resistance to virus infections by analysing the transcriptome of both the host and viruses in laboratory virus inoculation time course experiments.
WP3 – Identify potential virus adaptations over 20 years of natural selection by analysing historical host samples from the long-term surviving, mite-resistant honeybee population on Gotland, Sweden.
WP4 – Identify genomic regions and causative genes associated with disease resistance to develop marker-assisted selection by performing a Genome-wide association study using whole genome sequencing (WGS) of honeybee DNA from samples provided by a network of volunteer beekeepers recruited to facilitate large-scale phenotyping and sampling in different geographical environments.
The knowledge gained from this project can be used to improve honeybee health through disease resistance/tolerance breeding and remove the dependency on chemical treatments currently necessarily used in beekeeping today to reduce virus epidemics. This will lead to improved sustainability of pollination services provided by honeybees for both crop production and wild plant biodiversity. Therefore, the project is in-line with the European sustainable development goals for zero hunger, good health and well-being and life on land.
In this report, I will highlight the scientific progress of the first half of the ERC research project BEE NATURAL. The progress will be reported by corresponding to the work packages and tasks planned in the application.
WP1 – Reveal the phenotypic and genetic mechanisms of naturally adapted mite resistance
In this WP we set out to explore the underlying mechanisms behind reduced mite reproductive success observed in naturally selected mite-resistant honeybees. We have confirmed our hypothesis that this trait of reduced mite reproduction is due to adaptations of the host brood rather than traits of adult bees (Scaramella, et al., 2023). This is most likely due to altered expression patterns of pupal cuticular volatile compounds that trigger mite egg-laying. Our first task was to Identify differences in pupal volatile cuticular compounds between mite-resistant and -susceptible honeybees. We have successfully done this and a summary of brood volatile compounds that differ between mite-resistant and mite-susceptible honeybees over a time course is currently being prepared for publication. Our second task was to Identify transcriptomic response associated with alterations or differences in brood volatiles. We have a collection of pupal samples collected along a time-series through their development and during the sensitive time-window for mite egg-laying. We are currently extracting RNA from these samples for transcriptomic analysis. Tasks 3 and 4 involve identify the host transcriptome and the specific volatiles that are associated with disrupting mite reproduction. This work is planned for the second half of the project.
WP 2 – Characterise the molecular adaptations of tolerance and resistance to virus infections
In this WP we set out to phenotype the virus tolerance and resistance mechanisms in mite-resistant honeybee populations. The Gotland honeybee populations had demonstrated colony- and individual-level classical tolerance through reduced mortality despite high virus titres. We hypothesis that the genetic response of the host to virus infections is based on a molecular mechanism that can be identified in the RNA phase. Virus tolerance and resistance has not been explored in the Avignon and Oslo honeybee population but will be through the efforts of this WP in parallel with the Gotland population. The first task was to assess colony-level adaptation of virus tolerance and/or resistance in the other long-term surviving honeybee populations. We have produced a summary of colony-level virus tolerance/resistance phenotypes of different long-term naturally surviving honeybee populations, and this research paper is currently under production. Our second task was to determine individual-level virus susceptibility (Locke et al., 2021). We are currently investigating the host transcriptome from the individuals in this study to identify associations in immune gene responses with virus tolerance and/or resistance, in line with our final task of this WP.
WP 3 – Identify potential virus adaptations over 20 years of natural selection
The main task of this WP was to characterize any possible long-term virus co-evolution in the Gotland mite-resistant honeybee population. Data is currently being analyzed to produce a summary of clustering and phylogenetic analysis of DWV consensus sequences and variability profiles through 20+ years of natural selection for survival of the Swedish mite-resistant honeybee population.
WP4 – Identify genomic regions and causative genes associated with disease resistance to develop marker-assisted selection
Genome-wide association studies require a large sample size to produce a large set of Single Nucleotide Polymorphisms (SNPs) that can be linked to an extensively characterized expression gradient of a phenotype allowing for the consistent identification of genomic regions and/or potential causative genes that correlate with the phenotype. We have completed the first task of this WP, which was to establish a network of beekeepers to facilitate large-scale data collection. This has been done in collaboration with the Swedish beekeeping association. Tasks 2 (a genome-wide association study on disease resistance) and 3 (to identify gene-by-environment interactions on disease tolerance/resistance phenotypes) are planned for the second part of the project.
WP1 – Reveal the phenotypic and genetic mechanisms of naturally adapted mite resistance
In this WP we set out to explore the underlying mechanisms behind reduced mite reproductive success observed in naturally selected mite-resistant honeybees. We have confirmed our hypothesis that this trait of reduced mite reproduction is due to adaptations of the host brood rather than traits of adult bees (Scaramella, et al., 2023). This is most likely due to altered expression patterns of pupal cuticular volatile compounds that trigger mite egg-laying. Our first task was to Identify differences in pupal volatile cuticular compounds between mite-resistant and -susceptible honeybees. We have successfully done this and a summary of brood volatile compounds that differ between mite-resistant and mite-susceptible honeybees over a time course is currently being prepared for publication. Our second task was to Identify transcriptomic response associated with alterations or differences in brood volatiles. We have a collection of pupal samples collected along a time-series through their development and during the sensitive time-window for mite egg-laying. We are currently extracting RNA from these samples for transcriptomic analysis. Tasks 3 and 4 involve identify the host transcriptome and the specific volatiles that are associated with disrupting mite reproduction. This work is planned for the second half of the project.
WP 2 – Characterise the molecular adaptations of tolerance and resistance to virus infections
In this WP we set out to phenotype the virus tolerance and resistance mechanisms in mite-resistant honeybee populations. The Gotland honeybee populations had demonstrated colony- and individual-level classical tolerance through reduced mortality despite high virus titres. We hypothesis that the genetic response of the host to virus infections is based on a molecular mechanism that can be identified in the RNA phase. Virus tolerance and resistance has not been explored in the Avignon and Oslo honeybee population but will be through the efforts of this WP in parallel with the Gotland population. The first task was to assess colony-level adaptation of virus tolerance and/or resistance in the other long-term surviving honeybee populations. We have produced a summary of colony-level virus tolerance/resistance phenotypes of different long-term naturally surviving honeybee populations, and this research paper is currently under production. Our second task was to determine individual-level virus susceptibility (Locke et al., 2021). We are currently investigating the host transcriptome from the individuals in this study to identify associations in immune gene responses with virus tolerance and/or resistance, in line with our final task of this WP.
WP 3 – Identify potential virus adaptations over 20 years of natural selection
The main task of this WP was to characterize any possible long-term virus co-evolution in the Gotland mite-resistant honeybee population. Data is currently being analyzed to produce a summary of clustering and phylogenetic analysis of DWV consensus sequences and variability profiles through 20+ years of natural selection for survival of the Swedish mite-resistant honeybee population.
WP4 – Identify genomic regions and causative genes associated with disease resistance to develop marker-assisted selection
Genome-wide association studies require a large sample size to produce a large set of Single Nucleotide Polymorphisms (SNPs) that can be linked to an extensively characterized expression gradient of a phenotype allowing for the consistent identification of genomic regions and/or potential causative genes that correlate with the phenotype. We have completed the first task of this WP, which was to establish a network of beekeepers to facilitate large-scale data collection. This has been done in collaboration with the Swedish beekeeping association. Tasks 2 (a genome-wide association study on disease resistance) and 3 (to identify gene-by-environment interactions on disease tolerance/resistance phenotypes) are planned for the second part of the project.
The project is still in the early stages of producing data but we have results that we expect will progress the research field on honeybee disease resistance and tolerance beyond the state of the art.