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Characterisation of the genotype of honey bee colonies from pool sequences - S. Eynard

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  • Characterisation of the genotype of honey bee colonies from pool sequences - S. Eynard

    S. Eynard 1, C. Sann 2, F. Mondet 3,4, B. Basso 5, K. Canale-Tabet 1, R. Mahla 2, O. Bouchez 6, Y. Le Conte 3,4, Y. Poquet 2, F. Phocas 7, F. Guillaume 8, A. Decourtye 4,5, L. Genestout 2,8, A. Vignal 1, B. Servin 1

    1 GenPhySE, INRA, Université Toulouse, INPT, INP-ENVT, Castanet Tolosan, FRANCE, 2 Labogena, Jouy en Josas, FRANCE, 3 Abeilles et Environnement, INRA, Avignon, FRANCE, 4 UMT PrADE, INRA, Avignon, FRANCE, 5 ITSAP, Avignon, FRANCE, 6 US 1426, GeT-PlaGe, Genotoul, INRA, Castanet Tolosan, FRANCE, 7 GenAqua, GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy en Josas, FRANCE, 8 Evolution, Noyal-sur- vilaine, FRANCE

    Abstract: Characterizing the genetic diversity of populations allows to better understand their demographic history and their adaptation to selective pressures. In honey bees, this characterisation is facilitated by a relatively small genome size, but is hindered by the fact that often the unit of observation and sampling is the colony rather than a single individual. Moreover, performing large scale genetic analyses of honey bees is a real challenge, due to the specific reproduction mechanism including multi-male insemination, making the genotype of a bee colony a mixture of contribution from the queen and the mating drones. In this work we propose an approach to characterise the genotype of a colony based on pool sequencing of worker bees. We introduce statistical models for the analysis of pool sequence data allowing to reconstruct jointly individual queen genotypes of colonies and allele frequencies in bee populations. We demonstrate the performance of our approach using data on 1500 colonies collected throughout three years within the FranceAgriMer funded, BeeStrong project. Population admixture, in terms of queen sub-species composition, validation was accomplished using information on geographical and sociological organisation of the beekeepers. In addition to a better understanding of the population dynamics of honey bees, our approach to genotyping bee colonies promises to facilitate the genetic analysis of complex traits, and can be used for genome wide association studies on phenotypes of interests, for instance to assess Varroa resistance in honey bee populations.
    1. Phenotypic of 1500 bee colonies to search for genetic markers
    2. Data collection
      1. 103 beekeepers visited
      2. 1863 colonies phenotypes
      3. 987 colonies sequenced as of July 2019
      4. Phenotypes:
        1. Colony Dyamics Estimation
        2. SMR
        3. Mite Count of Phoretic V.D.
        4. Pool sequencing
    3. SMR Protocol
      1. Coloss protocol
      2. Goal 35 cells infested by. Single varroa founders
      3. In case of low infestation max 700 dissected cells
      4. Frames are selected during the coeval based on brood age
      5. Frames were collected between July and September
      6. Drawbacks
        1. Labor intensive
        2. Might not get 35 cells infested
        3. Only 55% of colonies had enough cells
        4. Correct SMR by empirical bates method
    4. SMR Distribution
      1. Falls between 30-40% in France
      2. Saw little difference between bee races for SMR
    5. Mechanism of SMR
      1. Reasons for no reproduction:
        1. Founder female produces no offspring
        2. Absence of male in the cell
        3. Delay in reproduction due to capping/uncapping
      2. No pattern of the above 3 types except #3
    6. Correlation of SMR
      1. SMR with recapping is small correlation but barely significant
    7. Needs for the future
      1. Validate sampling and SMR by screening full brood frame
      2. Looking at SMR on a brood cell
    Last edited by atollerson; 10-09-2019, 04:47 AM.
    Kalispell, Montana Zone 4a
    Certified Master Beekeeper