Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks
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RESEARCH ARTICLE
Open Access
Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks Perot Saelao1,2, Michael Simone-Finstrom1* , Arian Avalos1, Lelania Bilodeau1, Robert Danka1, Lilia de Guzman1, Frank Rinkevich1 and Philip Tokarz1
Abstract Background: The population genetics of U.S. honey bee stocks remain poorly characterized despite the agricultural importance of Apis mellifera as the major crop pollinator. Commercial and research-based breeding programs have made significant improvements of favorable genetic traits (e.g. production and disease resistance). The variety of bees produced by artificial selection provides an opportunity to characterize the genetic diversity and regions of the genome undergoing selection in commonly managed stocks. Results: Pooled sequencing of eight honey bee stocks found strong genetic similarity among six of the stocks. Two stocks, Pol-line and Hilo, showed significant differentiation likely due to their intense and largely closed breeding for resistance to the parasitic Varroa mite. Few variants were identified as being specific to any one stock, indicating potential admixture among the sequenced stocks. Juxtaposing the underlying genetic variation of stocks selected for disease- and parasite-resistance behavior, we identified genes and candidate regions putatively associated with resistance regulated by hygienic behavior. Conclusion: This study provides important insights into the distinct genetic characteristics and population diversity of honey bee stocks used in the United States, and provides further evidence of high levels of admixture in commercially managed honey bee stocks. Furthermore, breeding efforts to enhance parasite resistance in honey bees may have created unique genetic profiles. Genomic regions of interest have been highlighted for potential future work related to developing genetic markers for selection of disease and parasite resistance traits. Due to the vast genomic similarities found among stocks in general, our findings suggest that additional data regarding gene expression, epigenetic and regulatory information are needed to more fully determine how stock phenotypic diversity is regulated. Keywords: Apis mellifera, Pool-seq, FST, Single nucleotide polymorphism, Genetic diversity, Stock identification
Background Managing genetic diversity is critical for the success and sustainability of breeding programs of domesticated organisms. Retaining enough genetic diversity while simultaneously applying selection for desirable traits is a balance * Correspondence: [email protected] 1 USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820, USA Full list of author information is available at the end of the article
that ensures future success through reservoirs of standing variation and minimizes the likelihood of genetic bottlenecks [1–3]. Honey bees (Apis mellifera) are the predominant managed insect pollinator for a majority of food crop species and depend on high genetic diver
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