Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks

Perot Saelao,Philip Tokarz,Lelania Bilodeau,Michael Simone-Finstrom,Robert Danka,Arian Avalos,Frank Rinkevich,Lilia De Guzman

doi:10.1186/s12864-020-07111-x

Abstract

BackgroundThe 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.ResultsPooled 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.ConclusionThis 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.

Highlights

The population genetics of U.S honey bee stocks remain poorly characterized despite the agricultural importance of Apis mellifera as the major crop pollinator
We investigated the current patterns of genetic diversity of eight U.S honey bee stocks using whole genome sequencing of pooled individuals (Pool-seq) to determine genome-wide allele frequencies
In instances where we examined variation derived from targeted breeding efforts in the research stocks, we combined all three Italian stocks to form a common background under the assumption that their combined profile is representative of the broader genetic diversity of managed Italian bees across the U.S

Summary

Introduction

The population genetics of U.S honey bee stocks remain poorly characterized despite the agricultural importance of Apis mellifera as the major crop pollinator. The majority of queens that are commercially produced in the U.S originate from a relatively small number of queen producers in California, Hawaii and the southern U.S It has been suggested by previous work that a combined 500 breeder queens across operations are used to rear over a million daughter queens that are distributed throughout the U.S [13] While these do not all represent genetically distinct lines, the varied sources contribute to genetic diversity among stocks. A more comprehensive understanding of the genetic differentiation among commercially relevant stocks, is an important first step toward efforts to begin implementing genomic-based marker-assisted selection to rapidly and efficiently improve honey bee breeding programs

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Conclusion