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Improving bee health through genomics


Declines in bee populations across the world threaten food security and ecosystem function. It is currently not possible to routinely predict which specific stressors lead to declines in different populations or contexts, hindering efforts to improve bee health. Genomics has the potential to dramatically improve our ability to identify, monitor and predict the effects of stressors, as well as to mitigate their impacts through the use of marker-assisted selection, RNA interference and potentially gene editing. Here we discuss the most compelling recent applications of genomics to investigate the mechanisms underpinning bee population declines and to improve the health of both wild and managed bee populations.

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Fig. 1: Evolutionary relationships of bees depicting the number of published genomes per family.
Fig. 2: Population genomic approaches to study and improve bee health.
Fig. 3: Transcriptomic approaches to study, diagnose and improve bee health.
Fig. 4: Metagenomic approaches to study and improve bee health.
Fig. 5: Methods for manipulating gene function in bees.


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Research in the laboratory of C.M.G. is supported by funding from the US National Science Foundation and the US Department of Agriculture. Research in the laboratory of A.Z. is supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada, Large Scale Applied Research Projects (BeeOMICs and BeeCSI) from Genome Canada and a York University Research Chair in Genomics.

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Nature Reviews Genetics thanks D. de Graaf, K. Raymann and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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The authors contributed equally to all aspects of the article.

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Correspondence to Christina M. Grozinger or Amro Zayed.

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Structural but not necessarily functional enzyme variants that migrate at different rates during electrophoresis, which are the result of genetic changes in the enzyme-encoding gene.

Restriction fragment length polymorphisms

Genetic variations that create or abolish a restriction enzyme recognition site, leading to variation in DNA fragment sizes following digestion by restriction endonucleases, as revealed by gel electrophoresis.


Stretches of repetitive DNA with a core motif (typically two or three bases) that is repeated many times. Microsatellites have high mutation rates, leading to many alleles segregating within populations. Because of their polymorphic nature, they are naturally suited for DNA fingerprinting applications.


A genetic system in which females are diploid and males are haploid.

Population genomics

Analysis of genetic diversity at a genome scale in populations to estimate population genetic parameters or to link genotype with phenotype.


Analysis of transcripts within specific tissues using microarrays or RNA sequencing.


Analysis of DNA or RNA from communities of organisms using high-throughput sequencing approaches. Metagenomics does not require isolation of specific species or strains from collected samples before sequencing and thus can be used to identify all species or variants within a sample using bioinformatics.

Marker-assisted selection

Artificial selection programmes using predictive genetic markers to select individuals for breeding

Genome-wide association studies

(GWAS). Studies that investigate the association between genotypes across the genome and their influence on phenotypic traits in natural populations.

Effective population size

The size of an ‘ideal’ population (a random mating population of constant size with Poisson variation in family sizes) that would have the same genetic parameters as the actual population under study.

RNA interference

(RNAi). The application of double-stranded RNA molecules to reduce or silence the expression of target genes.

Single-nucleotide polymorphism

(SNP). A point mutation in a DNA sequence that introduces variation between individuals of a group or species.

Positive selection

An evolutionary force that increases the frequency of beneficial mutations within populations.

Selective sweeps

Processes by which strong positive selection on a mutation results in reduced genetic diversity at nearby linked loci.


Pertaining to genomes that have been generated by hybridization of typically distinct genomes.

Extinction via hybridization

The loss of naturally distinct evolutionary lineages as a result of hybridization with other — typically managed — populations.

Narrow sense heritability

The proportion of phenotypic variance attributed to additive genetic variance.

Quantitative trait loci

(QTLs). Genomic loci that contain variants influencing a quantitative trait. Quantitative traits exhibit continuous variation within populations, such as height in humans or the amount of pollen collected by bee colonies.

Haplotype blocks

Stretches of DNA characterized by high levels of linkage disequilibrium.

Thelytokous parthenogenesis

A form of asexual reproduction found in honeybees from the Cape region of South Africa. Worker bees have the ability to lay unfertilized diploid eggs that develop into daughter workers.

Adverse outcomes pathway

A conceptual framework that links a molecular phenotype (such as a change in gene expression or level of activity of a receptor) to a phenotypic change at another level of biological organization (such as physiology or behaviour) that is associated with a particular end point of interest (such as changes in survival, population demography or size). Adverse outcomes pathways are developed and refined using empirical data and are commonly used in ecotoxicological research.


A metagenomic method in which specific genomic regions (rather than whole genomes) are amplified and sequenced. These regions are selected to show high interspecific variation and low intraspecific variation, allowing identification of the different species within the sample. Metabarcoding is often used to minimize sequencing costs or to investigate fairly well-characterized communities.

Corbicular loads

Pollen loads that are carried on the modified pollen basket (that is, the corbicula) of some bees of the subfamily Apinae.


The taxonomic analysis of pollen grains.


Pertaining to genetic loci that affect two or more phenotypic traits.

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Grozinger, C.M., Zayed, A. Improving bee health through genomics. Nat Rev Genet 21, 277–291 (2020).

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