Establishing standards for genome wide association studies in eusocial insects through a case study in honey bees

As eusocial insects enter the post-genomic era, the availability of reference genomes and genomic datasets have facilitated Genome-wide Association Studies (GWAS) for traits measured on whole colonies. Several GWAS have been completed for traits like foraging and colony nesting behavior. However, no studies have addressed the specific challenges of applying GWAS to eusocial species. Eusocial species, such as honey bees, present several hurdles for traditional GWAS designs: they have high recombination rates, their social traits are generally polygenic, and the existence of multiple castes introduces additional layers of complexity in identifying genotype-phenotype associations. Moreover, many eusocial species are haplodiploid and polyandrous. To address these challenges, we used the honey bee (Apis mellifera) as a model to simulate GWAS scenarios for honey yield. We explored the influence of factors such as the number of quantitative trait loci (QTL), heritability level, number of SNP markers covering the genome, and sample size on QTL discovery. We also examined the impact of genotyping queens versus workers. Our results suggest that a p-value threshold of 1 × 10^- 6 and sample sizes of at least 1,000 are effective for identifying QTL for key traits. Including both queen and worker genotypes improved QTL discovery power, emphasizing the need to optimize GWAS methods for eusocial species. Our results should improve future GWAS in honey bees and highlights the need for additional simulations and standard-setting work in other eusocial species.