AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap

Area of Science:

• Genomics
• Population Genetics
• Entomology

Background:

• Honey bee (Apis mellifera) drones are haploid, inheriting alleles solely from their queen.
• This haploid nature makes them ideal for establishing known allele combinations (haplotypes).
• Existing haplotype resources for honey bees are limited.

Purpose of the Study:

• To create a comprehensive haplotype resource for honey bees using whole-genome sequencing data.
• To demonstrate the utility of this resource for genotype imputation and phasing.
• To provide a reference panel for population genetic and evolutionary analyses.

Main Methods:

• Collation of whole-genome sequence data from 1,407 honey bee drones across 19 countries and 8 subspecies.
• Alignment to the Amel_HAv3.1 reference genome.
• Variant calling and quality filtering to identify high-quality genetic variants.

Main Results:

• A high-quality variant dataset of 17.4 million variants across 1,328 samples was generated.
• The AmelHap resource achieved >95% concordance for genotype imputation, even with significant data loss.
• Demonstrated high accuracy for phasing diploid honey bee genomes.

Conclusions:

• The AmelHap resource is a valuable tool for honey bee genetic research.
• It facilitates accurate genotype imputation from low-depth sequencing or SNP chip data.
• It serves as a comprehensive reference panel for population genetics and evolutionary studies.