Abstract
The absence of a full pedigree can hinder selective breeding efforts. In honeybees, definitive maternity and especially paternity of queens is difficult to determine, even under managed mating schemes (e.g. using artificial insemination) due to the negative effects of single-drone mating on colony fitness. Here we genotyped 388 living queens from two beekeeping operations using Genotyping-by-Sequencing (GBS). We evaluate two methods to call single-nucleotide polymorphism (SNPs), Tassel 5 and Stacks, for their ability to supply SNPs that can recover known relationships. While Stacks discovered more SNPs (29,433), SNPs called with Tassel 5 (16,757) were found to be more accurate for the derivation of relationships. This methodology presents a low-cost genotyping approach and can be used to support commercial honeybee breeding schemes.