A SNP-based honey bee paternity assignment test for evaluating the effectiveness of mating stations and its application to the Ataun valley, Basque Country, Spain

Abstract Geographically isolated mating stations are deployed across Europe to facilitate controlled mating with selected drone-producing colonies. To assess the reliability of these stations, we developed a paternity assignment test using a custom Illumina genotyping chip with 6457 SNPs based on two metrics (number of mismatch alleles and kinship). The method demonstrated remarkable accuracy during validation with an independent dataset of known parent-offspring pairs, with an accuracy rate of 97.7%. We then applied the developed paternity assignment test to the Apis mellifera iberiensis mating station in the Ataun valley, Basque Country, Spain, in 2021. Drone-producing colonies in the valley were sampled and genotyped, as well as 156 worker offspring of queens mated at the station, and 56 drones collected in the drone congregation area. Out of the 156 worker samples, we could assign paternity of 120 (76.9%) to one of the drone-producing colonies in the valley, while 23.1% were of unknown patriline. Out of the 56 drones collected in the air, 52 (92.9%) were assigned to drone-producing colonies. We were also able to determine the colonies and apiaries that made the most significant contributions to the matings. This information aids in effective apiary management, including the selection of suitable mating station locations and the positioning of drone-producing colonies therein. Overall, our SNP-based paternity assignment test offers a valuable tool for evaluating mating station effectiveness across Europe, crucial for advancing breeding objectives in honey bee populations.