Survey of genetic diversity and pathogen prevalence in commercial beekeeping operations across southwest Saudi Arabia: Implications for management and selective breeding

The native honey bee subspecies, Apis mellifera jemenitica, is under threat from genetic pressure caused by exotic subspecies introduced through commercial beekeeping. Uncontrolled interbreeding risks compromising local adaptations, potentially producing populations unsuited to Saudi Arabia’s harsh climate. This study analyzed the mitochondrial lineage, Nosema spp. infections, Varroa destructor infestation levels, and honey bee-associated viral loads. Honey bee workers were sampled from five colonies at eleven apiaries between December 2022 and February 2023. Mitochondrial DNA was extracted for COI-COII region analysis, and the alcohol wash method was used to assess Varroa mite infestation. Nosema spp. were detected using PCR, with infection levels quantified via microscopy and RT-qPCR. Colonies were also screened for honey bee-associated viruses, representing the first survey of viral prevalence in Saudi Arabia. Mitochondrial analysis identified ten new haplotypes at four locations, suggesting interbreeding between lineages. Varroa mite infestation averaged 1.95 ± 0.96 mites per 100 workers and remained below the 3% threshold at nine of the eleven locations, indicating generally low infestation levels. Nosema spp. infections were absent at three apiaries, with an average spore count of 3.43 × 10⁶ ± 1.1 × 10³ spores per location. This preliminary assessment of genetic diversity and pathogen prevalence provides a foundation for developing a breeding program to enhance disease resistance and honey production in A. m. jemenitica colonies, ensuring their resilience in Southwestern Saudi Arabia's challenging environment.