Development of a cost-effective SNP tool to detect genetic pollution in honey bee spermatheca content

• Autor(a) principal: Soltani, Chiraz
• Data de Publicação: 2023
• Tipo de documento: Dissertação
• Idioma: eng
• Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
• Texto Completo: http://hdl.handle.net/10198/29205
• topic: Single nucleotide polymorphism; Introgression; Conservation; Apis Mellifera; Whole genome sequencing; NEBNext direct genotyping solution; Domínio/Área Científica::Engenharia e Tecnologia::Outras Engenharias e Tecnologias

The loss of genetic complexes adapted to local conditions through genetic introgression is one of the many threats affecting the honey bee (Apis mellifera). Large- scale displacement of honey bees has altered their native distribution. One extreme example is A. m. mellifera, a European subspecies that was once widespread but is now threatened with extinction in numerous countries due to introgression and replacement by the C lineage. As a result, conservation measures may be needed to preserve the genetic diversity of these subspecies. Acknowledging the significance of native genetic diversity, several conservation and breeding programs have been established. Their effectiveness hinges on the availability of accurate and cost-effective molecular tools for assessing subspecies introgression. Whole-genome data has offered valuable insights into honey bee evolution, yet its practical application is hampered by the need for specialized bioinformatics expertise and computational resources, often unavailable in conservation and breeding centers. To bridge this gap, a novel SNP (Single Nucleotide Polymorphism) tool, based on the NEBNext Direct Genotyping Solution, has been developed. This tool was designed from 228 whole-genome sequence data generated from 148 M-lineage drones and 80 C-lineage drones. From 5,007 highly differentiated SNPs, we selected 130 SNPs. After eliminating problematic SNPs, we retained 82 SNPs that demonstrated exceptional accuracy in estimating the degree of genetic introgression in known samples. This innovative tool represents a significant advancement in the genetic analysis of honey bee colonies, with applications spanning breeding and conservation efforts for A. m. mellifera, A. m. iberiensis, A. m. carnica and A. m. ligustica.