Genomic diversity and population structure of Carniolan honey bee in its native habitat

• Published in: BMC genomics Vol. 25; no. 1; pp. 849 - 13
• Main Authors: Lukic, Boris, Raguz, Nikola, Kovačić, Marin, Curik, Ino, Obšteter, Jana, Prešern, Janez, Bubnič, Jernej, Lužaić, Ras, Pihler, Ivan, Mirjanić, Goran, Pietropaoli, Marco, Puškadija, Zlatko
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 10-09-2024; BioMed Central; BMC
• Subjects: Agricultural ecosystems; Agricultural production; Analysis; Animals; Apiculture; Apis mellifera; Apis mellifera carnica; Bee breeding; Bee culture; Beekeeping; Bees; Bees - genetics; Best practice; Biological diversity; Breeding; Climate change; Climatic changes; Conservation; Datasets; Differentiation; Discriminant analysis; Diseases; Ecosystem; Ecosystem services; Ecosystems; Environmental changes; Gene Flow; Genetic analysis; Genetic aspects; Genetic diversity; Genetic factors; Genetic relationship; Genetic Variation; Genetics, Population; Genome, Insect; Genomes; Genomic analysis; Genomic diversity; Genomics; Genomics - methods; Growth; Heterozygosity; Home range; Homogeneity; Honey; Honeybee; Inbreeding; Methods; Mitochondrial DNA; Plant breeding; Polymorphism, Single Nucleotide; Population decline; Population genetics; Population structure; Population studies; Populations; Quality control; Sample size; Single nucleotide polymorphism (SNP); Single nucleotide polymorphisms; Single-nucleotide polymorphism; Hungary; Eastern Europe; Slovenia; Serbia; Bosnia and Herzegovina; Montenegro; Croatia; Europe; Bosnia-Hercegovina; Italy; Population structure; Genomic diversity; Single nucleotide polymorphism (SNP); Beekeeping; Conservation; Apis mellifera carnica
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10750-z

Research into the genetic diversity of honey bee (Apis mellifera L.) populations has become increasingly significant in recent decades, primarily due to population declines attributed to human activities and climate change. As a species of great importance, breeding programs that leverage understanding of genomic diversity could offer solutions to mitigate these challenges. The objective of this study was to examine the genomic diversity and population structure of Carniolan honey bees (Apis mellifera carnica) using the Illumina SNP chip on a large honey bee sample collected from Central and South-Eastern European countries. The study also aims to offer recommendations for future breeding programs.
Our analysis involved Discriminant Analysis of Principal Components (DAPC), heterozygosity, admixture analysis, fixation indices (F
), Neighbour-Joining tree, gene flow and Isolation-by-distance analysis. DAPC indicated distinct separation between the Carniolan and Italian honey bee (Apis mellifera ligustica) populations, whereas the admixture analysis revealed varying levels of gene flow and genetic admixture within the Carniolan honey bee populations, demonstrating closer relationships between specific geographic regions (confirmed by Isolation-by-distance analysis). Furthermore, the research of heterozygosity, genomic inbreeding, pairwise F
values, and Neighbour-Joining tree provided insights into the patterns of genetic differentiation and similarity among the populations of Carniolan honey bee within its natural habitat. We have observed genetic homogeneity of the Carniolan honey bee population when considered in a broader genetic/geographical context. However, the Carniolan honey bee has sufficient genetic diversity in its geographical home range that needs to be carefully monitored and maintained.
This study provides important insights into the genetic composition, differentiation, and relationships among Carniolan honey bee populations in Central and South-Eastern European countries. The findings are crucial for conservation efforts, breeding programs, and sustainable beekeeping practices. They emphasise the importance of considering genetic factors and population structure in the breeding and management of honey bees. By understanding these genetic relationships, we can develop strategies to preserve genetic diversity, improve breeding outcomes, and ensure the resilience of honey bee populations in the face of environmental changes and challenges. This knowledge can also inform policy makers and stakeholders on best practices to maintain healthy bee populations, which are vital for ecosystem services and agricultural productivity.