Banat Naked Neck is the most important indigenous breed of chickens in Serbia. Marginalized until recently, it is becoming increasingly popular due to its adaptability and good productivity in alternative production systems. However, its history and the current breeding model pose challenges for breed preservation and future improvement. This study aimed to assess the genetic diversity and structure of four subpopulations of Banat Naked Neck from different districts in Serbia (West Backa, North Banat, South Banat and Kolubara) using D-loop mitochondrial DNA sequences and a set of 30 microsatellite markers. Seven haplotypes in the phylogenetic analysis of D-loop mitochondrial DNA suggested maternal origin related to the Indian subcontinent, while haplotype and nucleotide diversity averaged 0.731 ± 0.053 and 0.0067 ± 0.0018, respectively. Microsatellite genotyping showed an average detected number of alleles per locus of 5.129 ± 0.237, while the observed and expected heterozygosity averaged 0.560 ± 0.018 and 0.631 ± 0.014, respectively. Genetic differentiation estimated through FST was 0.051 (p < .001). Two clusters in STRUCTURE analysis showed possible separation of two older subpopulations (South Banat and Kolubara) from the two more recent ones (West Backa and North Banat). This first comprehensive study of genetic diversity serves as the basis for future preservation, use and improvement of the Banat Naked Neck breed.
Keywords: Banat Naked Neck; Serbia; genetic diversity; microsatellites; mitochondrial DNA.