Mitochondrial DNA polymorphism in different populations of orloff spangled chicken breed

The genetic diversity of the Spangled Orloff chickens was for the first time studied by analyzing the polymorphism of the hypervariable region in the D-loop of mitochondrial DNA (mtDNA). Samples for the analysis were collected at the farms of the All-Russian Poultry Research and Technological Institute (VNITIP), the All-Russian Institute of Farm Animal Genetics and Breeding (VNIIGRZH), and the Moscow Zoo. The D-loop partial sequences (between nucleotide positions 57 and 523) were determined according to the reference sequence of Gallus gallus spadiceus mtDNA, NC_007235 in 39 individuals obtained from these populations (GenBank Accession nos. KM391754–KM391792). In the analyzed mtDNA fragment, a total of 20 polymorphic sites located between the positions 167 and 368, as well as at the position 446, were described in Orloff Spangled Chicken Breed. One polymorphic site at position 221 (haplogroup E, haplotype ORL-2) was unique. All of the identified nucleotide changes were transition-type substitutions. On the basis of the analysis of polymorphic sites in the hypervariable fragment of the D-loop of Spangled Orloff chicken mtDNA, we have found seven haplotypes belonging to four haplogroups (A, B, C, and E). Haplogroup E (haplotypes ORL-1, ORL-2, and ORL-3) was present in the majority of the studied individuals, with the frequencies of 0.77 in the total sample and 0.47 in the VNIIGRZH farm population. Haplogroups A (haplotypes ORL-4 and ORL-7), B (ORL-6), and C (ORL-5) were found only in samples from the VNIIGRZH farm. The studied mtDNA region revealed the lower level of polymorphism in the VNITIP and Moscow Zoo populations, which only had the ORL-1 and ORL-3 haplotypes belonging to Haplogroup E, respectively. Our data suggested that the studied Spangled Orloff chicken populations differed in the composition and frequencies of mtDNA haplogroups and haplotypes.