Mitogenomic characterisation of the Ispenc chicken: a genetically distinct Turkish miniature breed

1. The Ispenc chicken, a genetically undefined miniature breed in Türkiye, was analysed using mitochondrial DNA to clarify its maternal lineage and assess its distinction from European ornamental breeds (Sabelpoot and Barbu d'Anvers) as well as from the Sultan breed.2. Phylogenetic analysis of a 1508 bp mtDNA fragment spanning the D-loop identified five haplotypes (H1-H5): Ispenc individuals carried H2 and H3, Sultan chickens carried H4, while Sabelpoot and Barbu d'Anvers shared H5.3. Molecular variance analysis indicated strong population structure, with 98% of genetic variation occurring among populations (F_st = 0.98184). Two complete mitogenomes representing the H2 and H3 haplotypes of the Ispenc breed (16785 bp each) were assembled, each containing a 1232 bp D-loop and the standard set of 37 mitochondrial genes.4. Comparative mitogenome analysis identified 62 nucleotide differences among haplotypes: Ispenc differed from Sabelpoot and Barbu d'Anvers by 44-45 nucleotides, whereas these two breeds differed by only two nucleotides. Haplogroup analysis assigned Ispenc to haplogroup A and the European ornamental breeds to haplogroup E.5. These results demonstrated that the Ispenc chicken represents a distinct maternal lineage that is clearly differentiated from European miniature breeds. This underscored its value as a native genetic resource and highlighting the need to conserve both of its mtDNA lineages (H2 and H3).