High‑resolution recombination landscape in Iranian native chicken ecotypes: Elevated hotspot density and candidate...

The recombination landscape is a key genomic feature that influences genetic diversity and evolutionary dynamics, yet it remains largely unexplored in native chicken populations adapted to harsh environmental conditions. This study, for the first time, mapped high‑resolution recombination events in Iranian indigenous chicken ecotypes (Khazak, Lari, Marandi, and Naked neck) and compared them with two commercial breeds reared in Iran (Arian and Leghorn). The aim was to identify differences in recombination rates, hotspots distribution, and genes located within recombination hotspots. The average whole‑genome recombination rate in indigenous ecotypes and the Arian breed (16.78 ± 12.43 cM/Mb) was significantly higher than in Leghorn (5.12 ± 3.82 cM/Mb) (Kruskal‑Wallis, P < 2.2 × 10⁻¹⁶). Hotspot density was also much higher in indigenous populations and Arian (covering 22.70% of macrochromosomes) compared with Leghorn (1.10%). Recombination rates showed a strong concentration in telomeric regions (>100 cM/Mb) and a sharp decrease in central regions (<10 cM/Mb), a pattern consistently observed across all six populations, with greater peak intensity in native ecotypes and Arian. Protein-coding genes located within recombination hotspots included UNC13C, TRPM8, TLR3, TLR2, SLC6A19, NAALADL2, HSPB7, ETNPPL, CHORDC1, and ABCG2. This study provides the first high‑resolution recombination landscape for Iranian native chickens, revealing significantly higher recombination rates and hotspot densities in indigenous populations and the Arian breed compared to the Leghorn breed. The genes located within these hotspots represent a catalogue of loci that may be prioritized in future functional and association studies of environmental adaptation.