Persian fallow deer (Dama dama mesopotamica) is only found in a few protected and refuges areas in the northwest, north, and southwest of Iran. The aims of this study were analysis of inbreeding and morphometric parameters of semen in male Persian fallow deer to investigate the cause of reduced fertility of this endangered species in Dasht-e-Naz National Refuge, Sari, Iran. The Persian fallow deer semen was collected by an electroejaculator from four adult bucks randomly during the breeding season and from five dehorned and horned deer’s in non-breeding season. Twelve blood samples were taken and mitochondrial DNA was extracted, a non-coding region called d-loop was amplified, sequenced and then were considered for genetic analysis. The Persian fallow deer’s normal and abnormal spermatozoa were similar to that of domestic ruminants but very smaller and difficult to observe at the primary observation. The post-mating season collected ejaculates contained abnormal spermatozoa, debris and secretion of accessory glands in horned bucks and accessory glands secretion free of any spermatozoa in dehorned or early velvet budding bucks. Microscopic evaluation in all four bucks during the mating season showed the mean concentration of 9 × 106 spermatozoa/ml. The mean ± standard deviation of age, testes length and testes width was 4.60 ± 1.52 years, 3.58 ± 0.32 and 1.86 ± 0.09 cm, respectively. The results identified 1120 loci in which 377 were polymorphic. In conclusion, reduced fertility of male Persian fallow deer may be caused by inbreeding of the protected herd in a limited area of Dasht-e-Naz National Refuge.

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