Based on protein polymorphism and results obtained with RAPD-PCR and ISSR-PCR methods, the domestic and wild Artiodactyla and Perissodactyla (14 and 7 species, respectively) were compared. The marker-specific species differentiation in domestic and wild species was observed, leading to the hypothesis of the “subgenome” existing in domestic species. It is assumed that “subgenome” contains certain genes encoding important proteins and enzymes. In the past, the high variation of “subgenome” could play an essential role in domestication, leading to the wide morphological differentiation of contemporary domestic species.
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