Background. During the course of evolution, numerous taxa abandoned canonical sex and reproduced asexually. Examination of the Cobitis hankugensis - Iksookimia longicorpa asexual complex already revealed important evolutionary discoveries tackling phenomena like interspecific hybridization, non-Mendelian inheritance, polyploidy and asexuality. Yet, as in other similar cases, the investigation is hampered by the lack of easily accessible molecular tools for efficient differentiation among genomotypes.

Material and methods. Here, we tested the cross-species amplification of 23 microsatellite markers derived from distantly related species and investigated the extent to which such markers can facilitate the genome identification in non-model hybrid complex.

Results. We found that 21 out of 23 microsatellite markers amplified in all genomotypes. Five of them could be used for easy diagnosticity of parental species and their hybrids due to species-specific amplification profiles. We also noted that three markers, i.e. IC654 and IC783 derived from Cobitis choii and Iko_TTA01 from Iksookimia koreensis, had dosage-sensitive amplification efficiencies of species-specific alleles. This could be further used for reliable differentiation of genome composition in polyploids.

Conclusions. The present study introduces a noninvasive method applicable for diagnosis of ploidy and genome composition of hybrids, which are not clearly distinguished morphologically. We showed that very detailed information may be obtained even from markers developed in distantly related taxa.