Incidental and/or uncontrolled hybridization between silver carp (Hypophthalmichthys molitrix) and bighead (Aristichthys nobilis) represents a serious problem in Czechoslovak aquaculture. This fact affects fitness traits very negatively in successive generations of hybrids. To solve this problem, 1076 individuals in a total of both H. molitrix. A. nobilis, and their hybrids in 12 groups from six rearing facilities were analysed. Twelve protein systems representing 21 presumptive loci were studied to analyse the electrophoretic patterns of their products using horizontal starch gel electrophoresis of blood and tissue extracts. Both species displayed identical electrophoretic patterns in MYO‐I*, LDH‐A*, LDH‐B*, sMDH‐1*, sIDHP‐3*, GPI‐1*, and CK‐I* loci. For a reliable differentiation of both species products of the following nine loci are applicable ALB*, PA*, TF, sMDH‐2*, SOD*, NDH*, MYO‐IF, MYO‐III*, and CK‐2*. In addition, some polymorphic variants in slDHP‐1*, sIDHP‐2*, LDH‐C*, EST‐II*, and GPI‐2* loci are of use as auxillary markers while the other variants are common to both species. A high level of gene introgression was evident through hybridization between both species. All groups declared previously as ‘H. molifrix’ were actually confirmed biochemically to be H. molitrix. However, all groups declared as ‘A. nobilis’ were proved to be a mixture of A. nobilis and its hybrids of different level with H. molitrix. This suggests it is impossible to distinguish between A. nobilis and hybrids using their external morphology only.
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