The African mud catfish (Clarias gariepinus) is well known for its nutritional and economic importance and it’s the most important cultured fish species in Nigeria. Its sustainable production is being threatened by suspected inbreeding depression occasioned by the use and reuse of imported frys and fingerlings from exotic homogenous stocks. Morphological, genetic, and molecular studies were carried out to determine the residual genetic variability and assess the possibility of improving the fish quality through selective breeding of local strains. Three hundred and ninety two samples were collected with the aid of gill nets and analysed using multivariate tools of principal component analysis and Discriminate function analysis (DFA) for morphometric studies; Growth performance was examined by heterosis performance on Specific growth rate(SGR), Hatchability, survival and mean growth over a period of 26 weeks through reciprocal crossings of different strains, while the molecular analysis examined the selection traits through protein profiling using Sodium deodosulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis, and genetic differentiation using random amplified polymorphic DNA(RAPD) assay and microsatellite analysis. Morphological comparisons revealed morphometric homogeneity between C. gariepinus fish population in River Benue and River Niger and their tributaries which clustered into five considerably distinct populations. The growth performance analysis shows significant difference in mean weight gain, specific growth rates and survival rate (P<0.05). Sokoto sourced strains (SKT) gave the best growth of 595.00±4.33g, closely followed by its reciprocal hybrid with South African strains (SA ? X SKT ?) 554.00±6.22g, while the New Bussa strain had the lowest growth value (70.00±2.07g) at the grow-out level. The cross between the Dutch and Yola strains gave the highest positive mean heterosis of 28.54% (P<0.05). The data obtained from polypeptides of C. gariepinus revealed Sokoto (MW = 100kDa); Yola (MW = 40kDa, MW = 30kDa); Dutch (MW= 15kDa); SKT and YLA hybrid ((MW = 30kDa); Dutch and Yola (MW = 15kDa) as identifying negative marker bands. The DNA-RAPD analysis recorded an overall low polymorphism among and within the local and exotic populations of C. gariepinus in Nigerian freshwater bodies and their reciprocals (19.35%). However, considerably higher levels of polymorphism were detected between the Lokoja Ganija strains (29.67%) and Yola strains (12.09%). The nine microsatellite loci used to screen the wild C. gariepinus strains and their crosses germplasm revealed polymorphic information content (PIC) values that ranged from 0.077±0.231 to 0.395±0.399 with the local strains showing slightly higher allelic diversity than the three exotic strains. The among population heterozygosity deficit (FST) ranged from 0.0672 to 0.3171 with an average value of 0.1448. Estimation of effective population size (Ne) revealed that the Ne of the exotic strains was smaller than that of the local strains in Nigerian freshwater bodies. The low similarity coefficient (SC) value obtained in the phylogenetic dendograms indicates a high divergent of these strains from different water bodies.
Key Words: Clarias gariepinus, Cross breeding, Strains, Microsatellites, Genetic variation