Vol.:(0123456789) 1 3 Molecular Biology Reports https://doi.org/10.1007/s11033-018-4354-x ORIGINAL ARTICLE Genetic characterization of Benin’s wild populations of Sarotherodon melanotheron melanotheron Rüppell, 1852 T. Olivier Amoussou 1,2,3  · Issaka Youssao Abdou Karim 3  · Guiguigbaza‑Kossigan Dayo 1  · Ibrahim Imorou Toko 4  · Modou Séré 1  · Antoine Chikou 5  · Aboubacar Toguyéni 1,2 Received: 2 July 2018 / Accepted: 3 September 2018 © Springer Nature B.V. 2018 Abstract The Cichlid fsh Sarotherodon melanotheron is typically found in West and Central African estuaries and lagoons. It repre- sents a good candidate for promoting tilapia farming in brackish waters. Understanding the genetic diversity in its popula- tions from the hydrographical basins of Southern Benin is primordial before designing selective breeding programs. For this purpose, 202 samples collected from four rivers of Southern Benin and were genotyped using 15 polymorphic microsatellite DNA markers. Each river was split up into three sampling sites. We found signifcant global linkage disequilibrium across the genome of natural populations of this tilapia species overall the loci. However, when the loci that display aberrant Wright’s (F IS and F ST ) were removed from the data, a linkage disequilibrium was detected for the remaining 11 loci and became compatible with the null hypothesis. Null alleles explained at least 20.58% of F IS variation. We found a signifcant isolation by distance across subsamples. Efective population size averaged 210 individuals, with a range from 36 to 517 individuals. Assuming that 79% of heterozygote defcits are explained by sib mating lead to a rough estimate of r sm = 0.4 of mating rate between full sibs within S. melanotheron subpopulations. The fsh size correlated positively and signifcantly with the observed F IS (r = 0.58; p value = 0.04806). Reproduction system (endogamy) in S. melanotheron could explain the strong heterozygote defcit observed. Our results provide technical guidance for efcient management of this tilapia species’ genetic resources for breeding programs in fresh and brackish waters. Keywords Tilapia · Sarotherodon melanotheron · Genetic diversity · Geographic isolation · SSR · Linkage disequilibrium Introduction Nowadays, fshery catches are declining in many countries. This is attributable to the increased fshing intensity, pol- lution, destruction of habitats, introduction of new species and climate change [1–3]. Exploitation of aquatic natural resources is mainly regulated on the base of stock abundance Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-018-4354-x) contains supplementary material, which is available to authorized users. * T. Olivier Amoussou amssoliver@gmail.com Issaka Youssao Abdou Karim issaka.youssao@epac.uac.bj Ibrahim Imorou Toko ibrahim.imorou-toko@fa-up.bj Aboubacar Toguyéni toguyeni@univ-ouga.bf 1 Centre International de Recherche-Développement sur l’élevage en zone Subhumide (CIRDES), P.O. Box 01-454, Bobo-Dioulasso 01, Burkina Faso 2 Research Unit in Aquaculture and Aquatic Biodiversity, Nazi Boni University, P.O. Box 01-1091, Bobo-Dioulasso 01, Burkina Faso 3 Laboratory of Animal Sciences and Meat Technologies, Department of Animal Health and Production, University of Abomey-Calavi, P.O. Box 01-2009, Cotonou, Benin 4 Research Unit in Aquaculture and Aquatic Ecotoxicology, Department of Animal Production, Faculty of Agronomy, University of Parakou, P.O. Box 123, Parakou, Benin 5 Laboratory of Hydrobiology and Aquaculture, Faculty of Agronomic Sciences, University of Abomey-Calavi, P.O. Box 01-526, Cotonou, Benin