The Cichlid fish Sarotherodon melanotheron is typically found in West and Central African estuaries and lagoons. It represents a good candidate for promoting tilapia farming in brackish waters. Understanding the genetic diversity in its populations 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 significant 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 (FIS and FST) 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 FIS variation. We found a significant isolation by distance across subsamples. Effective population size averaged 210 individuals, with a range from 36 to 517 individuals. Assuming that 79% of heterozygote deficits are explained by sib mating lead to a rough estimate of rsm = 0.4 of mating rate between full sibs within S. melanotheron subpopulations. The fish size correlated positively and significantly with the observed FIS (r = 0.58; p value = 0.04806). Reproduction system (endogamy) in S. melanotheron could explain the strong heterozygote deficit observed. Our results provide technical guidance for efficient management of this tilapia species' genetic resources for breeding programs in fresh and brackish waters.
Keywords: Genetic diversity; Geographic isolation; Linkage disequilibrium; SSR; Sarotherodon melanotheron; Tilapia.