Abstract:Domestication and selective breeding become one of the main driving force of adaptive evolution for domestic animals. The introduced populations of Nile tilapia(Oreochromis niloticus) in China mainland have experienced a long-term domestication and selective breeding, which provide a unique opportunity to study adaptive evolution of fish species under domestication and selective breeding. In this study, we screened 12 polymorphic microsatellite loci in nine independent-reared strains (four of which were used for selective breeding and five for ranching) and their wild progenitor population of Nile tilapia to assess genetic diversity and genetic bottleneck across native, domesticated and selective breeding populations. The parameters of genetic variability in native, domesticated and selective breeding populations were summarized as follows:the average number of effective alleles (AE) was 5.433, 5.113-6.515, 3.239-6.734; the value of average expected heterozygosity (HE) was 0.812, 0.796-0.859, 0.657-0.858; the value of average polymorphism information content (PIC) was 0.768, 0.753-0.819, 0.601-0.818; the value of average Wright's inbreeding coefficient (FIS) was 0.323, 0.166-0.342, 0.249-0.314. LSD-t test showed that no significant differences were detected between native population and populations under artificial selection(domesticated and selective breeding populations) in terms of AE and HE. The HE values in three domesticated populations (EGY,WY and GD) were significantly higher than that in one selective breeding population(XJF).Analysis of bottleneck revealed that all populations have experienced a historical population bottleneck. Moreover, recent genetic population bottleneck was detected in native population, two domesticated populations (WY and EGY) and two selective breeding populations (JNM and XJF). The size of other historically bottlenecked populations may have been restored through new mutations and gene flow. The effective population sizes (NE) of native, domesticated and selective breeding populations were 177, 29-117 (an average of 57.4), 84-123 (an average of 102.8), respectively. The results of this study provided valuable information not only for the sustainable use of domesticated populations, but also for further genetic improvement of selective breeding populations of Nile tilapia. More importantly, the findings of this study provided a new reference basis for population structure and population dynamics of fish species under domestication and selective breeding.