In Silico Screening and Development of Microsatellite Markers for Genetic Analysis in Perca fluviatilis

SIMPLE SUMMARY: Perca fluviatilis is an economically important species of freshwater fish that has flavorsome meat with a high nutritional value. Microsatellite markers are widely used in the genetic structure analysis of aquatic animals due to their abundance, high polymorphism, and codominance. In this study, we screened, tested, and developed polymorphic markers and evaluated the genetic diversity of the main wild P. fluviatilis populations in China. From the P. fluviatilis genomic data, 98,425 pairs of microsatellites were identified. A total of 200 primer pairs for tetranucleotide microsatellites were synthesized and tested in randomly selected wild individuals. Among them, 152 microsatellite markers were found to be polymorphic. A total of 29 markers with clear amplified bands and high polymorphism were selected for the genetic analysis of the four populations. The results indicated a high level of genetic diversity in P. fluviatilis populations in Wulungu Lake, Jili Lake, and the Wulungu River and a medium level of genetic diversity in the Kalaeerqisi River. There was moderate genetic differentiation among the populations in Xinjiang. The results of this study provide important information on the genetic diversity and genetic population structuring of P. fluviatilis in China as well as a scientific basis for the protection and molecular marker-assisted breeding of P. fluviatilis. ABSTRACT: Perca fluviatilis is an economically important species of freshwater fish. To understand the genetic structure of P. fluviatilis in China, 268 samples were collected from Wulungu Lake (WL), Jili Lake (JL), the Wulungu River (WR), and the Kalaeerqisi River (KR). These samples were then analyzed using microsatellite markers. A total of 98,425 microsatellite markers were developed based on the genomic data, and 29 polymorphic microsatellite markers were selected to analyze genetic diversity in this study. The number of alleles (N(a)) and observed heterozygosity (H(o)) per population ranged from 4.621 (KR) to 11.172 (WL) and from 0.510 (KR) to 0.716 (JL), respectively. The results of the polymorphic information content (PIC) showed that the WL, JL, and WR populations were highly polymorphic (PIC ≥ 0.5) and that the KR population was moderately polymorphic (0.25 ≤ PIC < 0.5). The genetic differentiation coefficient (F(st)) among the four P. fluviatilis populations was 0.074, indicating moderate genetic differentiation among the populations in Xinjiang. The reason for the significant difference between the rivers and lakes could be the presence of a dam blocking the flow of P. fluviatilis. The development of microsatellite markers provides support for population genetics in the future. The evaluation of the genetic structure of P. fluviatilis in Xinjiang provides a reference for the reproduction and conservation of P. fluviatilis.