In Silico Screening and Development of Microsatellite Markers for Genetic Analysis in Perca 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 (Na) and observed heterozygosity (Ho) 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 (Fst) 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.

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

“…When several genome assemblies are available within the same species, in silico detection of polymorphic markers is resource-efficient in terms of time and cost. This approach has been successfully applied in sesame, spinach, and Perca fluviatilis (Dossa et al, 2017; Bhattarai et al, 2021; Xu et al, 2022). We compared the common SSR markers from the genomes of D. alata (TDa95/00328 and Kabusa) and obtained 93,92% polymorphic SSR markers.…”

Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus

“…The isolation of sufficient DNA quantity and quality collected non-invasively from such samples as fish scales or mucus has become of wide interest to researchers studying genetic diversity [ 5 ]. To study the genetic structure of fish populations, fish must be caught, and DNA extracted mainly from the muscle [ 31 ] or the fin [ 32 ] tissue. Such research is difficult to carry out on a large scale, as it requires the killing of many fish [ 33 ] or harming them.…”

Unlocking the genome of perch – From genes to ecology and back again

“…Other studies have documented the genetic divergence patterns at a broader geographical scale between waterbodies (Kánainé Sipos et al, 2021;Xu et al, 2022). In addition, microsatellites have been used to identify the genetic origin of perch for fish traceability (Pukk et al, 2016;Rolli et al, 2014) and to study the temporal changes and evolutionary consequences of overfishing (Pukk et al, 2013).…”

“…Based on microsatellite analysis, the evidence of significant population genetic structuring in perch was observed at both small geographical scales within lakes (Bergek & Olsson, 2009; Gerlach et al, 2001, but see also Kalous et al, 2017 on lack of genetic differentiation) and at small spatial scales in the Baltic Sea (Bergek et al, 2010; Bergek & Björklund, 2009; Olsson et al, 2011). Other studies have documented the genetic divergence patterns at a broader geographical scale between waterbodies (Kánainé Sipos et al, 2021; Xu et al, 2022). In addition, microsatellites have been used to identify the genetic origin of perch for fish traceability (Pukk et al, 2016; Rolli et al, 2014) and to study the temporal changes and evolutionary consequences of overfishing (Pukk et al, 2013).…”