Development and characterization of seventeen novel microsatellite markers in common hairfin anchovy (Setipinna tenuifilis) using third-generation sequencing technology

Common hairfin anchovy (Setipinna tenuifilis) is an economically and ecologically important pelagic fish in China's seas. However, the resources of S. tenuifilis have been greatly declined as a result of overfishing. Therefore, a large number of polymorphic molecular markers will be of benefit to a further investigation of the existing genetic resources. In this study, a total of 2,529,301 microsatellite loci were detected in the S. tenuifilis genome using third-generation sequencing technology. Seventeen microsatellite markers were successfully developed from the randomly selected 100 dinucleotide motifs and genotyped by capillary electrophoresis. Sixteen markers were detected to be high polymorphic (PIC > 0.5) in S. tenuifilis. The number of alleles (Na) and effective number (Ne) of alleles ranged from 8 to 29 (mean 18.471) and ranged from 2.149 to 19.619 (mean 9.921), respectively. The average Ho was 0.642 and ranged from 0.383 to 0.900, and the average He was 0.855 and ranged from 0.535 to 0.949. The PCoA result showed no significant genetic heterogeneity based on individual genetic distance. However, the analysis of the STRUCTURE displayed a discontinuity between northern and southern populations. The result showed that these polymorphic microsatellite markers could be applied to study genetic diversity and population differentiation of S. tenuifilis, facilitating the management and conservation of this species.