Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)

Abstract

The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of a population genetic structure of this species is limited by the low number of molecular markers currently described. In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We sequenced 60 individuals from three populations occurring in the Zagros basin. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16. (average = 7.89). The results showed that, the polymorphism information content (PCI) of these SSR loci varied from 0.254 to 0.888. The observed heterozygosity (Ho) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (He) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated signi cantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p< 0.05). These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate populations and other closely related species.

Development and characterization of microsatellite markers for Chaeturichthys stigmatias (Actinopterygii: Gobiiformes: Gobiidae) based on restriction site-associated DNA sequencing (RAD-seq)

“…Given its codominance, high reproducibility, rich polymorphism, wide distribution, high stability, and easy detection (Dou et al 2015;Song et al 2016;Parthiban et al 2018;), microsatellite markers have been used in a wide range of applications in population genetics, genetic breeding, evolutionary studies, identification of relations and individual identification (Lu et al 2005;Hayes et al 2007;Queirós et al 2015), which can provide data reference and research guidance for them. In addition, microsatellite markers are greatly effective tools in population genetic studies because they could reveal the distinct population segments even in fine-scale genetic structure studies (Gandomkar et al 2021). Therefore, it is essential to use microsatellite markers more conveniently and efficiently.…”

“…In fact, high-throughput sequencing for developing SSR does not require sequencing depth as high as genome assembly and annotation, so the cost of this method is relatively low. Recently, high-throughput sequencing has been used to develop microsatellite markers in many fish, such as Ctenopharyngodon idella (Valenciennes, 1844) (see Yu et al 2014), Coilia nasus Temminck et Schlegel, 1846 (see Fang et al 2015), Colossoma macropomum (Cuvier, 1816) (see Ariede et al 2018), Genypterus chilensis (Guichenot, 1848) (see González et al 2019), and Capoeta aculeata (Valenciennes, 1844) (see Gandomkar et al 2021).…”

“…Restriction site-associated DNA sequencing (RADseq) is a powerful tool to characterize the microsatellite and single nucleotide polymorphism (SNP) markers, which was based on the second-generation sequencing technology (Khoshkholgh and Nazari 2020;Gandomkar et al 2021). The reads generated by RAD-seq are grouped according to the enzyme recognition sequence, which could improve the precision and accuracy of contigs assembly, and improve the success rate of developing polymorphic microsatellite markers (Wei et al 2014).…”