Development of polymorphic microsatellites for Sillago sihama based on next-generation sequencing and transferability to Sillago japonica.

Sillago sihama (Forsskål, 1775), a commercially important marine fishery species in the Indo-West Pacific, is being developed as a target species for aquaculture and stock enhancement in China. However, due to the limitations of traditional isolation methods, the available microsatellite loci, or simple sequence repeats (SSRs), of S. sihama lack diversity. We used a stepwise approach including Illumina sequencing, primer screening, and SSR marker validation to develop diverse SSRs for S. sihama. A total of 853.48 Mb clean sequences were assembled with high coverage and sequencing depth, and 27,288 potential SSRs were identified. A set of 18 novel SSR markers with four type motifs including 11 di-, 1 tri-, 5 tetra-, and 1 hexanucleotide repeats were successfully isolated. The ranges of number of alleles per locus and observed and expected heterozygosities were 5-24, 0.226-0.968, and 0.319-0.950, respectively. The diversity parameters exhibited high levels of polymorphism in these 18 loci. Three loci with the presence of both null alleles and inbreeding showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni correction. Moreover, 13 loci developed in S. sihama showed high transferability to the closely related species Sillago japonica. The polymorphic SSR markers developed in this study may serve as valuable tools for further basic and applied research on the genetic resources of S. sihama as well as S. japonica. Our results indicate that this approach, based on next-generation sequencing technology, is convenient, cost-effective, and suitable for SSR marker isolation in other sillaginid fishes.