Abstract:The objective of this study was to identify microsatellites from the transcriptome sequences of Coilia ectenes using MISA software. These microsatellites could create very useful resources in the evaluation of germplasm resource and marker-assisted breeding of C. ectenes. The results showed that a total of 33,896 microsatellites were identified with repeating units, at lengths of 1~6 bases, from 71,869 unigenes. Different types of repeat SSRs had considerably different distribution characteristics. The majority of the microsatellite loci consisted of mono-, di-, and tri-nucleotide motifs (34.94%, 49.47%, and 13.34%, respectively). Dinucleotide microsatellite repeating units were the most abundant in the C. ectenes transcriptome, and the AC/GT repeating units were the most ascendant repeating unit (75.25%). The dominant repeating units for the mononucleotide and trinucleotide motifs were A/T (86.25%) and AGG/CCT (28.57%), respectively. Different nucleotide repeat motifs had different repetitions that had a reducing trend, with the increase in the number of nucleotides in repeat motifs. Among the 100 designed primer pairs, 16 pairs proved to be polymorphic microsatellite markers. In the present study, 16 polymorphic microsatellite loci were characterized to evaluate the genetic diversity of the selected C. ectenes (F3). The results showed that the average number of effective alleles (Ne), the average observed heterozygosity (Ho), the average expected heterozygosity (He), and the average Shannon´s information index (I) of the selected C.ectenes (F3) were 1.7580, 0.3414, 0.3977, and 0.6278, respectively. These results indicate that it is feasible to develop microsatellite markers based on the C. ectenes transcriptome and polymorphic microsatellite loci obtained in this study will facilitate further studies on the population genetic management and conservation of C. ectenes.
