Analysis on Microsatellite Loci of Daphnia similoides sinensis and Rapid Development of Primer Based on Transcriptome Sequencing

In this study, we performed transcriptome sequencing of D. similoides sinensis and developing of simple sequence repeats (SSRs) markers to identify valuable markers for Daphnia molecular genetics. The total length of D. similoides sinensis transcriptome sequence was 40093546 bp, which contained 12017 SSR markers and 21344 microsatellite loci. 2164 SSR primer pairs were obtained through design for 21344 sequences which contained the loci of SSRs. 60 primer pairs were randomly selected, 11 SSR primer pairs with polymorphism were obtained by polyacrylamide gel electrophoresis and capillary electrophoresis. Atotal of 88 alleles of SSRs were amplified, of which 52 belonged to polymorphic loci (the percentage of polymorphic loci was 59%). The polymorphism information content of the 11-pairs SSR primers ranged from 0.4 to 0.75, with an average of 0.58, indicating that these primers had rich polymorphism. The results suggested that the 11 primers pairs might provide important values in revealing the genetic diversity and phyletic evolution of D. similoides sinensis.