Development of Microsatellite DNA Markers Based on RAD-seq Data of Charybdis feriata
Charybdis feriata is an important marine aquatic species for conservation of germplasm resources in China,with a high economic value and a high genetic breeding value.Developing microsatellite DNA markers is helpful for studying the population ecology and germplasm resources of this species.In this study,the sim-plified genome information of C.feriata was obtained by restriction site-associated DNA sequencing(RAD-seq),and the microsatellite-related information was analyzed to develop microsatellite DNA markers.The re-sults showed that a total of 2 419 242 Simple Sequence Repeat(SSR)loci were identified,among which the di-nucleotide and mono-nucleotide motifs were the most,each accounting for 43.95％and 28.71％of the total loci.Hexanucleotide repeat motifs were the most diverse,amounting to 287 types;followed by pentanucleoti-de repeat motifs(275 types).The number of repeats varied among different types of motifs in SSR loci.A to-tal of 21 330 pairs of microsatellite primers for C.feriata were designed by primer3 v2.3.6,and 192 pairs of primers with high polymorphism were selected to be verified in 12 samples of C.feriata.The results showed that 14 pairs of primers had a single band and good polymorphism,and the number of alleles of each primer ranged from 4 to 14.The expected heterozygosity(He)and observed heterozygosity(Ho)were 0.503-0.892 and 0.167-1.000,respectively,and the Polymorphic Information Content(PIC)was 0.456-0.882.This study showcases that this method is feasible in screening SSR markers for C.feriata,and the obtained primers can be applied in the research of the genetic diversity and population genetics of C.feriata.
Charybdis feriataRADseqmicrosatellitedevelopment of primersgenetic diversity
万方数据
维普
