Development of simple sequence repeat markers and genetic diversity of Lutraria sieboldii along the northern Beibu Gulf

Abstract

Abstract Background Lutraria sieboldii is an economically important shellfish in the Beibu Gulf of China. However, genetic diversity has not been systematically reported, and the number of simple sequence repeat (SSR) markers is still limited. These issues seriously hinder germplasm utilization and genetic study.Methods and results SSR markers were identified and developed in the transcriptome, and then the genetic diversity was revealed along the northern Beibu Gulf. We identified a total of 438 SSR loci and designed 329 primers. Of them, 100 SSRs were synthesized and used to reveal genetic diversity. We detected Na of 19.583 with the range from 10 to 36, Ne of 9.139 with the range from 4.075 to 20.629, PIC of 0.861 with the range from 0.723 to 0.949, Ho of 0.516 with the range from 0.000 to 0.964 and He of 0.873 with the range from 0.755 to 0.952 in the population of 117 individuals; the genetic distances between populations ranged from 0.186 to 0.276; Fst ranged from 0.126 to 0.198, and Nm ranged from 1.014 to 1.737; the genetic structure was detected and the population was divided into five groups.Conclusion A total of 438 SSR loci were identified in the transcriptome, and 100 SSR primers of the 329 designed primers were synthesized. The genetic diversity and structure of L. sieboldii along the northern Beibu Gulf were revealed by 36 highly polymorphic SSR markers. These findings will provide useful tools and a solid foundation for the exploration and effective utilization of genetic resources in L. sieboldii.