Development of simple sequence repeat markers and genetic diversity of Sipunculus nudus in the Beibu Gulf of China

Background The marine species Sipunculus nudus , valued for its medicinal and commercial significance, faces critical research gaps due to a lack of molecular markers (notably simple sequence repeats (SSRs)) and insufficient genetic diversity data, hindering genetic studies and evidence-based breeding initiatives. Methods The software of Misa and Primer3 were adopted to detect SSRs and develop primer pairs, and then some primers of highly polymorphic loci in the genome were used to reveal the genetic diversity of S. nudus along the Beibu Gulf in China. Results From the genome, 277,264 SSRs were detected an d 198,902 primers were designed. Ninety-five of the synthesized 100 primers could amplify across samples, with 93 showing polymorphism. Thirty highly polymorphic primers were chosen to disclose the genetic diversity of 219 materials from Beibu Gulf, China. We detected 370 alleles with high genetic diversity: observed heterozygosity ( Ho ) = 0.905, expected heterozygosity ( He ) = 0.833, Shannon’s index ( I ) = 2.042, and polymorphism information content ( PIC ) = 0.811. The study also revealed varying levels of genetic differentiation and gene flow among different provenances. Structure analysis partitioned all samples into seven distinct genetic clusters. Conclusions We identified 277,264 SSRs in S. nudus and developed primers for 198,902 SSRs. Subsequently, 100 primers were validated for assessing genetic diversity and population differentiation. These will establish a critical foundation for advancing germplasm conservation and targeted breeding strategies in this species.