Conservation Genetics of the Asian Giant Soft-Shelled Turtle (Pelochelys cantorii) with Novel Microsatellite Multiplexes

SIMPLE SUMMARY: Pelochelys cantorii is critically endangered and rarely seen in the wild, and only 13 adults are being kept in captivity in China. For the purpose of reinforcing the conservation and management of P. cantorii, the Pearl River Fisheries Research Institute (Chinese Fishery Academy of Sciences) successfully bred more than 800 turtles from 2015 to 2020. In this study, we developed and characterized 10 simple sequence repeat markers from the RNA transcriptome of P. cantorii, established two multiplex PCR systems, and obtained the genetic structure and genetic diversity of the artificially conserved population. The aim was to obtain viable second-generation P. cantorii with the highest genetic diversity to implement population recovery plans for this species. ABSTRACT: To understand the genetic structure of the protected turtle species Pelochelys cantorii we used transcriptome data to design more than 30,000 tri- and tetranucleotide repeat microsatellite primer pairs, of which 230 pairs were used for laboratory experiments. After two screenings, only 10 microsatellite markers with good specificity, high amplification efficiency, and polymorphisms were obtained. Using the selected primers, two multiplex PCR systems were established to compare and analyze the genetic diversity of artificially assisted breeding generations from four parents (two females and two males) continuously bred over two years. A total of 25 alleles were detected among the 10 microsatellite loci of the offspring. The polymorphism information content (PIC) was 0.313–0.674, with an average of 0.401, among which two loci were highly polymorphic (PIC ≥ 0.5). The number of alleles was 2–5 and the number of effective alleles was 1.635–3.614. The observed heterozygosity was 0.341–0.813, with an average of 0.582, whereas the average expected heterozygosity was 0.389–0.725, with an average of 0.493. Moreover, on the basis of Nei’s genetic distance and the Bayesian clustering algorithm, the 182 offspring were divided into two subgroups, and the results corresponded to the two maternal lines. This is the first study to investigate the molecular markers of P. cantorii, and the results obtained can be used to protect genetic resources and provide a genetic basis for the design of population recovery plans.