EST-SSR development and genetic diversity in the medicinal plant Pseudostellaria heterophylla (Miq.) Pax

Pseudostellaria heterophylla is a perennial herb plant with high medicinal value. Germplasm development and improvement play a crucial role in the modern pseudostellaria industry. In present study, we genotyped 10 representative cultivars and 102 F1 hybrid individuals with developed markers in China, aiming at (1) screening a set of markers for correctly identifying P. heterophylla cultivars and F1 hybrid individuals, and (2) confirming the genetic diversity and parent-offspring (PO) relationships among them. The results showed that 360 EST-SSR markers were developed using transcriptome library. Based on genotyping data of 10 representative cultivars, 20 of them showed high fingerprinting power and genetic diversity with mean observed heterozygosity (Ho), Shannon's Information Index (I), PI and PIsibs value of 0.330, 0.560, 0.505 and 0.704, respectively. A combination of 20 markers could further reduce the value. of PI and PIsibs to 3.2 × 10−7 and 6.7 × 10−4, respectively. Furtherly, above 20 EST-SSR were recommended as a set marker for analyzing the genetic diversity and parentage of 102 F1 hybrid individuals. The results showed that the markers are highly polymorphic among the F1 individuals with an average Shannon's Information Index of 0.642. It was possible to discriminate 100 test samples by a combination of twenty markers, and the overall possibility of finding two random individuals having the same genotypes across the 20 loci was estimated to be 2.0 × 10−8. Meanwhile, parentage analysis based on the genotyping data confirmed 63 pairs of putative PO relationships, whereas the other 13 were identified as pseudo-hybrids relationships. Overall, this study will provide 20 credible EST-SSR marker and 102 hybrid materials for further germplasm conservation, genetic improvement, genetic mapping and functional gene location. •The new 102 progeny germplasm resources of Pseudostellaria heterophylla were cultivated.•The EST-SSR markers of P. heterophylla were developed for the first time.•Twenty novel EST-SSR markers were powerful tools for both genetic and parentage analysis in P. heterophylla.•The genetic relationship of 10 representative cultivars and 102 F1 hybrid individuals were observed in our study.