Objective This study aimed to develop SSR molecular markers for Platostoma palustre and analyze the genetic diversity of its germplasm resources, so as to provide theoretical support for the conservation of P. palustre germplasm resources and the breeding of elite varieties. Methods Based on the whole-genome sequence of P. palustre, the distribution characteristics of simple sequence repeats (SSRs) were mined and analyzed, and polymorphic SSR primers were developed to provide a theoretical basis for the evaluation of genetic diversity and analysis of population structure in P. palustre. Results A total of 122,699 SSR loci were identified in the P. palustre genome, with a genomic SSR density of 96.91 loci/Mb and a locus occurrence frequency of 10.32 kb/SSR. Dinucleotide repeat motifs were the dominant type, accounting for 68.3% of all repeat motifs. After polymorphism screening, 15 pairs of SSR primers with good polymorphism were obtained. Their polymorphism information content (PIC) ranged from 0.197 to 0.736, with an average value of 0.425. Genetic diversity analysis of 40 P. palustre germplasms showed that the number of alleles at the 15 SSR loci was higher than the number of effective alleles, and the alleles were unevenly distributed. There were differences in heterozygosity among different loci; the average observed heterozygosity was higher than the average expected heterozygosity with a certain gap between them, indicating that the tested population deviated from the Hardy-Weinberg equilibrium (HWE), with genetic variation and favorable overall genetic diversity, and the genotype frequencies of some loci in the population changed. Fixation index (F) analysis showed that F > 0 at 3 loci and F < 0 at 12 loci, indicating that the number of heterozygous individuals was higher than that of homozygous individuals in the population. The Shannon’s information index (I) ranged from 0.449 (TDF191) to 1.628 (TDF166), with an average of 0.887. A phylogenetic tree of the 40 P. palustre germplasms was constructed using Phylip software based on the UPGMA method, which divided the germplasms into two subgroups. A “0/1” DNA fingerprint was successfully constructed by digital assignment coding. Conclusion The abundant SSR loci information obtained in this study can provide important theoretical and technical support for the development of whole-genome SSR markers, molecular marker-assisted breeding, and genetic diversity research of P. palustre.

Platostoma palustre (Blume) A. J. Paton  /  SSR  /  germplasm resources  /  genetic diversity  /  DNA fingerprinting