Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (H_O) values, and the expected heterozygosity (H_E) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.

Ginseng (Panax ginseng) renowned as the king of medicinal plants. Ginseng grows slowly under shade conditions, requiring at least 4 years to produce a limited number of seeds. Molecular breeding of ginseng faces challenges due to its the tetraploid genome and the absence of an efficient molecular marker system. To overcome these obstacles, we adopted genotyping-by-sequencing to delve into genetic mapping and survey genetic diversity. We constructed a comprehensive genetic map comprising 24 linkage groups, each corresponding to one of the 24 chromosomes in the ginseng genome, based on 1216 nonredundant SNPs obtained from an F₂ mapping population. Additionally, 431 103 SNPs were identified from 119 diverse ginseng genotypes. From these, 192 informative subgenome-specific single copy SNPs were selected to develop a SNP chip. The SNP chip was used to genotype a large ginseng collection, encompassing registered cultivars, breeding lines, wild-simulated ginseng, and wild ginseng from various countries and regions. We evaluated the utility of the assay for molecular breeding with 919 ginseng genotypes. This breeder-friendly SNP chip promises versatility, enabling purity assessments of seeds and products, the authentication of species and cultivars, and the determination of homozygosity and homogeneity rates for breeding lines. Genotype data for 1200 ginseng genotypes are now stored in our database. This SNP chip lays the foundation for a molecular breeding in ginseng and will facilitate the breeding process in this medicinal crop.