Black soybean (Glycine max L.) has been used as a traditional medicine because its seed coat contains various natural phenolic compounds such as anthocyanins. The objective of this study was to reveal the genetic variation in the agricultural traits, phytochemicals, and antioxidant activity of 172 Korean black soybean landraces (KBSLs) and establish a relationship among them. The evaluation of three agricultural traits (days to 50% flowering, maturity, and 100-seed weight), six phytochemicals (delphinidin-3-glucoside, cyaniding-3-glucoside, petunidin-3-glucoside, daidzin, glycitin, and genestin), and four antioxidant activities (2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid)(ABTS), ferric-reducing antioxidant power (FRAP), and the total polyphenol content (TPC) of 172 KBSLs were analyzed in 2012 and 2015. The agricultural traits, phytochemicals, and antioxidant activities of the 172 KBSLs showed wide variation among the accessions and years. In correlation analysis, the agricultural traits and phytochemicals showed positive and negative correlations with phytochemicals and antioxidant activity, respectively. The principal component analyses result indicated that phytochemicals accounted for most of the variability in the KBSLs. In clustering analysis, the 172 KBSLs were classified into four clusters. These results could lead to expanding the knowledge of the agricultural traits, phytochemicals, and antioxidant activity of the KBSLs, which are valuable materials for the development of new soybean varieties.

Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 species-specific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.

Recently, within the Fabaceae family, the Vicia genus has been recognized for its vital role in sustainable agriculture. Vicia species are economically important grain and forage crops. However, the presence of complex morphological characteristics makes identification and recognition of native species difficult. In this study, the possibility of using DNA barcoding regions (ITS2, matK, and rbcL) to distinguish among 19 Vicia taxa (59 accessions) found in South Korea was evaluated. The sequence alignment analysis revealed considerable nucleotide diversity (π) between the loci, in which ITS2 showed the highest mean interspecific distance, whereas there was no intraspecific variability among the barcode regions in 12 of the 19 taxa. Phylogenetic analysis of combined barcoding regions revealed well-resolved phylogeny with the highest species level discrimination. Combinations of barcode loci were also used in classification at the subgenera and section levels. The results revealed that the combined barcoding regions can be used effectively to differentiate the following species: Vicia angustifolia var. segetilis, Vicia bungei, Vicia villosa, Vicia cracca, Vicia dasycarpa, Vicia hirsuta, Vicia tetrasperma, Vicia amurensis, Vicia hirticalycina, and Vicia chosenensis. However, it is difficult to differentiate the species of Vicia unijuga, Vicia unijuga var. kaussanensis, Vicia linearifolia, Vicia unijuga f. angustifolia, Vicia nipponica, Vicia amoena, Vicia venosa var. cuspidata, Vicia pseudo-orobus, and Vicia japonica with the tested barcode regions. These species come under sect. Vicilla and are found to be closely related or species that have recently undergone speciation; thus, it has limitation to distinguish with recommended barcodes. Hence, to differentiate the unclassified species, 39 morphological characteristics were investigated, in which 16 useful characteristics were selected for efficient classification. Finally, the 16 selected morphological useful traits efficiently differentiated all the Vicia species. In conclusion, a combination of barcoding loci together with morphological characteristics of this study efficiently discriminated all the Korean Vicia species.

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes.

Perilla seed oil has been attracting attention in South Korea as a health food. Five fatty acids of 100 Perilla accessions were identified as follows: palmitic acid (PA) (5.10–9.13%), stearic acid (SA) (1.70–3.99%), oleic acid (OA) (11.1–21.9%), linoleic acid (LA) (10.2–23.4%), and linolenic acid (LNA) (54.3–75.4%). Additionally, the 100 Perilla accessions were divided into two groups (high or low) based on the total fatty acid content (TFAC). By using an association analysis of 40 simple sequence repeat (SSR) markers and the six Perilla seed oil traits in the 100 Perilla accessions, we detected four SSR markers associated with TFAC, five SSR markers associated with LNA, one SSR marker associated with LA, two SSR markers each associated with OA and PA, and four SSR markers associated with SA. Among these SSR markers, four SSR markers (KNUPF14, KNUPF62, KNUPF72, KNUPF85) were all associated with TFAC and LNA. Moreover, two SSR markers (KNUPF62, KNUPF85) were both associated with TFAC, LNA, and OA. Therefore, these SSR markers are considered to be useful molecular markers for selecting useful accessions related to fatty acid contents in Perilla germplasm and for improving the seed oil quality of Perilla crop through marker-assisted selection (MAS) breeding programs.

Sweet potato (Ipomoea batatas L. Lam) is an important food crop widely cultivated in the world. In this study, nine chloroplast simple sequence repeat (cpSSR) markers were used to analyze the genetic diversity and relationships of 558 sweet potato accessions in the germplasm collection of the National Agrobiodiversity Center (NAC). Eight of the nine cpSSR showed polymorphisms, while Ibcp31 did not. The number of alleles per locus ranged from two to four. In general, the Shannon index for each cpSSR ranged from 0.280 to 1.123 and the diversity indices and unbiased diversity ranged from 0.148 to 0.626, and 0.210 to 0.627, respectively. Results of the median-joining network showed 33 chlorotypes in 558 sweet potato accessions. In factor analysis, 558 sweet potato accessions were divided into four clusters, with clusters I and II composed only of the sweet potato accessions from Korea, Japan, Taiwan, and the USA. The results of this study confirmed that the genetic diversity of the female parents of sweet potato accessions conserved at the NAC is low and therefore more sweet potato accessions need to be collected. These results will help to establish an efficient management plan for sweet potato genetic germplasms at the NAC.