Jung-Sook Sung

Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method

A genetic evaluation of safflower germplasm collections derived from different geographical regions and countries will provide useful information for sustainable conservation and the utilization of genetic diversity. However, the molecular marker information is limited for evaluation of genetic diversity of safflower germplasm. In this study, we acquired 509 putative genomic SSR markers for sufficient genome coverage using next‐generation sequencing methods and characterized thirty polymorphic SSRs in safflower collection composed of 100 diverse accessions. The average allele number and expected heterozygosity were 2.8 and 0.386, respectively. Analysis of population structure and phylogeny based on thirty SSR profiles revealed genetic admixture between geographical regions contrary to genetic clustering. However, the accessions from Korea were genetically conserved in distinctive groups in contrast to other safflower gene pool. In conclusion, these new genomic SSRs will facilitate valuable studies to clarify genetic relationships as well as conduct population structure analyses, genetic map construction and association analysis for safflower.

Analysis of molecular genetic diversity and population structure in Amaranthus germplasm using SSR markers

We assessed the molecular genetic diversity and population structure of Amaranthus species accessions using 11 simple sequence repeat markers. A total of 122 alleles were detected, and the number of alleles per marker (NA) ranged from 6 to 21 with an average of 11.1 alleles. The frequency of major alleles per locus ranged from 0.148 to 0.695, with an average value of 0.496 per marker. The overall polymorphic information content values were 0.436–0.898, with an average value of 0.657. The observed heterozygosity (HO) and expected heterozygosity (HE) ranged from 0.056 to 0.876 and from 0.480 to 0.907, with average values of 0.287 and 0.698, respectively. The average HO (0.240) was lower than the HE and gene flow (Nm), and showed substantial genetic variability among all populations of amaranth accessions. The sample groupings did not strictly follow the geographic affiliations of the accessions. A similar pattern was obtained using model-based structure analysis without grouping by species type. Knowledge of the genetic diversity and population structure of amaranth can be used to select representative genotypes and manage Amaranthus germplasm breeding programs.

Variation in Antioxidant Activity and Polyphenol Content in Tomato Stems and Leaves

Tomato was considered as one of the most widely cultivated vegetable crops in the world. Tomato plant has high antioxidant capacity which can be attributed to the high levels of carotenoids, phenols, vitamins C and E. However, most of tomato plants have been discarded as waste after fruit harvesting. In order to identify genetic resources with high antioxidant level for use in food or as feed additives, we investigated the ABTS, DPPH antioxidant activity and polyphenol content in tomato leaves and stems. A total of 112 tomato accessions were classified into three groups by latitude of their collected countries: 30°~60° North (50 accessions), 0°~30° North (40 accessions), and 0°~30° South (22 accessions). Stem and leaf extracts showed wide variation in ABTS antioxidant activity ranging from 1.6 ± 1.0 to 48.4 ± 6.1 μg Trolox mg -1 dw. The antioxidant activity of DPPH was in the range of 6.3 ± 0.2 to 40.0 ± 0.3 μg ASC mg -1 dw. Total polyphenol content ranged from 6.1 ± 0.2 to 38.9 ± 0.7 μg GAE mg -1 dw. ABTS, DPPH antioxidant activities and polyphenol content in accessions from 30°~60°N latitude were significantly higher (P<0.05) than those from 0°~30°N latitude. ABTS values showed a significant positive correlation (r = 0.700**) with DPPH activity. IT100506 (KOR) and 702959 (UKR) were recommended as potential sources of natural antioxidants due to their highest antioxidant activity among accessions. This study will provide valuable information for tomato breeders in developing and producing functional food or feed additives resources.

Effects of Temperature, Light and Chemical Reagent on Dormancy Breaking and Seed Germination of Three Species in Apiaceae

The seeds of Apiaceae have been known as having morphophysiological dormancy (MPD). It is a class of seed dormancy in which the embryo is both underdeveloped and physiologically dormant. This study was conducted to investigate the effects of the temperature, light and chemical reagent on dormancy breaking and seed germination of three species in Apiaceae (Peucedanum japonicum Thumb, Angelica tenuissima Nakai, Glehnia littoralis F. Schmidt et Miq.). Seed size of three species ranged from 5.57-9.7 mm in length and 3.7 mm in width. The 1000-seed weight ranged from 0.21 g in A. tenuissima to 17.53 g in G. littoralis. Maximum percent-germinations of P. japonicum, A. tenuissima, and G. littoralis were 62.6%, 43.3%, and 36.4%, respectively. In P. japonicum and A. tenuissima, prechilling (4C for 7 days) were only best effective on breaking dormancy and germination. The GA3 or KNO3 treatments were ineffective for breaking dormancy. The proper temperature for germination was constant 20C. In G. littoralis, gibberellin treatments were effective for germination. The seeds showed relatively good germinations at alternative 15/20C (16/8h) and constant 20C (dark).

Assessing phenolic content and antioxidant potential diversity in Allium plants using multivariate data analysis

The genus Allium includes hundreds of plant species and is regarded as one of the most cultivated vegetables. It is an important source of novel therapeutic compounds known for their beneficial effects on human health; however, there could be differences in content, composition, type, and bioactivity of the phytochemicals found among the Allium plants. The main purpose of this study was to acquire insights on the variation in antioxidant profiles and phenolic content between Allium accessions in different species, as well as between similar species of several varieties. We collected 112 accessions from more than 20 countries, and grew them under similar agronomic conditions. The antioxidant potential was evaluated by using 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS), 1,1-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and reducing power (RP) assays. The total phenolic content (TPC) was studied using the Folin–Ciocalteu method. TPC varied from 3.43 (accession 199897) to 22.19 (accession 273483) µg gallic acid equivalent/mg dry weight (DW) of the aerial organs of Allium. The antioxidant activity of Allium samples ranged from 4.37 (accession 806595) to 57.46 (accession number 711971) µg Trolox equivalent/mg DW; 0.35 (accession 117246) to 9.53 (accession 711971) µg ascorbic acid equivalents/mg DW; 2.92 (accession 199890) to 21.20 (accession 803493) µgAAE/mg DW; and 0.80 (accession 117260) to 31.13 (accession 803527) µgAAE/mg DW using ABTS, DPPH, FRAP, and RP assays, respectively. Accessions 273483 (A. cepa), 283346 (A. cepa ‘cepa’), and 803527 (unknown species) had the highest TPC, FRAP, and RP values among those tested, while the highest ABTS and DPPH radical scavenging activities were recorded in accession 711971 (A. ramosum). Pearson’s coefficient of correlations indicated that variables (TPC, ABTS, DPPH, FRAP, and RP values) correlated significantly each other, with r-values between 0.585 and 0.894. Principal component analysis plots and hierarchical cluster analysis indicated significant variability in antioxidant activity and phenolic content among all the accessions studied, as well as within similar species. Based on our results from principal component and hierarchical cluster analysis, accession 283346 (A. cepa ‘cepa’), K139348 (A. fistulosum), and 711971 (A. ramosum) are potential sources of phenolics and natural antioxidants. The variability in total phenolic and antioxidant activity among the Allium accessions can be used by breeders, food technologists, nutritionist, and researchers for assessing breeding lines for genetic selection and for monitoring levels of these factors during food storage and processing.

Transcriptome Characterization and Single Nucleotide Polymorphism (SNP) Identification in Vicia amurensis Oett. Using Next-Generation Sequencing Technology

Vicia amurensis is a perennial plant found in Northern China, Japan, and Korea that plays an important role in sustainable agricultural practices due to its ability to fix atmospheric nitrogen in a symbiotic association with rhizobia. 454 sequencing technology was used to sequence the V. amurensis transcriptome which yielded 26.41 Mb from 71,197 reads as a result of 24,959 valid singletons. In addition, 1743 contigs, with the largest contig size being 3534, and 26,702 unigenes were detected. The contig distributions in three non-mutually exclusive Gene Ontology classifications and clusters of orthologous gene classes showed that differentially expressed genes were generally overrepresented in general function and prediction alone (176, 14.47%), and posttranslational modifications, protein turnover, chaperones (162, 13.32%). In total, 12,656 single nucleotide polymorphism (SNP) types were detected; these variants contained 10,585 SNPs, 1513 indels and 558 variants involving more than one nucleotide. The 2383 SNP types with high confidence differences were identified. The present study provides invaluable information on the functional genomic resources and future biological research on V. amurensis. The SNPs identified in this study will provide a material basis for future mapping and marker-assisted breeding analyses.