Soon-Jae Kwon

Assessment of genetic diversity and population structure in mungbean

This study was carried out to assess the genetic diversity and to analyze the population genetic structure for a total of 692 mungbean accessions preserved at National Agrobiodiversity Center (NAC) of the Rural Development Administration (RDA), Korea. Mungbean accessions were collected from 27 countries in nine different geographic regions, and were genotyped using 15 microsatellite markers, which were developed in our previous study. A total of 66 alleles were detected among 692 accessions at all the loci with an average of 4.4 alleles per locus. All the microsatellite loci were found to be polymorphic. The expected heterozygosity (HE) and polymorphism information content (PIC) ranged from 0.081 to 0.588 (mean = 0.345) and from 0.080 to 0.544 (mean = 0.295), respectively. Of the 66 alleles, 17 (25.8%) were common (frequency range between 0.05 and 0.5), 15 (22.7%) were abundant (frequency range > 0.5), and 34 (51.5%) were rare (frequency range < 0.05). Locus GB-VR-7 provided the highest number of rare alleles(eight), followed by GB-VR-91(six) and GB-VR-113(four). Country-wide comparative study on genetic diversity showed that accessions from the USA possessed the highest genetic diversity (PIC) followed by Nepal, Iran, and Afghanistan. And region-wide showed that accessions from Europe possessed the highest average genetic diversity, followed by accessions from the USA, South Asia, West Asia, and Oceania. Twenty-seven countries were grouped into seven clades by phylogenetic relationship analysis, but clustering pattern did not strictly follow their geographical origin because of extensive germplasm exchange between/among countries and regions. As a result of a model-based analysis (STRUCTURE) of microsatellite data, two distinct genetic groups were identified which shared more than 75% membership with one of the two genetic groups. However the genetic group pattern did not reflect their geographical origin. The Duncan’s Multiple Range Test among these two genetic groups and an admixed group, with a mean of 16 phenotypic traits, showed significant difference in 12 quantitative and qualitative traits on the basis of ANOVA. These 15 newly developed SSR markers proved to be useful as DNA markers to detect genetic variation in mungbean germplasm for reasonable management and crossbreeding purposes.

Genetic diversity and relationship among faba bean ( Vicia faba L.) germplasm entries as revealed by TRAP markers

Target region amplification polymorphism markers were used to assess the genetic diversity and relationship among 151 worldwide collected faba bean (Vicia faba L.) entries (137 accessions maintained at the USDA‐ARS, Pullman, WA, 2 commercial varieties and 12 elite cultivars and advanced breeding lines obtained from Link of Georg-August University, Germany). Twelve primer combinations (six sets of polymerase chain reaction) amplified a total of 221 markers, of which 122 (55.2%) were polymorphic and could discriminate all the 151 entries. A high level of polymorphism was revealed among the accessions with an estimated average pairwise similarity of 63.2%, ranging from 36.9 to 90.2%. Cluster analysis divided the 151 accessions into five major groups with 2‐101 entries each and revealed a substantial association between the molecular diversity and the geographic origin. All 101 accessions in Group V are originated from China and 13 of the 15 accessions in Group II were from Afghanistan. Thirty-two individual plants were sampled from two entries to assess the intra-accession variation. It was found that the advanced inbred line (Hiverna/5-EP1) had very little variation (5.0%), while the original collection (PI 577746) possessed a very high amount of variation (47.1%). This is consistent with the previous reports that faba bean landraces have a high level of outcrossing in production fields and thus contain larger amount variation within each landrace. One implication of this observation for germplasm management is that a relatively larger population is needed in regeneration to mitigate the possible loss of genetic variation due to genetic drift.

Development of expressed sequence tag derived-simple sequence repeats in the genus Lilium

Although lily is the second largest flower crop in cutting flower commodity, only six simple sequence repeats SSRs have been reported. Thus, we developed expressed sequence tag derived-SSRs (EST-SSRs) for the Lilium genus. Among 2,235 unique ESTs, 754 ESTs contained SSR motifs, among which 165 ESTs were amenable to primer design. Among these 165 EST-SSRs, 131 EST-SSRs showed amplification in at least one Lilium species, and 76 EST-SSRs showed amplification in at least nine species. Of the 76 EST-SSRs, 47 showed amplification in all Lilium species analyzed. Using 10 breeding lines, we selected 21 EST-SSRs that had the highest number of alleles and polymorphism information content. The polymorphism information content values of these selected EST-SSRs ranged from 0.49 to 0.94 with an average of 0.76, which are higher than other plant species. The phylogenetic dendrogram derived from the amplification profiles of the 21 high polymorphic EST-SSRs was congruent with the genetic background of the 84 selected lily accessions and hybrids, which are available in commerce. Thus, the developed EST-SSRs will be very useful in germplasm management, genetic diversity analysis, cultivar finger printing, and molecular breeding in the lily.

LSGermOPA, a custom OPA of 384 EST-derived SNPs for high-throughput lettuce ( Lactuca sativa L.) germplasm fingerprinting

To deploy a high-throughput genotyping platform in germplasm management, we designed and tested a custom OPA (Oligo Pool All), LSGermOPA, for assessing the genetic diversity and population structure of the USDA cultivated lettuce (Lactuca sativa L.) germplasm collection using Illumina’s GoldenGate assay. This OPA contains 384 EST (expressed sequence tag)-derived SNP (single nucleotide polymorphism) markers selected from a large set of SNP markers experimentally validated and mapped by the Compositae Genome Project. Used for genotyping were DNA samples prepared from bulked leaves of five randomly-selected seedlings from each of 380 lettuce accessions. High-quality genotype data were obtained from 354 of the 384 SNPs. The reproducibility of automatic genotype calls was 99.8% as calculated from the four pairs of duplicated DNA samples in the assay. An unexpectedly high percentage of heterozygous genotypes at the polymorphic loci for most accessions indicated a high level of heterogeneity within accessions. Only 148 homogenous accessions, collectively comprising all five horticultural types, were used in subsequent analyses to demonstrate the usefulness of LSGermOPA. The results of phylogenetic relationship, population structure and genetic differentiation analyses were consistent with previous reports using other marker systems. This suggests that LSGermOPA is capable of revealing sufficient levels of polymorphism among lettuce cultivars and is appropriate for rapid assessment of genetic diversity and population structure in the lettuce germplasm collection. Challenges and strategies for effective genotyping and managing lettuce germplasm are discussed.

Intron loss mediated structural dynamics and functional differentiation of the polygalacturonase gene family in land plants

The polygalacturonase (PG) gene family is one of the largest gene families in plants. PGs are involved in various plant development steps. The evolutionary processes accounting for the functional divergence and the specialized functions of PGs in land plants are unclear. Whole sets of PG genes were retrieved from the genome web sites of model organisms in algae and land plants. The number of PG genes was expanded by lineage-specific manner with the biological complexity of the organism. Differentiation of PGs was related with phylogenetic hierarchy such as presence of rhamno-PGs from algae to plants, endo- and exo-PGs in land plants, exo-PGs in flowering plants. Gene structure analysis revealed that land plant PG genes resulted from differential intron gain and loss, with the latter event predominating. Differential intron losses partitioned the PGs into separate clades to be expressed differentially during plant development. Intron position and phase were not conserved between PGs of algae and land plants but conserved among PG genes of land plants from moss to vascular plants, indicating that the current introns in the PGs in land plants appeared after the split between unicellular algae and multicelluar land plants. The results demonstrate that the functional divergence and differentiation of PGs in land plants is attributable to intron losses.

Fruit Quality and Chemical Contents of Hybrid Boysenberry ( Rubus ursinus ) Lines Developed by Hybridization and Gamma Irradiation

The Rubus fruit is an economically important berry crop that contains various functional compounds. The objective of this study was to analyze fruit qualities (i.e., pH, soluble solids content, titratable acidity, and mineral content) as well as fatty acid and phenolic compounds (i.e., ellagic acid and anthocyanins) among hybrid boysenberry lines developed by hybridization and gamma irradiation. There were no significant differences in the hybrid boysenberry fruit pH and titratable acidity (%) among the tested genotypes. However, the soluble solids content was higher in the BSA119 and BSA144 mutants than in the original genotype (BS_Hybrid). Meanwhile, linoleic acid was the most abundant fatty acid in the analyzed hybrid boysenberry fruits. The fatty acid composition did not differ significantly among the genotypes. The ellagic acid content of all genotypes ranged from 8.72 mg/100 g to 46.10 mg/100 g, with the highest concentration observed for the BSB127 genotype. Additionally, cyanidin-3-O-sophoroside (M-H, 611 m/z) and cyanidin-3-O-glucoside (M-H, 449 m/z) were the two major anthocyanins detected in the boysenberry and mutant genotypes, while cyanidin-3-O-glucoside was the predominant blackberry anthocyanin. The total anthocyanin concentrations of four mutant genotypes (i.e., BSA036, BSA078, BSA101, and BSB127) were significantly higher than that of the original genotype (382.0 mg/100 g). The highest total anthocyanin concentration was observed for the BSA078 genotype (467.9 mg/100 g). These results may be useful for identifying the optimal genotypes for breeding new cultivars with enhanced qualities and potential health benefits.

Phytochemicals and antioxidant activity in the kenaf plant ( Hibiscus cannabinus L.)

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Chemical compounds from four different tissues of the kenaf plant (Hibiscus cannabinus), a valuable medicinal crop originating from Africa, were examined to determine its potential for use as a new drug material. Leaves, bark, flowers, and seeds were harvested to identify phytochemical compounds and measure antioxidant activities. Gas chromatography mass spectrometry analyses identified 22 different phytocompounds in hexane extracts of the different parts of the kenaf plant. The most abundant volatile compounds were E-phytol (32.4%), linolenic acid (47.3%), trisiloxane-1,1,1,5,5,5-hexamethyl3,3-bis[(trimethylsilyl)oxy] (16.4%), and linoleic acid (46.4%) in leaves, bark, flowers, and seeds, respectively. Ultra-high performance liquid chromatography identified the major compounds in the different parts of the kenaf plant as kaemperitrin, caffeic acid, myricetin glycoside, and p-hydroxybenzoic acid in leaves, bark, flowers, and seeds, respectively. Water extracts of flowers, leaves, and seeds exhibited the greatest DPPH radical scavenging activity and SOD activity. Our analyses suggest that water is the optimal solvent, as it extracted the greatest quantity of functional compounds with the highest levels of antioxidant activity. These results provide valuable information for the development of environmentally friendly natural products for the pharmaceutical industry.

Construction of mutation populations by gamma-ray and carbon beam irradiation in chili pepper ( Capsicum annuum L.)

Mutagenesis using ionizing radiation has been widely used for the development of genetic and breeding resources with novel characteristics. Although mutation breeding using X- and gamma-rays has been attempted in peppers, information on the effectiveness of other ionizing radiation and a comparative analysis of mutagenic effects of different forms of radiation is limited. Therefore, we investigated and compared the biological effectiveness and mutagenesis efficiency of gamma-rays and a carbon beam (a heavy ion beam) in a chili pepper landrace of Korea, ‘Yuwol-cho’. The survival and shoot growth rate obtained by irradiation at serial doses showed that the LD50 was about 140 and 35 Gy, and the RD50 was about 80 and 32 Gy for gamma rays and carbon beams, respectively. The optimal doses for mutation breeding for these forms of radiation were estimated to be 80-100 and 15-20 Gy for gamma rays and carbon beams, respectively. We also developed M2 populations consisting of 1,836 lines by gamma-ray irradiation (100 Gy) and 154 lines by carbon beam irradiation (20 Gy). The frequency of dwarf or male sterile individuals showed that the mutagenic effect of the carbon beam was higher than that of gamma-rays. We identified individuals in each population with various developmental mutations through phenotypic analysis and categorized the mutations into four groups (mutations in plant architecture and development, leaf, flower, or fruits). This study provides basic information for mutation breeding using ionizing radiation and useful materials for the identification of genes related to the diverse characteristics in chili pepper.

Morphological characteristics, chemical and genetic diversity of kenaf ( Hibiscus cannabinus L.) genotypes

The kenaf plant is used widely as food and in traditional folk medicine. This study evaluated the morphological characteristics, functional compounds, and genetic diversity of 32 kenaf cultivars from a worldwide collection. We found significant differences in the functional compounds of leaves from all cultivars, including differences in levels of chlorogenic acid isomer (CAI), chlorogenic acid (CA), kaempferol glucosyl rhamnoside isomer (KGRI), kaempferol rhamnosyl xyloside (KRX), kaemperitrin (KAPT) and total phenols (TPC). The highest TPC, KAPT, CA, and KRX contents were observed in the C22 cultivars. A significant correlation was observed between flowering time and DM yield, seed yield, and four phenolic compounds (KGRI, KRX, CAI, and TPC) (P < 0.01). To assess genetic diversity, we used 80 simple sequence repeats (SSR) primer sets and identified 225 polymorphic loci in the kenaf cultivars. The polymorphism information content and genetic diversity values ranged from 0.11 to 0.79 and 12 to 0.83, with average values of 0.39 and 0.43, respectively. The cluster analysis of the SSR markers showed that the kenaf genotypes could be clearly divided into three clusters based on flowering time. Correlations analysis was conducted for the 80 SSR markers; morphological, chemical and growth traits were found for 15 marker traits (corolla, vein, petal, leaf, stem color, leaf shape, and KGRI content) with significant marker-trait correlations. These results could be used for the selection of kenaf cultivars with improved yield and functional compounds.

Molecular dissection of the response of the rice Systemic Acquired Resistance Deficient 1 (SARD1) gene to different types of ionizing radiation

Abstract Purpose: Exposure to ionizing radiation induces plant defenses by regulating the expression of response genes. The systemic acquired resistance deficient 1 (SARD1) is a key gene in plant defense response. In this study, the function of Oryza sativa SARD1 (OsSARD1) was investigated after exposure of seeds/plants to ionizing radiation, jasmonic acid (JA) or salicylic acid (SA). Materials and methods: Rice seeds exposed to two types of ionizing radiations (gamma ray [GR] and ion beam [IB]) were analyzed by quantitative reverse transcription PCR (qRT-PCR) to identify the genes that are altered in response to ionizing radiation. Then, OsSARD1-overexpressing homozygous Arabidopsis plants were generated to assess the effects of OsSARD1 in the response to irradiation. The phenotypes of these transgenic plants, as well as control plants, were monitored after GR irradiation at doses of 200 and 300 Gray (Gy). Results: The OsSARD1 transcript was strongly downregulated after exposure to GR and IB irradiation. Previous phylogenetic analysis showed that the Arabidopsis SARD1 (AtSARD1) protein is closely related to Arabidopsis calmodulin-binding protein 60g (AtCBP60g), which is known to be required for activation of SA biosynthesis. In this study, phylogenetic analysis showed that OsSARD1 was grouped with AtSARD1. The OsSARD1 gene was induced after exposure to SA and JA. The biological phenotype of OsSARD1-overexpressing Arabidopsis plants was examined. OsSARD1-overexpressing plants displayed resistance to GR; in comparison with wild-type plants, the height and weight of OsSARD1-overexpressing plants were significantly greater after GR irradiation. In addition, OsSARD1 protein was abundantly accumulated in the nucleus. Conclusions: The results indicate that OsSARD1 plays an important role in the regulation of the defense responses to GR and IB irradiation and exhibits phytohormone induced expression.