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The leaves of roselle (Hibiscus sabdariffa L.) have been used as a traditional folk medicine that has diuretic and mild laxative effects. Roselle is cultivated in many countries for medicines and food. However, studies on the variation of functional compounds in different accessions are relatively limited. In this study, we investigated the phenolic compound content of leaf extracts from 49 different roselle accessions from a worldwide collection by ultra-high performance liquid chromatography mass spectrometry. The aim was to chemically classify and assess the pharmacological properties of the phenolic compounds in the leaves. The phenolic compounds were identified as neochlorogenic acid, cryptochlorogenic acid, rutin, rutin isomer, isoquercitin, kaempferol-3-O-rutinoside, kaempferol-3-O-glucoside, quercetin, quercetin isomer, and kaempferol. These compounds were present at significantly different levels among the accessions. The most abundant phenolic compound was rutin, which was found in 45 accessions where the total phenolic compound content was 18.75-46.51 mg/g (average 31.52 mg/g). The phenolic compounds were classified into four groups. The two accessions with the highest total phenolic compound content were from Ghana (PI286316) and Senegal (PI275413). The hierarchical cluster analysis of the 49 roselle accessions showed that they formed five groups according to their phenolic compound content. Our results will be useful for the selection of roselle genotypes with improved functional compounds.

Kenaf is a valuable fiber and medicinal crop. Here, we performed RNA-sequencing to obtain comprehensive transcriptome information and identify putative genes involved in biosynthetic pathways of anthocyanins and kaempferitrin in kenaf. A total of 39.6 Gb reads were generated for six kenaf accessions. Individual de novo assembly of each accession and clustering of whole transcriptome contigs finally yielded 299,880 representative transcripts having an average length of 1217 bp, of which 231,825 (77.3%) were annotated against various databases. Expression profiling of the transcripts identified 6,592 differentially expressed genes (DEGs) among the three accessions, C-14 (a local landrace) and two of its mutant varieties, Jeokbong (purple leaves and stems) and Baekma (light green leaves and stems). In addition to their altered coloration, leaves of these two mutants had significantly different anthocyanin and kaempferitrin contents. We constructed anthocyanin and kaempferitrin biosynthetic pathways and identified 671 transcripts mapping to the entire pathway. In addition, 29 DEGs assigned to eight structural genes and 41 DEGs related to three transcription factor families were identified in high anthocyanin- and kaempferitrin-accumulating mutant Jeokbong. Our results provide a large transcriptome library pool for understanding gene functions and should also be useful in further studies of flavonoid biosynthesis in kenaf.

The genus Hibiscus comprises approximately 300 diverse species whose genetic relationships have not been extensively clarified. In this study, we evaluated the cross-species transferability of 102 expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from the transcriptome of kenaf H. cannabinus L. and used them to assess the genetic diversity and inter-relationships of 87 accessions and 7 cultivars of 18 Hibiscus species. Among 102 markers, 100 (98%) were polymorphic in these 94 accessions/cultivars. The rates of cross-species transferability of the EST-SSR markers ranged from 83 H. trionum L. to 99% H. ponticus Rupr., with an average of 89.9%. A total of 871 alleles were detected using the 100 polymorphic EST-SSR markers; the number of alleles ranged from 2 (RBRC_Hc_ES_76) to 16 (RBRC_Hc_ES_80) and averaged 8.71. Polymorphism information content values varied from 0.15 (RBRC_Hc_ES_74) to 0.84 (RBRC_Hc_ES_3, RBRC_Hc_ES_95), with an average of 0.56. Phylogenetic and population structure analyses classified the 94 accessions/cultivars into two and two or three groups, respectively. Overall, our results demonstrate that the EST-SSR markers derived from the kenaf transcriptome were applied successfully to other Hibiscus species to provide useful information on the genetic diversity of this genus.

Background Soybean seeds contain 18-24% lipids, which are made up of 85% polyunsaturated fatty acids. Two of these (linoleic and linolenic acids) comprise essential fatty acids that are not synthesized in humans and animals. Linolenic acid plays a vital role in the maintenance of brain function and is a source of docosahexaenoic acid for retinal and nerve tissue, with its physiological functions being a focus of attention. Results We developed mutant soybean populations via gamma irradiation of Korean cultivars Danbaek and Daepung and evaluated the linolenic acid content of 78 and 154 M9 mutant progenies. We selected the four mutant lines with the highest linolenic acid contents based on 2 years of investigation of fatty acids. The selected mutant lines had linolenic acid contents that were 33.9% to 67.7% higher than those of the original cultivars and exhibited increased fatty acid desaturase (FAD) gene expression levels during seed development. We also identified nucleotide polymorphisms of FAD genes in the four mutant lines. Conclusion The present study found that linolenic acid content is related to significantly increased expression levels of the FAD3C and FAD3D genes in the endoplasmic reticulum, which was uncovered by radiation mutation breeding of soybean. © 2019 Society of Chemical Industry.

Sweet sorghum (Sorghum bicolor L. Moench) is one of the most important crops for bioethanol production and the provision of antioxidant compounds for human health. In this study, we investigated the 8 agronomic traits of 153 sweet sorghum germplasms, which demonstrated a variety of phenotypes. In particular, nine sweet sorghum germplasms exhibited a sugar content exceeding 20 Brix. Based on agronomic characteristics, we selected eight elite sweet sorghum germplasms that showed highperformance agronomic and growth characteristics such as tall height, large panicle size with short height, high sugar content, and seed-specific characteristics. The selected germplasms also showed significant differential amount of 3 antioxidant compounds of 3-deoxyanthocyanins, flavonoids, and tannins. SS113 contained the highest levels of total 3-deoxyanthocyanins with apigeninidin contents 3-9 fold higher than that of other germplasms, while SS129 had a white seed coat with the highest recorded total flavonoid level (7.52 mg/g) but no detectable 3-deoxyanthocyanins compounds. The characterization of the traits and compounds will be useful for basic research into the selection of suitable cultivars in the breeding of sweet sorghum.

Soybean seeds are consumed worldwide owing to their nutritional value and health benefits. In this study we investigated the metabolic properties of 208 soybean mutant diversity pool (MDP) lines by measuring the isoflavone and fatty acid contents of the seed. The total isoflavone content (TIC) ranged from 0.88 mg/g to 7.12 mg/g and averaged 3.08 mg/g. The proportion of oleic acid among total fatty acids (TFA) ranged from 0.38% to 24.66% and averaged 11.02%. Based on the TIC and TFA among the 208 MDP lines, we selected six lines with altered isoflavone content and six lines with altered oleic acid content compared with those of the corresponding wild-types for measuring gene expression. Each of twelve genes from the isoflavone and fatty acid biosynthesis pathways were analyzed at three different seed developmental stages. Isoflavone biosynthetic genes, including CHI1A, IFS1, and IFS2, showed differences in stages and expression patterns among individuals and wild-types, whereas MaT7 showed consistently higher expression levels in three mutants with increased isoflavone content at stage 1. Expression patterns of the 12 fatty acid biosynthetic genes were classifiable into two groups that reflected the developmental stages of the seeds. The results will be useful for functional analysis of the regulatory genes involved in the isoflavone and fatty acid biosynthetic pathways in soybean.

Rapeseed is the most important oil crop used in the food and biodiesel industries. In this study, based on single nucleotide polymorphism (SNP) identified from genotyping-by-sequencing (GBS), and an association study of flowering time, crude fat and fatty acid contents were investigated in 46 rapeseed mutant lines derived from gamma rays. A total of 623,026,394 clean data reads were generated with 6.6 million reads on average. A set of 37,721 filtered SNPs was used to perform gene ontology and phylogenetic analysis. Hierarchical cluster analysis of the rapeseed mutant lines gave eight groups based on flowering time and fatty acid compositions. Gene ontological analysis of the mutant lines showed that many genes displaying SNPs are involved in cellular processes, cellular anatomy, and binding. A total of 40 SNPs were significantly associated with flowering time (1 SNP), crude fat content (2 SNPs), and fatty acid content (37 SNPs). A total of 21 genes were annotated from fatty acid content SNPs, among them, nine genes were significantly enriched in reproductive processes, such as embryonic development, fruit development, and seed development. This study demonstrated that SNPs are efficient tools for mutant screening and it provides a basis that the improving the oil qualities of rapeseed.

L-3,4-dihydroxyphenylalanine (L-dopa)-rich faba (Vicia faba L.) tissues are a potentially useful source for its pharmaceutical purpose, although the species contains health curious vicine and convicine in the seeds. We determined the contents of L-dopa, vicine, and convicine in different tissues of faba plants throughout the entire growth period. The three compounds accumulated in germinating sprouts and showed high contents at 8 days of germination, especially in the epicotyl containing 132.33 mg∙g−1 DW of L-dopa, 19.81 mg∙g−1 DW of vicine, and 10.38 mg∙g−1 DW of convicine, respectively. We compared the contents of the three compounds among leaves of different ages in plants at different growth stages. The samples could be ranked, from highest to lowest content, ranging from 11.11 to 81.82 mg∙g−1 DW, as follows: new leaves &gt, young leaves &gt, old leaves, and vegetative &gt, flowering &gt, ripening. Vicine and convicine were not detected in leaves or flowers. The L-dopa content was high in flowers, especially young flower buds, ranging from 36.51 to 100.70 mg∙g−1 DW. In older flowers, the L-dopa content tended to decrease as the calyx and petal parts developed. In addition, the three compounds showed decreasing contents in pods, stems, and roots with increasing plant age. The results of this study provide information on the timing and extent of L-dopa, vicine, and convicine accumulation in different faba tissues, and indicate that various by-products, especially new/young leaves and flowers, are potential sources of natural L-dopa.

Transposable elements (TEs) are ubiquitous repetitive components of eukaryotic organisms that show mobility in the genome against diverse stresses. TEs contribute considerably to the size, structure, and plasticity of genomes and also play an active role in genome evolution by helping their hosts adapt to novel conditions by conferring useful characteristics. We developed a simple and rapid method for investigation of genetic mobility and diversity among TEs in combination with a target region amplification polymorphism (TE-TRAP) marker system in gamma-irradiated sorghum mutants. The TE-TRAP marker system reveals a high level of genetic diversity, which provides a useful marker resource for genetic mobility research.

Gordonia ajoucoccus strain A2, isolated from crude oil-contaminated soils, synthesizes yellow keto-γ-carotene from various n-alkanes as the sole carbon source. Its complete genome sequence consists of a single circular chromosome (5,090,254 bp, 67.3% G+C content). Seven putative genes were identified supporting the proposed keto-γ-carotene pathway of G. ajoucoccus A2.

DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.

Kenaf is a source of fiber and a bioenergy crop that is considered to be a third world crop. Recently, a new kenaf cultivar, "Jangdae," was developed by gamma irradiation. It exhibited distinguishable characteristics such as higher biomass, higher seed yield, and earlier flowering than the wild type. We sequenced and analyzed the transcriptome of apical leaf and stem using Pacific Biosciences single-molecule long-read isoform sequencing platform. De novo assembly yielded 26,822 full-length transcripts with a total length of 59 Mbp. Sequence similarity against protein sequence allowed the functional annotation of 11,370 unigenes. Among them, 10,100 unigenes were assigned gene ontology terms, the majority of which were associated with the metabolic and cellular process. The Kyoto encyclopedia of genes and genomes (KEGG) analysis mapped 8875 of the annotated unigenes to 149 metabolic pathways. We also identified the majority of putative genes involved in cellulose and lignin-biosynthesis. We further evaluated the expression pattern in eight gene families involved in lignin-biosynthesis at different growth stages. In this study, appropriate biotechnological approaches using the information obtained for these putative genes will help to modify the desirable content traits in mutants. The transcriptome data can be used as a reference dataset and provide a resource for molecular genetic studies in kenaf.

Ionizing radiation combined with in vitro tissue culture has been used for development of new cultivars in diverse crops. The effects of ionizing radiation on mutation induction have been analyzed on several orchid species, including Cymbidium. Limited information is available on the comparison of mutation frequency and spectrum based on phenotypes in Cymbidium species. In addition, the stability of induced chimera mutants in Cymbidium is unknown. In this study, we analyzed the radiation sensitivity, mutation frequency, and spectrum of mutants induced by diverse &gamma, ray treatments, and analyzed the stability of induced chimera mutants in the Cymbidium hybrid cultivars RB003 and RB012. The optimal &gamma, irradiation conditions of each cultivar differed as follows: RB003, mutation frequency of 4.06% (under 35 Gy/4 h), RB012, 1.51% (20 Gy/1 h). Re-irradiation of &gamma, rays broadened the mutation spectrum observed in RB012. The stability of leaf-color chimera mutants was higher than that of leaf-shape chimeras, and stability was dependent on the chimera type and location of a mutation in the cell layers of the shoot apical meristem. These results indicated that short-term &gamma, irradiation was more effective to induce mutations in Cymbidium. Information on the stability of chimera mutants will be useful for mutation breeding of diverse ornamental plants.

Mutation breeding is useful for improving agronomic characteristics of various crops. In this study, we conducted a genetic diversity and association analysis of soybean mutants to assess elite mutant lines. On the basis of phenotypic traits, we chose 208 soybean mutants as a mutant diversity pool (MDP). We then investigated the genetic diversity and inter-relationships of these MDP lines using target region amplification polymorphism (TRAP) markers. Among the different TRAP primer combinations, polymorphism levels and polymorphism information content (PIC) values averaged 59.71% and 0.15, respectively. Dendrogram and population structure analyses divided the MDP lines into four major groups. According to an analysis of molecular variance (AMOVA), the percentage of inter-population variation among mutants was 11.320 (20.6%), whereas mutant intra-population variation ranged from 0.231 (0.4%) to 14.324 (26.1%). Overall, intra-population genetic similarity was higher than that of inter-populations. In an analysis of the association between TRAP markers and agronomic traits using three different statistical approaches based on the single factor analysis (SFA), the Q general linear model (GLM), and the mixed linear model (Q+K MLM), we detected six significant marker&ndash, trait associations involving five phenotypic traits. Our results suggest that the MDP has great potential for soybean genetic resources and that TRAP markers are useful for the selection of soybean mutants for soybean mutation breeding.

Wheat grain is recognized as a rich source of nutrients, including proteins, vitamins, minerals, fibers and antioxidants. In recent years, the focus of wheat breeding has been to increase the content of bioactive compounds to improve human health and prevent diseases. RESULTS Five novel wheat mutant lines with variable seed color were developed using gamma irradiation of hexaploid wheat inbred line K4191 (purple seed color). The total anthocyanin contents of three mutant lines (L47, L167 and L925) were significantly higher than those of wild-type lines, including K4191 and ?Keumkang? (white seed color). L925 showed the highest total anthocyanin content, and cyanidin-3-glucoside was presented as the most predominant anthocyanin. Compared with ?Keumkang?, the expression of anthocyanin biosynthesis genes was significantly up-regulated in purple seed mutant lines. The highest antioxidant activity was observed in L925 extracts. The expression of a few antioxidant-related genes and total anthocyanin content were positively correlated with antioxidant capacity. These data suggest that anthocyanins and phenolic compounds in wheat grains contribute to the antioxidant potential. CONCLUSION Purple grain color is associated with higher anthocyanin accumulation and antioxidant capacity in wheat. Wheat mutants developed in this study may serve as a valuable source of antioxidants. ? 2018 Society of Chemical Industry

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.

Vibrio parahaemolyticus and V. vulnificus are the most common pathogens causing seafood-borne illnesses in Korea. This study determines the abundance and antimicrobial resistance of pathogenic Vibrio species in seawater and zooplankton samples from the Geoje Island coast in Korea, which is an important area for coastal fisheries, the fishing industry, and tourism. The two Vibrio species were detected more in mesozooplankton samples than in seawater samples. V. parahaemolyticus isolates showed greater resistance than those of V. vulnificus for antimicrobials. Of V. parahaemolyticus isolates, 93.3% exhibited resistance to three or more antimicrobial agents. Conversely, more than 80% of V. vulnificus isolates showed susceptibility to all antimicrobials examined, with the exception of rifampicin. Our findings show that strong antimicrobial resistance of V. parahaemolyticus in the surveyed area was exposed to conventionally used antibiotics, therefore necessitating proper surveillance programs for the monitoring of antimicrobial resistance patterns in seawater bodies and aquatic animals.

The faba bean, one of the few crops that produces L-3,4-dihydroxy-phenylalanine (L-dopa) naturally, is also a good source of fatty acids and isoflavones. This study analyzed fatty acids, L-dopa and isoflavones in the leaves, immature pods and seeds of selected high-yielding faba bean genotypes spring-sown in Korea. The most abundant fatty acids in the leaves, immature pods and seeds were linolenic acid (58.6-63.7%), linoleic acid (46.9-58.9%), and linoleic acid (45.7-63.6%), respectively. The L-dopa content was highest in the leaf for all the faba bean genotypes except PI430715 and PI614810 where it was highest in the immature pods. The α-linolenic acid and L-dopa contents of the seed and immature pod of the PI430715 and PI614810 genotypes were the highest of all the genotypes. Four isoflavones (daidzin, genistin, daidzein and genistein) were detected with levels of daidzin and genistin generally higher than those of daidzein and genistein in each part of the faba bean. The L-dopa content was correlated (P ≤ 0.05) with those of five fatty acids (oleic, gondoic, phytanic, α-linolenic, and behenic acid). Overall, the PI430715 and PI614810 faba bean genotypes with their higher L-dopa and α-linolenic acid contents were the most functional. This study may help identify optimal genotypes for breeding new cultivars which provide functional compounds to treat Parkinson’s disease or use in foods.

Kenaf is a multipurpose crop, but a lack of genetic information hinders genetic and molecular research. In this study, we aimed to develop EST-SSR markers from mutant and wild-type cultivars, and to assess the genetic diversity of the kenaf resources. A total of 33 Gb of sequence data comprising 130,480 unigenes was assembled by de novo RNA-sequencing of six kenaf cultivars, and 5619 SSRs were identified. Tri-nucleotide motifs occurred most frequently (82.67%) followed by di-, tetra-, and penta-motifs. In total, 515 polymorphic EST-SSRs were derived by pairwise comparisons of the cultivars based on in silico analyses. Of these, 70 markers were successfully validated among six cultivars. We used the six cultivars, together with 39 kenaf accessions from worldwide to assess genetic diversity and to characterize the EST-SSRs. The number of alleles per locus ranged from 2 to 8. PIC and genetic diversity values ranged from 0.08 to 0.79 and 0.08–0.82, respectively. The phylogenetic and population structure showed that the 45 accessions could be clearly divided into three groups based on different days to flowering (DTF). Genetic differentiation among the DTF groups showed a proportionally high level of variance. Association analysis between the DTF and the markers revealed three significant associations. Furthermore, using a multiplex PCR with three markers, DTF could be perfectly discriminated. These markers will be useful in marker-assisted selection after further validation with segregating populations of kenaf.

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).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).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.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.

Salinity stress affects plants by reducing the water potential and causing ion imbalance or disturbances in ion homeostasis and toxicity. Salinity stress frequently causes both osmotic and ionic stress in plants, resulting in the increase or decrease of certain secondary metabolites in plants. In this study, the effect of NaCl treatment on the nutritional quality of tartary buckwheat plants was studied by conducting an HPLC analysis of phenylpropanoid and anthocyanin content. It was observed that there was no significant change of color in tartary buckwheat during salt treatment. The accumulation of most phenylpropanoid compounds increased slightly in response to the NaCl concentration. The total phenylpropanoid content in tartary buckwheat was the highest at 100 mM NaCl treatment. Seven-day-old wheat plantlets treated with 100 mM NaCl for 2, 4, 6, and 8 days showed the highest accumulation of total phenylpropanoids at day 8 after treatment, while the content of most phenylpropanoids was higher than that in the control during this period. Although the development of tartary buckwheat slightly decreased with NaCl treatment and the accumulation of anthocyanin compounds did not change in plants with a diffident NaCl concentration and time treatment, the results suggest that the salinity treatment of tartary buckwheat causes antioxidant activity improvement by inducing an accumulation of flavonoid and phenolic compounds. However, since the anthocyanin content did not increase, the antioxidant effect of the treatment is not expected to be significant.

Microorganism selection is critical to deglycosylation in soybean fermentation for producing beneficial phytochemicals. This study investigated isoflavone bioconversion in soybean extract inoculated with Lactobacillus plantarum K2-12 and Lactobacillus curvatus JD0-31 exhibiting different enzyme activities. L. plantarum showed higher esterase (C4), esterase (C8), β-galactosidase, α-glucosidase, β-glucosidase, and N-acetyl-β-glucosaminase activities. We found that isoflavone bioconversion was distinguished into isoflavone backbone structure types. Malonyl- and acetyl- types of isoflavones except for malonyl daidzin were not significantly differed their contents between lactobacilli. Deglycosylating severity was observed in malonyl genistin in both lactobacilli, resulting mass production of genistein. On the other hand, daidzein glycosides were dependable to lactobacilli, in which L. plantarum efficiently degraded malonyl daidzin and daidzin in fast time. Glycitein was most degradable among the three aglycones by fermentation. These results suggest that efficient control of isoflavone deglycosylation by Lactobacillus species should be controlled to the inoculation period and select target isoflavones.

The development of soybean with high antioxidant activities for use in the food and cosmetics industries is a target of breeding programs. In soybean, antioxidants are associated with seed color, although the metabolic basis for seed coloration remains incompletely understood. We selected six γ-ray-induced mutant lines that exhibited black, partially black, brown, partially brown, or yellowish-white pigmentation in the seed coat. Antioxidant activity and contents of anthocyanins, flavan-3-ols, and isoflavones were evaluated in the seed coat and cotyledons. The lines with black or brown seeds showed the highest antioxidant activities. The cotyledons showed no significant differences in seed coat components or antioxidant activities among lines. Black and brown seed coat components showed the highest antioxidant activities. The black seed coat contained five anthocyanins, whereas seed coats of brown- and yellow-seeded lines entirely lacked anthocyanins. Both black and brown seeds were rich in flavan-3-ols, including catechin and epicatechin, which were the predominant antioxidant contributors in brown seeds. Isoflavone contents showed weaker correlations with antioxidant activity than anthocyanins and flavan-3-ols. These results demonstrated that antioxidant activities were determined by anthocyanins in black seeds and flavan-3-ols in brown and black seeds, whereas relatively low antioxidant activities in yellow seeds reflected their high isoflavone contents.

Transposable elements (TEs)—major components of eukaryotic genomes—have the ability to change location within a genome. Because of their mobility, TEs are important for genome diversification and evolution. Here, a simple rapid method, using the consensus terminal inverted repeat sequences of PONG, miniature inverted-repeat transposable element (MITE)-Tourist (M-t) and MITE-Stowaway (M-s) as target region amplification polymorphism (TE-TRAP) markers, was employed to investigate the mobility of TEs in a gamma-irradiated soybean mutant pool. Among the different TE-TRAP primer combinations, the average polymorphism level and polymorphism information content value were 57.98% and 0.14, respectively. Only the PONG sequence separated the mutant population into three major groups. The inter-mutant population variance, determined using the PONG marker (3.151 and 29%) was greater than that of the M-t (2.209 and 20%) and M-s (2.766 and 18%) markers, whereas the reverse was true for the intra-mutant population variations, with M-t and M-s values, being 15.151 (82%) and 8.895 (80%), respectively, compared with the PONG marker (7.646 and 71%). Thus, the MITE markers revealed more dynamic and active mobility levels than the PONG marker in gamma-ray irradiated soybean mutant lines. The TE-TRAP technique associated with sensitive MITEs is useful for investigating genetic diversity and TE mobilization, providing tools for mutant selection in soybean mutation breeding.

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.

Blackberries (Rubus fruticosus L.) are a good source of antioxidants and contain appreciable levels of functional compounds. This study was carried out to evaluate fruit qualities (pH, soluble solids content, titratable acidity, and minerals), functional compounds (total phenolic content, total flavonoid content, anthocyanins, and ellagic acid), and antioxidant activity among five mutated blackberry lines over three ripening stages to examine the effect of fruit maturation on functional compounds and antioxidant activity. The content of sugars, total phenolic content, total flavonoid content, and anthocyanins (cyanidin-3-O-glucoside, cyanidin-3-O-xyloside, cyanidin-3-O-malonylglucoside, and cyanidin-3-O-dioxalylglucoside) increased as fruit development advanced, whereas the ellagic acid content decreased as the fruit became more mature. Among the minerals tested, potassium showed the highest concentrations at all stages of development. The antioxidant activity was correlated with total phenolic content (P≤0.01), total flavonoid content (P≤0.01), and total anthocyanins (P≤0.05). The results indicate that Maple and B201 lines contained the highest anthocyanin content and exhibited greater antioxidant activity.

The chemical composition of the different plant parts of green ( Hibiscus cannabinus L. cv. Jangdae) and purple ( H. cannabinus L. cv. Jeokbong) kenaf cultivars were investigated using high-performance liquid chromatography. Ten carotenoid and phenolic compounds were quantified in the different parts of green and purple kenaf. The accumulation of carotenoids and phenolic compounds in the different parts of both cultivars was slightly different. The total carotenoid content in all parts of purple kenaf was higher than that in green kenaf. In particular, lutein, β-carotene, and 9Z-β-carotene were found in all the plant parts of both purple and green kenaf. Most levels of these 3 carotenoids were higher in all parts of the purple cultivar than those found in the green cultivar. According to the detected phenolic compound content, the leaves of the green cultivar contained a higher level of total phenolics, even though the most levels of the individual phenolic compounds were higher in the purple cultivar due to the level of kaempferitrin, a major compound found in kenaf, being much higher than the levels observed for the other phenolic compounds. However, the flowers and stems of the purple cultivar had a higher level of total phenolics. Among the 10 different phenolic compounds, 7 (4-hydroxybenzoic acid, chlorogenic acid, p-coumaric acid, ferulic acid, benzoic acid, rutin, and kaempferol) were present in all the plant parts of both kenaf cultivars. Purple kenaf leaves contain higher levels of 4-hydroxybenzoic acid, chlorogenic acid, and rutin, whereas the purple cultivar flowers have higher levels of p-coumaric acid, ferulic acid, and benzoic acid. This study provides valuable information on the chemical composition of different plant parts of green and purple kenaf cultivars.

Hibiscus species are rich in phenolic compounds and have been traditionally used for improving human health through their bioactive activities. The present study investigated the phenolic compounds of leaf extracts from 18 different H. acetosella accessions and evaluated their biofunctional properties, focusing on antioxidant and antibacterial activity. The most abundant phenolic compound in H. acetosella was caffeic acid, with levels ranging from 14.95 to 42.93 mg/100 g. The antioxidant activity measured by the ABTS assay allowed the accessions to be classified into two groups: a high activity group with red leaf varieties (74.71&ndash, 84.02%) and a relatively low activity group with green leaf varieties (57.47&ndash, 65.94%). The antioxidant activity was significantly correlated with TAC (0.933), Dp3-Sam (0.932), Dp3-Glu (0.924), and Cy3-Sam (0.913) contents (p &lt, 0.001). The H. acetosella phenolic extracts exhibited antibacterial activity against two bacteria, with zones of inhibition between 12.00 and 13.67 mm (Staphylococcus aureus), and 10.67 and 13.33 mm (Pseudomonas aeruginosa). All accessions exhibited a basal antibacterial activity level (12 mm) against the Gram-positive S. aureus, with PI500758 and PI500764 exhibiting increased antibacterial activity (13.67 mm), but they exhibited a more dynamic antibacterial activity level against the Gram-negative P. aeruginosa.

The unicellular green alga Chlamydomonas reinhardtti is a promising source of bioenergy and understanding its carbon metabolism is important. In this organism, carbon accumulation can be manipulated with nitrogen supply. Chlamydomonas reinhardtii is a mixotroph that can act as an autotroph or heterotroph, depending on conditions. Fructose-1,6-bisphosphate aldolases (FBAs) are important enzymes in energy pathways of algae; they convert fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Expression of both CrFBA1 and CrFBA2 was less under nitrogen-deplete conditions than under nitrogen-replete conditions in Chlamydomonas cells. To explore CrFBA1 function, CrFBA1-overexpressing Chlamydomonas lines were generated. Compared to wild-type, transformed cells grew more slowly in photoautotrophic conditions, but at the same rate in mixotrophic condition. We suggest that overexpression of CrFBA1 affected photosynthetic carbon fixation in the Calvin-Benson cycle. The CrFBA1-overexpressing lines had less starch than the wild-type under mixotrophic, low-nitrogen conditions, but more fatty acids. In the transgenic cells, expression of granule bound starch synthase 1 (GBSS1) determined by quantitative reverse transcription-polymerase chain reaction was down-regulated, but acetyl-CoA synthetases (ACS1 and ACS2) and phosphoglucomutase (PGM) were up-regulated compared to wild-type. We propose three possible explanations for the observed low starch and high fatty acid content of the transgenic cells. Firstly, abnormal carbon flux by CrFBA1 overexpression leads to GBSS1 down-regulation in a feed-forward regulation, which resulted in the low starch accumulation. Secondly, increase of exogenous acetate assimilation by ACS1 and ACS2 up-regulation results in high accumulation of total fatty acid in transformants, perhaps due to compensation for reduced-carbon fixation. Lastly, activation of glycolytic pathway by CrFBA1 overexpression enhances conversion of starch to fatty acid. We conclude that overexpression of CrFBA1 deregulates carbon metabolism in Chlamydomonas reinhardtii.

The effect of salinity (NaCl treatment) on the nutritive value of wheat sprouts was investigated by analyzing the expression of phenylpropanoid biosynthetic pathway genes and the levels of phenylpropanoid compounds. Treatment with various concentrations of NaCl (50, 100, and 200 mM) resulted in increased epicatechin levels but decreased accumulation of catechin hydrate, benzoic acid, and quercetin compounds in the sprouts compared with the control (0 mM). The trans-cinnamic acid, 4-hydroxybenzoic acid, ferulic acid, epicatechin, and total phenylpropanoid level in wheat sprout was the highest at 50 mM of NaCl treatment. Six-day-old wheat plantlets exposed to 50 mM NaCl for 6, 12, 24, 48, and 72 h, showed that the total phenylpropanoids accumulation was the highest at 48 h after the treatment and most of the treatments showed higher phenylpropanoid content than the control at the same time points. Although the shoot and root length and the fresh weight of wheat sprouts decreased with NaCl treatment, these results suggest that treatment of 50 mM NaCl improves the nutritional quality of wheat sprouts, due to increased phenylpropanoid concentrations.

Ginsenosides are the principal active components of ginseng and are considered attractive candidates for combination cancer therapy because they can kill tumors and have favorable safety profiles. However, the overall benefit of ginsenosides remains unclear, particularly in cancer immunosurveillance, considering the controversial results showing repression or promotion of immune responses. Here we identify a potentiating role of ginsenoside F1 (G-F1) in cancer surveillance by natural killer (NK) cells. Among 15 different ginsenosides, G-F1 most potently enhanced NK cell cytotoxicity in response to diverse activating receptors and cancer cells. G-F1 also improved cancer surveillance in mouse models of lymphoma clearance and metastatic melanoma that rely on NK cell activity. G-F1-treated NK cells exhibited elevated cytotoxic potential such as upregulation of cytotoxic mediators and of activation signals upon stimulation. NK cell potentiation by G-F1 was antagonized by insulin-like growth factor (IGF)-1 blockade and recapitulated by IGF-1 treatment, suggesting the involvement of IGF-1. Thus, our results suggest that G-F1 enhances NK cell function and may have chemotherapeutic potential in NK cell-based immunotherapy. We anticipate our results to be a starting point for further comprehensive studies of ginsenosides in the immune cells mediating cancer surveillance and the development of putative therapeutics.

Phenylpropanoids and flavonoids belong to a large group of secondary metabolites, and are considered to have antioxidant activity, which protects the cells against biotic and abiotic stresses. However, the accumulation of phenylpropanoids and flavonoids in bitter melon has rarely been studied. Here, we identify ten putative phenylpropanoid and flavonoid biosynthetic genes in bitter melon. Most genes were highly expressed in leaves and/or flowers. HPLC analysis showed that rutin and epicatechin were the most abundant compounds in bitter melon. Rutin content was the highest in leaves, whereas epicatechin was highly accumulated in flowers and fruits. The accumulation patterns of trans-cinnamic acid, p-coumaric acid, ferulic acid, kaempferol, and rutin coincide with the expression patterns of McPAL, McC4H, McCOMT, McFLS, and Mc3GT, respectively, suggesting that these genes play important roles in phenylpropanoid and flavonoid biosynthesis in bitter melon. In addition, we also investigated the optimum light conditions for enhancing phenylpropanoid and flavonoid biosynthesis and found that blue light was the most effective wavelength for enhanced accumulation of phenylpropanoids and flavonoids in bitter melon.

Rice blast disease, caused by Magnaporthe oryzae, results in an extensive loss of rice productivity. Previously, we identified a novel M. oryzae secreted protein, termed MSP1 which causes cell death and pathogen-associated molecular pattern (PAMP)-triggered immune (PTI) responses in rice. Here, we report the transcriptome profile of MSP1-induced response in rice, which led to the identification of 21,619 genes, among which 4,386 showed significant changes (P < 0.05 and fold change > 2 or < 1/2) in response to exogenous MSP1 treatment. Functional annotation of differentially regulated genes showed that the suppressed genes were deeply associated with photosynthesis, secondary metabolism, lipid synthesis, and protein synthesis, while the induced genes were involved in lipid degradation, protein degradation, and signaling. Moreover, expression of genes encoding receptor-like kinases, MAPKs, WRKYs, hormone signaling proteins and pathogenesis-related (PR) proteins were also induced by MSP1. Mapping these differentially expressed genes onto various pathways revealed critical information about the MSP1-triggered responses, providing new insights into the molecular mechanism and components of MSP1-triggered PTI responses in rice.

Kenaf (Hibiscus cannabinus L.) is an annual herbaceous crop and the third largest fiber crop of economic importance, after cotton and jute. In view of recent global environmental challenges, multipurpose uses of kenaf have been developed, such as animal feed, bio-plastics, bio-fuels, and phytoremediation. We cloned genes related to monolignol biosynthesis using a reverse transcriptase PCR (RT-PCR) strategy. ‘Auxu’ cultivars in the seedling phase were used as the experimental source material. The 4-coumarate:CoAligase (4CL), cinnamoyl-CoA reductase (CCR), ferulate 5-hydroxylase (F5H), caffeic acid O-methyltransferase (COMT), cinnamyl alcohol dehydrogenase (CAD), encoding hydroxycinnamoyl transferase (HCT), ρ-coumarate 3-hydroxylase (C3H) and caffeoyl-CoA-O-methyltransferase (CCoAOMT), cDNAs had open reading frames of 1623, 1017, 1179, 921, 1107, 1323, 1527 and 744 bp, encoding polypeptides of 540, 338, 392, 306, 368, 441, 508 and 247 amino acid residues, respectively. We submitted the five gene sequences (4CL, CCR, F5H, COMT, and CAD) to the GenBank database. A phylogenetic tree showed that lignin biosynthesis genes had the closest relationships with Gossypium and Theobroma cacao. Expression levels of the genes 4CL, HCT, C3H, CCoAOMT, CCR, F5H, COMT, and CAD in stems from plants harvested at four different growth stages were evaluated. Expression levels of 4CL, HCT, C3H, CCoAOMT, CCR, F5H, COMT, and CAD were gradually increased during the vegetative growth of kenaf stem. Similarly with the gene expression, lignin amounts were also increased during the stem growth. Thus, these six genes may be directly involved in lignin biosynthesis. These results will be useful basic data for molecular breeding to enhance bio-mass production.

The phytohormone abscisic acid (ABA) enables plants to adapt to adverse environmental conditions through the modulation of metabolic pathways and of growth and developmental programs. We used comparative microarray analysis to identify genes exhibiting ABA-dependent expression and other hormone-dependent expression among them in Oryza sativa shoot and root. We identified 854 genes as significantly up- or down-regulated in root or shoot under ABA treatment condition. Most of these genes had similar expression profiles in root and shoot under ABA treatment condition, whereas 86 genes displayed opposite expression responses in root and shoot. To examine the crosstalk between ABA and other hormones, we compared the expression profiles of the ABA-dependently regulated genes under several different hormone treatment conditions. Interestingly, around half of the ABA-dependently expressed genes were also regulated by jasmonic acid based on microarray data analysis. We searched the promoter regions of these genes for cis-elements that could be responsible for their responsiveness to both hormones, and found that ABRE and MYC2 elements, among others, were common to the promoters of genes that were regulated by both ABA and JA. These results show that ABA and JA might have common gene expression regulation system and might explain why the JA could function for both abiotic and biotic stress tolerance.

Carotenoids, found in the fruit and different organs of bitter melon (Momordica charantia), have attracted great attention for their potential health benefits in treating several major chronic diseases. Therefore, study related to the identification and quantification of the medically important carotenoid metabolites is highly important for the treatment of various disorderes. The present study involved in the identification and quantification of the various carotenoids present in the different organs of M. charantia and the identification of the genes responsible for the accumulation of the carotenoids with respect to the transcriptome levels were investigated. In this study, using the transcriptome database of bitter melon, a partial-length cDNA clone encoding geranylgeranyl pyrophosphate synthase (McGGPPS2), and several full-length cDNA clones encoding geranylgeranyl pyrophosphate synthase (McGGPPS1), zeta-carotene desaturase (McZDS), lycopene beta-cyclase (McLCYB), lycopene epsilon cyclases (McLCYE1 and McLCYE2), beta-carotene hydroxylase (McCHXB), and zeaxanthin epoxidase (McZEP) were identified in bitter melon. The expression levels of the mRNAs encoding these eight putative biosynthetic enzymes, as well as the accumulation of lycopene, α-carotene, lutein, 13Z-β-carotene, E-β-carotene, 9Z-β-carotene, β-cryptoxanthin, zeaxanthin, antheraxanthin, and violaxanthin were investigated in different organs from M. charantia as well as in the four different stages of its fruit maturation. Transcripts were found to be constitutively expressed at high levels in the leaves where carotenoids were also found at the highest levels. Collectively, these results indicate that the putative McGGPPS2, McZDS, McLCYB, McLCYE1, McLCYE2, and McCHXB enzymes might be key factors in controlling carotenoid content in bitter melon. In conclusion, the over expression of the carotenoid biosynthetic genes from M. charantia crops to increase the yield of these medically important carotenoids.

Background Mesenchymal stem cells (MSCs) have broad-spectrum therapeutic effects in various diseases, and thus have many clinical applications. However, it is difficult to produce sufficient numbers of MSCs for clinical use, and improved culture systems are required. Here, we report the effects of calcium (Ca2+) and hypoxia on the proliferation of human umbilical cord blood-derived MSCs (hUCB-MSCs). In addition, we determined the optimal conditions of these two factors for the large-scale culture of hUCB-MSCs. Methods hUCB-MSCs were maintained under hypoxic conditions (3% O2) with 1.8 mM Ca2+ during long-term culture, and their proliferation was evaluated. To characterize the underlying mechanisms, the effects on hypoxia-inducible factor (HIF)-1α and the extracellular signal-regulated kinase (ERK) signaling pathways were investigated. The therapeutic effects in a mouse emphysema model were analyzed and compared with those of naive MSCs. Results The proliferation of Ca2+/hypoxia-treated hUCB-MSCs was increased compared with that observed using either calcium or hypoxia culture alone, without loss of stem cell marker expression or differentiation ability. The enhancement of the proliferation capacity of hUCB-MSCs by the synergistic effects of Ca2+ and hypoxia was dependent on the expression of HIF-1α and the ERK signaling pathway. The proliferation of Ca2+/hypoxia-treated hUCB-MSCs resulted in a delayed senescence phenotype and increased the expression levels of stemness genes such as Oct4 and Nanog compared to those observed in conventional culture conditions. In addition, Ca2+/hypoxia-treated MSCs transplantation in the mouse emphysema model showed the same therapeutic effects as observed with naive MSCs. Conclusions These findings suggest that a Ca2+/hypoxia-based expansion system has applications for the large-scale production of MSCs for therapeutic purposes. Electronic supplementary material The online version of this article (doi:10.1186/s40169-017-0168-z) contains supplementary material, which is available to authorized users.

Mevalonate (MVA) is a key compound of living organisms including bacteria, plants, and humans. MVA and mevalonolactone (MVL), a lactonized form of MVA, are important for pharmaceutical, cosmeceutical, and biotechnological applications. Although (R, S)-MVA with 50% enantiomeric purity is mainly produced by chemical synthesis, recently, microbial fermentation processes for MVA production have been considered as an alternative to the chemical synthesis because of high enantiomeric purity [(R)-MVA] and high titer. In the present study, bio-MVA produced by a fermentative process was decolorized by a charcoal-based method and then chemically transformed into bio-MVL without byproducts by means of phosphoric acid as an acid catalyst. The final bio-MVL was (R)-MVL with over 99% enantiomeric purity according to 1H NMR analysis.

Background Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Results Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. Conclusion This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2734-y) contains supplementary material, which is available to authorized users.

NF-κB is a key transcription factor that dictates the outcome of diverse immune responses. How NF-κB is regulated by multiple activating receptors that are engaged during natural killer (NK)-target cell contact remains undefined. Here we show that sole engagement of NKG2D, 2B4 or DNAM-1 is insufficient for NF-κB activation. Rather, cooperation between these receptors is required at the level of Vav1 for synergistic NF-κB activation. Vav1-dependent synergistic signalling requires a separate PI3K-Akt signal, primarily mediated by NKG2D or DNAM-1, for optimal p65 phosphorylation and NF-κB activation. Vav1 controls downstream p65 phosphorylation and NF-κB activation. Synergistic signalling is defective in X-linked lymphoproliferative disease (XLP1) NK cells entailing 2B4 dysfunction and required for p65 phosphorylation by PI3K-Akt signal, suggesting stepwise signalling checkpoint for NF-κB activation. Thus, our study provides a framework explaining how signals from different activating receptors are coordinated to determine specificity and magnitude of NF-κB activation and NK cell responses., NK cell activation requires multiple signals. Here the authors show that while NKG2D, 2B4, or DNAM-1 receptor activation is insufficient to induce cytokine production, these signals synergize by Vav-1-mediated NF-κB multiphosphorylation, and this signaling checkpoint is defective in X-linked lymphoproliferative disease.

This study evaluated the chemical and genetic diversity of high-seed-yield sorghum germplasms from Korea, the United States, and South Africa. We identified significant differences in the chemical contents of whole plants at the heading stage in all cultivars, including differences in crude protein, fat, fiber, ash, neutral detergent fiber, acid detergent fiber, mineral, and fatty acid contents. Our results suggest that Banwoldang is the most appropriate cultivar for roughage because of its high protein yield. We identified significant differences in the tannin, flavonoid, amylose, mineral, crude fat, fatty acid, and 3-deoxyanthocyanin contents in the whole grain from all cultivars, but not in the mineral or crude fat contents. Tannin levels were generally low. IS645 contained the highest levels of flavonoids and linolenic acid compounds, and Moktak had the highest amylose and deoxyanthocyanidin content in the grain. To assess genetic diversity, we used 10 simple sequence repeat (SSR) primer sets to identify 38 alleles with 3-8 alleles per locus. Based on phylogenetic analysis of the SSR markers, the sorghum cultivars were divided into three major groups. Comparison of clusters based on chemical compositions with those based on SSRs showed that the groups formed by the three native Korean cultivars clustered similarly in molecular dendrograms. Association analysis was conducted for the 10 SSR marker; 48 chemical and growth traits were present for two marker traits (seed color and whole plant fatty acid content) with significant marker-trait associations. These markers could be used to select sorghum cultivars for breeding programs.

Under certain circumstances, transposable elements (TE) can create or reverse mutations and alter the genome size of a cell. Sorghum (Sorghum bicolor L.) is promising for plant transposon tagging due to its small genome size and its low content of repetitive DNA. We developed a marker system based on targeted region amplification polymorphisms (TE-TRAP) that uses the terminal inverted repeats (TIRs) of transposons. A total of 3816 class 2 transposons belonging to the PIF/Harbinger family were identified from the whole sorghum genome that produced five primers, including eight types of TIRs. To define the applicability and utilization of TE-TRAP, we used 21 individuals that had been bred after ɤ-ray irradiation. In total, 31 TE-TRAP, 16 TD, and 21 AFLP primer combinations generated 1133, 223, and 555 amplicons, respectively. The percent polymorphic marker was 62.8, 51.1, and 59.3% for the TE-TRAP, TD, and AFLP markers, respectively. Phylogenetic and principal component analyses revealed that TE-TRAP divided the 21 individuals into three groups. Analysis of molecular variance suggested that TE-TRAP had a higher level of genetic diversity than the other two marker systems. After verifying the efficiency of TE-TRAP, 189 sorghum individuals were used to investigate the associations between the markers and the ɤ-ray doses. Two significant associations were found among the polymorphic markers. This TE-based method provides a useful marker resource for mutation breeding research.