Development and Validation of SNP and InDel Markers for Pod-Shattering Tolerance in Soybean.

Pod-shattering causes a significant yield loss in many soybean cultivars. Shattering-tolerant cultivars provide the most effective approach to minimizing this loss. We developed molecular markers for pod-shattering and validated them in soybeans with diverse genetic backgrounds. The genes Glyma.16g141200, Glyma.16g141500, and Glyma.16g076600, identified in our previous study by quantitative trait locus (QTL) mapping and whole-genome resequencing, were selected for marker development. The whole-genome resequencing of three parental lines (one shattering-tolerant and two shattering-susceptible) identified single nucleotide polymorphism (SNP) and/or insertion/deletion (InDel) regions within or near the selected genes. Two SNPs and one InDel were converted to Kompetitive Allele-Specific PCR (KASP) and InDel markers, respectively. The accuracy of the markers was examined in the two recombinant inbred line populations used for the QTL mapping, as well as the 120 varieties and elite lines, through allelic discrimination and phenotyping by the oven-drying method. Both types of markers successfully discriminated the pod shattering-tolerant and shattering-susceptible genotypes. The prediction accuracy, which was as high as 90.9% for the RILs and was 100% for the varieties and elite lines, also supported the accuracy and usefulness of these markers. Thus, the markers can be used effectively for genetic and genomic studies and the marker-assisted selection for pod-shattering tolerance in soybean.

Protein, Amino Acid, Oil, Fatty Acid, Sugar, Anthocyanin, Isoflavone, Lutein, and Antioxidant Variations in Colored Seed-Coated Soybeans.

Different physiological and genetic studies show that the variations in the accumulation of pigment-stimulating metabolites result in color differences in soybean seed coats. The objective of this study was to analyze the nutrient contents and antioxidant potential in black, brown, and green seed-coated soybeans. Significant variations in protein (38.9-43.3%), oil (13.9-20.4%), total sugar (63.5-97.0 mg/g seed), total anthocyanin (3826.0-21,856.0 µg/g seed coat), total isoflavone (709.5-3394.3 µg/g seed), lutein (1.9-14.8 µg/g), total polyphenol (123.0-385.8 mg gallic acid/100 g seed), total flavonoid (22.1-208.5 mg catechin/100 g seed), 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid (ABTS; 275.0-818.8 mg Trolox/100 g seed), and 2,2-diphenyl-1-picrylhydrazyl (DPPH; 96.3-579.7 mg Trolox/100 g seed) were found among the soybean genotypes. Ilpumgeomjeong2 contained the lowest protein but the highest oil and total sugar. The lowest oil-containing Wonheug had the highest protein content. Socheong2 was rich in all four variables of antioxidants. Anthocyanins were detected only in black soybeans but not in brown and green soybeans. The variation in isoflavone content was up to 5-fold among the soybean genotypes. This study could be a valuable resource for the selection and improvement of soybean because an understanding of the nutrient content and antioxidant potentials is useful to develop effective strategies for improving the economic traits; for example, the major emphasis of soybean breeding for fatty acids is to enhance the oleic and linoleic acid contents and to decrease linolenic acid content.

Quantitative Trait Locus Mapping for Drought Tolerance in Soybean Recombinant Inbred Line Population.

Improving drought stress tolerance of soybean could be an effective way to minimize the yield reduction in the drought prevailing regions. Identification of drought tolerance-related quantitative trait loci (QTLs) is useful to facilitate the development of stress-tolerant varieties. This study aimed to identify the QTLs for drought tolerance in soybean using a recombinant inbred line (RIL) population developed from the cross between a drought-tolerant 'PI416937' and a susceptible 'Cheonsang' cultivar. Phenotyping was done with a weighted drought coefficient derived from the vegetative and reproductive traits. The genetic map was constructed using 2648 polymorphic SNP markers that distributed on 20 chromosomes with a mean genetic distance of 1.36 cM between markers. A total of 10 QTLs with 3.52-4.7 logarithm of odds value accounting for up to 12.9% phenotypic variance were identified on seven chromosomes. Five chromosomes-2, 7, 10, 14, and 20-contained one QTL each, and chromosomes 1 and 19 harbored two and three QTLs, respectively. The chromosomal locations of seven QTLs overlapped or located close to the related QTLs and/or potential candidate genes reported earlier. The QTLs and closely linked markers could be utilized in maker-assisted selection to accelerate the breeding for drought tolerance in soybean.

QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max).

Pod shattering is an important reproductive process in many wild species. However, pod shattering at the maturing stage can result in severe yield loss. The objectives of this study were to discover quantitative trait loci (QTLs) for pod shattering using two recombinant inbred line (RIL) populations derived from an elite cultivar having pod shattering tolerance, namely "Daewonkong", and to predict novel candidate QTL/genes involved in pod shattering based on their allele patterns. We found several QTLs with more than 10% phenotypic variance explained (PVE) on seven different chromosomes and found a novel candidate QTL on chromosome 16 (qPS-DS16-1) from the allele patterns in the QTL region. Out of the 41 annotated genes in the QTL region, six were found to contain SNP (single-nucleotide polymorphism)/indel variations in the coding sequence of the parents compared to the soybean reference genome. Among the six potential candidate genes, Glyma.16g076600, one of the genes with known function, showed a highly differential expression levels between the tolerant and susceptible parents in the growth stages R3 to R6. Further, Glyma.16g076600 is a homolog of AT4G19230 in Arabidopsis, whose function is related to abscisic acid catabolism. The results provide useful information to understand the genetic mechanism of pod shattering and could be used for improving the efficiency of marker-assisted selection for developing varieties of soybeans tolerant to pod shattering.

Changes occurring in nutritional components (phytochemicals and free amino acid) of raw and sprouted seeds of white and black sesame (Sesamum indicum L.) and screening of their antioxidant activities.

The present study is the first to investigate the germination properties regarding phytochemicals, amino acids, total phenolics, and antioxidant capacities of white and black sesame seeds. Nutritional components and antioxidant effects showed considerable differences. Sesamine and sesamolin composition decreased (white: 4.21→1.72, 3.57→1.57 mg/g; black: 2.43→0.58, 1.36→0.45 mg/g) during germination. Moreover, catechin displayed the predominant composition in sprouted seeds with values of 13.50 mg/g (white) and 19.09 (black) mg/g followed by (-)-epicatechin and sinapic acid. Total phenolics increased by approximately 4 times upon germination, i.e., 503.1±27.1→ 2085.0±56.7 (white) and 645.8±31.5→2480.1±49.5 (black), mg GAE/g. Amino acids also remarkably increased in sprouted white (7.04→31.69mg/g) and black (6.55→26.97mg/g) seeds, with individual composition occurring in the following order: asparagine>arginine>tryptophan>leucine>alanine. In particular, arginine and tryptophan exhibited the greatest variations. The antioxidant effects against DPPH radical were stronger in sprouted seeds depending on the phytochemicals. Therefore, sprouted sesame can be utilized as an excellent source for functional foods.

Analysis of yield of eleutherosides B and E in Acanthopanax divaricatus and A. koreanum grown with varying cultivation methods.

An analysis of the yield of eleutherosides B and E in Acanthopanax divaricatus and A. koreanum was performed using high performance liquid chromatography to evaluate production by different cultivation methods. In A. divaricatus and A. koreanum, the total content of eleutherosides B and E was 2.466-7.360 mg/g varying by plant section, 3.886-11.506 mg/g by pinching site, 3.655-10.083 mg/g by planting time, and 3.652-10.108 mg/g by fertilizer ratio. Thus the total content of eleutherosides B and E in A. divaricatus and A. koreanum differed depending on cultivation methods. These results present useful information for high eleutheroside content applications in A. divaricatus and A. koreanum. This information can affect selection of plant section and cultivation methods for nutraceutical, pharmaceutical, and cosmeceutical material development.

Attenuation by a Vigna nakashimae extract of nonalcoholic fatty liver disease in high-fat diet-fed mice.

A Vigna nakashimae (VN) extract has been shown to have antidiabetic and anti-obesity effects. However, the mechanism underlying the effect of a VN extract on hepatic inflammation and endoplasmic reticulum (ER) stress remains unclear. In the present study, we investigated how a VN extract protects against the development of non-alcoholic fatty liver disease (NAFLD). A VN extract for 12 weeks reduced the body weight, serum metabolic parameters, cytokines, and hepatic steatosis in high-fat diet (HFD)-fed mice. A VN extract decreased HFD-induced hepatic acetyl CoA carboxylase and glucose transporter 4 expressions. In addition to the levels of high-mobility group box 1 and receptor for advanced glycation, the hepatic expression of ATF4 and caspase-3 was also reduced by a VN extract. Thus, these data indicate that a chronic VN extract prevented NAFLD through multiple mechanisms, including inflammation, ER stress, and apoptosis in the liver.

Rapid characterisation and comparison of saponin profiles in the seeds of Korean Leguminous species using ultra performance liquid chromatography with photodiode array detector and electrospray ionisation/mass spectrometry (UPLC-PDA-ESI/MS) analysis.

The present work was reported on investigation of saponin profiles in nine different legume seeds, including soybean, adzuki bean, cowpea, common bean, scarlet runner bean, lentil, chick pea, hyacinth bean, and broad bean using ultra performance liquid chromatography with photodiode array detector and electrospray ionisation/mass spectrometry (UPLC-PDA-ESI/MS) technique. A total of twenty saponins were characterised under rapid and simple conditions within 15min by the 80% methanol extracts of all species. Their chemical structures were elucidated as soyasaponin Ab (1), soyasaponin Ba (2), soyasaponin Bb (3), soyasaponin Bc (4), soyasaponin Bd (5), soyasaponin αg (6), soyasaponin ßg (7), soyasaponin ßa (8), soyasaponin γg (9), soyasaponin γa (10), azukisaponin VI (11), azukisaponin IV (12), azukisaponin II (13), AzII (14), AzIV (15), lablaboside E (16), lablaboside F (17), lablaboside D (18), chikusetusaponin IVa (19), and lablab saponin I (20). The individual and total saponin compositions exhibited remarkable differences in all legume seeds. In particular, soyasaponin ßa (8) was detected the predominant composition in soybean, cowpea, and lentil with various concentrations. Interestingly, soybean, adzuki bean, common bean, and scarlet runner bean had high saponin contents, while chick pea and broad bean showed low contents.

IAA-producing Penicillium sp. NICS01 triggers plant growth and suppresses Fusarium sp.-induced oxidative stress in sesame (Sesamum indicum L.).

Application of rhizospheric fungi is an effective and environmentally friendly method of improving plant growth and controlling many plant diseases. The current study was aimed to identify phytohormone-producing fungi from soil, to understand their roles in sesame plant growth, and to control Fusarium disease. Three predominant fungi (PNF1, PNF2, and PNF3) isolated from the rhizospheric soil of peanut plants were screened for their growth-promoting efficiency on sesame seedlings. Among these isolates, PNF2 significantly increased the shoot length and fresh weight of seedlings compared with controls. Analysis of the fungal culture filtrate showed a higher concentration of indole acetic acid in PNF2 than in the other isolates. PNF2 was identified as Penicillium sp. on the basis of phylogenetic analysis of ITS sequence similarity. The in vitro biocontrol activity of Penicillium sp. against Fusarium sp. was exhibited by a 49% inhibition of mycelial growth in a dual culture bioassay and by hyphal injuries as observed by scanning electron microscopy. In addition, greenhouse experiments revealed that Fusarium inhibited growth in sesame plants by damaging lipid membranes and reducing protein content. Co-cultivation with Penicillium sp. mitigated Fusarium-induced oxidative stress in sesame plants by limiting membrane lipid peroxidation, and by increasing the protein concentration, levels of antioxidants such as total polyphenols, and peroxidase and polyphenoloxidase activities. Thus, our findings suggest that Penicillium sp. is a potent plant growthpromoting fungus that has the ability to ameliorate damage caused by Fusarium infection in sesame cultivation.

Penicillium sp. mitigates Fusarium-induced biotic stress in sesame plants.

Fusarium-infected sesame plants have significantly higher contents of amino acids (Asp, Thr, Ser, Asn, Glu, Gly, Ala, Val, Met, Ile, Leu, Tyr, Phe, Lys, His, Try, Arg, and Pro), compared with their respective levels in the healthy control. These higher levels of amino acids induced by Fusarium infection were decreased when Penicillium was co-inoculated with Fusarium. Compared with the control, Fusarium-infected plants showed higher contents of palmitic (8%), stearic (8%), oleic (7%), and linolenic acids (4%), and lower contents of oil (4%) and linoleic acid (11%). Co-inoculation with Penicillium mitigated the Fusarium-induced changes in fatty acids. The total chlorophyll content was lower in Fusarium- and Penicillium-infected plants than in the healthy control. The accumulation of carotenoids and γ-amino butyric acid in Fusarium-infected plants was slightly decreased by co-inoculation with Penicillium. Sesamin and sesamolin contents were higher in Penicillium- and Fusarium- infected plants than in the control. PURPOSE OF WORK: To clarify the mechanism of the biocontrol effect of Penicillium against Fusarium by evaluating changes in primary and secondary metabolite contents in sesame plants.

Identification, characterisation, and quantification of phenolic compounds in the antioxidant activity-containing fraction from the seeds of Korean perilla (Perilla frutescens) cultivars.

The present research was the first to investigate phenolic compound profiles and antioxidant properties in the seeds of various perilla (Perilla frutescens) cultivars. The 80% methanol extract (50 µg/ml) of this species showed potent antioxidant activities against 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) radicals. Phenolic compounds were characterised by nuclear magnetic resonance (NMR) spectroscopy, and ultra performance liquid chromatography with photodiode array detector and electrospray ionisation/mass (UPLC-PDA-ESI/MS) analysis. Nine compounds were elucidated as caffeic acid-3-O-glucoside (1), caffeic acid (2), luteolin-7-O-glucoside (3), apigenin-7-O-glucoside (4), rosmarinic acid-3-O-glucoside (5), rosmarinic acid (6), luteolin (7), apigenin (8), and chrysoeriol (9). The individual and total phenolic contents were remarkably different, especially rosmarinic acid-3-O-glucoside (5) and rosmarinic acid (6) which were the predominant compounds (>95%) in all perilla cultivars. Additionally, Yeupsil cultivar exhibited the highest phenolic content (5029.0 µg/g) and antioxidant activity, whereas the lowest was shown by Dasil (2138.7 µg/g). Therefore, these results suggest that antioxidant effects of perilla seeds are correlated with phenolic contents.

Slow-binding inhibition of soybean lipoxygenase-1 by luteolin.

Luteolin, isolated from the seeds of Perilla frutescens (perilla seeds), inhibited the peroxidation of linoleic acid catalyzed by soybean lipoxygenase-1 (EC 1.13.11.12, Type 1) with an IC(50) of 5.0 M (1.43 µg/mL) noncompetitively. The progress curves for an enzyme reaction indicate that luteolin shows slow binding kinetics. Both the initial velocity and steady-state rate in the progress curve were decreased with increasing the concentration of luteolin. The kinetic parameters, which described the inhibition by luteolin, were evaluated by nonlinear regression fits.

Isolation and identification of phenolic compounds from the seeds of Perilla frutescens (L.) and their inhibitory activities against α-glucosidase and aldose reductase.

Five phenolic compounds were isolated from the seeds of Perilla (Perilla frutescens L.) using gradient solvent fractionation, silica gel column chromatography, and preparative high-performance liquid chromatography (HPLC). Their chemical structures were identified as caffeic acid-3-O-glucoside (1), rosmarinic acid-3-O-glucoside (2), rosmarinic acid (3), luteolin (4), and apigenin (5) using NMR spectroscopy and HPLC-ESI/MS analysis. Among them, luteolin (4) inhibited α-glucosidase (EC 3.2.1.20) with IC(50) value of 45.4µM. The inhibition kinetic analysed by Dixon plot indicate that luteolin is a noncompetitive inhibitor, and the inhibition constant K(I) was calculated at 45.0µM. Moreover, rosmarinic acid (3) and luteolin (4) inhibited recombinant human aldose reductase (EC 1.1.1.21) with IC(50) values of 11.2 and 0.6µM, respectively. Notably, the inhibition kinetic of luteolin (4) follows a hyperbolic dependence on aldose reductase inhibition by Dixon plot. Thus, inhibition kinetic indicates that luteolin (4) is a mixed-type inhibitor.

Chemometric Approach to Fatty Acid Profiles in Soybean Cultivars by Principal Component Analysis (PCA).

The purpose of this study was to investigate the fatty acid profiles in 18 soybean cultivars grown in Korea. A total of eleven fatty acids were identified in the sample set, which was comprised of myristic (C14:0), palmitic (C16:0), palmitoleic (C16:1, ω7), stearic (C18:0), oleic (C18:1, ω9), linoleic (C18:2, ω6), linolenic (C18:3, ω3), arachidic (C20:0), gondoic (C20:1, ω9), behenic (C22:0), and lignoceric (C24:0) acids by gas-liquid chromatography with flame ionization detector (GC-FID). Based on their color, yellow-, black-, brown-, and green-colored cultivars were denoted. Correlation coefficients (r) between the nine major fatty acids identified (two trace fatty acids, myristic and palmitoleic, were not included in the study) were generated and revealed an inverse association between oleic and linoleic acids (r=-0.94, p<0.05), while stearic acid was positively correlated to arachidic acid (r=0.72, p<0.05). Principal component analysis (PCA) of the fatty acid data yielded four significant principal components (PCs; i.e., eigenvalues>1), which together account for 81.49% of the total variance in the data set; with PC1 contributing 28.16% of the total. Eigen analysis of the correlation matrix loadings of the four significant PCs revealed that PC1 was mainly contributed to by oleic, linoleic, and gondoic acids, PC2 by stearic, linolenic and arachidic acids, PC3 by behenic and lignoceric acids, and PC4 by palmitic acid. The score plots generated between PC1-PC2 and PC3-PC4 segregated soybean cultivars based on fatty acid composition.

Identification and characterization of anthocyanins in yard-long beans (Vigna unguiculata ssp. sesquipedalis L.) by High-performance liquid chromatography with diode array detection and electrospray ionization/mass spectrometry (HPLC-DAD-ESI/MS) analysis.

Anthocyanins play an important role in physiological functions related to human health. The objective of this study was to investigate the profiles of anthocyanins in the immature purple pods and black seeds of yard-long beans ( Vigna unguiculata ssp. sesquipedalis L.) using high-performance liquid chromatography (HPLC) with diode array detection and electrospray ionization/mass spectrometry (DAD-ESI/MS) analysis. The individual anthocyanins were identified by comparing their mass spectrometric data and retention times. In the purple pods, five individual anthocyanins were identified: delphinidin-3-O-glucoside (2), cyanidin-3-O-sambubioside (4), cyanidin-3-O-glucoside (5), pelargonidin-3-O-glucoside (7), and peonidin-3-O-glucoside (8). From the black seed coat of the yard-long beans, seven anthocyanins were identified, including delphinidin-3-O-galactoside (1), cyanidin-3-O-galactoside (3), petunidin-3-O-glucoside (6), and malvidin-3-O-glucoside (9), together with compounds 2, 5, and 8. In this study, we report for the first time anthocyanin profiles for the pod and seed coat of yard-long beans.