Gel-based and gel-free proteome data associated with controlled deterioration treatment of Glycine max seeds.

Data presented here are associated with the article: "In-depth proteomic analysis of soybean (Glycine max) seeds during controlled deterioration treatment (CDT) reveals a shift in seed metabolism" (Min et al., 2017) [1]. Seed deterioration is one of the major problems, affecting the seed quality, viability, and vigor in a negative manner. Here, we display the gel-based and gel-free proteomic data, associated with the CDT in soybean seeds. The present data was obtained from 2-DE, shotgun proteomic analysis (label-free quantitative proteomic analysis) using Q-Exactive, and gene ontology analysis associated with CDT in soybean seeds (Min et al., 2017) [1].

In-depth proteomic analysis of Glycine max seeds during controlled deterioration treatment reveals a shift in seed metabolism.

Seed aging is one of the major events, affecting the overall quality of agricultural seeds. To analyze the effect of seed aging, soybean seeds were exposed to controlled deterioration treatment (CDT) for 3 and 7days, followed by their physiological, biochemical, and proteomic analyses. Seed proteins were subjected to protamine sulfate precipitation for the enrichment of low-abundance proteins and utilized for proteome analysis. A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins. Of these identified proteins, 146 showed significant changes in protein abundance, where 5 and 141 had increased and decreased abundances, respectively while 352 proteins were completely degraded during CDT. Gene ontology and KEGG analyses suggested the association of differential proteins with primary metabolism, ROS detoxification, translation elongation and initiation, protein folding, and proteolysis, where most, if not all, had decreased abundance during CDT. Western blotting confirmed reduced level of antioxidant enzymes (DHAR, APx1, MDAR, and SOD) upon CDT. This in-depth integrated study reveals a major downshift in seed metabolism upon CDT. Reported data here serve as a resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality. BIOLOGICAL SIGNIFICANCE: Controlled deterioration treatment (CDT) is one of the major events that negatively affects the quality and nutrient composition of agricultural seeds. However, the molecular mechanism of CDT is largely unknown. A combination of gel-based and gel-free proteomic approach was utilized to investigate the effects of CDT in soybean seeds. Moreover, we utilized protamine sulfate precipitation method for enrichment of low-abundance proteins, which are generally masked due to the presence of high-abundance seed storage proteins. Reported data here serve as resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality.

One-step multiplex reverse transcription-polymerase chain reaction for the simultaneous detection of three rice viruses.

Rice stripe virus (RSV), Rice black-streaked dwarf virus (RBSDV), and Rice dwarf virus (RDV) are major rice-infecting viruses in Korea that can cause serious crop losses. A one-step multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for the simultaneous detection of these rice viruses. Three sets of specific primers targeted to the capsid protein coding genes of RSV, RBSDV, and RDV were used to amplify fragments that were 703 bp, 485 bp, and 252 bp, respectively. The one-step mRT-PCR assay proved to be a sensitive and rapid method for detecting the three rice viruses. This method could be used to facilitate better control of rice viruses.

Effect of the growth stage and cultivar on policosanol profiles of barley sprouts and their adenosine 5'-monophosphate-activated protein kinase activation.

Adenosine 5'-monophosphate-activated protein kinase (AMPK) is an intracellular sensor that can regulate glucose levels within the cell. For this reason, it is well-known to be a target for drugs against diabetes and obesity. AMPK was activated significantly by the hexane extract of barley sprouts. This AMPK activation emerges across the growth stages of the sprout, becoming most significant (3 times above the initial stages) 10 days after sprouting. After this time, the activation decreased between 13 and 20 days post-sprouting. Analysis of the hexane extracts by gas chromatography-mass spectrometry showed that the amounts of policosanols (PCs, which are linear, primary aliphatic alcohols with 20-30 carbons) in the plant dramatically increased between 5 days (109.7 mg/100 g) and 10 days (343.7 mg/100 g) post-sprouting and then levels fell back down, reaching 76.4 mg/100 g at 20 days post-sprouting. This trend is consistent with PCs being the active ingredient in the barley plants. We validate this by showing that hexacosanol is an activator of AMPK. The richest cultivar for PCs was found to be the Daejin cultivar. Cultivars had a significant effect on the total PC content (113.2-183.5 mg/100 g) within the plant up to 5 days post-sprouting. However this dependence upon the cultivar was not so apparent at peak stages of PC production (10 days post-sprouting). The most abundant PC in barley sprout, hexacosanol, contributed 62-80% of the total PC content at every stage. These results are valuable to determine the optimal times of harvest to obtain the highest yield of PCs.

Dual inhibition of γ-oryzanol on cellular melanogenesis: inhibition of tyrosinase activity and reduction of melanogenic gene expression by a protein kinase A-dependent mechanism.

The in vitro effects on melanogenesis of γ-oryzanol (1), a rice bran-derived phytosterol, were investigated. The melanin content in B16F1 cells was significantly and dose-dependently reduced (-13% and -28% at 3 and 30 µM, respectively). Tyrosinase enzyme activity was inhibited by 1 both in a cell-free assay and when analyzed based on the measurement of cellular tyrosinase activity. Transcriptome analysis was performed to investigate the biological pathways altered by 1, and it was found that gene expression involving protein kinase A (PKA) signaling was markedly altered. Subsequent analyses revealed that 1 stimulation in B16 cells reduced cytosolic cAMP concentrations, PKA activity (-13% for cAMP levels and -40% for PKA activity), and phosphorylation of the cAMP-response element binding protein (-57%), which, in turn, downregulated the expression of microphthalmia-associated transcription factor (MITF; -59% for mRNA and -64% for protein), a key melanogenic gene transcription factor. Accordingly, tyrosinase-related protein 1 (TRP-1; -69% for mRNA and -82% for protein) and dopachrome tautomerase (-51% for mRNA and -92% for protein) in 1-stimulated B16F1 cells were also downregulated. These results suggest that 1 has dual inhibitory activities for cellular melanogenesis by inhibiting tyrosinase enzyme activity and reducing MITF and target genes in the PKA-dependent pathway.

Fine mapping and identification of candidate rice genes associated with qSTV11(SG), a major QTL for rice stripe disease resistance.

Rice stripe disease, caused by rice stripe virus (RSV) is a serious constraint to rice production in subtropical regions of East Asia. We performed fine mapping of a RSV resistance QTL on chromosome 11, qSTV11 ( SG ), using near-isogenic lines (NILs, BC(6)F(4)) derived from a cross between the highly resistant variety, Shingwang, and the highly susceptible variety, Ilpum, using 11 insertion and deletion (InDel) markers. qSTV11 ( SG ) was localized to a 150-kb region between InDel 11 (17.86 Mbp) and InDel 5 (18.01 Mbp). Among the two markers in this region, InDel 7 is diagnostic of RSV resistance in 55 Korean japonica and indica rice varieties. InDel 7 could also distinguish the allele type of Nagdong, Shingwang, Mudgo, and Pe-bi-hun from Zenith harboring the Stv-b ( i ) allele. As a result, qSTV11 ( SG ) is likely to be the Stv-b ( i ) allele. There were 21 genes in the 150-kb region harboring the qSTV11 ( SG ) locus. Three of these genes, LOC_Os11g31430, LOC_Os11g31450, and LOC_Os11g31470, were exclusively expressed in the susceptible variety. These expression profiles were consistent with the quantitative nature along with incomplete dominance of RSV resistance. Sequencing of these genes showed that there were several amino acid substitutions between susceptible and resistant varieties. Putative functions of these candidate genes for qSTV11 (SG) are discussed.

Structural and quantitative analysis of antioxidant and low-density lipoprotein-antioxidant flavonoids from the grains of sugary rice.

Grains of sugary rice were extracted with 80% aqueous methanol, and the concentrated extracts were successively partitioned using ethyl acetate, n-butanol, and water. From the n-butanol fractions, four flavonoid glycosides were isolated through repeated silica gel, octadecyl silica gel, and Sephadex LH-20 column chromatographies. Based on the nuclear magnetic resonance, mass spectrometry, and infrared spectroscopic data, the chemical structures of the compounds were determined to be taxifolin-7-O-ß-d-glucopyranoside (1), hyperin (2), isoquercitrin (3), and quercetin gentiobioside (4). These compounds were isolated from the grains of sugary rice for the first time. All isolated compounds were tested for antioxidant activity and low-density lipoprotein (LDL)-antioxidative activity using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and LDL assays. Compound 1 exhibited a strong scavenging effect on DPPH, with a 50% inhibition concentration (IC(50)) value of 8.1 µM, and also inhibited LDL oxidation with an IC(50) value of 40.0±20 µM. A simple and efficient high-performance liquid chromatography/diode array detection method for the simultaneous determination of the four bioactive flavonoids (1-4) has been developed and applied to their content determination in the sugary rice. The grains were extracted by 80% methanol, and the contents of 1, 2, 3, and 4 were determined to be 1.12±0.045, 0.65±0.011, 0.68±0.032, and 0.89±0.021 mg/g, respectively.

Rice varieties in relation to rice bread quality.

BACKGROUND: It is difficult to predict rice bread quality only from the amylose content (AC) or dough characteristics of new lines produced by rice breeding programmes. This study investigated the AC relative to bread baking quality of rice varieties developed in Korea, and identified specific characteristics that contribute to rice bread quality. RESULTS: Manmibyeo, Jinsumi, Seolgaeng and Hanareumbyeo were classified as low AC, YR24088 Acp9, Suweon517, Chenmaai and Goamibyeo as intermediate AC and Milyang261 as high AC. Suweon517, Milyang261 and Manmibyeo had a high water absorption index (WAI), while Goamibyeo, YR24088 Acp9, Jinsumi, Seolgaeng, Hanareumbyeo and Chenmaai had a low WAI. The gelatinisation enthalpy of flour varied from 9.2 J g(-1) in Milyang261 to 14.8 J g(-1) in YR24088 Acp9. After 7 days of storage the rate of flour retrogradation and crumb firmness were weakly correlated, with the exception of Jinsumi. Bread volumes of Jinsumi, Chenmaai, YR24088 Acp9 and Goamibyeo were comparable to that of wheat flour, but the rest were unsuited to bread making because of their low volume and hard crumb texture. CONCLUSION: Based on volume, texture and crumb firmness ratio, Chenmaai and Goamibyeo were the most appropriate varieties for making bread. An intermediate AC and low WAI were the primary indicators of rice bread flour quality.