Comparison of the contents of phenolic compounds including flavonoids and antioxidant activity of rice (Oryza sativa) and Chinese wild rice (Zizania latifolia)

Integrative phenomics, metabolomics and genomics analysis provides new insights for deciphering the genetic basis of metabolism in polished rice

BACKGROUND

Metabolomics is one of the most widely used omics tools for deciphering the functional networks of the metabolites for crop improvement. However, it is technically demanding and costly.

RESULTS

We propose a relatively inexpensive approach for metabolomics analysis in which metabolomics is combined with hyperspectral imaging via machine learning. This approach can be used to target important steps in flavonoid and lipid biosynthesis in rice. We extract 1848 hyperspectral indices and 887 metabolites from polished grains of 533 Oryza sativa accessions. Hyperspectral indices are then linked to metabolites through correlation analysis and modelling. Based on this, a total of 554 metabolites and 1313 hyperspectral indices are identified for further genome-wide association study (GWAS). By GWAS, we detect 17,509 significant locus-trait associations with 2882 single nucleotide polymorphisms (SNPs). Colocalization analysis links these SNPs to the corresponding metabolites and hyperspectral indices. We detect 6415 pairs of metabolites and hyperspectral indices within a linkage disequilibrium of 300 kb in the Oryza sativa genome. We then characterize 1761 candidate genes colocalized to these loci by transcriptomic analysis. We further verify novel candidate genes encoding a novel flavonoid (LOC_Os09g18450) and a flavonoid/lipid (LOC_Os07g11020) respectively by gene editing and overexpression in rice.

CONCLUSION

Our findings indicate that hyperspectral imaging combined with machine learning methods could serve as a powerful tool for quickly and inexpensively assessing crop metabolites.

Variations in the End-Use Quality of Whole Grain Flour Are Closely Related to the Metabolites in the Grains of Pigmented Wheat (Triticum aestivum L.)

Whole grain flour is considered a part of a healthy diet, especially when produced with pigmented wheat (Triticum aestivum). However, the specific metabolic pathways and mechanisms by which these metabolites affect the end-use quality of pigmented wheat varieties still need to be better understood. This study examined the relationship between metabolite concentrations and the end-use quality of three wheat varieties: common wheat (CW, JM20), black wheat (BW, HJ1), and green wheat (GW, HZ148). The study's findings revealed significant differences in the accumulation of metabolic substances among the various pigmented wheat varieties. Specifically, BW and GW exhibited notably higher levels of amino acids, derivatives, and lipids than CW. The study's findings revealed significant differences in the accumulation of metabolic substances among the various pigmented wheat varieties. Specifically, BW and GW exhibited notably higher levels of amino acids and their derivatives and lipids than CW. Amino acid derivatives, such as glutathione and creatine, are compounds formed through chemical modifications of amino acids and play crucial roles in antioxidative defense and energy metabolism. The gliadin and glutenin content of BW increased by 12% and 2%, respectively, compared to CW, due to elevated levels of amino acids and their derivatives, whereas GW was notable for its higher globulin content (an increase of 11.6%). BW was also distinguished by its exceptionally high anthocyanin content, including cyanidin-3-O-(6-O-malonyl-beta-D-glucoside) (23.2 μg g-1), cyanidin-3-O-glucoside (6.5 μg g-1), and peonidin-3-O-glucoside (2.3 μg g-1), which surpassed the levels found in both CW and GW (which approached zero). However, BW had lower gluten content, resulting in a greater weakening and reduced development and stability times. Conversely, GW exhibited an increased lipid metabolism, which was associated with a higher starch and gluten content, improving the maximum tensile resistance. Overall, the pigmented wheat varieties offer superior nutritional profiles and processing advantages, necessitating further research to optimize their commercial use.

Changes of polyphenols and their antioxidant activities in non-pigmented, red and black rice during in vitro digestion

Polyphenols, a major bioactive constituent in rice grain, require processing and digestion before being absorbed by human body. Free and bound phenolics, flavonoids and their antioxidant activities in non-pigmented, red and black rice after cooking and INFOGEST digestions of oral, gastric and intestinal phases were investigated. It showed that cooking caused great losses of polyphenols and antioxidant activity. Free ferulic, isoferulic and p-coumaric acid in most rice were highest at intestinal phase (p < 0.05). Bound ferulic acid in three colored rice, bound p-coumaric acid in black rice and catechin in red rice were higher at oral and/or gastric phase. After cooking, total flavonoids of non-pigmented and pigmented rice were highest at intestinal and gastric phase, respectively. Cyanidin-3-O-glucoside, peonidin-3-O-glucoside and quercetin peaked at intestinal phase in black rice. It suggested that black rice has a greater potential to be used in meal balance and functional product development.

Overexpression of ZlMYB1 and ZlMYB2 increases flavonoid contents and antioxidant capacity and enhances the inhibition of α-glucosidase and tyrosinase activity in rice seeds

Anthocyanins are natural flavonoids with a high antioxidant power and many associated health benefits, but most rice produce little amounts of these compounds. In this study, 141 MYB transcription factors in 15 chromosomes, including the nucleus-localised ZlMYB1 (Zla03G003370) and ZlMYB2 (Zla15G015220), were discovered in Zizania latifolia. Overexpression of ZlMYB1 or ZlMYB2 in rice seeds induced black pericarps, and flavonoid content, antioxidant capacity, and α-glucosidase and tyrosinase inhibition effects significantly increased compared to those in the control seeds. ZlMYB1 and ZlMYB2 overexpression induced the upregulation of 764 and 279 genes, respectively, and the upregulation of 162 and 157 flavonoids, respectively, linked to a black pericarp phenotype. The expression of flavonoid 3'-hydroxylase and UDP-glycose flavonoid glycosyltransferase, as well as the activities of these enzymes, increased significantly in response to ZlMYB1 or ZlMYB2 overexpression. This study systematically confirmed that the overexpression of ZlMYB1 and ZlMYB2 promotes flavonoid biosynthesis (especially of anthocyanins) in rice.

Metabolomic analysis of rice cultivars from diverse production areas

Rice grown in Yunnan Province is known for its excellent taste and consumer preference. However, the metabolite composition of this unique rice remains unclear. In this study, the metabolic profile of different rice planted in various producing regions was evaluated. A total of 1,005 metabolites were identified, including nucleotides and their derivatives, amino acids and their derivatives, alkaloids, organic acids, phenolic acids, lignans and coumarins, lipids, terpenoids, quinones, flavones, tannins, and others. Procucing region and varieties can be clearly distinguished on the PCA diagram. Differential metabolites accumulated in the MSD502 vs. MSR88 (138)/LHHG (234)/LHR88 (188) comparison groups. The results in this study provide scientific information for the origin tracing and variety differentiation of raw rice materials.

Comparative study for metabolomics, antioxidant activity, and molecular docking simulation of the newly bred Korean red rice accessions

This study analyzed the metabolite profiles and antioxidant capacities of two waxy and non-waxy Korean red rice accessions newly bred. Fifteen phenolic compounds were detected in the rice samples. Accession1 had high fatty acids, phytosterols, and vitamin E; accession3 had high vitamin E and phytosterol; and accession4 had a high total flavonoid. The correlation analysis findings from this study validated the positive association between all the metabolites and antioxidant activity. in silico results revealed that protocatechuic acid had a docking score of -9.541, followed by luteolin, quercetin, and caffeic acid, all of which had significant docking scores and a significant number of contacts. Similarly, molecular dynamics simulations showed that phytochemicals had root mean square deviation values of <2.8 Å with Keap 1, indicating better stability. This study provides valuable insights into potential directions for future investigations and improvements in the functional qualities of other colored rice varieties.

Role of phenylpropanoid pathway in genetic regulation and physiological adaptation in arsenic stressed rice genotypes

This study investigates the role of the phenylpropanoid pathway in arsenic (As) contaminated rice genotypes under natural conditions, exploring the intricate relationship between genetic regulation and physiological adaptation. Differential approaches adapted by rice genotypes to counteract As exposure are elucidated here through analysis of enzyme activities and related gene expression patterns, docking simulations, and nutrient dynamics. Enzymatic analysis from the phenylpropanoid pathway revealed significant variations across rice genotypes, with Mini mansoori exhibiting notably higher activity levels of key enzymes (PAL, C4H, 4CL, CHI, DFR and F3H) compared to Sampoorna and Pioneer. Additionally, the gene expression profiling unveiled differential responses, with Mini mansoori and Pioneer demonstrating higher expression of genes (OsPAL, OsCHS, OsCHI, OsF3H, OsF3'H, OsFLS, OsDFR, and OsLAR) associated with As resistance and tolerance, compared to Sampoorna. Enrichment analysis emphasized the involvement of cinnamic acid biosynthesis and related pathways. Molecular docking depicted certain proteins, such as Os4CL, OsFLS, OsDFR, and OsLAR susceptible to As binding, potentially affecting enzymatic activity. Ionomic analysis unveiled that Mini mansoori maintained higher levels of essential nutrients such as Na, Ca, P, Mn, Mg, and Zn in grains. However, this contrasted with Pioneer and Sampoorna, which experienced nutrient imbalance likely due to higher As accumulation. Chlorophyll fluorescence analysis depicted that Mini mansoori and Pioneer maintained better photosynthetic efficiency under As toxicity compared to Sampoorna. Moreover, network analysis highlights the critical role of Mg and Na interaction with essential phenolics and flavonoids, in combating the stress. Harnessing this understanding, targeted breeding effort could yield As-resistant rice varieties with enhanced nutrient and flavonoid contents, addressing both food safety and malnutrition in affected regions.

Chemical and Bioactive Properties of Red Rice with Potential Pharmaceutical Use

Red rice has been proposed as a super-food. Accordingly, the nutritional properties (AOAC), as well as its chemical composition, including sugars (HPLC-RI), organic acids (UFLC-PDA), tocopherols (HPLD-FD), and phenolic compounds (LC-DAD-ESI/MSn), together with the main bioactive properties (antioxidant, cytotoxic, antiproliferative, and antibacterial activities), were evaluated to access its nutritional benefits and health improvement potential. The most abundant macronutrients found were carbohydrates (87.2 g/100 g dw), proceeded by proteins (9.1 g/100 g dw), fat (2.6 g/100 g dw), and ash (1.1 g/100 g dw). Sucrose and raffinose were the only detected sugars, with sucrose presenting the maximum concentration (0.74 g/100 g dw). MUFAs and PUFAs were the predominant fatty acids (40.7% and 31%, respectively). Among the two detected tocopherol isoforms, γ-tocopherol (0.67 mg/100 g dw) predominated over α-tocopherol. The phenolic compounds profile, majorly composed of flavan-3-ols, should be associated with the detected bioactivities, which may provide biological benefits to human health beyond the primary nutritional effect. Overall, the bioactive potential of red rice was comprehensively accessed.

Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice

Pigmented rice stands out for its nutritional value and is gaining more and more attention. Wild rice, domesticated red rice, and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype. We performed population genetic analyses using 5104 worldwide rice accessions, including 2794 accessions with red or black pericarps, 85 of which were newly sequenced in this study. The results suggested an evolutionary trajectory of red landraces originating from wild rice, and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years. Cultivated red rice was found to feralize to weedy rice, and weedy rice could be further re-domesticated to cultivated red rice. A genome-wide association study based on the 2794 accessions with pigmented pericarps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization. Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.

Chemical Structure Diversity and Extensive Biological Functions of Specialized Metabolites in Rice

Rice (Oryza sativa L.) is thought to have been domesticated many times independently in China and India, and many modern cultivars are available. All rice tissues are rich in specialized metabolites (SPMs). To date, a total of 181 terpenoids, 199 phenolics, 41 alkaloids, and 26 other types of compounds have been detected in rice. Some volatile sesquiterpenoids released by rice are known to attract the natural enemies of rice herbivores, and play an indirect role in defense. Momilactone, phytocassane, and oryzalic acid are the most common diterpenoids found in rice, and are found at all growth stages. Indolamides, including serotonin, tryptamine, and N-benzoylserotonin, are the main rice alkaloids. The SPMs mainly exhibit defense functions with direct roles in resisting herbivory and pathogenic infections. In addition, phenolics are also important in indirect defense, and enhance wax deposition in leaves and promote the lignification of stems. Meanwhile, rice SPMs also have allelopathic effects and are crucial in the regulation of the relationships between different plants or between plants and microorganisms. In this study, we reviewed the various structures and functions of rice SPMs. This paper will provide useful information and methodological resources to inform the improvement of rice resistance and the promotion of the rice industry.

Toxicity of bisphenol A (BPA) and its analogues BPF and BPS on the free-floating macrophyte Salvinia biloba

Evidence linking the toxicity of bisphenol A (BPA) to environmental and public-health issues has led to restrictions on its use. This compound has been gradually replaced with analogues proposed as a safer alternative, normally bisphenol F (BPF) and bisphenol S (BPS), but these substitutes are structurally almost identical to BPA, suggesting they may pose similar risks. The effects of BPA and these analogues were compared for antioxidant activity, lipid peroxidation, free-radical generation, photosynthetic pigments, and chlorophyll fluorescence in Salvinia biloba Raddi (S. biloba) plants exposed to environmentally relevant and sublethal concentrations (1, 10, 50, 100 and 150 μM). Bisphenol exposure promoted alterations in most of the physiological parameters investigated, with BPS toxicity differing slightly from that of the analogues. Furthermore, S. biloba removed similar levels of BPA and BPF from aqueous solutions with ≈70% removed at the 150 μM concentration, while BPS was less effectively removed, with only 23% removed at 150 μM. These findings show that high concentrations of bisphenols (10≥) are toxic to S. biloba, and even typical environmental levels (≤1 μM) can induce metabolic changes in plants, bringing to light that both BPA and its substitutes BPF and BPS pose risks to aquatic ecosystems.

Comparison of Metabolites and Main Nutritional Components between Uncooked and Cooked Purple Rice

Cooking can lead to varying degrees of nutrient loss in purple rice. For this investigation, two varieties of purple rice (YZN1 and YZ6) were chosen as the focal points to explore the metabolites associated with rice nutrition post cooking using nontargeted and targeted metabolomics techniques. The results showed that after cooking the two purple rice varieties, the contents of the flavonoids; OPC; TP; total antioxidant capacity; and K, Na, Fe, Mn, Zn, Cu, Ca, and Mg significantly decreased. Compared with YZN1U (YZN1 uncooked), the amino acid and mineral element contents in YZN1C (YZN1 cooked) decreased to varying degrees. After cooking YZ6, the contents of seven amino acids significantly decreased. Following the preparation of purple rice, the metabolites primarily engaged in the pathways of flavonoid synthesis and flavone and flavonol synthesis. Flavonoids, total antioxidant capacity, mineral elements, and amino acids showed a strong correlation with delphinidin and luteolin. The ROC analysis demonstrated that the value of the area under the curve for delphinidin and luteolin was 1 when comparing YZ6C (YZ6 cooked) and YZ6U (YZ6 uncooked), as well as YZN1C and YZN1U. Delphinidin and luteolin can be used as potential biomarkers of nutrient loss after cooking purple rice. This study holds significant implications for the balanced nutrition and healthy development of human dietary grains.

Integrated transcriptome and metabolome analysis unveil the response mechanism in wild rice (Zizania latifolia griseb.) against sheath rot infection

Sheath rot disease (SRD) is one of the most devastating diseases of Manchurian wild rice (MWR) (Zizania latifolia Griseb). Pilot experiments in our laboratory have shown that an MWR cultivar "Zhejiao NO.7"exhibits signs of SRD tolerance. To explore the responses of Zhejiao No. 7 to SRD infection, we used a combined transcriptome and metabolome analysis approach. A total of 136 differentially accumulated metabolites (DAMs, 114 up- and 22 down-accumulated in FA compared to CK) were detected. These up-accumulated metabolites were enriched in tryptophan metabolism, amino acid biosynthesis, flavonoids, and phytohormone signaling. Transcriptome sequencing results showed the differential expression of 11,280 genes (DEGs, 5,933 up-, and 5,347 downregulated in FA compared to CK). The genes expressed in tryptophan metabolism, amino acid biosynthesis, phytohormone biosynthesis and signaling, and reactive oxygen species homeostasis confirmed the metabolite results. In addition, genes related to the cell wall, carbohydrate metabolism, and plant-pathogen interaction (especially hypersensitive response) showed changes in expression in response to SRD infection. These results provide a basis for understanding the response mechanisms in MWR to FA attack that can be used for breeding SRD-tolerant MWR.

Domestication, breeding, omics research, and important genes of Zizania latifolia and Zizania palustris

Wild rice (Zizania spp.), an aquatic grass belonging to the subfamily Gramineae, has a high economic value. Zizania provides food (such as grains and vegetables), a habitat for wild animals, and paper-making pulps, possesses certain medicinal values, and helps control water eutrophication. Zizania is an ideal resource for expanding and enriching a rice breeding gene bank to naturally preserve valuable characteristics lost during domestication. With the Z. latifolia and Z. palustris genomes completely sequenced, fundamental achievements have been made toward understanding the origin and domestication, as well as the genetic basis of important agronomic traits of this genus, substantially accelerating the domestication of this wild plant. The present review summarizes the research results on the edible history, economic value, domestication, breeding, omics research, and important genes of Z. latifolia and Z. palustris over the past decades. These findings broaden the collective understanding of Zizania domestication and breeding, furthering human domestication, improvement, and long-term sustainability of wild plant cultivation.

NtLTPI.38, a plasma membrane-localized protein, mediates lipid metabolism and salt tolerance in Nicotiana tabacum

Non-specific lipid transfer proteins (nsLTPs) typically have conserved structural resemblance, low sequence identity, and broad biological functions in plant growth and stress resistance. Here, a plasma membrane-localized nsLTP, NtLTPI.38, was identified in tobacco plants. Multi-omics integrated analysis revealed that NtLTPI.38 overexpression or knock out significantly changed glycerophospholipid and glycerolipid metabolism pathways. NtLTPI.38 overexpression remarkably increased phosphatidylcholine, phosphatidylethanolamine, triacylglycerol, and flavonoid levels, but decreased ceramides compared to wild type and mutant lines. Differentially expressed genes were associated with lipid metabolite and flavonoid synthesis. Many genes related to Ca²⁺ channels, abscisic acid (ABA) signal transduction, and ion transport pathways were upregulated in overexpressing plants. NtLTPI.38 overexpression in salt-stressed tobacco triggered a Ca²⁺ and K⁺ influx in leaves, increased the contents of chlorophyll, proline, flavonoids, and osmotic tolerance, and raised enzymatic antioxidant activities as well as the expression level of related genes. However, mutants accumulated more O₂^- and H₂O_2, exhibited ionic imbalance, gathered excess Na⁺, Cl^-, and malondialdehyde, with more severe ion leakage. Therefore, NtLTPI.38 enhanced salt tolerance in tobacco by regulating lipid and flavonoid synthesis, antioxidant activity, ion homeostasis, and ABA signaling pathways.

Investigation of some bioactive compounds, in vitro bioaccessibility, and sensory acceptability of couscous produced by pre-gelatinized rice flour

BACKGROUND

The purpose of this study was to investigate the sensory properties, antioxidant capacities, total phenolic content, and their bioaccessibility in gluten-free rice couscous that is produced without additives. Since rice does not contain gluten, pre-gelatinized rice flour (GRF) was added instead of gum and enzymes in order to provide the desired structure in the couscous samples.

RESULTS

According to the results, the total phenolic content of couscous samples was increased with GRF addition. The highest extractable and hydrolyzable antioxidant capacity values were observed in the couscous samples supplemented with 30% GRF using the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical cation, cupric-reducing antioxidant capacity, and ferric reducing antioxidant capacity methods. The bioaccessibility of antioxidant capacity was found to be significantly higher (P < 0.05) than the control sample in all methods except the 1,1-diphenyl-2-picrylhydrazyl free radical method in the couscous samples.

CONCLUSION

According to the data obtained, it has been determined that couscous, which has a very small round shape, can be produced with GRF without additives. In this context, gluten-free rice couscous could be used as an alternative valuable food in terms of nutrition and can be an alternative traditional food for celiac diseases as well as for individuals preferring the consumption of gluten-free products. © 2022 Society of Chemical Industry.

Effect of different doses of nitrogen fertilization on bioactive compounds and antioxidant activity of brown rice

Brown rice as a whole grain food is associated with various chronic diseases' reduced risks. In this study, the effects of different doses of nitrogen fertilization (0, 160, 210, 260, 315, and 420 kg N/ 100 m²) on bioactive compounds and antioxidant activity of brown rice (yanfeng47) were investigated. At nitrogen level of 210-260 kg N/100 m², the content of TFC (302.65 mg/100 g), β-sitosterol (1762.92 mg/100 g), stigmasterol (1358.735 mg/100 g), DPPH (74.57%), and OH free radical scavenging (74.19%) was the highest. The major phenolic acid was p-hydroxybenzoic acid. There were significant positive linear relationships between TFC (0.872, 0.843), β-sitosterol (0.896, 0.657), stigmasterol (0.543, 0.771), p-hydroxybenzoic acid (0.871, 0.875), and DPPH, OH antioxidant activity. These indicated that TFC and phytosterols were the most important components in brown rice that had strong antioxidant activity. Composite score of principal components indicated 210 Kg N/100 m² exhibited a more ideal dose of nitrogen for nutritional composition and antioxidant activity of brown rice.

Comparative analysis of rice reveals insights into the mechanism of colored rice via widely targeted metabolomics

Pigmented rice, particularly black rice, has attracted widespread global interest due to its high nutritional value. To obtain a better understanding of differential metabolites between pigmented rice and white rice, we used a widely-targeted metabolomics-based approach to investigate the metabolite profiling of black, red, glutinous, and common white rice. In total, 732 metabolites were identified, of which 281, 305, 241, 267, and 265 differential metabolites were screened by comparing the following group: glutinous/white vs black, glutinous/white vs red, and red vs black. Venn diagram demonstrated that 69 metabolites were shared between pigmented and non-pigmented rice, and 117 between glutinous/white/red vs black. Additionally, metabolic pathways analysis of differential metabolites in glutinous/white/red vs black revealed that the flavonoid biosynthesis, anthocyanin biosynthesis, and flavone and flavonol biosynthesis are differential enrichment metabolic pathways. As such, identifying these different metabolites contribute to a better understanding of the function and nutritional value of various rice strains.

Metabolic profiling and transcriptome analysis provide insights into the accumulation of flavonoids in chayote fruit during storage

Chayote (Sechium edulel) fruits are rich in flavonoids, folate, and low-calorie food. However, studies about the flavonoids and the corresponding regulatory mechanism of flavonoid synthesis in chayote fruits was still unclear. In present study, an integrated transcriptome and metabolite analysis of chayote fruits at three different storage stages were conducted to explore the flavonoid compositions and gene expression associated with flavonoid synthesis. Through the UPLC-MS/MS analysis, a total of 57 flavonoid compounds were detected. Of these, 42 flavonoid glycosides were significantly differential accumulation in chayote fruits at three different storage stages. Many genes associated with flavonoid synthesis were differentially expressed in chayote fruits at three different storage stages through RNA-seq analysis, including structural genes and some TFs. There was a high correlation between RNA-seq analysis and metabolite profiling, and the expression level of candidate genes in the flavonoid synthesis pathway were consistent with the dynamic changes of flavonoids. In addition, one R2R3-MYB transcription factor, FSG0057100, was defined as the critical regulatory gene of flavonoid synthesis. Furthermore, exogenous application of phenylalanine increased the total content of flavonoids and promoted some flavonoid biosynthesis-related gene expression in chayote fruits. The above results not only make us better understand the molecular mechanism of flavonoid synthesis in chayote fruits, but also contribute to the promotion and application of chayote products.

Systematic Analysis of BELL Family Genes in Zizania latifolia and Functional Identification of ZlqSH1a/b in Rice Seed Shattering

The loss of seed shattering is an important event in crop domestication, and elucidating the genetic mechanisms underlying seed shattering can help reduce yield loss during crop production. This study is the first to systematically identify and analyse the BELL family of transcription factor-encoding genes in Chinese wild rice (Zizania latifolia). ZlqSH1a (Zla04G033720) and ZlqSH1b (Zla02G027130) were identified as key candidate genes involved in seed shattering in Z. latifolia. These genes were involved in regulating the development of the abscission layer (AL) and were located in the nucleus of the cell. Over-expression of ZlqSH1a and ZlqSH1b resulted in a complete AL between the grain and pedicel and significantly enhanced seed shattering after grain maturation in rice. Transcriptome sequencing revealed that 172 genes were differentially expressed between the wild type (WT) and the two transgenic (ZlqSH1a and ZlqSH1b over-expressing) plants. Three of the differentially expressed genes related to seed shattering were validated using qRT-PCR analysis. These results indicate that ZlqSH1a and ZlqSH1b are involved in AL development in rice grains, thereby regulating seed shattering. Our results could facilitate the genetic improvement of seed-shattering behaviour in Z. latifolia and other cereal crops.

Metabolomics and proteomics reveal the molecular basis of colour formation in the pericarp of Chinese wild rice (Zizania latifolia)

Chinese wild rice (Zizania latifolia) is rich in flavonoids and the characteristic colour of its pericarp is attributed to the flavonoids. In this study, the molecular basis of the colour change in the pericarp of Chinese wild rice was studied using metabolomics and proteomics. Whole seeds in three developmental stages (10, 20, and 30 days after flowering) were characterised based on phenolic contents, free amino acids (FAAs), and the expression level and activities of enzymes critical in flavonoid biosynthesis. The total phenolic and proanthocyanidin contents of Chinese wild rice increased gradually, whereas total flavonoid and FAA contents decreased during seed development. Metabolomic analysis revealed gradual upward trends for 57 flavonoids (sub classes 1, 3, and 10) related to colour change in the pericarp. Proteomic analysis showed that the phenylpropanoid biosynthesis metabolic pathway was enriched with differentially expressed proteins and was associated with flavonoid biosynthesis. Proteomic data suggested that leucoanthocyanidin reductase and WD40 repeat protein may be involved in flavonoid biosynthesis in Chinese wild rice, which was also verified by real-time quantitative PCR. Our results provide new insights into the understanding of the colour formation in the pericarp of Chinese wild rice.

Polyphenol Composition and Antioxidant Activity of Japonica Rice Cultivars and Intake Status

Japonica rice is produced mainly in northeast China, Japan, and the Korean Peninsula. Polyphenols and flavonoids are the main antioxidants in japonica rice. This study reported the polyphenol content and antioxidant activity of nine brown and white japonica rice cultivars. The total phenolic and flavonoid contents of brown rice were in the ranges of 241.98-296.76 GAE mg/100 g, and 225.30-276.80 RE mg/100 g, respectively. These values were significantly higher than that of white rice by 118.98-206.06% and 135.0-217%, respectively. The bound fraction from phenolics and flavonoids contributed 41.1-63.6% and 62.22-78.19% of the total phenolic and flavonoid content in brown rice, respectively, while these ranges were 55.5-73.5% and 46.07-66.83% in white rice, respectively. p-Hydroxybenzonic acid was the predominant phenolic acid in japonica rice. All four antioxidant capacities of brown rice (DPPH, ABTS, OH, FRAP) were higher by up to 1.68-2.85 times than those of white rice. The PZ21 (Yanfeng 47) japonica rice variety has outstanding antioxidant capacity based on the weights of each antioxidant index. According to the differences of functional substances among varieties, it can provide guidance for consumers and theoretical basis for the production of healthy food.

Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

BACKGROUND

Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development.

RESULTS

In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation.

CONCLUSIONS

Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.

Role of Nutrients and Foods in Attenuation of Cardiac Remodeling through Oxidative Stress Pathways

Cardiac remodeling is defined as a group of molecular, cellular, and interstitial changes that manifest clinically as changes in the heart’s size, mass, geometry, and function after different injuries. Importantly, remodeling is associated with increased risk of ventricular dysfunction and heart failure. Therefore, strategies to attenuate this process are critical. Reactive oxygen species and oxidative stress play critical roles in remodeling. Importantly, antioxidative dietary compounds potentially have protective properties against remodeling. Therefore, this review evaluates the role of nutrients and food as modulators of cardiac remodeling.

Effect of enzymatic hydrolysis on digestibility and morpho-structural properties of hydrothermally pre-treated red rice starch

The objective of this work was to evaluate the effects of enzymatic hydrolysis on digestibility and morphological and structural properties of hydrothermally pre-treated (HPT) red rice starch. The pre-treatments were performed in autoclave and cooking for the modification of rice grains and native starch. In vitro starch digestibility was performed consecutively and semi-simultaneously using α-amylase and amyloglucosidase. A first-order mathematical model was used to adjust the hydrolysis kinetic data, which made it possible to calculate the surface area, hydrolysis index, and glycemic index of the starch. Scanning electron microscopy images (SEM), Fourier transform infrared (FTIR) spectra and X-ray diffraction (XRD) were also performed to investigate the characteristics of the post-hydrolysis starch samples. The autoclaved starch HSS-A3, which was subjected to 121 °C/1.08 bar for 10 min, showed the highest in vitro digestibility values (80.08 %). Both starch samples showed increase of particle size and enzymatic digestibility after HPT. FTIR spectra of the starch samples showed that there was no appearance of new functional groups. However, XRD evidenced that HPT changed the intensity of the peaks and the type of crystallinity was changed for autoclaved starch (A3) from type A to Vh, with crystallinity ranging from 21.71 % to 26.42 %. The semi-simultaneous approach showed more advantages due to the highest in vitro digestibility as well as reducing the processing time and use of reagents.

Metabolomics based inferences to unravel phenolic compound diversity in cereals and its implications for human gut health

Background

Scope and approach

Key findings and conclusion

•

Phenolic compounds are critical in avoiding metabolic disorders associated with oxidative stress.

•

Breeding cereal crops to enrich phenolic compounds in grains contributes to personalized nutrition.

•

A diet rich in cereal phenolics likely to increase human gut health, thereby lowering the risk of non-communicable illness.

Optimization of the pulse electric field assisted extraction of black rice grain for antioxidant and sirtuin1 enzyme stimulation activities

Cyanidin-3-glucoside (C3G) and peonidin-3-glucoside (P3G) in black rice grain (BRG) demonstrate many beneficial health effects, including antioxidant and anti-aging properties. This research aimed to study on pulsed electric field assisted water extraction (PEF-AWE) on BRG using pre-treatment technique, which was determined for enhanced yields of C3G and P3G, antioxidant and sirtuin1 enzyme stimulation activities. The effects of operating parameters for PEF-AWE (intensity of electric field, X₁: 3–5 kV/cm, number of pulse, X₂: 1000–3000 pulse and BRG/water ratio, X₃: 0.1–0.5 g/mL) were determined using regression analysis and optimized PEF-AWE condition using the response surface methodology. Regression models showed the intensity of electric field and BRG/water ratio were the strong influence parameters significantly on C3G (p < 0.01). The results highlighted optimized conditions of PEF-AWE followed by 5 kV/cm, 3000 pulse and 0.5 g/mL leading to achieve higher C3G (92.59 ± 4.79 mg/g) and P3G (4.59 ± 0.27 mg/g) than no pre-treatment by PEF process, approximately 60%. Additionally, PEF extracts of BRG can modulate the ability of surtuin1 enzyme to deacetylate substrate proteins (26.78 ± 0.50 FIR). Thus, PEF-AWE can be applied to produce BRG extract as natural antioxidant compound and functional ingredient.

Comparative metabolomics study of Tartary (Fagopyrum tataricum (L.) Gaertn) and common (Fagopyrum esculentum Moench) buckwheat seeds

Tartary buckwheat has higher health-promoting value than common buckwheat. However, the related metabolites information except flavonoids is largely deficient. Here, we compared the seed metabolomes of the two species using a UHPLC-QqQ-MS-based metabolomics approach. In total, 722 metabolites were obtained, of which 84 and 78 were identified as the key active ingredients of Traditional Chinese Medicines and the active pharmaceutical ingredients for six major diseases-resistance, respectively. Comparative analysis showed there were obviously difference in metabolic profiles between the two buckwheat species, and further found 61 flavonoids and 94 non-flavonoids metabolites displayed significantly higher contents (≥2 fold) in Tartary buckwheat than in common buckwheat. Our results suggest that Tartary and common buckwheat seeds are rich in metabolites beneficial to human health, and non-flavonoids metabolites also contributed to Tartary buckwheat's higher health-promoting value than common buckwheat. This study provides valuable information for the development of new functional foods of Tartary buckwheat.

Chemical Composition Analysis, Cytotoxic, Antimicrobial and Antioxidant Activities of Physalis angulata L.: A Comparative Study of Leaves and Fruit

Physalis angulata L. belongs to the family Solanaceae and is distributed throughout the tropical and subtropical regions. Physalis angulata leaf and fruit extracts were assessed for in vitro anticancer, antioxidant activity, and total phenolic and flavonoid content. The GC-MS technique investigated the chemical composition and structure of bioactive chemicals reported in extracts. The anticancer activity results revealed a decrease in the percentage of anticancer cells' viability in a concentration- and time-dependent way. We also noticed morphological alterations in the cells, which we believe are related to Physalis angulata extracts. Under light microscopy, we observed that as the concentration of ethanolic extract (fruit and leaves) treated HeLa cells increased, the number of cells began to decrease.

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Chinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7-31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.

The nutritional profile and human health benefit of pigmented rice and the impact of post-harvest processes and product development on the nutritional components: A review

Pigmented rice has attracted considerable attention due to its nutritional value, which is in large conferred by its abundant content of phenolic compounds, considerable micronutrient concentrations, as well as its higher resistant starch and thereby slower digestibility properties. A wide range of phenolic compounds identified in pigmented rice exhibit biological activities such as antioxidant activity, anti-inflammatory, anticancer, and antidiabetic properties. Post-harvest processes significantly reduce the levels of these phytochemicals, but recent developments in processing methods have allowed greater retention of their contents. Pigmented rice has also been converted to different products for food preservation and to derive functional foods. Profiling a large set of pigmented rice cultivars will thus not only provide new insights into the phytochemical diversity of rice and the genes underlying the vast array of secondary metabolites present in this species but also provide information concerning their nutritional benefits, which will be instrumental in breeding healthier rice. The present review mainly focuses on the nutritional composition of pigmented rice and how it can impact human health alongside the effects of post-harvest processes and product development methods to retain the ambient level of phytochemicals in the final processed form in which it is consumed.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.

Comparison of Phenolic and Flavonoid Compound Profiles and Antioxidant and α-Glucosidase Inhibition Properties of Cultivated Soybean (Glycine max) and Wild Soybean (Glycine soja)

Wild soybean (Glycine soja Sieb.et Zucc; WS) has been used as a traditional food in China for many years and contains significantly higher levels of isoflavones than cultivated soybean (Glycine max; CS), but the secondary metabolites, including flavonoids and the phenolic composition differences between them, remain unclear. The results showed that WS possessed significantly higher total phenolic and flavonoid content and exhibited better antioxidant and α-glucosidase inhibition activities as well as excellent protective effects against H₂O₂-induced oxidative injury in a human endothelial cell line. Through metabolomic analysis, 642 metabolites were identified, and 238 showed differential expression, with 151 upregulated and 87 downregulated. A total of 79 flavonoid compounds were identified, 42 of which were upregulated in WS. 2'-Hydroxygenistein, garbanzol, protocatechuic aldehyde, ligustilide, and resveratrol were the most discriminated compounds in WS. The metabolic pathway analysis of differential metabolites related to the biosynthesis of flavonoids and phenolic acids were the biosynthesis of phenylpropanoids, flavonoids, isoflavonoids, flavones, and flavonols. This study substantially elucidated differences in the content of flavonoids and biological activities between WS and CS, which is useful information for the effective utilization of these two black soybean species in food processing.

The Total Antioxidant Capacity and the Total Phenolic Content of Rice Using Water as a Solvent

Background

The present study evaluates the antioxidant properties of some Sri Lankan red rice varieties using water extracts.

Methods

Water extracts of rice varieties Attakkari, Bg2907, and Bg407 were used in this study. The total antioxidant capacity was measured by ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, and reducing power assays. The total phenolic content (TPC), total flavonoid content (TFC), monomeric anthocyanin, and condensed tannin contents were measured by Folin-Ciocalteu, aluminium chloride, pH differential, and vanillin assays, respectively.

Results

It was observed that mean FRAP, DPPH, reducing power, TPC, TFC, monomeric anthocyanin content, and condensed tannin content were in the range of 0.561 ± 0.113 to 0.695 ± 0.077 mmol/100 g fresh weight (FW), 26.07 ± 3.08 to 53.66 ± 7.61 mg/mL FW, 33.49 ± 4.105.14 to 40.81 ± 3.65 mg/mL, 0.676 ± 0.078 to 0.900 ± 0.057 mg tannic acid equivalent (TAE)/g, 5.36 ± 0.75 to 6.38 ± 0.82 mg TAE/g FW, 0.0202 ± 0.005 to 0.0292 ± 0.009 mg/g FW, and 0.078 ± 0.015 to 0.104 ± 0.017 mg TAE/g FW, respectively. Significant differences were observed in DPPH, reducing power, and TPC among rice varieties (p < 0.05). Rice variety Attakkari had the highest total antioxidant capacity (TAC), scavenging activity, reducing power, TPC, TFC, monomeric anthocyanin content, and condensed tannin content followed by Bg2907 and Bg406.

Conclusion

Total phenolic compounds, total flavonoid, and condensed tannin are the major antioxidants in all three varieties of rice while the monomeric anthocyanin is only a minor antioxidant.