Dynamic Metabolomics and Transcriptomics Analyses for Characterization of Phenolic Compounds and Their Biosynthetic Characteristics in Wheat Grain

Untargeted metabolomic and transcriptomic analysis in spring and durum wheat reveals potential mechanisms associated with the early stem solidness phenotype and resistance to wheat stem sawfly

Wheat stem sawfly (WSS) causes devastating yield loss in both common bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum L. var durum) in the North American Great Plains. The early stem solidness phenotype confers solid stems early in plant development coinciding with the flight period of WSS and provides protection to plants during the critical oviposition period. With this phenotype, pith is lost as the plant develops, which may allow for enhanced biological control of surviving larvae by braconid parasitoids Bracon cephi (Gahan) and Bracon lissogaster Muesebeck, as well as having additional potential yield benefits from utilizing reabsorbed pith components. Here, we use an untargeted transcriptomics and metabolomics approach to explore the mechanisms related to the early stem solidness phenotype in three cultivars of spring wheat and two cultivars of durum wheat in addition to three near- isogenic pairs of spring wheat and two near- isogenic pairs of durum wheat. We identified effects of growth stage and allele on expression of metabolites and transcripts associated with stem solidness, development of cell walls and programmed cell death. A caffeic acid methylesterase and pectin methylesterase were upregulated in hollow stemmed Reeder and lines with the 3BLa allele, which likely influences lignin subunit proportions as well as the production of volatile semiochemicals that impact the behavior of adult WSS. TaVPE3cB, a gene associated with programmed cell death and thickening of cell walls, also had increased expression in hollow stemmed lines and is likely partially responsible for the hollow stemmed phenotype observed. Growth stage and allele also affected the expression of transcripts and metabolites involved in the phenylpropanoid pathway, carbohydrate and glycoside biosynthesis and lipid biosynthesis, implicating the involvement of these pathways in resistance and plant response to infestation by WSS.

Dynamic Metabolomic Changes in the Phenolic Compound Profile and Antioxidant Activity in Developmental Sorghum Grains

Phenolic compounds (PC) were analyzed by UHPLC-ESI-QTOF-MSE in two sorghum genotypes, harvested in two growing seasons (GS) at five distinct days after flowering (DAF) to evaluate how genotype/GS influences the PC synthesis and antioxidant capacity during grain growth. Total phenolic contents were strongly correlated with antioxidant capacity (r > 0.9, p < 0.05). Globally, 97 PC were annotated, including 20 PC found irrespective of the grain developmental stage and genotype/GS. The phenolic profile clearly differs between stages: phenolic acids were the most abundant class in early stages (50%), and flavonoid accumulation becomes predominant in late ones (3/5 of total ion abundance). Dimeric and trimeric tannins were identified even in 10DAF grains. Chemometry revealed great PC variability between genotypes (27%) and important biomarkers of GS differentiation (e.g., ferulic acid). This work can input open databases of PC and paves the way to understand biosynthetic pathways of PC in sorghum and future sorghum selection.

Unrevealing the mechanisms behind the cardioprotective effect of wheat polyphenolics

Cardiovascular diseases pose a major threat to both life expectancy and quality of life worldwide, and a concerning level of disease burden has been attained, particularly in middle- and low-income nations. Several drugs presently in use lead to multiple adverse events. Thus, it is urgently needed to develop safe, affordable, and effective management of cardiovascular diseases. Emerging evidence reveals a positive association between polyphenol consumption and cardioprotection. Whole wheat grain and allied products are good sources of polyphenolic compounds bearing enormous cardioprotective potential. Polyphenolic extract of the entire wheat grain contains different phenolic compounds viz. ferulic acid, caffeic acid, chlorogenic acid, p-coumaric acid, sinapic acid, syringic acid, vanillic acid, apigenin, quercetin, luteolin, etc. which exert cardioprotection by reducing oxidative stress and interfering with different toxicological processes. The antioxidant capacity has been thought to exert the cardioprotective mechanism of wheat grain polyphenolics, which predominantly suppresses oxidative stress, inflammation and fibrosis by downregulating several pathogenic signaling events. However, the combined effect of polyphenolics appears to be more prominent than that of a single molecule, which might be attained due to the synergy resulting in multimodal cardioprotective benefits from multiple phenolics. The current article covers the bioaccessibility and possible effects of wheat-derived polyphenolics in protecting against several cardiovascular disorders. This review discusses the mechanistic pharmacology of individual wheat polyphenols on the cardiovascular system. It also highlights the comparative superiority of polyphenolic extracts over a single phenolic.

Integrative metabolome and transcriptome profiling provide insights into elucidation of the synthetic mechanisms of phenolic compounds in Yunnan hulled wheat (Triticum aestivum ssp. yunnanense King)

BACKGROUND

Yunnan hulled wheat grains (YHWs) have abundant phenolic compounds (PCs). However, a systematic elucidation of the phenolic characteristics and molecular basis in YHWs is currently lacking. The aim of the study, for the first time, was to conduct metabolomic and transcriptomic analyses of YHWs at different developmental stages.

RESULTS

A total of five phenolic metabolite classes (phenolic acids, flavonoids, quinones, lignans and coumarins, and tannins) and 361 PCs were identified, with flavonoids and phenolic acids being the most abundant components. The relative abundance of the identified PCs showed a dynamic decreasing pattern with grain development, and the most significant differences in accumulation were between the enlargement and mature stage, which is consistent with the gene regulation patterns of the corresponding phenolic biosynthesis pathway. Through co-expression and co-network analysis, PAL, HCT, CCR, F3H, CHS, CHI and bZIP were identified and predicted as candidate key enzymes and transcription factors.

CONCLUSION

The results broaden our understanding of PC accumulation in wheat whole grains, especially the differential transfer between immature and mature grains. The identified PCs and potential regulatory factors provide important information for future in-depth research on the biosynthesis of PCs and the improvement of wheat nutritional quality. © 2024 Society of Chemical Industry.

Metabolome and Transcriptome Association Analysis Reveals Mechanism of Synthesis of Nutrient Composition in Quinoa (Chenopodium quinoa Willd.) Seeds

Quinoa (Chenopodium quinoa Willd.) seeds are rich in nutrition, superior to other grains, and have a high market value. However, the biosynthesis mechanisms of protein, starch, and lipid in quinoa grain are still unclear. The objective of this study was to ascertain the nutritional constituents of white, yellow, red, and black quinoa seeds and to employ a multi-omics approach to analyze the synthesis mechanisms of these nutrients. The findings are intended to furnish a theoretical foundation and technical support for the biological breeding of quinoa in China. In this study, the nutritional analysis of white, yellow, red, and black quinoa seeds from the same area showed that the nutritional contents of the quinoa seeds were significantly different, and the protein content increased with the deepening of color. The protein content of black quinoa was the highest (16.1 g/100 g) and the lipid content was the lowest (2.7 g/100 g), among which, linoleic acid was the main fatty acid. A combined transcriptome and metabolome analysis exhibited that differentially expressed genes were enriched in "linoleic acid metabolism", "unsaturated fatty acid biosynthesis", and "amino acid biosynthesis". We mainly identified seven genes involved in starch synthesis (LOC110716805, LOC110722789, LOC110738785, LOC110720405, LOC110730081, LOC110692055, and LOC110732328); five genes involved in lipid synthesis (LOC110701563, LOC110699636, LOC110709273, LOC110715590, and LOC110728838); and nine genes involved in protein synthesis (LOC110710842, LOC110720003, LOC110687170, LOC110716004, LOC110702086, LOC110724454 LOC110724577, LOC110704171, and LOC110686607). The data presented in this study based on nutrient, transcriptome, and metabolome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa, and provide candidate genes for further genetic improvements to improve the nutritional value of quinoa seeds.

Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars

BACKGROUND

The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in proteins, amino acids, lipids, carbohydrates. Walnut had a variety endopleura color as yellow, red, and purple. However, the regulation of walnut endopleura color remains little known.

RESULTS

To understand the process of coloration in endopleura, we performed the integrative analysis of transcriptomes and metabolomes at two developmental stages of walnut endopleura. We obtained total of 4,950 differentially expressed genes (DEGs) and 794 metabolites from walnut endopleura, which are involved in flavonoid and phenolic biosynthesis pathways. The enrichment analysis revealed that the cinnamic acid, coniferyl alcohol, naringenin, and naringenin-7-O-glucoside were important metabolites in the development process of walnut endopleura. Transcriptome and metabolome analyses revealed that the DEGs and differentially regulated metabolites (DRMs) were significantly enriched in flavonoid biosynthesis and phenolic metabolic pathways. Through co-expression analysis, CHS (chalcone synthase), CHI (chalcone isomerase), CCR (cinnamoyl CoA reductase), CAD (cinnamyl alcohol dehydrogenase), COMT (catechol-Omethyl transferase), and 4CL (4-coumaroyl: CoA-ligase) may be the key genes that potentially regulate walnut endopleura color in flavonoid biosynthesis and phenolic metabolic pathways.

CONCLUSIONS

This study illuminates the metabolic pathways and candidate genes that underlie the endopleura coloration in walnuts, lay the foundation for further study and provides insights into controlling nut's colour.

Influence of lactic acid fermentation on the phenolic profile, antioxidant activities, and volatile compounds of black chokeberry (Aronia melanocarpa) juice

Lactic acid fermentation is an effective method for improving the quality of black chokeberry. This study aimed to investigate the influence of lactic acid bacteria on the phenolic profile, antioxidant activities, and volatiles of black chokeberry juice. Initially, 107  cfu/mL of Lactiplantibacillus plantarum, Lactobacillus acidophilus, and Lacticaseibacillus rhamnosus were inoculated into pasteurized black chokeberry juice and fermented for 48 h at 37°C. All these strains enhanced the total phenolic and total flavonoid contents, with La. acidophilus showing the highest total phenolic (1683.64 mg/L) and total flavonoid (659.27 mg/L) contents. Phenolic acids, flavonoids, and anthocyanins were identified using ultrahigh-performance liquid chromatography-tandem mass spectrometry. The prevalent phenolic acid, flavonoid, and anthocyanin in the lactic-acid-fermented black chokeberry juice were cinnamic acid, rutin, and cyanidin-3-O-rutinoside, respectively. Furthermore, following fermentation, the DPPH and ABTS scavenging capacity, as well as the reducing power capacity, increased from 59.98% to 92.70%, 83.06% to 94.95%, and 1.24 to 1.82, respectively. Pearson's correlation analysis revealed that the transformation of phenolic acids, flavonoids, and anthocyanins probably contributed to enhancing antioxidant activities and color conversation in black chokeberry juice. A total of 40 volatiles were detected in the fermented black chokeberry juice by gas chromatography-ion mobility spectrometry. The off-flavor odors, such as 1-penten-3-one and propanal in the black chokeberry juice, were weakened after fermentation. The content of 2-pentanone significantly increased in all fermented juice, imparting an ethereal flavor. Hence, lactic acid fermentation can effectively enhance black chokeberry products' flavor and prebiotic value, offering valuable insights into their production. PRACTICAL APPLICATION: The application of lactic acid bacteria in black chokeberry juice not only enhances its flavor but also improves its health benefits. This study has expanded the range of black chokeberry products and offers a new perspective for the development of the black chokeberry industry.

Integrated Metabolome and Transcriptome Analyses Reveal Amino Acid Biosynthesis Mechanisms during the Physiological Maturity of Grains in Yunnan Hulled Wheat (Triticum aestivum ssp. yunnanense King)

Yunnan hulled wheat (YHW) possesses excellent nutritional characteristics; however, the precise amino acid (AA) composition, contents, and molecular mechanisms underlying AA biosynthesis in YHW grains remain unclear. In this study, we aimed to perform metabolomic and transcriptomic profiling to identify the composition and genetic factors regulating AA biosynthesis during the physiological maturation of grains of two YHW genotypes, Yunmai and Dikemail, with high and low grain protein contents, respectively. A total of 40 and 14 differentially accumulated amino acids (AAs) or AA derivatives were identified between the waxy grain (WG) and mature grain (MG) phenological stages of Yunmai and Dikemail, respectively. The AA composition differed between WG and MG, and the abundance of AAs-especially that of essential AAs-was significantly higher in WG than in MG (only 38.74-58.26% of WG). Transcriptome analysis revealed differential regulation of structural genes associated with the relatively higher accumulation of AAs in WG. Weighted gene co-expression network analysis and correlation analyses of WG and MG indicated differences in the expression of clusters of genes encoding both upstream elements of AA biosynthesis and enzymes that are directly involved in AA synthesis. The expression of these genes directly impacted the synthesis of various AAs. Together, these results contribute to our understanding of the mechanism of AA biosynthesis during the different developmental stages of grains and provide a foundation for further research to improve the nutritional value of wheat products.

The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.

Antioxidant Capacity and Profiles of Phenolic Acids in Various Genotypes of Purple Wheat

The total phenolic content, phenolic compositions, and antioxidant capacity in the grain of 40 purple wheat genotypes were studied. In this study, purple wheats were investigated in terms of their composition of free and bound phenolic acids and 2,2-diphenyl-1-picrylhydrazyl radical scavenging capacity. The free phenolic content ranged from 164.25 to 271.05 mg GAE/100 g DW and the bound phenolic content was between 182.89-565.62 mg GAE/100 g wheat. The total phenolic content of purple wheat samples ranged from 352.65 to 771.83 mg GAE/100 g wheat. Gallic acid, protocatechuic acid, catechin, 4-hydroxybenzoic acid, syringic acid, ellagic acid, m-coumaric acid, o-coumaric acid, chrysin, caffeic acid, p-coumaric acid, ferulic acid, quercetin, kaempferol, rutin, sinapic acid, and chlorogenic acid were detected by HPLC system. Gallic acid, benzoic acid derivatives, and dominant phenolics, which are frequently found in cereals, were also dominant in purple wheat samples and were found in free fractions. The antioxidant capacity was assessed using the DPPH method. The antioxidant capacity (AA%) in the free phenolic extracts of the purple wheats was between 39.7% and 59.5%, and the AA% values of bound phenolic extract of the purple wheat varied between 42.6% and 62.7%. This study suggested that purple wheat samples have high phenolic compound content as antioxidant potential and therefore consumption of purple wheat-containing food products may provide health benefits.

QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing

The size, shape, and color of wheat seeds are important traits that are associated with yield and flour quality (size, shape), nutritional value, and pre-harvest sprouting (coat color). These traits are under multigenic control, and to dissect their molecular and genetic basis, quantitative trait loci (QTL) analysis is used. We evaluated 114 recombinant inbred lines (RILs) in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative, ITMI/MP) grown in 2014 season. We used digital image analysis for seed phenotyping and obtained data for seven traits describing seed size and shape and 48 traits of seed coat color. We identified 212 additive and 34 pairs of epistatic QTLs on all the chromosomes of wheat genome except chromosomes 1A and 5D. Many QTLs were overlapping. We demonstrated that the overlap between QTL regions was low for seed size/shape traits and high for coat color traits. Using the literature and KEGG data, we identified sets of genes in Arabidopsis and rice from the networks controlling seed size and color. Further, we identified 29 and 14 candidate genes for seed size-related loci and for loci associated with seed coat color, respectively.