Characterization of factors underlying the metabolic shifts in developing kernels of colored maize

Integrative transcriptome and metabolome analysis reveals the mechanisms of light-induced pigmentation in purple waxy maize

Introduction

Waxy maize, mainly consumed at the immature stage, is a staple and vegetable food in Asia. The pigmentation in the kernel of purple waxy maize enhances its nutritional and market values. Light, a critical environmental factor, affects anthocyanin biosynthesis and results in pigmentation in different parts of plants, including in the kernel. SWL502 is a light-sensitive waxy maize inbred line with purple kernel color, but the regulatory mechanism of pigmentation in the kernel resulting in purple color is still unknown.

Methods

In this study, cyanidin, peonidin, and pelargonidin were identified as the main anthocyanin components in SWL502, evaluated by the ultra-performance liquid chromatography (UPLC) method. Investigation of pigment accumulation in the kernel of SWL502 was performed at 12, 17, and 22 days after pollination (DAP) under both dark and light treatment conditions via transcriptome and metabolome analyses.

Results

Dark treatment affected genes and metabolites associated with metabolic pathways of amino acid, carbohydrate, lipid, and galactose, biosynthesis of phenylpropanoid and terpenoid backbone, and ABC transporters. The expression of anthocyanin biosynthesis genes, such as 4CL2, CHS, F3H, and UGT, was reduced under dark treatment. Dynamic changes were identified in genes and metabolites by time-series analysis. The genes and metabolites involved in photosynthesis and purine metabolism were altered in light treatment, and the expression of genes and metabolites associated with carotenoid biosynthesis, sphingolipid metabolism, MAPK signaling pathway, and plant hormone signal transduction pathway were induced by dark treatment. Light treatment increased the expression level of major transcription factors such as LRL1, myc7, bHLH125, PIF1, BH093, PIL5, MYBS1, and BH074 in purple waxy maize kernels, while dark treatment greatly promoted the expression level of transcription factors RVE6, MYB4, MY1R1, and MYB145.

Discussion

This study is the first report to investigate the effects of light on waxy maize kernel pigmentation and the underlying mechanism at both transcriptome and metabolome levels, and the results from this study are valuable for future research to better understand the effects of light on the regulation of plant growth.

High-quality genome assembly and multi-omics analysis of pigment synthesis pathway in Auricularia cornea

Owing to its great market potential for food and health care, white Auricularia cornea, a rare edible fungus, has received increased attention in recent years. This study presents a high-quality genome assembly of A. cornea and multi-omics analysis of its pigment synthesis pathway. Continuous Long Reads libraries, combined with Hi-C-assisted assembly were used to assemble of white A. cornea. Based on this data, we analyzed the transcriptome and metabolome of purple and white strains during the mycelium, primordium, and fruiting body stages. Finally, we obtained the genome of A.cornea assembled from 13 clusters. Comparative and evolutionary analysis suggests that A.cornea is more closely related to Auricularia subglabra than to Auricularia heimuer. The divergence of white/purple A.cornea occurred approximately 40,000 years ago, and there were numerous inversions and translocations between homologous regions of the two genomes. Purple strain synthesized pigment via the shikimate pathway. The pigment in the fruiting body of A. cornea was γ-glutaminyl-3,4-dihydroxy-benzoate. During pigment synthesis, α-D-glucose-1P, citrate, 2-Oxoglutarate, and glutamate were four important intermediate metabolites, whereas polyphenol oxidase and other 20 enzyme genes were the key enzymes. This study sheds light on the genetic blueprint and evolutionary history of the white A.cornea genome, revealing the mechanism of pigment synthesis in A.cornea. It has important theoretical and practical implications for understanding the evolution of basidiomycetes, molecular breeding of white A.cornea, and deciphering the genetic regulations of edible fungi. Additionally, it provides valuable insights for the study of phenotypic traits in other edible fungi.

Integrative metabolomic and transcriptomic analyses reveal the mechanisms of Tibetan hulless barley grain coloration

Cereal grains accumulate anthocyanin during developmental process. The anthocyanin content increases at grain filling stages to develop grain coloration in cereals. However, anthocyanin biosynthesis responsible for grain coloring and its regulatory mechanisms controlled by structural and functional genes remain unclear. Therefore, this study aimed to explore the global map of metabolic changes linked to grain coloration of Tibetan hulless barley (qingke) using an integrative metabolome and transcriptome approach. Grains from three colored qingke cultivars at different developmental stages were considered for molecular and metabolic investigations. A total of 120 differentially accumulated metabolites (DAMs) and 8,327 differentially expressed genes (DEGs) were filtered. DEGs were mainly enriched in the phenylpropanoid and flavonoid pathways. The transcript levels of anthocyanin biosynthesis genes (PAL, C4H, 4CL, CHS, FLS, F3H, F3'H, DFR, ANS, GT, OMT, and MAT) significantly upregulate in colored qingke compared to the non-colored variety. During grain development and maturation, the strong correlation of HvMYC2 expression with anthocyanin contents and anthocyanin biosynthesis genes suggested it as a critical gene in anthocyanin accumulation. Further results confirmed that HvMYC2 could be activated by HvMYB and be a positive regulator of UV-B and cold tolerance in qingke. In addition, verification based on enzymatic assays indicated that six key modifier enzymes could catalyze glycosylation, malonylation, and methylation of anthocyanins, thereby dissecting the major anthocyanin modification pathway in colored qingke. Overall, our study provides global insight into anthocyanin accumulation and the mechanism underlying grain coloration in qingke.

A newly characterized allele of ZmR1 increases anthocyanin content in whole maize plant and the regulation mechanism of different ZmR1 alleles

The novel ZmR1^CQ01 allele for maize anthocyanin synthesis was identified, and the biological function and regulatory molecular mechanisms of three ZmR1 alleles were unveiled. Anthocyanins in maize are valuable to human health. The R1 gene family is one of the important regulatory genes for the tissue-specific distribution of anthocyanins. R1 gene allelic variations are abundant and its biological function and regulatory molecular mechanisms are not fully understood. By exploiting genetic mapping and transgenic verification, we found that anthocyanin pigmentation in maize leaf midrib was controlled by ZmR1 on chromosome 10. Allelism test of maize zmr1 EMS mutants confirmed that anthocyanin pigmentation in leaf sheath was also controlled by ZmR1. ZmR1^CQ01 was a novel ZmR1 allelic variation obtained from purple maize. Its overexpression caused the whole maize plant to turn purple. ZmR1^B73 allele confers anthocyanin accumulation in near ground leaf sheath rather than in leaf midribs. The mRNA expression level of ZmR1^B73 was low in leaf midribs, resulting in no anthocyanin accumulation. ZmR1^B73 overexpression promoted anthocyanin accumulation in leaf midribs. Loss of exon 5 resulted in ZmR1^ZN3 allele function destruction and no anthocyanin accumulation in leaf midrib and leaf sheath. DNA affinity purification sequencing revealed 1010 genes targeted by ZmR1^CQ01, including the bz2 in anthocyanin synthesis pathway. RNA-seq analysis showed 55 genes targeted by ZmR1^CQ01 changed the expression level significantly, and the expression of genes encoding key enzymes in flavonoid and phenylpropanoid biosynthesis pathways were significantly up-regulated. ZmR1 functional molecular marker was developed. These results revealed the effects of transcriptional regulation and sequence variation on ZmR1 function and identified the genes targeted by ZmR1^CQ01 at the genome-wide level.

Maize Flavonoid Biosynthesis, Regulation, and Human Health Relevance: A Review

Maize is one of the most important crops for human and animal consumption and contains a chemical arsenal essential for survival: flavonoids. Moreover, flavonoids are well known for their beneficial effects on human health. In this review, we decided to organize the information about maize flavonoids into three sections. In the first section, we include updated information about the enzymatic pathway of maize flavonoids. We describe a total of twenty-one genes for the flavonoid pathway of maize. The first three genes participate in the general phenylpropanoid pathway. Four genes are common biosynthetic early genes for flavonoids, and fourteen are specific genes for the flavonoid subgroups, the anthocyanins, and flavone C-glycosides. The second section explains the tissue accumulation and regulation of flavonoids by environmental factors affecting the expression of the MYB-bHLH-WD40 (MBW) transcriptional complex. The study of transcription factors of the MBW complex is fundamental for understanding how the flavonoid profiles generate a palette of colors in the plant tissues. Finally, we also include an update of the biological activities of C3G, the major maize anthocyanin, including anticancer, antidiabetic, and antioxidant effects, among others. This review intends to disclose and integrate the existing knowledge regarding maize flavonoid pigmentation and its relevance in the human health sector.

Widely Targeted Metabolomics Analysis Reveals Key Quality-Related Metabolites in Kernels of Sweet Corn

Sweet corn (Zea mays convar. saccharata var. rugosa) is a major economic vegetable crop. Different sweet corn cultivars vary largely in flavor, texture, and nutrition. The present study performed widely targeted metabolomics analysis based on the HPLC-MS/MS technology to analyze the metabolic profiles in three sweet corn cultivars widely grown in China. A total of 568 metabolites in the three sweet corn cultivars were detected, of which 262 differential metabolites significantly changed among cultivars. Carbohydrates, organic acids, and amino acids were the majority detected primary metabolites. Organic acids were mainly concentrated on shikimate, benzoic acids, and quinic acid with aromatic groups. And the essential amino acids for the human body, methionine and threonine, were highly accumulated in the high-quality cultivar. In addition, phenylpropanoids and alkaloids were the most enriched secondary metabolites while terpenes were low-detected in sweet corn kernels. We found that the flavonoids exist in both free form and glycosylated form in sweet corn kernels. PCA and HCA revealed clear separations among the three sweet corn cultivars, suggesting distinctive metabolome profiles among three cultivars. The differential metabolites were mapped into flavonoid biosynthesis, phenylpropanoid biosynthesis, biosynthesis of amino acids, and other pathways according to the KEGG classification. Furthermore, we identified skimmin, N',N^″-diferuloylspermidine, and 3-hydroxyanthranilic acid as the key quality-related metabolites related to grain quality traits in sweet corn. The results suggested variations of metabolic composition among the three cultivars, providing the reference quality-related metabolites for sweet corn breeding.

Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges

Simple Summary

This review summarizes the status, applications, and challenges of plant metabolomics in the context of crop breeding, food quality and safety, and human nutrition and health. It also highlights the importance of plant metabolomics in elucidating biochemical and genetic bases of traits associated with nutritive and healthy beneficial foods and other plant products to secure food supply, to ensure food quality, to protect humans from malnutrition and other diseases. Meanwhile, this review calls for comprehensive collaborations to accelerate relevant researches and applications in the context of human nutrition and health.

Abstract

Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.

The Application of Metabolomics for the Study of Cereal Corn (Zea mays L.)

Corn (Zea mays L.) is an important cereal crop indigenous to the Americas, where its genetic biodiversity is still preserved, especially among native populations from Mesoamerica and South America. The use of metabolomics in corn has mainly focused on understanding the potential differences of corn metabolomes under different biotic and abiotic stresses or to evaluate the influence of genetic and environmental factors. The increase of diet-linked non-communicable diseases has increased the interest to optimize the content of bioactive secondary metabolites in current corn breeding programs to produce novel functional foods. This review provides perspectives on the role of metabolomics in the characterization of health-relevant metabolites in corn biodiversity and emphasizes the integration of metabolomics in breeding strategies targeting the enrichment of phenolic bioactive metabolites such as anthocyanins in corn kernels.

Anthocyanin Profiling of Maize Grains Using DIESI-MSQD Reveals That Cyanidin-Based Derivatives Predominate in Purple Corn, whereas Pelargonidin-Based Molecules Occur in Red-Pink Varieties from Mexico

Corn seeds contain natural pigments and antioxidants, such as the molecular variants of flavonoids and carotenoids. The aleurone and pericarp tissues from pigmented genotypes were extracted for metabolic fingerprinting and evaluated using UV-vis and mass spectrometry (MS). MS ionomic fingerprints classified samples according to genetic background and kernel color. The MS/MS fragmentation pattern (Daughter and Neutral Loss methods) allowed the tentative identification of 18 anthocyanins with glycosyl, malonyl, and succinyl moieties, including 535 m/z for cyanidin-3-O-(6″-malonyl-glucoside) and 621 m/z for cyanidin-3-O-(3″,6″-dimalonyl-glucoside). We also detected 663 m/z for pelargonidin-3-O-(disuccinyl-glucoside) and 633 m/z for peonidin-3-O-(disuccinyl-glucoside). Cyanidin-based anthocyanins were the most abundant in dark purple colored kernels, while pelargonidins predominated in the red-pink kernels of the "Elote occidental" landrace. Grains of "Conico negro" had a simultaneous pigmentation of aleurone and pericarp, while Vitamaize had purple pigmentation only in the aleurone layer. Most landraces had a white endosperm, while Vitamaize had a yellow endosperm and a dark seed coat. We conclude that Vitamaize grains contain both carotenes and anthocyanins, and therefore it is proposed as a nontransgenic agronomically improved variety of tropical purple maize, a good source for organic superfoods.

Integrated Metabolome and Transcriptome Analysis Uncovers the Role of Anthocyanin Metabolism in Michelia maudiae

Michelia maudiae Dunn is one of the important ornamental plants in the Magnoliaceae family, and the color of its flowers usually appears naturally pure white. The discovery of a rubellis flower named M. maudiae Dunn var. rubicunda provides an opportunity to reveal the metabolism of the flavonoids and anthocyanins of this “early angiosperm” plant. Combined metabolome and transcriptome analyses were applied using white and rubellis mutant tepals. Seven stages have been divided for flower development, and forty-eight differentially altered metabolites were identified between white and rubellis tepals at a later stage. The major anthocyanins including peonidin O-hexoside, cyanidin O-syringic acid, cyanidin 3,5-O-diglucoside, cyanidin 3-O-glucoside, and pelargonidin 3-O-glucoside were upregulated over 157-fold in the mutant. Conversely, the highly significant accumulation of the colorless procyanidin or the slightly yellow epicatechin and catechin was found in white flowers. Putative homologues of color-related genes involved in the phenylpropanoid and flavonoid biosynthesis pathway were identified in the transcriptome. The increasing expression of dihydroflavonol 4-reductase (DFR) might play an important role in the occurrence of rubellis pigments, while the overexpression of anthocyanidin reductase (ANR) in white flowers may promote the biosynthesis of proanthocyanidins. Additionally, several coloration-related repressor R2R3-MYB transcription factors showed different expression levels in the tepals of the rubellis mutant. This study provides a comprehensive analysis relating color compounds to gene expression profiles of the Magnoliids plant M. maudiae. The newly generated information will provide a profound effect on horticultural applications of Magnoliaceae.

Intra-Kernel Reallocation of Proteins in Maize Depends on VP1-Mediated Scutellum Development and Nutrient Assimilation

During maize (Zea mays) seed development, the endosperm functions as the major organ for storage of photoassimilate, serving to nourish the embryo. α-Zeins and globulins (GLBs) predominantly accumulate in the maize endosperm and embryo, respectively. Here, we show that suppression of α-zeins by RNA interference (αRNAi) in the endosperm results in more GLB1 being synthesized in the embryo, thereby markedly increasing the size and number of protein storage vacuoles. Glb genes are strongly expressed in the middle-to-upper section of the scutellum, cells of which are significantly enlarged by αRNAi induction. Elimination of GLBs caused an apparent reduction in embryo protein level, regardless of whether α-zeins were expressed or suppressed in the endosperm, indicating that GLBs represent the dominant capacity for storage of amino acids allocated from the endosperm. It appears that protein reallocation is mostly regulated at the transcriptional level. Genes differentially expressed between wild-type and αRNAi kernels are mainly involved in sulfur assimilation and nutrient metabolism, and many are transactivated by VIVIPAROUS1 (VP1). In vp1 embryos, misshapen scutellum cells contain notably less cellular content and are unable to respond to αRNAi induction. Our results demonstrate that VP1 is essential for scutellum development and protein reallocation from the endosperm to embryo.

Transcriptome analysis reveals novel enzymes for apo-carotenoid biosynthesis in saffron and allows construction of a pathway for crocetin synthesis in yeast

Crocus sativus is generally considered the source of saffron spice which is rich in apo-carotenoid compounds such as crocins, crocetin, picrocrocin, and safranal, which possess effective pharmacological activities. However, little is known about the exact genes involved in apo-carotenoid biosynthesis in saffron and the potential mechanism of specific accumulation in the stigma. In this study, we integrated stigmas at different developmental stages to perform in-depth transcriptome and dynamic metabolomic analyses to discover the potential key catalytic steps involved in apo-carotenoid biosynthesis in saffron. A total of 61 202 unigenes were obtained, and 28 regulators and 32 putative carotenogenic genes were captured after the co-expression network analysis. Moreover, 15 candidate genes were predicted to be closely related to safranal and crocin production, in which one aldehyde dehydrogenase (CsALDH3) was validated to oxidize crocetin dialdehyde into crocetin and a crocetin-producing yeast strain was created. In addition, a new branch pathway that catalyses the conversion of geranyl-geranyl pyrophosphate to copalol and ent-kaurene by the class II diterpene synthase CsCPS1 and three class I diterpene synthases CsEKL1/2/3 were investigated for the first time. Such gene to apo-carotenoid landscapes illuminate the synthetic charactersistics and regulators of apo-carotenoid biosynthesis, laying the foundation for a deep understanding of the biosynthesis mechanism and metabolic engineering of apo-carotenoids in plants or microbes.

Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field

BACKGROUND

Drought and heat stress effects on rice have been extensively studied, in particular during the sensitive flowering and grain-filling stages. However, in the field these stresses usually occur together because reduced transpirational cooling under drought conditions results in increased plant tissue temperature. In addition, environmental stresses are usually transient and the ability to efficiently recover from stress may be at least as important for overall stress tolerance as the direct stress response itself. Nevertheless, nothing is known about recovery mechanisms after drought and heat stress in rice under field conditions.

RESULTS

We have used gas chromatography-mass spectrometry-based metabolomics to elucidate the metabolic responses of flag leaves, flowering spikelets, and developing seeds from 3 rice cultivars differing in their drought and heat tolerance to rewatering after stress in the field. Within 60 hours after rewatering, many stress-responsive metabolites returned to their control levels, although recovery was not complete. In addition, control plants showed developmental differences that were revealed by metabolite profiles during 60 hours of post-stress sampling, in particular in developing seeds. Correlation analysis identified several metabolites as marker candidates for the stability of grain yield or quality under conditions of combined drought and heat stress.

CONCLUSIONS

The rewatering responses of stressed plants seemed to be a combination of the reversal of stress effects and reinitiation of development after stress relief. The identified potential markers can be useful in efforts to breed stress-tolerant rice germplasm to ensure food availability under changing climate conditions.

Isolation and Characterization of Three Chalcone Synthase Genes in Pecan (Carya illinoinensis)

Phenolics are a group of important plant secondary metabolites that have been proven to possess remarkable antioxidant activity and to be beneficial for human health. Pecan nuts are an excellent source of dietary phenolics. In recent years, many studies have focused on the separation and biochemical analysis of pecan phenolics, but the molecular mechanisms of phenolic metabolism in pecans have not been fully elucidated, which significantly hinders quality breeding research for this plant. Chalcone synthase (CHS) plays crucial roles in phenolic biosynthesis. In this study, three Carya illinoinensisCHSs (CiCHS1, CiCHS2, and CiCHS3), were isolated and analyzed. CiCHS2 and CiCHS3 present high expression levels in different tissues, and they are also highly expressed at the initial developmental stages of kernels in three pecan genotypes. A correlation analysis was performed between the phenolic content and CHSs expression values during kernel development. The results indicated that the expression variations of CiCHS2 and CiCHS3 are significantly related to changes in total phenolic content. Therefore, CiCHSs play crucial roles in phenolic components synthesis in pecan. We believe that the isolation of CiCHSs is helpful for understanding phenolic metabolism in C. illinoinensis, which will improve quality breeding and resistance breeding studies in this plant.