Metabolomics analysis reveals differences in evolution between maize and rice

Uncovering fruit flavor and genetic diversity across diploid wild Fragaria species via comparative metabolomics profiling

Wild Fragaria resources exhibit extensive genetic diversity and desirable edible traits, such as high soluble solid content and flavor compounds. However, specific metabolites in different wild strawberry fruits remain unknown. In this study, we characterized 1008 metabolites covering 11 subclasses among 13 wild diploid resources representing eight species, including F. vesca, F. nilgerrensis, F. viridis, F. nubicola, F. pentaphylla, F. mandschurica, F. chinensis, and F. emeiensis. Fifteen potential metabolite biomarkers were identified to distinguish fruit flavors among the 13 diploid wild Fragaria accessions. A total of nine distinct modules were employed to explore key metabolites related to fruit quality through weighted gene co-expression module analysis, with significant enrichment in amino acid biosynthesis pathway. Notably, the identified significantly different key metabolites highlighted the close association of amino acids, sugars, and anthocyanins with flavor formation. These findings offer valuable resources for improving fruit quality through metabolome-assisted breeding.

PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant species

Comparative metabolomics plays a crucial role in investigating gene function, exploring metabolite evolution, and accelerating crop genetic improvement. However, a systematic platform for intra- and cross-species comparison of metabolites is currently lacking. Here, we report the Plant Comparative Metabolome Database (PCMD; http://yanglab.hzau.edu.cn/PCMD), a multilevel comparison database based on predicted metabolic profiles of 530 plant species. The PCMD serves as a platform for comparing metabolite characteristics at various levels, including species, metabolites, pathways, and biological taxonomy. The database also provides a number of user-friendly online tools, such as species comparison, metabolite enrichment, and ID conversion, enabling users to perform comparisons and enrichment analyses of metabolites across different species. In addition, the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite numbering. The PCMD is the most species-rich comparative plant metabolomics database currently available, and a case study demonstrates its ability to provide new insights into plant metabolic diversity.

GABA promotes peroxisome proliferation in Triticum monococcum leaves

Although peroxisomes are integral for both primary and secondary metabolism, how developmental changes affect activity of peroxisomes remains poorly understood. Here, we used published RNA-seq data to analyze the expression patterns of genes encoding 21 peroxisome metabolic pathways at successive developmental stages of Zea mays and Oryza sativa. Photorespiration was the most represented pathway in adult leaf relative to the juvenile stages. Components of reactive oxygen species (ROS)/reactive nitrogen species (RNS) metabolism, NADPH regeneration, and catabolism of polyamines were also enriched at later stages of leaf differentiation. The most commonly upregulated gene in differentiated leaves across all datasets of both species was BETAINE ALANINE DEHYDROGENASE (BADH). BADH functions in catabolism of polyamines where it converts 4-aminobutyraldehyde (ABAL) to 4-aminobutyrate (GABA). We tested the outcome of RNA-seq analysis by qRT-PCR in developing Triticum monococcum ssp. monococcum (Einkorn) seedlings. Consistent with the outcomes of RNA-seq analysis, transcription of BADH and CATALASE3 (CAT3) were upregulated in older seedlings. CAT3 is an essential peroxisome biogenesis factor and a key enzyme of ROS homeostasis. Furthermore, exogenous application of GABA resulted in higher peroxisome abundance and transcriptional upregulation of BADH and a gene encoding another peroxisome biogenesis factor responsible for peroxisome fission, PEROXIN11C (PEX11C), in leaves. We propose that GABA contributes to regulation of peroxisome fission machinery during leaf differentiation.

Characterization of microbial community assembly in parasitic plant systems and the influence of microorganisms on metabolite accumulation in parasitic plants: case study of Cistanche salsa and Kalidium foliatum

Introduction

Cistanche salsa (C.A.Mey.) G. Beck is a perennial holoparasitic herb recognized for its medicinal properties, particularly in kidney-tonifying and laxative treatments. Despite its therapeutic potential, little is known about the endophyte communities inhabiting C. salsa and its host plants, and how these microorganisms may impact the production and accumulation of metabolites in C. salsa.

Methods

We conducted a dual analysis focusing on metabolomics of wild C. salsa and microbiome characterization of both C. salsa and its host plant, Kalidium foliatum (Pall.) Moq. The metabolomics analysis revealed variations in metabolite composition across different parts of C. salsa. Additionally, the microbiome analysis involved studying endophytic bacteria and fungi, comparing their community structures between parasitic C. salsa and its host plant.

Results

Significant variations in metabolite composition were observed through metabolomic profiling, which identified 93 secondary metabolites and 398 primary metabolites across various parts of C. salsa. Emphasis was placed on differences in metabolite composition within the flowers. Microbiome analysis revealed differential community compositions of endophytic bacteria between the parasitic and host plants, whereas differences in endophytic fungi were less pronounced. Certain endophytes, such as Bacteroidota, Proteobacteria, Ascomycota, and Basidiomycota, were associated with the production of specific secondary metabolites in C. salsa, including the plant-specific compound salsaside.

Discussion

Our findings highlight the intricate relationship between C. salsa and its endophytic microbiota, suggesting a potential role of these microorganisms in modulating the biosynthesis of bioactive compounds. The differential preferences of endophytic bacteria and fungi across various microenvironments within the parasitic plant system underscore the complexity of these interactions. Further elucidation of these dynamics could enhance our understanding of C. salsa's medicinal properties and its ecological adaptations as a holoparasitic herb.

Comparative metabolomics combined with genome sequencing provides insights into novel wolfberry-specific metabolites and their formation mechanisms

Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.

Combining association with linkage mapping to dissect the phenolamides metabolism of the maize kernel

Phenolamides are important secondary metabolites in plant species. They play important roles in plant defense responses against pathogens and insect herbivores, protection against UV irradiation and floral induction and development. However, the accumulation and variation in phenolamides content in diverse maize lines and the genes responsible for their biosynthesis remain largely unknown. Here, we combined genetic mapping, protein regulatory network and bioinformatics analysis to further enhance the understanding of maize phenolamides biosynthesis. Sixteen phenolamides were identified in multiple populations, and they were all significantly correlated with one or several of 19 phenotypic traits. By linkage mapping, 58, 58, 39 and 67 QTLs, with an average of 3.9, 3.6, 3.6 and 4.2 QTLs for each trait were mapped in BBE1, BBE2, ZYE1 and ZYE2, explaining 9.47%, 10.78%, 9.51% and 11.40% phenotypic variation for each QTL on average, respectively. By GWAS, 39 and 36 significant loci were detected in two different environments, 3.3 and 2.8 loci for each trait, explaining 10.00% and 9.97% phenotypic variation for each locus on average, respectively. Totally, 58 unique candidate genes were identified, 31% of them encoding enzymes involved in amine and derivative metabolic processes. Gene Ontology term analysis of the 358 protein-protein interrelated genes revealed significant enrichment in terms relating to cellular nitrogen metabolism, amine metabolism. GRMZM2G066142, GRMZM2G066049, GRMZM2G165390 and GRMZM2G159587 were further validated involvement in phenolamides biosynthesis. Our results provide insights into the genetic basis of phenolamides biosynthesis in maize kernels, understanding phenolamides biosynthesis and its nutritional content and ability to withstand biotic and abiotic stress.

RefMetaPlant: a reference metabolome database for plants across five major phyla

Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC-MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A 'Reference Metabolome Database for Plants' (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like 'LC-MS/MS Query', 'RefMetaBlast' and 'CompoundLibBlast' for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.

Isotope effects on radical pair performance in cryptochrome: A new hypothesis for the evolution of animal migration: The quantum biology of migration

Mechanisms occurring at the atomic level are now known to drive processes essential for life, as revealed by quantum effects on biochemical reactions. Some macroscopic characteristics of organisms may thus show an atomic imprint, which may be transferred across organisms and affect their evolution. This possibility is considered here for the first time, with the aim of elucidating the appearance of an animal innovation with an unclear evolutionary origin: migratory behaviour. This trait may be mediated by a radical pair (RP) mechanism in the retinal flavoprotein cryptochrome, providing essential magnetic orientation for migration. Isotopes may affect the performance of quantum processes through their nuclear spin. Here, we consider a simple model and then apply the standard open quantum system approach to the spin dynamics of cryptochrome RP. We changed the spin quantum number (I) and g-factor of hydrogen and nitrogen isotopes to investigate their effect on RP's yield and magnetic sensitivity. Strong differences arose between isotopes with I = 1 and I = 1/2 in their contribution to cryptochrome magnetic sensitivity, particularly regarding Earth's magnetic field strengths (25-65 µT). In most cases, isotopic substitution improved RP's magnetic sensitivity. Migratory behaviour may thus have been favoured in animals with certain isotopic compositions of cryptochrome.

Comparative metabolomics study on areca nut from China and Southeast Asia (Thailand and Indonesia)

INTRODUCTION

Areca nut is an economic crop and an important component in traditional Chinese medicine (TCM) and ethnomedicine. The crop is rich in alkaloids and flavonoids. Most previous studies have focused on the chemical components, especially alkaloids, in crops from certain areca nut-producing areas.

OBJECTIVE

The purpose of this study was to compare the differences in areca nut seeds in two main cultivation areas, identify differential metabolites, and evaluate seed quality in different production areas.

METHODS

A widely targeted metabolomics method based on ultrahigh-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-QQQ-MS), combined with the TCM systems pharmacology (TCMSP) database and multivariate statistical analysis, was used in this study to maximise the differentiation between quality characteristics of areca nut seeds from China and Southeast Asian regions.

RESULTS

Altogether, 1031 metabolites were identified in areca nut seeds; by querying the TCMSP database, 375 metabolites were identified as the main active ingredients. Moreover, the research showed that the metabolic profiles of areca nut seeds from China (ASCN) and Southeast Asia (ASSA) exhibit significant differences, and the difference is mainly reflected in 318 compounds. The relative content of 146 metabolites in ASCN was significantly higher than that in ASSA. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) comparative analysis, areca nut seed metabolites in Chinese production areas were determined to have a wider metabolic pathway.

CONCLUSION

The areca nut seeds from cultivation areas possess many metabolites that are beneficial for health, including alkaloids, amino acids, phenolic acids, and lipids. Thus, compared with ASSA, ASCN have a higher medicinal value. This study provides a direction for the subsequent development and utilisation of areca nut seeds.

Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking

The process of crop domestication leads to a dramatic reduction in the gene expression associated with metabolic diversity. Genes involved in specialized metabolism appear to be particularly affected. Although there is ample evidence of these effects at the genetic level, a reduction in diversity at the metabolite level has been taken for granted despite having never been adequately accessed and quantified. Here we leveraged the high coverage of ultra high performance liquid chromatography-high-resolution mass spectrometry based metabolomics to investigate the metabolic diversity in the common bean (Phaseolus vulgaris). Information theory highlights a shift towards lower metabolic diversity and specialization when comparing wild and domesticated bean accessions. Moreover, molecular networking approaches facilitated a broader metabolite annotation than achieved to date, and its integration with gene expression data uncovers a metabolic shift from specialized metabolism towards central metabolism upon domestication of this crop.

Evaluation of sugarcane promising clones based on the morphophysiological traits developed from fuzz

Sugarcane is one of the critical commercial crops and principal sources of ethanol and sugar worldwide. Unfavorable conditions and poor seed setting rates hinder variety development in sugarcane. Countries like Pakistan directly import fuzz (true seed) and other propagation material from the USA, China, Brazil, etc. In this study, we imported fuzz from China, developed 29 genotypes germinating in the glasshouse, and evaluated at field conditions along with two local checks (CPF-251 and HSF-240). Morphophysiological data were recorded, including plant height (PH), cane length (CL), internodal length (IL), tiller number (TN), brix percentage (B), cane diameter (CD), chlorophyll a (Chl. a), chlorophyll b (Chl. b), and total chlorophyll (T. Chl). Results showed highly significant (p < 0.001) differences among the sugarcane accessions for all the studied traits. High broad-sense heritability (81.89% to 99.91%) was recorded for all the studied parameters. Genetic Advance (GA) ranges from 4.6% to 65.32%. The highest GA was observed for PH (65.32%), followed by CL (63.28%). Chlorophyll leaching assay was also performed at different time points (0, 50, 100, 150, and 200 min). All the genotypes showed the same leaching trend at all times, and better performing genotypes showed less leaching compared to poor performing, indicating the high amount of cutin and wax on the leaf surface. Correlation analysis showed that PH, CL, IL, and TN had significant associations. Principal components analysis (PCA) further confirms these results. Based on PCA and correlation results, PH, CL, IL, and TN can be utilized as a selection criterion for sugarcane improvement. Genotypes such as NS-4a, NS-5, NS-6, NS-8, NS-9, and NS-15 are recommended for future breeding programs related to sugarcane variety development.

Natural variation of diterpenoid phytoalexins in rice: Aromatic diterpenoid phytoalexins in specific cultivars

Rice (Oryza sativa L.) plants accumulate antimicrobial compounds known as phytoalexins in response to pathogen attack. To date, more than 20 compounds have been isolated as phytoalexins from rice, mostly diterpenoids. However, the quantitative analysis of diterpenoid phytoalexins in various cultivars has revealed that the cultivar 'Jinguoyin' does not accumulate these compounds at detectable concentrations. Therefore, in this study, we attempted to detect a new class of phytoalexins from Bipolaris oryzae infected leaves of 'Jinguoyin'. We detected five compounds in the leaves of the target cultivar, whereas these compounds were not detected in the leaves of 'Nipponbare' or 'Kasalath', which are representative cultivars of the japonica and indica subspecies. Subsequently, we isolated these compounds from ultraviolet (UV)-light-irradiated leaves and determined their structures by spectroscopic analysis and the crystalline sponge method. All the compounds were diterpenoids containing a benzene ring and were detected from the pathogen-infected rice leaves for the first time. Because the compounds showed antifungal activity against B. oryzae and Pyricularia oryzae, we propose that they function as phytoalexins in rice and named them abietoryzins A-E. The abietoryzins tended to accumulate at high concentrations in cultivars that accumulated low levels of known diterpenoid phytoalexins after UV-light irradiation. Of the total of 69 cultivars in the WRC, 30 cultivars accumulated at least one of the abietoryzins, and, in 15 cultivars, the amounts of some abietoryzins were the highest among those of the analyzed phytoalexins. Therefore, abietoryzins are a major phytoalexin group in rice, although their presence has, to date, been overlooked (252 words).

Responses of Aroma Related Metabolic Attributes of Opisthopappus longilobus Flowers to Environmental Changes

Opisthopappus longilobus (Opisthopappus) and its descendant species, Opisthopappus taihangensis, commonly thrive on the Taihang Mountains of China. Being typical cliff plants, both O. longilobus and O. taihangensis release unique aromatics. To determine the potential differentiation and environmental response patterns, comparative metabolic analysis was performed on O. longilobus wild flower (CLW), O. longilobus transplant flower (CLT), and O. taihangensis wild flower (TH) groups. Significant differences in the metabolic profiles were found, not within O. longilobus, but between O. longilobus and O. taihangensis flowers. Within these metabolites, twenty-eight substances related to the scents were obtained (one alkene, two aldehydes, three esters, eight phenols, three acids, three ketones, three alcohols, and five flavonoids), of which eugenol and chlorogenic were the primary aromatic molecules and enriched in the phenylpropane pathway. Network analysis showed that close relationships occurred among identified aromatic substances. The variation coefficient (CV) of aromatic metabolites in O. longilobus was lower than O. taihangensis. The aromatic related compounds were significantly correlated with the lowest temperatures in October and in December of the sampled sites. The results indicated that phenylpropane, particularly eugenol and chlorogenic, played important roles in the responses of O. longilobus species to environmental changes.

Comparative metabolomics of root-tips reveals distinct metabolic pathways conferring drought tolerance in contrasting genotypes of rice

Background

The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown.

Results

This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways.

Conclusion

Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.

Characterization of 35 Masson pine (Pinus massoniana) half-sib families from two provinces based on metabolite properties

Plant metabolism is an important functional trait, and its metabolites have physiological and ecological functions to adapt to the growth environment. However, the physiological and ecological functions of metabolites from different provinces of the same plant species are still unclear. Therefore, this study aimed to determine whether metabolites from different provinces of Masson pine (Pinus massoniana Lamb.) have the corresponding metabolic traits. The gas chromatography–mass spectrometry technique and metabonomic analysis methods were used to characterize 35 Masson pine half-sib families from two provinces. A total of 116 metabolites were putatively identified in 35 families of Masson pine, among which the average content of organic acids was the highest, followed by saccharides and alcohols, and phosphoric acids. Comparative analysis of metabolite groups showed that organic acids, amines, and others were significantly different between the Masson pine families from Guangxi and Guizhou provinces. Six differential metabolites were found between the provinces from Guizhou and Guangxi, namely caffeic acid, L-ascorbic acid, gentiobiose, xylitol, d-pinitol, and β-sitosterol. The most significantly enriched pathways among differentially expressed metabolites between the two provinces were steroid biosynthesis, phenylpropanoid biosynthesis, glutathione metabolism, pentose and glucuronate interconversions. Overall, the results showed that Masson pine half-sib families from different geographical provinces have different metabolite profiles and their metabolites are affected by geographical provenance and growth environment adaptability. This study revealed that the breeding of Masson pine families from different provinces changed the metabolite profiles, providing a reference for the multipurpose breeding of Masson pine.

Analysis of chemotypes and their markers in leaves of core collections of Eucommia ulmoides using metabolomics

The leaves of Eucommia ulmoides contain various active compunds and nutritional components, and have successively been included as raw materials in the Chinese Pharmacopoeia, the Health Food Raw Material Catalogue, and the Feed Raw Material Catalogue. Core collections of E. ulmoides had been constructed from the conserved germplasm resources basing on molecular markers and morphological traits, however, the metabolite diversity and variation in this core population were little understood. Metabolite profiles of E. ulmoides leaves of 193 core collections were comprehensively characterized by GC-MS and LC-MS/MS based non-targeted metabolomics in present study. Totally 1,100 metabolites were identified and that belonged to 18 categories, and contained 120 active ingredients for traditional Chinese medicine (TCM) and 85 disease-resistant metabolites. Four leaf chemotypes of the core collections were established by integrated uses of unsupervised self-organizing map (SOM), supervised orthogonal partial least squares discriminant analysis (OPLS-DA) and random forest (RF) statistical methods, 30, 23, 43, and 23 chemomarkers were screened corresponding to the four chemotypes, respectively. The morphological markers for the chemotypes were obtained by weighted gene co-expression network analysis (WGCNA) between the chenomarkers and the morphological traits, with leaf length (LL), chlorophyll reference value (CRV), leaf dentate height (LDH), and leaf thickness (LT) corresponding to chemotypes I, II, III, and IV, respectively. Contents of quercetin-3-O-pentosidine, isoquercitrin were closely correlated to LL, leaf area (LA), and leaf perimeter (LP), suggesting the quercetin derivatives might influence the growth and development of E. ulmoides leaf shape.

Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives

Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

Analysis of metabolic differences in maize in different growth stages under nitrogen stress based on UPLC-QTOF-MS

Introduction

Maize has a high demand for nitrogen during the growth period. The study of metabolic changes in maize can provide a theoretical basis for rational nitrogen nutrition regulation.

Methods

In order to investigate the changes of different metabolites and their metabolic pathways in maize leaves under nitrogen stress, we used ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) for metabolomic analysis of maize leaves under different nitrogen treatments at three critical growth stages (V4, V12 and R1) in a pot experiment under natural conditions.

Results and discussion

The results showed that nitrogen stress significantly affected sugar metabolism and nitrogen metabolism, and affected carbon and nitrogen balance, and the effects of stress on maize leaves metabolism increased with the growth process. Metabolic pathways such as the TCA cycle and starch and sucrose metabolism were mainly affected at the seeding stage (V4). The stress response to nitrogen deficiency also showed significant upregulation of flavonoids such as luteolin and astragalin during the booting stage (V12) and anthesis-silking stage (R1). During R1 stage, the synthesis of tryptophan and phenylalanine and the degradation of lysine were significantly affected. Compared with nitrogen stress, the metabolic synthesis of key amino acids and jasmonic acid were intensified and the TCA cycle was promoted under nitrogen sufficiency conditions. This study initially revealed that the response mechanism of maize to nitrogen stress at the metabolic level.

Mass Spectrometry-Based Nontargeted and Targeted Analytical Approaches in Fingerprinting and Metabolomics of Food and Agricultural Research

Mass spectrometry (MS)-based techniques have been extensively applied in food and agricultural research. This review aims to address the advances and applications of MS-based analytical strategies in nontargeted and targeted analysis and summarizes the recent publications of MS-based techniques, including flow injection MS fingerprinting, chromatography-tandem MS metabolomics, direct analysis using ambient mass spectrometry, as well as development in MS data deconvolution software packages and databases for metabolomic studies. Various nontargeted and targeted approaches are employed in marker compounds identification, material adulteration detection, and the analysis of specific classes of secondary metabolites. In the newly emerged applications, the recent advances in computer tools for the fast deconvolution of MS data in targeted secondary metabolite analysis are highlighted.

A novel method for efficient screening and annotation of important pathway-associated metabolites based on the modified metabolome and probe molecules

植物次生代谢物在抵御生物/非生物胁迫、生物间互作以及信息传递等方面发挥重要作用,次生代谢途径解析对植物分子育种、天然产物合成等方面具有重要意义。液相色谱-高分辨串联质谱(LC-HRMS/MS)为次生代谢物鉴定及途径表征提供了技术手段。非靶向LC-HRMS/MS方法可获得丰富的质谱信号,包括一级质谱和二级质谱(MS, MS/MS),但受质谱数据库规模以及次生代谢物复杂性的制约,次生代谢物注释十分困难。该研究以玉米叶片中苯丙烷途径代谢物为例,发展用于非靶向代谢组数据中重要途径代谢物的高效筛选和注释新方法。首先,利用公共代谢途径数据库及文献获取参与苯丙烷代谢途径的61种修饰反应类型,进而从非靶向实验数据中筛选出修饰代谢组。其次,获取开源串联质谱数据中的苯丙烷类化合物作为探针分子,构建探针分子质谱数据库。将探针分子与修饰代谢组共建分子网络,锁定目标途径代谢物并注释结构。该方法在正、负离子模式下分别筛选出玉米叶片中392个和417个苯丙烷途径候选代谢物,去冗余后共注释出129个代谢物,涉及苯丙烷代谢的主要分支途径,如黄酮途径的8个类黄酮、19个氧苷类黄酮和32个碳苷类黄酮,31个羟基肉桂酸途径代谢物以及22个木脂素途径代谢物;其中26个在PubChem和SciFinder数据库中未见收录。该研究利用探针分子结合修饰组可快速锁定途径代谢物,且有助于快速、准确的网络传播注释,可显著提高目标途径代谢物筛选与注释效率,为植物次生代谢途径的深入解析提供分析手段。

Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Flavonoid Accumulation and Its Underlying Mechanism in Fruits of Distinct Canarium album Cultivars

Canarium album fruit has great potential to be consumed as a raw material not only for food but also medicine. The diverse active metabolites composition and content of C. album fruits greatly affect their pharmacological effects. However, up to now, there has been no report on the global metabolome differences among fruits from distinct C. album cultivars. In our present study, by using non-targeted metabolomics techniques, we identified 87 DAMs (differentially accumulated metabolites) including 17 types of flavonoids from fruits of four different C. album cultivars. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that the flavone and flavonol biosynthesis- and flavonoid biosynthesis-related DAMs were major factors determining their metabolome differences. Comparative transcriptomic analysis revealed that 15 KEGG pathways were significantly enriched by genes of the identified 3655 DEGs (differentially expressed genes) among different C. album cultivars. Consistent with the metabolome data, flavonoid biosynthesis-related DEGs, including eight key structural genes (such as FLS, CCoAOMT, CHI, C4H, DFR, LAR, and C3′H, etc.) and several regulatory transcription factor (TF) genes (including 32 MYBs and 34 bHLHs, etc.), were found to be significantly enriched (p < 0.01). Our study indicated that the differential expression of flavonoid biosynthesis-related genes and accumulation of flavonoids played dominant roles in the various metabolome compositions of fruits from different C. album cultivars.

Transcriptome and Metabolome Analyses Reveal Differences in Terpenoid and Flavonoid Biosynthesis in Cryptomeria fortunei Needles Across Different Seasons

Cryptomeria fortunei (Chinese cedar) has outstanding medicinal value due to its abundant flavonoid and terpenoid contents. The metabolite contents of C. fortunei needles differ across different seasons. However, the biosynthetic mechanism of these differentially synthesized metabolites (DSMs) is poorly understood. To improve our understanding of this process, we performed integrated non-targeted metabolomic liquid chromatography and gas chromatography mass spectrometry (LC-MS and GC-MS), and transcriptomic analyses of summer and winter needles. In winter, the C. fortunei needle ultrastructure was damaged, and the chlorophyll content and F _v/F _m were significantly (p < 0.05) reduced. Based on GC-MS and LC-MS, we obtained 106 and 413 DSMs, respectively; based on transcriptome analysis, we obtained a total of 41.17 Gb of clean data and assembled 33,063 unigenes, including 14,057 differentially expressed unigenes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DSMs/DEGs were significantly (p < 0.05) enriched in many biosynthesis pathways, such as terpenoids, photosynthates, and flavonoids. Integrated transcriptomic and metabonomic analyses showed that seasonal changes have the greatest impact on photosynthesis pathways, followed by terpenoid and flavonoid biosynthesis pathways. In summer Chinese cedar (SCC) needles, DXS, DXR, and ispH in the 2-methyl-pentaerythritol 4-phosphate (MEP) pathway and GGPS were highly expressed and promoted the accumulation of terpenoids, especially diterpenoids. In winter Chinese cedar (WCC) needles, 9 genes (HCT, CHS, CHI, F3H, F3'H, F3'5'H, FLS, DFR, and LAR) involved in flavonoid biosynthesis were highly expressed and promoted flavonoid accumulation. This study broadens our understanding of the metabolic and transcriptomic changes in C. fortunei needles caused by seasonal changes and provides a reference regarding the adaptive mechanisms of C. fortunei and the extraction of its metabolites.

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.

Metabolomic Analysis Reveals Nutritional Diversity among Three Staple Crops and Three Fruits

More than 2 billion people worldwide are under threat of nutritional deficiency. Thus, an in-depth comprehension of the nutritional composition of staple crops and popular fruits is essential for health. Herein, we performed LC-MS-based non-targeted and targeted metabolome analyses with crops (including wheat, rice, and corn) and fruits (including grape, banana, and mango). We detected a total of 2631 compounds by using non-targeted strategy and identified more than 260 nutrients. Our work discovered species-dependent accumulation of common present nutrients in crops and fruits. Although rice and wheat lack vitamins and amino acids, sweet corn was rich in most amino acids and vitamins. Among the three fruits, mango had more vitamins and amino acids than grape and banana. Grape and banana provided sufficient 5-methyltetrahydrofolate and vitamin B6, respectively. Moreover, rice and grape had a high content of flavonoids. In addition, the three crops contained more lipids than fruits. Furthermore, we also identified species-specific metabolites. The crops yielded 11 specific metabolites, including flavonoids, lipids, and others. Meanwhile, most fruit-specific nutrients were flavonoids. Our work discovered the complementary pattern of essential nutrients in crops and fruits, which provides metabolomic evidence for a healthy diet.

Rice metabolic regulatory network spanning the entire life cycle

As one of the most important crops in the world, rice (Oryza sativa) is a model plant for metabolome research. Although many studies have focused on the analysis of specific tissues, the changes in metabolite abundance across the entire life cycle have not yet been determined. In this study, combining both targeted and nontargeted metabolite profiling methods, a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle. The contents of metabolites in different tissues of rice were significantly different, with various metabolites accumulating in the plumule and radicle during seed germination. Combining these data with transcriptome data obtained from the same time period, we constructed the Rice Metabolic Regulation Network. The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across development. Using this dataset, we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity. This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agronomic traits.

The arches and spandrels of maize domestication, adaptation, and improvement

People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop.

Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis

Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F₁ hybrids by crossing 488 diverse inbred lines with two elite testers. Genome-wide association study identified hundreds of quantitative trait loci associated with phenotypic plasticity variation across diverse F₁ hybrids, the majority of which contributed very little variance, in accordance with the polygenic nature of these traits. We identified several quantitative trait locus regions that may have been selected during the tropical-temperate adaptation process. We also observed heterosis in terms of phenotypic plasticity, in addition to the traditional genetic value differences measured between hybrid and inbred lines, and the pattern of which was affected by genetic background. Our results demonstrate a landscape of phenotypic plasticity in maize, which will aid in the understanding of its genetic architecture, its contribution to adaptation and heterosis, and how it may be exploited for future maize breeding in a rapidly changing environment.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).

Using precision phenotyping to inform de novo domestication

An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.

Evolutionary History of Plant Metabolism

Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO₂ and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.

Domestication of Crop Metabolomes: Desired and Unintended Consequences

The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.

Cross-Species Comparison of Metabolomics to Decipher the Metabolic Diversity in Ten Fruits

Fruits provide humans with multiple kinds of nutrients and protect humans against worldwide nutritional deficiency. Therefore, it is essential to understand the nutrient composition of various fruits in depth. In this study, we performed LC-MS-based non-targeted metabolomic analyses with ten kinds of fruit, including passion fruit, mango, starfruit, mangosteen, guava, mandarin orange, grape, apple, blueberry, and strawberry. In total, we detected over 2500 compounds and identified more than 300 nutrients. Although the ten fruits shared 909 common-detected compounds, each species accumulated a variety of species-specific metabolites. Additionally, metabolic profiling analyses revealed a constant variation in each metabolite’s content across the ten fruits. Moreover, we constructed a neighbor-joining tree using metabolomic data, which resembles the single-copy protein-based phylogenetic tree. This indicates that metabolome data could reflect the genetic relationship between different species. In conclusion, our work enriches knowledge on the metabolomics of fruits, and provides metabolic evidence for the genetic relationships among these fruits.

Metabolomics Analyses of Cotyledon and Plumule Showing the Potential Domestic Selection in Lotus Breeding

Lotus (Nelumbo nucifera) seeds are widely consumed as functional food or herbal medicine, of which cotyledon (CL) is the main edible part, and lotus plumule (LP) is commonly utilized in traditional Chinese medicine. However, few studies have been conducted to investigate the chemical components of CL and LP in dry lotus seeds, not to mention the comparison between wild and domesticated varieties. In this study, a widely targeted metabolomics approach based on Ultra Performance Liquid Chromatography-electrospray ionization-Tandem mass spectrometry (UPLC-ESI-MS/MS) was utilized to analyze the metabolites in CL and LP of China Antique (“CA”, a wild variety) and Jianxuan-17 (“JX”, a popular cultivar). A total of 402 metabolites were identified, which included flavonoids (23.08% to 27.84%), amino acids and derivatives (14.18–16.57%), phenolic acids (11.49–12.63%), and lipids (9.14–10.95%). These metabolites were classified into ten clusters based on their organ or cultivar-specific characters. Most of these metabolites were more abundant in LP than in CL for both varieties, except for metabolites belonging to organic acids and lipids. The analysis of differentially accumulated metabolites (DAMs) demonstrated that more than 25% of metabolites detected in our study were DAMs in CL and LP comparing “JX” with “CA”, most of which were less abundant in “JX”, including 35 flavonoids in LP, 23 amino acids and derivatives in CL, 7 alkaloids in CL, and 10 nucleotides and derivatives in LP, whereas all of 11 differentially accumulated lipids in LP were more abundant in “JX”. Together with the fact that the seed yield of “JX” is much higher than that of “CA”, these results indicated that abundant metabolites, especially the functional secondary metabolites (mainly flavonoids and alkaloids), were lost during the process of breeding selection.

Genetic dissection of maize drought tolerance for trait improvement

Maize is one of the most important crops, but its production is threatened by drought stress worldwide. Thus, increased drought tolerance has been a major goal of maize breeding. Conventional breeding strategies have led to significantly increase of maize yields; however, these strategies often fail to meet the need for drought stress tolerance enhancement. Here, we focus on progress related to the genetic dissection of drought tolerance in maize at different developmental stages achieved through linkage mapping and association mapping. Moreover, recent molecular breeding systems, including transgenic, genome-wide marker-assisted selection, and genome editing technologies, have provided a more direct, efficient, and accurate approach for trait improvement. We also provide perspectives on future directions regarding multi-omics studies and maize improvement. Overall, the application of acquired knowledge will facilitate maize breeding to meet the challenges.

Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding

Crop domestication has fundamentally altered the course of human history, causing a shift from hunter-gatherer to agricultural societies and stimulating the rise of modern civilization. A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner. Here, we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice, two major staple food crops that feed the world. We propose that maize and rice might have evolved distinct genetic solutions toward domestication. Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms. Rice domestication tended to select de novo, loss-of-function, coding variation, while maize domestication more frequently favored standing, gain-of-function, regulatory variation. At the gene network level, distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication, during which different central genes were utilized, orthologous genes played different evolutionary roles, and unique genes or regulatory modules were acquired for establishing new traits. Finally, we discuss how the knowledge gained from past domestication processes, together with emerging technologies, could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.

Hepatopancreatic metabolomics shedding light on the mechanism underlying unsynchronized growth in giant freshwater prawn, Macrobrachium rosenbergii

The giant freshwater prawn, Macrobrachium rosenbergii (M. rosenbergii) as an important freshwater aquaculture species with high commercial value, exhibited unsynchronized growth. However, the potentially metabolic mechanism remains unclear. In this study, we used liquid chromatography tandem mass spectrometry (LC-MS/MS) to investigate the hepatopancreatic metabolic profiles of twenty giant freshwater prawns between the fast-growing group and slow-growing group. In the metabolomics assay, we isolated 8,293 peaks in positive and negative iron mode. Subsequently, 44 significantly differential metabolites were identified. Functional pathway analysis revealed that these metabolites were significantly enriched in three key metabolic pathways. Further integrated analysis indicated that glycerophospholipid metabolism and aminoacyl-tRNA biosynthesis have significant impact on growth performance in M.rosenbergii. Our findings presented here demonstrated the critical metabolites and metabolic pathways involved in growth performance, moreover provided strong evidence for elucidating the potentially metabolic mechanism of the unsynchronized growth in M. rosenbergii.