Lipidomics reveals associations between rice quality traits

Identification of crucial metabolites in colored grain wheat (Triticum aestivum L.) regulated by nitrogen application

Colored wheats have drawn attention due to their nutritional compounds. However, limited information is obtained on the effects of nitrogen fertilizer on crucial metabolites and grain quality of wheats with different color grain. In the study, the pot experiment was conducted with white (W), blue (B), and purple (P) grain wheats treated with three levels of N (LN, 0 g kg-1; MN, 0.05 g kg-1; HN, 0.1 g kg-1). Higher N level could promote wheat growth, improve grain indexes, and nutrient uptake. SPAD values of flag leaves remained in the order HN > MN > LN across all wheat varieties, and maintained increasing during tested stages under purple wheat. Metabolomics analysis showed that the annotated 358 metabolites mainly belonged to 29 classes, including carboxylic acids and their derivatives, fatty acids, flavonoids, and phenols. 35, 39, and 70 differential accumulated metabolites were respectively found between the WLN vs. WHN, the BHN vs. BLN, and the PHN vs. PLN, which were mainly enriched in "biosynthesis of plant secondary metabolites", "cGMP-PKG signaling pathway", "sphingolipid signaling pathway", "biosynthesis of alkaloids derived from histidine and purine", and "biosynthesis of plant hormones". Additionally, erucic acid was dominated in the three wheat cultivars, and was decreased after treated with high N levels. Our study preliminarily revealed the different response mechanisms to different N levels in the white, blue, and purple grain wheats, and lay a theoretical foundation for further breeding of excellent colored grain varieties.

Improving Rice Grain Quality Through Ecotype Breeding for Enhancing Food and Nutritional Security in Asia-Pacific Region

Rice grain is widely consumed as a staple food, providing essential nutrition for households, particularly marginalized families. It plays a crucial role in ensuring food security, promoting human nutrition, supporting good health, and contributing to global food and nutritional security. Addressing the diverse quality demands of emerging diverse and climate-risked population dietary needs requires the development of a single variety of rice grain that can meet the various dietary and nutritional requirements. However, there is a lack of concrete definition for rice grain quality, making it challenging to cater to the different demands. The lack of sufficient genetic study and development in improving rice grain quality has resulted in widespread malnutrition, hidden hunger, and micronutrient deficiencies affecting a significant portion of the global population. Therefore, it is crucial to identify genetically evolved varieties with marked qualities that can help address these issues. Various factors account for the declining quality of rice grain and requires further study to improve their quality for healthier diets. We characterized rice grain quality using Lancastrians descriptor and a multitude of intrinsic and extrinsic quality traits. Next, we examined various components of rice grain quality favored in the Asia-Pacific region. This includes preferences by different communities, rice industry stakeholders, and value chain actors. We also explored the biological aspects of rice grain quality in the region, as well as specific genetic improvements that have been made in these traits. Additionally, we evaluated the factors that can influence rice grain quality and discussed the future directions for ensuring food and nutritional security and meeting consumer demands for grain quality. We explored the diverse consumer bases and their varied preferences in Asian-Pacific countries including India, China, Nepal, Bhutan, Vietnam, Sri Lanka, Pakistan, Thailand, Cambodia, Philippines, Bangladesh, Indonesia, Korea, Myanmar and Japan. The quality preferences encompassed a range of factors, including rice head recovery, grain shape, uniform size before cooking, gelatinization, chalkiness, texture, amylose content, aroma, red-coloration of grain, soft and shine when cooked, unbroken when cooked, gelatinization, less water required for cooking, gelatinization temperature (less cooking time), aged rice, firm and dry when cooked (gel consistency), extreme white, soft when chewed, easy-to-cook rice (parboiled rice), vitamins, and minerals. These preferences were evaluated across high, low, and medium categories. A comprehensive analysis is provided on the enhancement of grain quality traits, including brown rice recovery, recovery rate of milled rice, head rice recovery, as well as morphological traits such as grain length, grain width, grain length-width ratio, and grain chalkiness. We also explored the characteristics of amylose, gel consistency, gelatinization temperature, viscosity, as well as the nutritional qualities of rice grains such as starch, protein, lipids, vitamins, minerals, phytochemicals, and bio-fortification potential. The various factors that impact the quality of rice grains, including pre-harvest, post-harvest, and genotype considerations were explored. Additionally, we discussed the future direction and genetic strategies to effectively tackle these challenges. These qualitative characteristics represent the fundamental focus of regional and national breeding strategies employed by different countries to meet consumer preference. Given the significance of rice as a staple food in Asia-Pacific countries, it is primarily consumed domestically, with only a small portion being exported internationally. All the important attributes must be clearly defined within specific parameters. It is crucial for geneticists and breeders to develop a rice variety that can meet the diverse demands of consumers worldwide by incorporating multiple desirable traits. Thus, the goal of addressing global food and nutritional security, and human healthy can be achieved.

Lipidomic analysis of grain quality variation in high quality aromatic japonica rice

To maintain the purity of the seeds and rice quality of the high-quality rice varieties, five lines with similar field and yield traits were selected from the Nanjing46 population in Liyang and used as study materials, and the original progeny were used as the control material for comparing rice quality and lipid metabolites in this study. The rice quality of the five lines still differed compared to CKN1. The Badh2-E2 gene was detected in all five lines, but its 2-AP content differed. The C11:0 content in CKN1 and VN1 was significantly greater than that in the other four lines. Most of the differentially abundant metabolites were phospholipids, including PA(16:0/18:2), PC(15:0/16:0) and PG(16:0/16:0). These metabolites can be used as potential metabolic markers for identifying quality variation. This study presents a novel methodology and theoretical framework for investigating varietal degradation and ensuring seed purity authentication.

Insertion of a miniature inverted-repeat transposable element into the promoter of OsTCP4 results in more tillers and a lower grain size in rice

A class I PCF type protein, TCP4, was identified as a transcription factor associated with both grain size and tillering through a DNA pull-down-MS assay combined with a genome-wide association study. This transcription factor was found to have a significant role in the variations among the 533 rice accessions, dividing them into two main subspecies. A Tourist-like miniature inverted-repeat transposable element (MITE) was discovered in the promoter of TCP4 in japonica/geng accessions (TCP4M+), which was found to suppress the expression of TCP4 at the transcriptional level. The MITE-deleted haplotype (TCP4M-) was mainly found in indica/xian accessions. ChIP-qPCR and EMSA demonstrated the binding of TCP4 to promoters of grain reservoir genes such as SSIIa and Amy3D in vivo and in vitro, respectively. The introduction of the genomic sequence of TCP4M+ into different TCP4M- cultivars was found to affect the expression of TCP4 in the transgenic rice, resulting in decreased expression of its downstream target gene SSIIa, increased tiller number, and decreased seed length. This study revealed that a Tourist-like MITE contributes to subspecies divergence by regulating the expression of TCP4 in response to environmental pressure, thus influencing source-sink balance by regulating starch biosynthesis in rice.

Influence of Nitrogen-Modified Atmosphere Storage on Lipid Oxidation of Peanuts: From a Lipidomic Perspective

The effect of nitrogen-modified atmosphere storage (NS) on peanut lipid oxidation was investigated in this paper. Non-targeted lipidomics was employed to detect the lipid metabolites in peanuts with the aim of exploring the mechanism of lipid oxidation in peanuts under different storage conditions. The results showed that compared with conventional storage (CS), NS significantly (p < 0.05) delayed the increase in acid value, carbonyl value, and 2-thiobarbituric acid value and the decrease in vitamin E content. However, the storage time has a much greater effect on lipid oxidation than the oxygen level in the storage environment. Lipidomics analysis revealed that there were significant differences in metabolite changes between CS and NS. NS reduced the decline of most glycerophospholipids by regulating lipid metabolism in peanuts. NS maintained higher levels of Diacylglycerol (DAG), sulfoquinovosyl diacylglycerol (SQDG), lysophophatidylcholine (LPC), lysophosphatidylethanolamine (LPE) and phosphatidylinositol (PI) compared to CS. This work provided a basis for the application of NS technology to peanut storage.

Untargeted Lipidomics Reveal Quality Changes in High-Moisture Japonica Brown Rice at Different Storage Temperatures

Low temperatures are an effective way of delaying grain rancidity and deterioration. However, little is known about the difference in quality changes in high-moisture japonica brown rice at different storage temperatures. In this study, the storage quality changes in japonica brown rice with a 15.50% moisture content stored at 15 °C, 20 °C, and 25 °C were investigated. In addition, an untargeted lipidomics analysis coupled with gas chromatography and mass spectrometry (GC-MS) was applied to analyze the volatile compounds and metabolite changes in the high-moisture japonica brown rice. The results showed that storage at 15 °C could well maintain the color and aroma stability of the brown rice and delay the increase in fatty acid value (FAV). The lipidomics results showed that storage at 15 °C delayed glycerolipid and sphingolipid metabolism and reduced glycerophospholipid catabolism in the brown rice. The low-temperature environment regulated these three metabolic pathways to maintain higher contents of triglycerides (TG), phosphatidylserine (PS), abd phosphatidylethanolamine (PE), and lower contents of diglycerides (DG), OAcyl-(gamma-hydroxy) FA (OAHFA), ceramides (Cer), and glycosylceramides (Hex1Cer) in the high-moisture japonica brown rice, which maintained the storage stability of the brown rice. Our results proposed the cryoprotection mechanism of postharvest brown rice from the perspective of volatile compounds and metabolite changes, providing a foothold for the further exploration of low-temperature storage as a safe and efficient cryoprotectant in the grain storage field.

Metabolomic study on the quality differences and physiological characteristics between rice cultivated in drought and flood conditions

The differences between dry- and flood-cultivated rice and the reason behind low-quality dry-cultivated rice were clarified. The physiological traits, starch synthase activity, and grain metabolomics of 'Longdao 18' were measured and analyzed at four growth stages. The brown, milled, and whole-milled rice rates and AGPase, SSS, and SBE activity were lower after drought treatment than during flood cultivation, while the chalkiness, chalky grain rate, amylose (16.57-20.999%), protein (7.99-12.09%), and GBSS activity were higher. Related enzymatic gene expression showed significant differences. Metabolic results showed pyruvate, glycine, and methionine upregulation at 8DAF and higher citric, pyruvic, and α-ketoglutaric acid content at 15DAF. Therefore, 8DAF-15DAF represented the crucial quality formation period for dry-cultivated rice. At 8DAF, the respiratory pathways used amino acids as signaling molecules and alternative substrates to adapt to energy shortages, arid environments and rapid protein accumulation and synthesis. Excessive amylose synthesis at 15DAF accelerated reproductive growth, promoting rapid premature aging.

Novel Grade Classification Tool with Lipidomics for Indica Rice Eating Quality Evaluation

The eating quality evaluation of rice is raising further concerns among researchers and consumers. This research is aimed to apply lipidomics in determining the distinction between different grades of indica rice and establishing effective models for rice quality evaluation. Herein, a high-throughput ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight (UPLC-QTOF/MS) method for comprehensive lipidomics profiling of rice was developed. Then, a total of 42 significantly different lipids among 3 sensory levels were identified and quantified for indica rice. The orthogonal partial least-squares discriminant analysis (OPLS-DA) models with the two sets of differential lipids showed clear distinction among three grades of indica rice. A correlation coefficient of 0.917 was obtained between the practical and model-predicted tasting scores of indica rice. Random forest (RF) results further verified the OPLS-DA model, and the accuracy of this method for grade prediction was 90.20%. Thus, this established approach was an efficient method for the eating grade prediction of indica rice.

Lipidomic Profiling of Rice Bran after Green Solid-Liquid Extractions for the Development of Circular Economy Approaches

Rice bran is a rather underutilized by-product of the rice industry that nowadays is far from being valorized. In this study, the lipidomic profile of bran of the Italian rice variety, Roma, has been evaluated through ultra performance liquid chromatography-tandem mass spectrometry. Crude lipid extracts were obtained from rice bran treated with different green solvents (1-butanol, ethanol and methyl tert-butyl ether/methanol mixture) in combination with an ultrasonic pre-treatment, and then compared with extracts obtained with standard solvents (chloroform/methanol mixture). Lipid yield, number and type of lipids and composition of prevalent lipid classes extracted were evaluated in order to provide an exhaustive lipid profile of the rice bran and to identify the most efficient green solvent for solid-liquid extractions. Twelve different lipid classes and a maximum of 276 lipids were identified. Ethanol and methyl tert-butyl ether/methanol solvents provided higher lipid extraction yields, the former being the most effective solvent for the extraction of triglycerides and N-acylethanolamines and the latter the most effective for the extraction of diglycerides, phospholipids and ceramides at 4 °C. Moreover, extraction with ethanol at 20 °C gave similar results as at 4 °C in terms of lipid yield and for most of the classes of lipids extracted. Taken together, our results indicate ethanol and methyl tert-butyl ether/methanol as excellent solvents for lipid extraction from rice bran, with the aim to further valorize this food by-product in the perspective of a circular economy.

Nutritional lipidomics for the characterization of lipids in food

Lipids represent one out of three major macronutrient classes in the human diet. It is estimated to account for about 15-20% of the total dietary intake. Triacylglycerides comprise the majority of them, estimated 90-95%. Other lipid classes include free fatty acids, phospholipids, cholesterol, and plant sterols as minor components. Various methods are used for the characterization of nutritional lipids, however, lipidomics approaches become increasingly attractive for this purpose due to their wide coverage, comprehensiveness and holistic view on composition. In this chapter, analytical methodologies and workflows utilized for lipidomics profiling of food samples are outlined with focus on mass spectrometry-based assays. The chapter describes common lipid extraction protocols, the distinct instrumental mass-spectrometry based analytical platforms for data acquisition, chromatographic and ion-mobility spectrometry methods for lipid separation, briefly mentions alternative methods such as gas chromatography for fatty acid profiling and mass spectrometry imaging. Critical issues of important steps of lipidomics workflows such as structural annotation and identification, quantification and quality assurance are discussed as well. Applications reported over the period of the last 5years are summarized covering the discovery of new lipids in foodstuff, differential profiling approaches for comparing samples from different origin, species, varieties, cultivars and breeds, and for food processing quality control. Lipidomics as a powerful tool for personalized nutrition and nutritional intervention studies is briefly discussed as well. It is expected that this field is significantly growing in the near future and this chapter gives a short insight into the power of nutritional lipidomics approaches.

Assessment of the Characteristics of Waxy Rice Mutants Generated by CRISPR/Cas9

The cooking and eating quality of rice grains is a major focus from a consumer's perspective and is mainly determined by the apparent amylose content (AAC) of the starch. Waxy rice, a type of rice with an AAC of less than 2%, is an important goal for the breeding of high-quality rice. In recent years, the cloning of the Waxy (Wx) gene has revealed the molecular mechanism of the formation of waxy traits in rice. However, there have been limited studies on the physicochemical properties, such as gelatinization temperature, rapid viscosity analyzer profile, and amylopectin fine structure of wx mutants. In the current study, a rapid and highly efficient strategy was developed through the CRISPR/Cas9 gene-editing system for generating wx mutants in the background of five different rice varieties. The wx mutation significantly reduced the AAC and starch viscosity but did not affect the major agronomic traits (such as plant height, panicle number per plant, grain number per panicle, and seed-setting frequency). Incorporation of the wx mutation into varieties with low initial AAC levels resulted in further reduction in AAC, but without significantly affecting the original, desirable gelatinization traits and amylopectin structure types, suggesting that parents with low initial AAC should be preferred in breeding programs.

Analysis of Related Metabolites Affecting Taste Values in Rice under Different Nitrogen Fertilizer Amounts and Planting Densities

The aim of this study was to explore the differences in metabolites related to rice quality formation under different nitrogen (N) fertilizers and planting densities. In this study, Yangnongxiang 28 was used as the experimental material with the following conditions: high nitrogen and low density (HNLD; high nitrogen: 360 kg·hm−2, low density: the row spacing of rice plants was 16 cm × 30 cm), medium nitrogen and medium density (MNMD; medium nitrogen: 270 kg·hm−2, medium density: the row spacing of rice plants was 13 cm × 30 cm), and low nitrogen and high density (LNHD; low nitrogen: 270 kg·hm−2, high density: the row spacing of rice plants was 10 cm × 30 cm). The rice quality indexes, including the processing quality, amylose content, and taste value, were compared under different treatments, and we analyzed their relationship with the metabolites. The results show that the milled rice rate of HNLD was 13.85% and was 1.89% higher than that of LNHD and MNMD, respectively. The head milled rice rate of HNLD was 32.45% and 6.39% higher than that of LNHD and MNMD, respectively. The milled rice rate and head milled rice rate of HNLD and MNMD were significantly higher than those of LNHD. This study identified 22 differential metabolites (DMs) in HNLD and LNHD, 38 DMs in HNLD and MNMD, and 23 DMs in LNHD and MNMD. Most of the identified differential metabolites were lipid metabolites, which were mainly enriched in the lipid metabolic pathways and amino acid metabolic pathways. The correlation analysis showed that the lipid metabolite physapubescin was significantly negatively correlated with the taste value. The lipid metabolites 2-undecen-1-ol, lucidenic acid F, and 8-deoxy-11,13-dihydroxygrosheimin were significantly positively correlated with the taste value. Lipids may be important substances that lead to differences in taste under different nitrogen fertilizer and density treatments.

Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century

The eating and cooking quality (ECQ) of rice is critical for determining its economic value in the marketplace and promoting consumer acceptance. It has therefore been of paramount importance in rice breeding programs. Here, we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in rice. Innovations in gene- and genome-editing techniques have enabled improvements in rice ECQ. Significant genes and quantitative trait loci (QTLs) have been shown to regulate starch composition, thereby affecting amylose content and thermal and pasting properties. A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and aroma. Marker-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ properties. The post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.

Adverse Effects of Arsenic Uptake in Rice Metabolome and Lipidome Revealed by Untargeted Liquid Chromatography Coupled to Mass Spectrometry (LC-MS) and Regions of Interest Multivariate Curve Resolution

Rice crops are especially vulnerable to arsenic exposure compared to other cereal crops because flooding growing conditions facilitates its uptake. Besides, there are still many unknown questions about arsenic’s mode of action in rice. Here, we apply two untargeted approaches using liquid chromatography coupled to mass spectrometry (LC-MS) to unravel the effects on rice lipidome and metabolome in the early stages of growth. The exposure is evaluated through two different treatments, watering with arsenic-contaminated water and soil containing arsenic. The combination of regions of interest (ROI) and multivariate curve resolution (MCR) strategies in the ROIMCR data analyses workflow is proposed and complemented with other multivariate analyses such as partial least square discriminant analysis (PLS-DA) for the identification of potential markers of arsenic exposure and toxicity effects. The results of this study showed that rice metabolome (and lipidome) in root tissues seemed to be more affected by the watering and soil treatment. In contrast, aerial tissues alterations were accentuated by the arsenic dose, rather than with the watering and soil treatment itself. Up to a hundred lipids and 40 metabolites were significantly altered due to arsenic exposure. Major metabolic alterations were found in glycerophospholipids, glycerolipids, and amino acid-related pathways.

Enhancing health benefits of milled rice: current status and future perspectives

Milled rice is an essential part of the regular diet for approximately half of the world's population. Its remarkable commercial value and consumer acceptance are mostly due to its promising cooking qualities, appealing sensory properties, and longer shelf life. However, the significant loss of the nutrient-rich bran layer during milling makes it less nutritious than the whole grain. Thus, enhancing the nutritive value of milled rice is vital in improving the health and wellbeing of rice consumers, particularly for those residing in the low-economic zones where rice is the primary source of calories and nutrition. This article provides a critical review on multiple frontiers of recent interventions, such as (1) infusing the genetic diversity to enrich amylose and resistant starch to reduce glycaemic index, (2) enhancing the minerals and vitamins through complementary fortification and biofortification as short and long-term interventions, and (3) developing transgenic solutions to improve the nutrient levels of milled rice. Additionally, the review highlights the benefits of functional ingredients of milled rice to human health and the potential of enhancing them in rice to address the triple burden of malnutrition. The potential merit of milled rice concerning food safety is also reviewed in this article.

Down-Regulation of FAD2-1 Gene Expression Alters Lysophospholipid Composition in the Endosperm of Rice Grain and Influences Starch Properties

Small quantities of lipids accumulate in the white rice grains. These are grouped into non-starch lipid and starch lipid fractions that affect starch properties through association with starch. Lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) are two major lipid classes in the two fractions. Using high-oleic rice grains, we investigated the fatty-acid composition in flour and starch by LC-MS and evaluated its impact on starch properties. In the wild-type grain, nearly 50% of fatty acids in LPC and LPE were palmitic acid (C16:0), over 20% linoleic acid (C18:2) and less than 10% oleic acid (C18:1). In the high-oleic rice grain, C18:1 increased at the expense of C18:2 and C16:0. The compositional changes in starch lipids suggest that LPC and LPE are transported to an amyloplast with an origin from endoplasmic reticulum-derived PC and PE during endosperm development. The high-dissociation temperature of the amylose-lipid complex (ALC) and restricted starch swelling power in the high-oleic rice starch indicates that the stability of the ALC involving C18:1 is higher than that of C18:2 and C16:0. This study provides insight into the lipid deposition and starch properties of rice grains with optimized fatty-acid composition.

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.