Metabolomic analysis of pathways related to rice grain chalkiness by a notched-belly mutant with high occurrence of white-belly grains

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Genetic control of grain appearance quality in rice

Grain appearance, one of the key determinants of rice quality, reflects the ability to attract consumers, and is characterized by four major properties: grain shape, chalkiness, transparency, and color. Mining of valuable genes, genetic mechanisms, and breeding cultivars with improved grain appearance are essential research areas in rice biology. However, grain appearance is a complex and comprehensive trait, making it challenging to understand the molecular details, and therefore, achieve precise improvement. This review highlights the current findings of grain appearance control, including a detailed description of the key genes involved in the formation of grain appearance, and the major environmental factors affecting chalkiness. We also discuss the integration of current knowledge on valuable genes to enable accurate breeding strategies for generation of rice grains with superior appearance quality.

Nitrogen Application Rate Affects the Accumulation of Carbohydrates in Functional Leaves and Grains to Improve Grain Filling and Reduce the Occurrence of Chalkiness

Chalkiness, which is highly affected by nitrogen (N) management during grain filling, is critical in determining rice appearance quality and consumer acceptability. We investigated the effects of N application rates 75 (N₁), 150 (N₂), and 225 (N₃) kg ha^-1 on the source-sink carbohydrate accumulation and grain filling characteristics of two indica hybrid rice cultivars with different chalkiness levels in 2019 and 2020. We further explored the relationship between grain filling and formation of chalkiness in superior and inferior grains. In this study, carbohydrates in the functional leaves and grains of the two varieties, and grain filling parameters, could explain 66.2%, 68.0%, 88.7%, and 91.6% of the total variation of total chalky grain rate and whole chalkiness degree, respectively. They were primarily concentrated in the inferior grains. As the N fertilizer application rate increased, the chalky grain rate and chalkiness degree of both the superior and inferior grains decreased significantly. This interfered with the increase in total chalky grain rate and chalkiness. Moreover, the carbohydrate content in the functional leaves increased significantly in N₂ and N₃ compared with that in N₁. The transfer of soluble sugar from the leaves to the grains decreased the soluble sugar and increased total starch contents, accelerated the development of grain length and width, increased grain water content, and effectively alleviated the contradiction between source and sink. These changes promoted the carbohydrate partition in superior and inferior grains, improved their average filling rate in the middle and later stages, optimized the uniformity of inferior grain fillings, and finally led to the overall reduction in rice chalkiness.

Amino Acids in Rice Grains and Their Regulation by Polyamines and Phytohormones

Rice is one of the most important food crops in the world, and amino acids in rice grains are major nutrition sources for the people in countries where rice is the staple food. Phytohormones and plant growth regulators play vital roles in regulating the biosynthesis of amino acids in plants. This paper reviewed the content and compositions of amino acids and their distribution in different parts of ripe rice grains, and the biosynthesis and metabolism of amino acids and their regulation by polyamines (PAs) and phytohormones in filling grains, with a focus on the roles of higher PAs (spermidine and spermine), ethylene, and brassinosteroids (BRs) in this regulation. Recent studies have shown that higher PAs and BRs (24-epibrassinolide and 28-homobrassinolide) play positive roles in mediating the biosynthesis of amino acids in rice grains, mainly by enhancing the activities of the enzymes involved in amino acid biosynthesis and sucrose-to-starch conversion and maintaining redox homeostasis. In contrast, ethylene may impede amino acid biosynthesis by inhibiting the activities of the enzymes involved in amino acid biosynthesis and elevating reactive oxygen species. Further research is needed to unravel the temporal and spatial distribution characteristics of the content and compositions of amino acids in the filling grain and their relationship with the content and compositions of amino acids in different parts of a ripe grain, to elucidate the cross-talk between or among phytohormones in mediating the anabolism of amino acids, and to establish the regulation techniques for promoting the biosynthesis of amino acids in rice grains.

Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape

Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes have been cloned to date. In this study, the candidate gene GSE5 of a major quantitative trait locus (QTL) for rice chalkiness, qDEC5, was identified by map-based cloning. Phenotyping and haplotype analysis of proActin:GSE5 transgenic line, gse5-cr mutant, and 69 rice varieties further confirmed that GSE5 had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed GSE5 was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to GSE5 was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that GSE5 played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by GSE5 to affect the formation of chalkiness, including some newly discovered genes, such as OsCESA9, OsHSP70, OsTPS8, OsPFK04, OsSTA1, OsERdj3A, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly; OsDjC10 and OsSUS3 were upregulated at 6 and 12 DAP, respectively, and OsGSTL2 was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of qDEC5 dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.

Metabolic Disturbance Induced by the Embryo Contributes to the Formation of Chalky Endosperm of a Notched-Belly Rice Mutant

Grain chalkiness is a key quality trait of the rice grain, whereas its underlying mechanism is still not thoroughly understood because of the complex genetic and environmental interactions. We identified a notched-belly (NB) mutant that has a notched-line on the belly of grains. The line dissects the endosperm into two distinct parts, the upper translucent part, and the bottom chalky part in the vicinity of the embryo. Using this mutant, our previous studies clued the negative influence of embryo on the biochemical makeup of the endosperm, suggesting the need for the in-depth study of the embryo effect on the metabolome of developing endosperm. This study continued to use the NB mutant to evolve a novel comparison method to clarify the role of embryo in the formation of a chalky endosperm. Grain samples of the wild-type (WT) and NB were harvested at 10, 20, and 30 days after fertilization (DAF), and then divided into subsamples of the embryo, the upper endosperm, and the bottom endosperm. Using non-targeted metabolomics and whole-genome RNA sequencing (RNA-seq), a nearly complete catalog of expressed metabolites and genes was generated. Results showed that the embryo impaired the storage of sucrose, amino acid, starch, and storage proteins in the bottom endosperm of NB by enhancing the expression of sugar, amino acids, and peptide transporters, and declining the expression of starch, prolamin, and glutelin synthesis-related genes. Importantly, the competitive advantage of the developing embryo in extracting the nutrients from the endosperm, transformed the bottom endosperm into an "exhaustive source" by diverting the carbon (C) and nitrogen (N) metabolism from synthetic storage to secondary pathways, resulting in impaired filling of the bottom endosperm and subsequently the formation of chalky tissue. In summary, this study reveals that embryo-induced metabolic shift in the endosperm is associated with the occurrence of grain chalkiness, which is of relevance to the development of high-quality rice by balancing the embryo-endosperm interaction.

Grain chalkiness traits is affected by the synthesis and dynamic accumulation of the storage protein in rice

BACKGROUOND

Grain chalkiness lowers the market value of rice. Alleviating grain chalkiness is the most challenging issue in many rice-producing areas of the world. Nitrogen (N) metabolism has received increasing attention as a result of its relationship with grain chalkiness, although little information is available on the mechanism of N-induced grain chalk.

RESULTS

A highly chalky rice variety OM052 was used to explore the protein synthesis and its accumulation in the grain exposed to N topdressing (N+) at the panicle initiation stage and a control (N-). The results showed that chalky kernels were stimulated by the N+ treatment and more prone to occur on the top and primary rachis. The grain protein content was increased because of the increased average and maximum rates of protein accumulation during grain filling, which was related to the enhanced activities of glutamine synthetase, glutamate synthase, glutamic oxalo-acetic transaminase and glutamate pyruvate transaminase under the N+ treatment. The activities of these enzymes at 15 days after flowering (DAF) were notably positively correlated with grain chalky traits and protein content.

CONCLUSION

N topdressing regulates the synthesis and accumulation of the protein by affecting the key enzymes, especially at 15 DAF, which is attributed to grain chalkiness in rice. © 2021 Society of Chemical Industry.

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

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

GC-MS-based metabolite profiling of key differential metabolites between superior and inferior spikelets of rice during the grain filling stage

BACKGROUND

The asynchronous filling between superior spikelets (SS) and inferior spikelets (IS) in rice has become a research hotspot. The stagnant development and poor grain filling of IS limit yields and the formation of good quality rice. A large number of studies on this phenomenon have been carried out from the genome, transcriptome and proteome level, indicating that asynchronous filling of SS and IS filling is a complex, but orderly physiological and biochemical process involving changes of a large number of genes, protein expression and modification. However, the analysis of metabolomics differences between SS and IS is rarely reported currently.

RESULTS

This study utilized untargeted metabolomics and identified 162 metabolites in rice spikelets. Among them, 17 differential metabolites associated with unsynchronized grain filling between SS and IS, 27 metabolites were related to the stagnant development of IS and 35 metabolites related to the lower maximum grain-filling rate of IS compared with the SS. We found that soluble sugars were an important metabolite during grain filling for SS and IS. Absolute quantification was used to further analyze the dynamic changes of 4 types of soluble sugars (sucrose, fructose, glucose, and trehalose) between SS and IS. The results showed that sucrose and trehalose were closely associated with the dynamic characteristics of grain filling between SS and IS. The application of exogenous sugar showed that trehalose functioned as a key sugar signal during grain filling of IS. Trehalose regulated the expression of genes related to sucrose conversion and starch synthesis, thereby promoting the conversion of sucrose to starch. The difference in the spatiotemporal expression of TPS-2 and TPP-1 between SS and IS was an important reason that led to the asynchronous change in the trehalose content between SS and IS.

CONCLUSIONS

The results from this study are helpful for understanding the difference in grain filling between SS and IS at the metabolite level. In addition, the present results can also provide a theoretical basis for the next step of using metabolites to regulate the filling of IS.

Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants

C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.

Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time

Background

The primary and secondary metabolites of fungi are critical for adaptation to environmental stresses, host pathogenicity, competition with other microbes, and reproductive fitness. Drought-derived reactive oxygen species (ROS) have been shown to stimulate aflatoxin production and regulate in Aspergillus flavus, and may function in signaling with host plants. Here, we have performed global, untargeted metabolomics to better understand the role of aflatoxin production in oxidative stress responses, and also explore isolate-specific oxidative stress responses over time.

Results

Two field isolates of A. flavus, AF13 and NRRL3357, possessing high and moderate aflatoxin production, respectively, were cultured in medium with and without supplementation with 15 mM H₂O₂, and mycelia were collected following 4 and 7 days in culture for global metabolomics. Overall, 389 compounds were described in the analysis which encompassed 9 biological super-pathways and 47 sub-pathways. These metabolites were examined for differential accumulation. Significant differences were observed in both isolates in response to oxidative stress and when comparing sampling time points.

Conclusions

The moderately high aflatoxin-producing isolate, NRRL3357, showed extensive stimulation of antioxidant mechanisms and pathways including polyamines metabolism, glutathione metabolism, TCA cycle, and lipid metabolism while the highly aflatoxigenic isolate, AF13, showed a less vigorous response to stress. Carbohydrate pathway levels also imply that carbohydrate repression and starvation may influence metabolite accumulation at the later timepoint. Higher conidial oxidative stress tolerance and antioxidant capacity in AF13 compared to NRRL3357, inferred from their metabolomic profiles and growth curves over time, may be connected to aflatoxin production capability and aflatoxin-related antioxidant accumulation. The coincidence of several of the detected metabolites in H₂O₂-stressed A. flavus and drought-stressed hosts also suggests their potential role in the interaction between these organisms and their use as markers/targets to enhance host resistance through biomarker selection or genetic engineering.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1580-x) contains supplementary material, which is available to authorized users.

Easy sectioning of whole grain of rice using cryomicrotome

To obtain a clear intact section of a ripened rice grain, which is suitable for biochemical and histological analysis, the Kawamoto method using a specific adhesive film was applied using a cryomicrotome. The longitudinal and sagittal sections were easily obtained together with the cross-section, and cell characteristics were clearly discerned in the ripened grain. It was demonstrated that the Kawamoto method is readily applicable for intact sectioning of hard tissue, including ripened grain. Intact section sampling may be useful for enzymatic analysis and transcriptomic analysis of plant tissue.

Plant Systems Biology at the Single-Cell Level

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.