Rice metabolic regulatory network spanning the entire life cycle

Yang, Chenkun; Shen, Shuangqian; Shen, Zhou; Li, Yufei; Mao, Yong; Zhou, Junjie; Shi, Yi; An, Longxu; Zhou, Qianqian; Peng, Weiming; Lyu, Yuanyuan; Liu, Xuemei; Chen, Wei; Wang, Shouchuang; Qu, Lianghuan; Liu, Xianqing; Fernie, Alisdair R.

doi:10.1016/j.molp.2021.10.005

Cited by 69 publications

(53 citation statements)

References 79 publications

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“…KEGG pathway enrichment analysis further showed that a large number of metabolites, namely, phenylpropanoid biosynthesis, flavonoid biosynthesis, and flavone and flavonol biosynthesis pathways were enriched in the DEMs. This finding is in consonance with a previous study, wherein it documented that metabolites such as phospholipids, amino acids and most lipids and fatty acids were enriched during rice seed germination ( Yang et al, 2022 ), suggesting that flavonoids play an important role in distinguishing the two phenotypes of sugarcane.…”

Section: Discussionsupporting

confidence: 92%

“…Flavonoids are also the largest and the most studied group of plant phenols with variable phenolic structures which could be further divided into flavones, isoflavones, flavonols, flavanols, flavanones, and anthocyanins ( Panche et al, 2016 ). For instance, Yang et al (2022) revealed that flavonoids in vegetative tissues of rice were observed to be abundant. Correspondingly, we found that flavonoids were the most dominant metabolites in the two sugarcane cultivars, exhibiting distinct distribution patterns in the various plant tissues.…”

Section: Discussionmentioning

confidence: 99%

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Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties

et al. 2022

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Metabolic composition can have potential impact on several vital agronomic traits, and metabolomics, which represents the bioactive compounds in plant tissues, is widely considered as a powerful approach for linking phenotype–genotype interactions. However, metabolites related to cane traits such as sugar content, rind color, and texture differences in different sugarcane cultivars using metabolome integrated with transcriptome remain largely inconclusive. In this study, metabolome integrated with transcriptome analyses were performed to identify and quantify metabolites composition, and have better insight into the molecular mechanisms underpinning the different cane traits, namely, brix, rind color, and textures in the stems (S) and leaves (L) of sugarcane varieties FN41 and 165402. We also identified metabolites and associated genes in the phenylpropanoid and flavonoid biosynthesis pathways, starch and sucrose metabolism. A total of 512 metabolites from 11 classes, with the vast majority (122) belonging to flavonoids were identified. Moreover, the relatively high amount of D-fructose 6-p, D-glucose6-p and glucose1-p detected in FN41L may have been transported and distributed by source and sink of the cane, and a majority of them reached the stem of sugarcane FN41L, thereby promoting the high accumulation of sugar in FN41S. Observations also revealed that genes such as C4H, CHS, F3H, F3’H, DFR, and FG2 in phenylpropanoid and flavonoid biosynthesis pathways were the major factors impacting the rind color and contrasting texture of FN41 and 165204. Further analysis revealed that weighted gene co-expression network analysis (WGCNA) hub genes and six transcription factors, namely, Tify and NAC, MYB-related, C2C2-Dof, WRKY, and bHLH play a key role in phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, starch and sucrose metabolism. Additionally, metabolites such as L-phenylalanine, tyrosine, sinapaldehyde, pinobanksin, kaempferin, and nictoflorin were the potential drivers of phenotypic differences. Our finding also demonstrated that genes and metabolites in the starch and sucrose metabolism had a significant effect on cane sugar content. Overall, this study provided valuable insight into the molecular mechanisms underpinning high sugar accumulation and rind color in sugarcane, which we believe is important for future sugarcane breeding programs and the selection of high biomass varieties.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties

et al. 2022

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“…The supernatants were collected and filtration (SCAA-104, 0.22 mm pore size; ANPEL, Shanghai, China, (accessed on 21 January 2021)) before the LC-MS analysis. The samples were equally mixed into multiple quality control samples for testing the instrument stability [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

“…In addition, through tomato breeding, the content of glycoalkaloids in modern cultivated tomatoes was greatly reduced, and the nutrients such as flavonoids and vitamins also decreased compared with wild tomatoes [ 18 ]. A rice metabolism database covering the entire growth period of a plant provides a basis for systematically understanding the dynamics and changes of the rice metabolome throughout a growing season [ 19 ]. Previously, a metabolomic analysis of various tissues in rice showed significant differences in the accumulation of 90 flavonoids and 16 phenolamides in rice seedlings, leaves, culms, panicles, and roots [ 20 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice

Zhang

Deng

et al. 2022

Metabolites

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Rice (Oryza sativa L.) is one of the most globally important crops, nutritionally and economically. Therefore, analyzing the genetic basis of its nutritional quality is a paramount prerequisite for cultivating new varieties with increased nutritional health. To systematically compare the nutritional quality differences between landraces and cultivated rice, and to mine key genes that determine the specific nutritional traits of landraces, a seed metabolome database of 985 nutritional metabolites covering amino acids, flavonoids, anthocyanins, and vitamins by a widely targeted metabolomic approach with 114 rice varieties (35 landraces and 79 cultivars) was established. To further reveal the molecular mechanism of the metabolic differences in landrace and cultivated rice seeds, four cultivars and six landrace seeds were selected for transcriptome and metabolome analysis during germination, respectively. The integrated analysis compared the metabolic profiles and transcriptomes of different types of rice, identifying 358 differentially accumulated metabolites (DAMs) and 1982 differentially expressed genes (DEGs), establishing a metabolite–gene correlation network. A PCA revealed anthocyanins, flavonoids, and lipids as the central differential nutritional metabolites between landraces and cultivated rice. The metabolite–gene correlation network was used to screen out 20 candidate genes postulated to be involved in the structural modification of anthocyanins. Five glycosyltransferases were verified to catalyze the glycosylation of anthocyanins by in vitro enzyme activity experiments. At the same time, the different mechanisms of the anthocyanin synthesis pathway and structural diversity in landrace and cultivated rice were systematically analyzed, providing new insights for the improvement and utilization of the nutritional quality of rice landrace varieties.

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“…In the multivariate analysis of metabolites (Figure 7.5), we observed that the organ was the main factor explaining the variability in the data, as previously reported in durum wheat (Vergara-Diaz et Martínez-Peña et al, 2022 (sse chapter 6)) and rice (Lawas et al, 2019;Yang et al, 2022a).…”

Section: Metabolite Profiles In Foliar and Non-foliar Photosynthetic ...supporting

confidence: 83%

Ear metabolism and genotype-by-environment interaction in field-grown durum wheat: identification of novel traits for crop improvement

Peña¹

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Today's world faces many challenges, such as population growth, economic instability, resource scarcity and impending climate change. This raises the need to make more efficient use of our resources and develop our resilience, primarily to ensure our food security, as one of the main challenges facing agricultural research in this century.Climate change projections predict an increase in average land surface temperature, more frequent and severe heavy rainfall events, and periods of drought leading to water scarcity and soil degradation, which will affect plant growth and development and impact agricultural productivity and yields in many regions of the world. Durum wheat, is one of the most important crops for human consumption, grown mainly in semi-arid climates with limited availability of nutrients and water resources. Its cultivation represents a valuable source of nutrients for the human diet, such as proteins, carbohydrates, essential vitamins and minerals. As part of human history, durum wheat was a key crop in the Neolithic Revolution that supported the dawn of civilisation. This crop has spread worldwide from the Middle East, and currently, the central cultivated regions are concentrated in few suitable areas, being the Mediterranean Basin the most representative. In addition, a wide variety of products can be obtained from its semolina, some with strong cultural background, such as pasta, burghul a, couscous and unleavened bread. All indications show that durum wheat will remain a staple food crop in the future.The environmental conditions of the current climate scenario will aggravate these constraints, especially in the semi-arid Mediterranean regions typical of our geographical environment. To maintain crop yields, short-term solutions are usually taken, such as increasing the application of nitrogen fertilisers, which in the long-term will undoubtedly be economically costly and harmful to the environment, generating water and soil pollution problems. To cope with this scenario, it is estimated that the demand for cereals, both for food and feed, must increase by 70% by 2050, which will require new strategies and innovative approaches to achieve a Golden Revolution in agriculture.The stagnation or even reduction of land suitable for cultivation, the problems of contamination, and the lack of genetic gains present in some areas lead us to be more creative in our research and seek new avenues of study and objectives. In this sense, one of the biggest challenges for physiologists, molecular biologists, agronomists, and breeders will be identifying traits or attributes to select cereal varieties that maximise their production under climate change conditions in specific areas, as there will be different climatic variations depending on the area in which we are located. To achieve this goal, it will first be necessary to perform holistic studies to understand the response of key physiological, biochemical and molecular processes occurring in the different organs of the plant to individual and combined env...

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Rice metabolic regulatory network spanning the entire life cycle

Cited by 69 publications

References 79 publications

Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties

Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties

Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice

Ear metabolism and genotype-by-environment interaction in field-grown durum wheat: identification of novel traits for crop improvement

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