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Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice.

ABSTRACT: Enhancing the dietary properties of rice is crucial to contribute to alleviating hidden hunger and non-communicable diseases in rice-consuming countries. Germination is a bioprocessing approach to increase the bioavailability of nutrients in rice. However, there is a scarce information on how germination impacts the overall nutritional profile of pigmented rice sprouts (PRS). Herein, we demonstrated that germination resulted to increase levels of certain dietary compounds, such as free phenolics and micronutrients (Ca, Na, Fe, Zn, riboflavin, and biotin). Metabolomic analysis revealed the preferential accumulation of dipeptides, GABA, and flavonoids in the germination process. Genome-wide association studies of the PRS suggested the activation of specific genes such as CHS1 and UGT genes responsible for increasing certain flavonoid compounds. Haplotype analyses showed a significant difference (P < 0.05) between alleles associated with these genes. Genetic markers associated with these flavonoids were incorporated into the random forest model, improving the accuracy of prediction of multi-nutritional properties from 89.7% to 97.7%. Deploying this knowledge to breed rice with multi-nutritional properties will be timely to address double burden nutritional challenges.

SUBMITTER: Tiozon RJN

PROVIDER: S-EPMC10545681 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice.

Tiozon Rhowell Jr N RJN Sreenivasulu Nese N Alseekh Saleh S Sartagoda Kristel June D KJD Usadel Björn B Fernie Alisdair R AR

Communications biology 20231002 1

Enhancing the dietary properties of rice is crucial to contribute to alleviating hidden hunger and non-communicable diseases in rice-consuming countries. Germination is a bioprocessing approach to increase the bioavailability of nutrients in rice. However, there is a scarce information on how germination impacts the overall nutritional profile of pigmented rice sprouts (PRS). Herein, we demonstrated that germination resulted to increase levels of certain dietary compounds, such as free phenolics ...[more]

PMID: 37783812

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Project description:Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Project description:Natural hazards are diverse and uneven in time and space, therefore, understanding its complexity is key to save human lives and conserve natural ecosystems. Reducing the outputs obtained after each modelling analysis is key to present the results for stakeholders, land managers and policymakers. So, the main goal of this survey was to present a method to synthesize three natural hazards in one multi-hazard map and its evaluation for hazard management and land use planning. To test this methodology, we took as study area the Gorganrood Watershed, located in the Golestan Province (Iran). First, an inventory map of three different types of hazards including flood, landslides, and gullies was prepared using field surveys and different official reports. To generate the susceptibility maps, a total of 17 geo-environmental factors were selected as predictors using the MaxEnt (Maximum Entropy) machine learning technique. The accuracy of the predictive models was evaluated by drawing receiver operating characteristic-ROC curves and calculating the area under the ROC curve-AUCROC. The MaxEnt model not only implemented superbly in the degree of fitting, but also obtained significant results in predictive performance. Variables importance of the three studied types of hazards showed that river density, distance from streams, and elevation were the most important factors for flood, respectively. Lithological units, elevation, and annual mean rainfall were relevant for detecting landslides. On the other hand, annual mean rainfall, elevation, and lithological units were used for gully erosion mapping in this study area. Finally, by combining the flood, landslides, and gully erosion susceptibility maps, an integrated multi-hazard map was created. The results demonstrated that 60% of the area is subjected to hazards, reaching a proportion of landslides up to 21.2% in the whole territory. We conclude that using this type of multi-hazard map may be a useful tool for local administrators to identify areas susceptible to hazards at large scales as we demonstrated in this research.

Project description:IntroductionHeat stress is a vital factor which restricts rice seed quality and yield. However, the response mechanism to heat stress in the mid filling stage of rice seed is unclear.MethodsIn the present study we integrated phenotypic analysis with biochemical, hormone, and gene expression analysis in order to explore technologies for improving rice seeds heat tolerance and subsequent seed germination.ResultsSpermidine (Spd) application effectively alleviated the damage of heat stress treatment during mid-filling stage (HTM, 12-20 days after pollination) on seed development, promoted subsequent seed germination and seedlings establishment. Spd significantly increased seed dry weight, starch and amylose contents during seed development under heat stress, and improved seed germinate, seedlings establishment and seedling characteristics during germination time. Biochemical analysis indicated that, HTM significantly decreased the activities of several starch synthase enzymes and led to a decrease in starch content. While Spd treatment significantly enhanced the activities of ADP-glucose pyrophosphorylas and granule-bound starch synthase, as well as the corresponding-genes expressions in HTM rice seeds, resulting in the increases of amylose and total starch contents. In addition, Spd significantly increased the catalase and glutathione reductase activities together with corresponding-genes expressions, and lowered the overaccumulation of H2O2 and malondialdehyde in HTM seeds. In the subsequent seed germination process, HTM+Spd seeds exhibited dramatically up-regulated levels of soluble sugars, glucose, ATP and energy charges. Consistently, HTM+Spd seeds showed significantly increased of α-amylose and α-glucosidase activities as well as corresponding-genes expressions during early germination. Moreover, HTM evidently increased the abscisic acid (ABA) content, decreased the gibberellin (GA) content, and accordingly significantly declined the GA/ABA ratio during early rice seeds germination. However, Spd treatment did not significantly affect the metabolism of GA and ABA in seed germination stage.DiscussionThe present study suggested that Spd treatment could effectively alleviate the negative impact of HTM on seed development and the subsequent seed germination, which might be closely correlated with starch synthesis and antioxidant defense during seed filling period, starch decomposition and energy supply in seed germination period.

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Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice.

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Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice.

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