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ABSTRACT:
PROVIDER: PRJNA575957 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Foxtail millet, domesticated from the wild species green foxtail, provides a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail millet grains, we generated and analyzed datasets encompassing genomes, transcriptomes, metabolomes and anti-inflammatory indices from 398 foxtail millet accessions. We identified hundreds of common variants that influence numerous secondary metabolites, with significant heterogeneity in the natural variation of metabolites and their underlying genetic architectures between different sub-groups of foxtail millet. The combined results from variations in genome, transcriptome and metabolome illustrated how breeding has altered foxtail millet metabolite content. Selection for alleles of genes associated with yellow grains led to altered metabolite profiles, such as carotenoids and endogenous hormones. The importance of PSY1 (phytoene synthase 1) for millet color was validated using CRISPR-Cas9. The in vitro cell inflammation assay showed that 83 metabolites have anti-inflammatory effects. This multi-omics study illustrates how the breeding history of foxtail millet has impacted metabolites. It provides some fundamental resources for understanding how grain quality could be associated with different metabolites, and highlights future perspectives on millet genetic research and metabolome-assisted improvement.
2022-05-09 | ST002168 | MetabolomicsWorkbench
Project description:High temperature during the grain-filling stage causes deleterious effects on storage material accumulation and grain quality. But it is still unclear how high temperature affects storage materials accumulation. In this study, we systemically analyzed the expression pattern of rice genes under high temperture during the grain-filling stage.
2015-10-19 | GSE73220 | GEO
Project description:De novo Transcriptome Sequencing to Dissect Candidate Genes Associated with Pearl Millet Grain Quality
| PRJNA625418 | ENA
Project description:Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size. We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway. These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.
2024-06-30 | GSE256331 | GEO
Project description:In wheat, the main staple crop in many regions of the word, one major challenge is to improve the yield potential while maintaining the grain quality, which is mainly defined by its protein concentration and composition. To achieve this goal, it is essential to considerate the nitrogen (N) and sulfur (S) nutrition, which strongly influences the grain storage protein (GSP) composition. Nowadays, the limitation of nitrogen inputs and the sulfur deficiency recently observed in soils represent major difficulties to control the grain quality. Thus, identification of the molecular mechanisms that control the accumulation of GSP in response to N and S supply is necessary. In this study, we applied four post-anthesis N and S treatments to an einkorn (Triticum monococcum) culture. Effects of the treatments on the grain transcriptome and metabolome were evaluated at different times during grain development. From the 386 differentially expressed genes and the 21 metabolites differentially accumulated, our results have revealed a strong impact of a high-N supply without any added S. A large majority of genes were transiently influenced by the treatments while others showed strong modifications of their kinetics of expression during grain filling. We hypothesized the role of several genes (e.ge.g. sulfate transporters, transcriptional regulators) in the adjustment of the N-to-S ratio in response to a S deficiency. These genes could coordinate the amino acid pool necessary for GSP synthesis. These new results contribute in facing the challenge of maintaining wheat grain quality for the development of more sustainable agriculture.
2018-12-01 | GSE107807 | GEO
Project description:Durum wheat requires high nitrogen inputs to obtain the high protein concentration necessary to satisfy pasta and semolina quality criteria. Optimizing plant nitrogen use efficiency is therefore of major importance for wheat grain quality. Here, we studied the impact on grain yield, protein concentration, and for the first time on protein composition of a marine (DPI4913) and a fungal (AF086) biostimulants applied to plant leaves. Plants were grown in a greenhouse and sampled at maturity for grain analysis. The protein concentration and quantity in grains per plant were determined, as well as water-use efficiency. A large-scale quantitative proteomics study of wheat flour samples was performed to determine the effect of biostimulant treatment on grain protein composition. Grain dry biomass and protein quantity were increased by 23.9% and 24.8% respectively with DPI4913, and by 27.4% and 25.9%, respectively, with AF086. A total of 1471 proteins were identified and 1391 were quantified. Quantitative proteomics analysis revealed 26 and 38 proteins with a significantly varying abundance after DPI4913 and AF086 treatment, respectively. Among these, 14 proteins were affected by both DPI4913 and AF086 treatments. The highest variations in proteins abundances were found for proteins involved in grain technological properties such as grain hardness, in storage functions with the substantial over-representation of the gluten protein gamma-gliadin, in regulation processes with the over-representation of proteins that play a transcription regulator role, and in stress responses with the over-representation of proteins implied in biotic and abiotic stress defense. The involvement of biostimulants in the abiotic stress response is suggested by the increase in water-use efficiency for DPI4913 treatment (15.4%) and for AF086 treatment (9.9%). In conclusion, our work, performed in greenhouse, has shown that DPI4913 and AF086 treatments promote grain yield while maintaining protein concentration in grains, and positively affect protein composition in term of grain quality. This study suggests that these biostimulants could be used to optimize durum wheat production and quality in field conditions.
2019-03-29 | PXD012469 | Pride
Project description:Introgression of a high molecular weight glutenin subunit (HMW-GS) gene, 1Ay21*, into commercial wheat cultivars increased overall grain protein content and bread-making quality by unknown mechanisms. As well as increased abundance of 1Ay HMW-GS, 115 differentially expressed proteins (DEPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines (NILs). Functional category analysis showed that the DEPs were predominantly other storage proteins, and proteins involved in protein synthesis, protein folding, protein degradation, stress response and grain development. Nearly half the genes encoding the DEPs showed strong co-expression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between these cis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the 1Ay21* improves grain protein content, but also directs selection of protein candidates for future wheat quality breeding programmes.
2021-05-30 | PXD021706 | Pride