A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity

Individual and binary exposure of embryonic zebrafish (Danio rerio) to single-walled and multi-walled carbon nanotubes in the absence and presence of dissolved organic matter

The available toxicological information was inadequate to assess the potential ecological risk of a mixture of different nanostructured carbon nanotubes (CNTs) to aquatic organisms, especially for the co-existence of mixed CNTs with dissolved organic matter (DOM). Herein, we investigated individual and binary exposure of zebrafish (Danio rerio) embryos to single-walled (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) in the absence and presence of DOM. Results indicated that embryonic chorions were more resistant to mixed-type CNTs than to single-type CNTs, yet the addition of DOM decreased this resistance. The mixed-type CNTs increased the antioxidant capacity of zebrafish embryos by increasing superoxide dismutase activity in comparison to the single-type CNTs. Furthermore, the mixed-type CNTs caused oxidative damage to the zebrafish embryos, characterized by an increase in malondialdehyde level. Nevertheless, the activation of the antioxidant defense system was modulated by the presence of DOM. Transcriptome sequencing analysis showed that the number of unique genes (UGs) and differentially expressed genes (DEGs) between the mixed-type CNTs and control groups was significantly enhanced compared to the single-type CNTs. DOM increased the number of UGs and up-regulated DEGs, but decreased the number of down-regulated DEGs. GO classification analysis revealed that the mixed-type CNTs mainly altered the cellular component process of single-type CNTs to induce joint effects. DOM generally enhanced the GO enrichment of DEGs in D. rerio embryos exposed to the mixed-type CNTs during the biological process. KEGG pathway enrichment analysis for the mixed-type CNTs showed enrichment of DEGs encoding ether lipid metabolism, glycerophospholipid metabolism, glycerolipid metabolism, citrate cycle, and biosynthesis of nucleotide sugars. However, DOM allowed more specific KEGG pathways towards the mixed-type CNTs to be identified. Despite the mixed-type CNTs exhibiting differential expression of functional genes compared to the control and single-type CNTs, DOM could regulate the expression of these functional genes associated with oxidative stress response, carbohydrate metabolism, endoplasmic reticulum stress, neuroendocrine, osmotic stress, and DNA damage and repair. Our study thus paves a solid way for exploring the molecular mechanism of aquatic toxicity of multiple nanomaterials under field-relevant conditions.

Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture.

10th Anniversary of Plants-Recent Advances and Further Perspectives

Published for the first time in 2012, Plants will celebrate its 10th anniversary [...].

Transcriptional Changes in the Developing Rice Seeds Under Salt Stress Suggest Targets for Manipulating Seed Quality

Global sea-level rise, the effect of climate change, poses a serious threat to rice production owing to saltwater intrusion and the accompanying increase in salt concentration. The reclaimed lands, comprising 22.1% of rice production in Korea, now face the crisis of global sea-level rise and a continuous increase in salt concentration. Here, we investigated the relationship between the decrease in seed quality and the transcriptional changes that occur in the developing rice seeds under salt stress. Compared to cultivation on normal land, the japonica rice cultivar, Samgwang, grown on reclaimed land showed a greatly increased accumulation of minerals, including sodium, magnesium, potassium, and sulfur, in seeds and a reduced yield, delayed heading, decreased thousand grain weight, and decreased palatability and amylose content. Samgwang showed phenotypical sensitivity to salt stress in the developing seeds. Using RNA-seq technology, we therefore carried out a comparative transcriptome analysis of the developing seeds grown on reclaimed and normal lands. In the biological process category, gene ontology enrichment analysis revealed that the upregulated genes were closely associated with the metabolism of biomolecules, including amino acids, carboxylic acid, lignin, trehalose, polysaccharide, and chitin, and to stress responses. MapMan analysis revealed the involvement of upregulated genes in the biosynthetic pathways of abscisic acid and melatonin and the relationship of trehalose, raffinose, and maltose with osmotic stress. Interestingly, many seed storage protein genes encoding glutelins and prolamins were upregulated in the developing seeds under salt stress, indicating the negative effect of the increase of storage proteins on palatability. Transcription factors upregulated in the developing seeds under salt stress included, in particular, bHLH, MYB, zinc finger, and heat shock factor, which could act as potential targets for the manipulation of seed quality under salt stress. Our study aims to develop a useful reference for elucidating the relationship between seed response mechanisms and decreased seed quality under salt stress, providing potential strategies for the improvement of seed quality under salt stress.