An alanine to valine mutation of glutamyl-tRNA reductase enhances 5-aminolevulinic acid synthesis in rice

Analysis of the Transcriptome Provides Insights into the Photosynthate of Maize Response to Salt Stress by 5-Aminolevulinic Acid

Salt stress is a significant environmental factor that impedes maize growth and yield. Exogenous 5-aminolevulinic acid (ALA) has been shown to mitigate the detrimental effects of various environmental stresses on plants. However, its regulatory role in the photosynthesis mechanisms of maize seedlings under salt stress remains poorly understood. Transcriptome sequencing and physiological index measurements were conducted on the leaves of the "Zhengdan 958" cultivar subjected to three different treatments. Differential expression analysis revealed 4634 differentially expressed genes (DEGs), including key transcription factor (TF) families such as NAC, MYB, WRKY, and MYB-related, across two comparisons (SS_vs_CK and ALA_SS_vs_SS). Significant enrichment was observed in the metabolic pathways related to porphyrin metabolism, photosynthesis-antenna proteins, photosynthesis, and carbon fixation in photosynthetic organisms. ALA treatment modulated the expression of photosynthesis-related genes, increased photosynthetic pigment content, and enhanced the activities of superoxide dismutase (SOD) and catalase (CAT), thereby mitigating the excessive accumulation of reactive oxygen species (ROS). Furthermore, ALA increased starch content under salt stress. These findings establish a foundational understanding of the molecular mechanisms through which ALA regulates photosynthesis under salt stress in maize seedlings. Collectively, exogenous ALA enhances maize's salt tolerance by regulating photosynthesis-related pathways.

Alleviatory efficacy of achillea millefolium L. in etoxazole-mediated toxicity in allium cepa L

The application of pesticides may adversely impact a variety of non-target organisms. The use of side-effect-free herbal remedies to protect against the toxicity of harmful pesticides such as etoxazole has gained attention in recent times. The current study aimed to reveal the potential mitigating efficacy of Achillea millefolium L. extract against etoxazole toxicity in Allium cepa L. A. cepa bulbs in the control group were applied with tap water, while bulbs in the treatment groups were applied with etoxazole at dose of 0.5 m/L and two different doses of A. millefolium extract (200 mg/L and 400 mg/L). The impact of the treatments on certain parameters was evaluated. The molecular docking analysis was employed to investigate the potential interactions of etoxazole with DNA species, DNA topoisomerases, tubulin proteins, glutamate-1-semialdehyde aminotransferase, and protochlorophyllide reductase. The phenolic profile of A. millefolium was assessed. Etoxazole exposure reduced rooting percentage, root length, weight gain, mitotic index, and levels of chlorophyll a and chlorophyll b. Conversely, etoxazole treatment led to an increase in chromosomal aberrations and micronuclei occurrence. The most frequently observed chromosomal aberrations induced by etoxazole, which serve as bioindicators of genotoxicity, were fragment, vagrant chromosome, sticky chromosome, unequal chromatin distribution, bridge, reverse polarization, and vacuolated nucleus. The levels of malondialdehyde and antioxidant enzyme (superoxide dismutase and catalase) activities were also elevated. Epidermis cell damage, flattened cell nucleus, thickened cortex cell wall, and thickened conduction tissue were the meristematic cell disorders triggered by etoxazole. Molecular docking studies showed that etoxazole can interact directly with DNA, tubulins, and the enzymes mentioned above. A. millefolium extract was found to contain a substantial quantity of phenolic compounds. A. millefolium extract, when co-administered with etoxazole, attenuated all toxic effects of etoxazole dose-dependently. In conclusion, A. millefolium may potentially serve as a reliable pharmacological shield against the toxicity of pesticides in non-target organisms.

MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization

BACKGROUND

Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest.

RESULTS

We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature.

CONCLUSIONS

MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available.

AVAILABILITY AND IMPLEMENTATION

MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools .

Yellow-Green Leaf 19 Encoding a Specific and Conservative Protein for Photosynthetic Organisms Affects Tetrapyrrole Biosynthesis, Photosynthesis, and Reactive Oxygen Species Metabolism in Rice

Chlorophyll is the main photosynthetic pigment and is crucial for plant photosynthesis. Leaf color mutants are widely used to identify genes involved in the synthesis or metabolism of chlorophyll. In this study, a spontaneous mutant, yellow-green leaf 19 (ygl19), was isolated from rice (Oryza sativa). This ygl19 mutant showed yellow-green leaves and decreased chlorophyll level and net photosynthetic rate. Brown necrotic spots appeared on the surface of ygl19 leaves at the tillering stage. And the agronomic traits of the ygl19 mutant, including the plant height, tiller number per plant, and total number of grains per plant, were significantly reduced. Map-based cloning revealed that the candidate YGL19 gene was LOC_Os03g21370. Complementation of the ygl19 mutant with the wild-type CDS of LOC_Os03g21370 led to the restoration of the mutant to the normal phenotype. Evolutionary analysis revealed that YGL19 protein and its homologues were unique for photoautotrophs, containing a conserved Ycf54 functional domain. A conserved amino acid substitution from proline to serine on the Ycf54 domain led to the ygl19 mutation. Sequence analysis of the YGL19 gene in 4726 rice accessions found that the YGL19 gene was conserved in natural rice variants with no resulting amino acid variation. The YGL19 gene was mainly expressed in green tissues, especially in leaf organs. And the YGL19 protein was localized in the chloroplast for function. Gene expression analysis via qRT-PCR showed that the expression levels of tetrapyrrole synthesis-related genes and photosynthesis-related genes were regulated in the ygl19 mutant. Reactive oxygen species (ROS) such as superoxide anions and hydrogen peroxide accumulated in spotted leaves of the ygl19 mutant at the tillering stage, accompanied by the regulation of ROS scavenging enzyme-encoding genes and ROS-responsive defense signaling genes. This study demonstrates that a novel yellow-green leaf gene YGL19 affects tetrapyrrole biosynthesis, photosynthesis, and ROS metabolism in rice.

Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes

Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.

Indole-3-acetic acid and zinc synergistically mitigate positively charged nanoplastic-induced damage in rice

Recent research has shown that polystyrene nanoplastics (PS-NPs) can inhibit plant growth and the development of crops, such as rice. In this study, we aimed to investigate the effects of PS-NPs of different particle sizes (80 nm, 200 nm, and 2 µm) and charges (negative, neutral, and positive) on rice growth, and to explore the underlying mechanisms and potential strategies for mitigating their impacts. Two-week-old rice plants were planted in a standard ½ Murashige-Skoog liquid medium holding 50 mg/L of different particle sizes and/or charged PS-NPs for 10 days, and the liquid medium without PS-NPs was used as control. The results showed that positively charged PS-NPs (80 nm PS-NH2) had the greatest impact on plant growth and greatly reduced the dry biomass, root length, and plant height of rice by 41.04%, 46.34%, and 37.45%, respectively. The positively charged NPs with a size of 80 nm significantly decreased the zinc (Zn) and indole-3-acetic acid (IAA, auxin) contents by 29.54% and 48.00% in roots, and 31.15% and 64.30% in leaves, respectively, and down-regulated the relative expression level of rice IAA response and biosynthesis genes. Moreover, Zn and/or IAA supplements significantly alleviated the adverse effects of 80 nm PS-NH2 on rice plant growth. Exogenous Zn and/or IAA increased seedlings' growth, decreased PS-NPs distribution, maintained redox homeostasis, and improved tetrapyrrole biosynthesis in rice treated with 80 nm PS-NH2. Our findings suggest that Zn and IAA synergistically alleviate positively charged NP-induced damage in rice.