Coregulation of glutamine synthetase1;2 (GLN1;2) and NADH-dependent glutamate synthase (GLT1) gene expression in Arabidopsis roots in response to ammonium supply

Melatonin improves cadmium tolerance in Salix viminalis by enhancing amino acid and saccharide metabolism, and increasing polyphenols

As a short-rotation woody plant, Salix viminalis has the potential for phytoremediation of cadmium (Cd), but it has poor tolerance to high Cd concentrations. Melatonin (MEL), a candidate bio-promoter, was considered to play an active role in plant responses to Cd. However, the molecular mechanism by which MEL regulates metabolic processes in plants to defend against Cd stress remain unclear. Transcriptomics and global untargeted metabolomic sequencing were used to investigate the rapid response of S. viminalis to high Cd concentrations during initial growth stage after foliar application of MEL. Four treatments were set up in a pot experiment involving foliar application of MEL on the first day, followed by irrigation with a Cd solution the next day. Significant variations in the relevant defence genes and metabolites in leaves exposed to Cd were observed between willows treated with and without MEL. Foliar application of MEL upregulated sulphur metabolism-related genes such as methionine and S-adenosylmethionine synthases in leaves exposed to Cd; glutamine content, which is the key point of nitrogen assimilation, also increased. Additionally, glycolysis and sucrose metabolic genes, including hexokinase, sucrose synthase, invertase, and the inositol phosphate metabolic gene myo-inositol-1-phosphate synthase were also upregulated in leaves. Moreover, MEL also upregulated genes related to the synthesis of flavonoids, anthocyanins, and proanthocyanins in the leaves. These results demonstrated that MEL improved amino acid and saccharide metabolism in the leaves of S. viminalis in response to Cd. It also improved the antioxidant capacity and Cd tolerance in S. viminalis leaves by enhancing synthetic capacity of polyphenol compounds. MEL may be involved in processes of photorespiration, ethylene metabolism, GABA shunt, nitric oxide metabolism, osmotic adjustment, and the synthesis of glutathione and ascorbate in S. viminalis under Cd stress. This series of metabolic changes in S. viminalis occurred within 24 h of the foliar application of MEL, which provided a sufficient substrate for subsequent defence reactions to cope with Cd stress. Our findings will help elucidate the molecular mechanism by which MEL regulates metabolic processes in plants in response to Cd challenges and guide the application of MEL to improve Cd phytoremediation efficiency.

Glutamine Synthetase and Glutamate Synthase Family Perform Diverse Physiological Functions in Exogenous Hormones and Abiotic Stress Responses in Pyrus betulifolia Bunge (P.be)

The unscientific application of nitrogen (N) fertilizer not only increases the economic input of pear growers but also leads to environmental pollution. Improving plant N use efficiency (NUE) is the most effective economical method to solve the above problems. The absorption and utilization of N by plants is a complicated process. Glutamine synthetase (GS) and glutamate synthase (GOGAT) are crucial for synthesizing glutamate from ammonium in plants. However, their gene family in pears has not been documented. This study identified 29 genes belonging to the GS and GOGAT family in the genomes of Pyrus betulaefolia (P.be, 10 genes), Pyrus pyrifolia (P.py, 9 genes), and Pyrus bretschneideri (P.br, 10 genes). These genes were classified into two GS subgroups (GS1 and GS2) and two GOGAT subgroups (Fd-GOGAT and NADH-GOGAT). The similar exon-intron structures and conserved motifs within each cluster suggest the evolutionary conservation of these genes. Meanwhile, segmental duplication has driven the expansion and evolution of the GS and GOGAT gene families in pear. The tissue-specific expression dynamics of PbeGS and PbeGOGAT genes suggest significant roles in pear growth and development. Cis-acting elements of the GS and GOGAT gene promoters are crucial for plant development, hormonal responses, and stress reactions. Furthermore, qRT-PCR analysis indicated that PbeGSs and PbeGOGATs showed differential expression under exogenous hormones (GA3, IAA, SA, ABA) and abiotic stress (NO3- and salt stress). In which, the expression of PbeGS2.2 was up-regulated under hormone treatment and down-regulated under salt stress. Furthermore, physiological experiments demonstrated that GA3 and IAA promoted GS, Fd-GOGAT, and NADH-GOGAT enzyme activities, as well as the N content. Correlation analysis revealed a significant positive relationship between PbeGS1.1, PbeGS2.2, PbeNADH-GOGATs, and the N content. Therefore, PbeGS1.1, PbeGS2.2, and PbeNADH-GOGATs could be key candidate genes for improving NUE under plant hormone and abiotic stress response. To the best of our knowledge, our study provides valuable biological information about the GS and GOGAT family in the pear for the first time and establishes a foundation for molecular breeding aimed at developing high NUE pear rootstocks.

Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits

The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.

Characterization and genetic differences analysis in adventitious roots development of 38 Populus germplasm resources

To select poplar clones with excellent adventitious roots development (ARD) and deepen the understanding of its molecular mechanism, a comprehensive evaluation was conducted on 38 Populus germplasm resources with cuttings cultured in the greenhouse. Genetic differences between poplar clones with good ARD and with poor ARD were explored from the perspectives of genomics and transcriptomics. By cluster analysis of the seven adventitious roots (AR) traits, the materials were classified into three clusters, of which cluster I indicated excellent AR developmental capability and promising breeding potential, especially P.×canadensis 'Guariento', P. 'jingtong1', P. deltoides 'Zhongcheng5', P. deltoides 'Zhongcheng2'. At the genomic level, the cross-population composite likelihood ratio (XP-CLR) analysis identified 1944 positive selection regions related to ARD, and variation detection analysis identified 3426 specific SNPs and 687 specific Indels in the clones with good ARD, 3212 specific SNPs and 583 specific Indels in the clones with poor ARD, respectively. Through XP-CLR, variation detection, and weighted gene co-expression network analysis based on transcriptome data, eight major putative genes associated with poplar ARD were primary identified, and a co-expression network of eight genes was constructed, it was discovered that CSD1 and WRKY6 may be important in the ARD. Subsequently, we confirmed that SWEET17 had a non-synonymous mutation at the site of 928,404 in the clones with poor ARD, resulting in an alteration of the amino acid. After exploring phenotypic differences and the genetic variation of adventitious roots development in different poplar clones, this study provides valuable reference information for future poplar breeding and genetic improvement.

Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction

Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.

The Arabidopsis Target of Rapamycin (TOR) kinase regulates ammonium assimilation and glutamine metabolism

In eukaryotes, Target of Rapamycin (TOR) is a well conserved kinase that controls cell metabolism and growth in response to nutrients and environmental factors. Nitrogen (N) is an essential element for plants, and TOR functions as a crucial N and amino acid sensor in animals and yeast. However, knowledge on the connections between TOR and the overall N metabolism and assimilation in plants is still limited. In this study, we investigated the regulation of TOR in Arabidopsis (Arabidopsis thaliana) by the N source as well as the impact of TOR deficiency on N metabolism. Inhibition of TOR globally decreased ammonium uptake while triggering a massive accumulation of amino acids, such as Gln, but also of polyamines. Consistently, TOR complex mutants were hypersensitive to Gln. We also showed that the glutamine synthetase inhibitor glufosinate abolishes Gln accumulation resulting from TOR inhibition and improves the growth of TOR complex mutants. These results suggest that a high level of Gln contributes to the reduction in plant growth resulting from TOR inhibition. Glutamine synthetase activity was reduced by TOR inhibition while the enzyme amount increased. In conclusion, our findings show that the TOR pathway is intimately connected to N metabolism and that a decrease in TOR activity results in glutamine synthetase-dependent Gln and amino acid accumulation.