Comparative root transcriptome analysis of two soybean cultivars with different cadmium sensitivities reveals the underlying tolerance mechanisms

Insights into the ameliorative effect of ZnONPs on arsenic toxicity in soybean mediated by hormonal regulation, transporter modulation, and stress responsive genes

Arsenic (As) contamination of agricultural soils poses a serious threat to crop productivity and food safety. Zinc oxide nanoparticles (ZnONPs) have emerged as a potential amendment for mitigating the adverse effects of As stress in plants. Soybean crop is mostly grown on marginalized land and is known for high accumulation of As in roots than others tissue. Therefore, this study aimed to elucidate the underlying mechanisms of ZnONPs in ameliorating arsenic toxicity in soybean. Our results demonstrated that ZnOB significantly improved the growth performance of soybean plants exposed to arsenic. This improvement was accompanied by a decrease (55%) in As accumulation and an increase in photosynthetic efficiency. ZnOB also modulated hormonal balance, with a significant increase in auxin (149%), abscisic acid (118%), gibberellin (160%) and jasmonic acid content (92%) under As(V) stress assuring that ZnONPs may enhance root growth and development by regulating hormonal signaling. We then conducted a transcriptomic analysis to understand further the molecular mechanisms underlying the NPs-induced As(V) tolerance. This analysis identified genes differentially expressed in response to ZnONPs supplementation, including those involved in auxin, abscisic acid, gibberellin, and jasmonic acid biosynthesis and signaling pathways. Weighted gene co-expression network analysis identified 37 potential hub genes encoding stress responders, transporters, and signal transducers across six modules potentially facilitated the efflux of arsenic from cells, reducing its toxicity. Our study provides valuable insights into the molecular mechanisms associated with metalloid tolerance in soybean and offers new avenues for improving As tolerance in contaminated soils.

Molecular-Assisted Breeding of Cadmium Pollution-Safe Cultivars

Cadmium (Cd) contamination in edible agricultural products, especially in crops intended for consumption, has raised worldwide concerns regarding food safety. Breeding of Cd pollution-safe cultivars (Cd-PSCs) is an effective solution to preventing the entry of Cd into the food chain from contaminated agricultural soil. Molecular-assisted breeding methods, based on molecular mechanisms for cultivar-dependent Cd accumulation and bioinformatic tools, have been developed to accelerate and facilitate the breeding of Cd-PSCs. This review summarizes the recent progress in the research of the low Cd accumulation traits of Cd-PSCs in different crops. Furthermore, the application of molecular-assisted breeding methods, including transgenic approaches, genome editing, marker-assisted selection, whole genome-wide association analysis, and transcriptome, has been highlighted to outline the breeding of Cd-PSCs by identifying critical genes and molecular biomarkers. This review provides a comprehensive overview of the development of Cd-PSCs and the potential future for breeding Cd-PSC using modern molecular technologies.

Transcriptome studies on cadmium tolerance and biochar mitigating cadmium stress in muskmelon

Cadmium pollution in agricultural soil is a great threat to crop growth and human health. In this research, with 1%, 3% and 5% biochar applied to control soil cadmium pollution, melon was selected to be the experimental object for physiological detection and transcriptome analysis, through which we explored the mechanism of cadmium tolerance and biochar mitigating cadmium stress in muskmelon. Three set concentrations of biochar have a mitigative effect on muskmelon cadmium stress, and 5% biochar and 3% biochar respectively have the best and the worst alleviative effect. The alleviation of biochar to cadmium stress on muskmelon is primarily in the manner of inhibiting cadmium transfer, while the resistance of muskmelon to cadmium stress is through activating phenylpropanoid pathway and overexpressing stress related genes. Under cadmium treatment, 11 genes of the phenylpropane pathway and 19 stress-related genes including cytochrome P450 family protein genes and WRKY transcription factor genes were up-regulated, while 1%, 3%, 5% biochar addition significantly downregulated 3, 0, 7 phenylpropane pathway genes and 17, 5, 16 stress-related genes, respectively. Genes such as cytochrome P450 protein family genes, WRKY transcription factor genes, and annexin genes may play a key role in muskmelon's resistance to cadmium stress. The results show the key pathways and genes of cadmium stress resistance and the effect of different concentrations of biochar in alleviating cadmium stress, which provide a reference for the research of cadmium stress resistance in crops and the application of biochar in cadmium pollution in agricultural soil.

Physiological and transcriptomic study reveal SeNPs-mediated AsIII stress detoxification mechanisms involved modulation of antioxidants, metal transporters, and transcription factors in Glycine max L. (Merr.) roots

Physiological changes and genome-wide alteration in gene expression were performed in soybean (Glycine max [L.] Merr.) roots exposed to AsⅢ (25 μmol/L) alone and supplemented with selenium nanoparticles (SeNPs) at the concentration of 10 and 25 μmol/L at the V2 growth stage. Excessive arsenic in the root zone poses a potential threat to soybean yield, particularly to roots, due to the limited translocation of AsIII from root to shoot in the case of soybean. We hypothesized that SeNPs can relieve AsⅢ toxicity to soybean root by reducing the AsⅢ uptake and regulating the internal tolerance mechanism of the plants. Results accomplished that SeNPs had positive impact on soybean dry weight and roots parameters under AsⅢ stress. Then, we further evaluated physiological indexes, whole genome transcriptomic analysis and quantitative real-time PCR to elucidate the underlying mechanism of AsⅢ tolerance under SeNPs supplementation. Under the condition of AsⅢ-stress, SeNPs exposure significantly reduced the electrolyte leakage, O₂^-•, H₂O₂ and MDA accumulation while increasing the antioxidants level. The RNA-seq dataset revealed total of 5819 up and 7231 down expressed DEGs across all libraries. The number of exclusively regulated genes were higher under As + SeNP10 (4909) treatment than in the AsⅢ-alone (4830) and As + SeNP25 (3311) treatments. The KEGG and GO analyses revealed that stress responsive DEGs such as glutathione S-transferase, glutathione peroxidase, ascorbate, glutaredoxin, thioredoxin, and phytochelatins synthase are responsible for AsⅢ tolerance under the SeNPs supplementation. Similarly, sulfate transporter, and ABC transporters (ATP-binding cassettes) expression were induced, and aquaporin channels related DEGs expression were reduced under SeNPs application in AsⅢ exposure condition. Furthermore, the expression of molecular chaperones (HSP) and transcription factors (MYB, bZIP, bHLH, and HSFs) were increased in SeNPs treatment groups. These results provide vital information of AsⅢ tolerance mechanism in response to SeNPs in soybean. We suggest that functional characterization of these genes will help us learn more about the SeNPs responsive arsenic tolerance mechanism in soybean.

Improvement of heat stress tolerance in soybean (Glycine max L), by using conventional and molecular tools

The soybean is a significant legume crop, providing several vital dietary components. Extreme heat stress negatively affects soybean yield and quality, especially at the germination stage. Continuous change in climatic conditions is threatening the global food supply and food security. Therefore, it is a critical need of time to develop heat-tolerant soybean genotypes. Different molecular techniques have been developed to improve heat stress tolerance in soybean, but until now complete genetic mechanism of soybean is not fully understood. Various molecular methods, like quantitative trait loci (QTL) mapping, genetic engineering, transcription factors (TFs), transcriptome, and clustered regularly interspaced short palindromic repeats (CRISPR), are employed to incorporate heat tolerance in soybean under the extreme conditions of heat stress. These molecular techniques have significantly improved heat stress tolerance in soybean. Besides this, we can also use specific classical breeding approaches and different hormones to reduce the harmful consequences of heat waves on soybean. In future, integrated use of these molecular tools would bring significant results in developing heat tolerance in soybean. In the current review, we have presented a detailed overview of the improvement of heat tolerance in soybean and highlighted future prospective. Further studies are required to investigate different genetic factors governing the heat stress response in soybean. This information would be helpful for future studies focusing on improving heat tolerance in soybean.