Comparative transcriptomic analysis reveals the important process in two rice cultivars with differences in cadmium accumulation

Combined effects of polyamide microplastic and sulfamethoxazole in modulating the growth and transcriptome profile of hydroponically grown rice (Oryza sativa L.)

The use of reclaimed water from wastewater treatment plants for irrigation has a risk of introducing micropollutants such as microplastics (MPs) and antimicrobials (AMs) into the agroecosystem. This study was conducted to investigate the effects of single and combined treatment of 0.1 % polyamide (PA ∼15 μm), and varying sulfamethoxazole (SMX) levels 0, 10, 50, and 150 mg/L on rice seedlings (Oryza sativa L.) for 12 days. The study aimed to assess the impact of these contaminants on the morphological, physiological, and biochemical parameters of the rice plants. The findings revealed that rice seedlings were not sensitive to PA alone. However, SMX alone or in combination with PA, significantly inhibited shoot and root growth, total biomass, and affected photosynthetic pigments. Higher concentrations of SMX increased antioxidant enzyme activity, indicating oxidative stress. The roots had a higher SMX content than the shoots, and the concentration of minerals such as iron, copper, and magnesium were reduced in roots treated with SMX. RNA-seq analysis showed changes in the expression of genes related to stress, metabolism, and transport in response to the micropollutants. Overall, this study provides valuable insights on the combined impacts of MPs and AMs on food crops, the environment, and human health in future risk assessments and management strategies in using reclaimed water.

Comparative transcriptomics reveals the key pathways and genes of cadmium accumulation in the high cadmium-accumulating rice (Oryza Sativa L.) line

The high cadmium (Cd)-accumulating rice line Lu527-8 (H8) has already been proven to exhibit elevated Cd concentration and translocation over the normal rice line Lu527-4 (N4). H8 and N4 are sister lines that diverged from the same parents, while the molecular mechanisms underlying the genotypic differences in Cd enrichment between the two rice lines remains unclear. Here an in-depth exploration was performed via transcriptome analysis with 2919 and 2563 differentially expressed genes (DEGs) in H8 and N4 identified, respectively. Gene ontology(GO) enrichment revealed that Cd-stressed rice both exhibited enhanced defense and antioxidant responses, while N4 displayed unique categories related to cell wall biosynthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 5 mutual pathways between H8 and N4. Many genes associated with cell wall biosynthesis were identified as the Cd-responsive DEGs. Enhanced phenylpropanoid biosynthesis and unique diterpenoid biosynthesis resulted in intensified lignin biosynthesis, which likely led to apoplastic barrier formation, subsequently blocked Cd inflow and reduced radial Cd transport in the root, thereby limited Cd translocation into aerial parts in N4. The key genes OsPAL6 and OsPAL8 that encode phenylalanine ammonia lyase (PAL), and gibberellin (GA) biosynthesis-related key genes including OsCPS2, OsCPS4, OsKSL4, OsKSL7 and some CYP superfamily members played vital roles in the process. Meanwhile, the greater upregulation of Cd transporters, such as OsIRT1/2, some OsABCs, OsYSLs, and OsZIPs in H8, accounted for the higher root absorption of Cd compared to N4. These findings unveil the molecular basis of the differential Cd concentration and translocation between the two rice lines, contributing valuable insights to the theory of Cd accumulation in rice.

Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants

Cadmium (Cd) is one of the most toxic heavy metals faced by plants and, additionally, via the food chain, threatens human health. It is principally dispersed through agro-ecosystems via anthropogenic activities and geogenic sources. Given its high mobility and persistence, Cd, although not required, can be readily assimilated by plants thereby posing a threat to plant growth and productivity as well as animal and human health. Thus, breeding crop plants in which the edible parts contain low to zero Cd as safe food stuffs and harvesting shoots of high Cd-containing plants as a route for decontaminating soils are vital strategies to cope with this problem. Recently, multiomics approaches have been employed to considerably enhance our understanding of the mechanisms underlying (i) Cd toxicity, (ii) Cd accumulation, (iii) Cd detoxification and (iv) Cd acquisition tolerance in plants. This information can be deployed in the development of the biotechnological tools for developing plants with modulated Cd tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. The aim of this review is to provide a current update about the mechanisms involved in Cd uptake by plants and the recent developments in the area of multiomics approach in terms of Cd stress responses, as well as in the development of Cd tolerant and low Cd accumulating crops.

Effects and mechanisms of different exogenous organic matters on selenium and cadmium uptake by rice in natural selenium-cadmium-rich soil

Many natural selenium (Se)-rich rice plants are being polluted by cadmium (Cd). In this study, for reducing Cd concentrations in rice grains while maintaining Se concentrations, the effects of different exogenous organic matters (OMs), such as humic acid (HA), cow manure (CM), and vermicompost (VC), on Se and Cd uptake in rice growing in natural Se-Cd-rich paddy soils were investigated by pot experiments. The Se and Cd concentrations in the soil solution, their species in the soil, and their concentrations and translocations in rice tissues were determined. Results showed that different exogenous OMs exhibited distinct percentage changes in Se and Cd levels in rice grains with amplitudes of -19.42 % and -56.90 % (significant, p < 0.05) in the HA treatments, +10.79 % and -1.72 % in the CM treatments, and +15.83 % and -15.52 % in the VC treatments, respectively. Correlation analysis showed that the concentrations of Se and Cd in rice grains might be primarily influenced by their concentrations in the soil solution, rather than the Se/Cd molar ratios in the soil solution or their translocations in rice tissues. HA decreased Se and Cd bioavailability in soil by increasing HA-bound Se and residual Cd, respectively. Meanwhile, HA increased soil solution pH, which was negative for Cd bioavailability but positive for Se bioavailability. This additive effect made HA lowered Cd concentration more than Se concentration in both soil solution and grain. CM and VC did not have this additive effect and thus have limited effects on grain Se and Cd concentrations. In addition, according to grain Se and Cd concentrations, to prioritize reducing Cd in rice, use HA; to prioritize increasing Se in rice, use VC. This study enhances the understanding of Se and Cd uptake mechanisms in rice with the applications of various OMs and offers potential remediation methods for Se-Cd-rich paddy soils.

Comparison of Transcriptome Differences between Two Rice Cultivars Differing in Cadmium Translocation from Spike-Neck to Grain

At present, the mechanism of varietal differences in cadmium (Cd) accumulation in rice is not well understood. Two rice cultivars, ZZY (high translocation-high grain Cd) and SJ18 (low translocation-low grain Cd), were used to analyze transcriptome differences in the spike-neck tissue in field trials. The results showed that, compared with ZZY, 22,367 differentially expressed genes (DEGs) were identified in SJ18, including 2941 upregulated and 19,426 downregulated genes. GO analysis enriched 59 downregulated terms, concerning 24 terms enriched for more than 1000 DEGs, including cellular and metabolic processes, biological regulation, localization, catalytic activity, transporter activity, signaling, etc. KEGG enrichment identified 21 significant downregulated pathways, regarding the ribosome, metabolic pathways, biosynthesis of secondary metabolism, signaling transduction, cell membrane and cytoskeleton synthesis, genetic information transfer, amino acid synthesis, etc. Weighted gene co-expression network analysis (WGCNA) revealed that these DEGs could be clustered into five modules. Among them, the yellow module was significantly related to SJ18 with hub genes related to OsHMA and OsActin, whereas the brown module was significantly related to ZZY with hub genes related to mitogen-activated protein kinase (MAPK), CBS, and glutaredoxin. This suggests that different mechanisms are involved in the process of spike-neck-grain Cd translocation among varieties. This study provides new insights into the mechanisms underlying differences in Cd transport among rice varieties.