Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity

AcEXPA1, an α-expansin gene, participates in the aluminum tolerance of carpetgrass (Axonopus compressus) through root growth regulation

KEY MESSAGE

AcEXPA1, an aluminum (Al)-inducible expansin gene, is demonstrated to be involved in carpetgrass (Axonopus compressus) root elongation under Al toxicity through analyzing composite carpetgrass plants overexpressing AcEXPA1. Aluminum (Al) toxicity is a major mineral toxicity that limits plant productivity in acidic soils by inhibiting root growth. Carpetgrass (Axonopus compressus), a dominant warm-season turfgrass widely grown in acidic tropical soils, exhibits superior adaptability to Al toxicity. However, the mechanisms underlying its Al tolerance are largely unclear, and knowledge of the functional genes involved in Al detoxification in this turfgrass is limited. In this study, phenotypic variation in Al tolerance, as indicated by relative root elongation, was observed among seventeen carpetgrass genotypes. Al-responsive genes related to cell wall modification were identified in the roots of the Al-tolerant genotype 'A58' via transcriptome analysis. Among them, a gene encoding α-expansin was cloned and designated AcEXPA1 for functional characterization. Observed Al dose effects and temporal responses revealed that Al induced AcEXPA1 expression in carpetgrass roots. Subsequently, an efficient and convenient Agrobacterium rhizogenes-mediated transformation method was established to generate composite carpetgrass plants with transgenic hairy roots for investigating AcEXPA1 involvement in carpetgrass root growth under Al toxicity. AcEXPA1 was successfully overexpressed in the transgenic hairy roots, and AcEXPA1 overexpression enhanced Al tolerance in composite carpetgrass plants through a decrease in Al-induced root growth inhibition. Taken together, these findings suggest that AcEXPA1 contributes to Al tolerance in carpetgrass via root growth regulation.

Identification and expression pattern of aluminium-responsive genes in roots of rice genotype with reference to Al-sensitivity

Aluminium (Al) is the third most abundant element in the Earth's crust. Globally, acidic soil occupies 30-40% of ice-free land areas; Al toxicity is a major threat to crops. The first symptom of Al toxicity is the inhibition of root growth followed by poor root hair development, swollen root apices, necrosis of leaves and reduced yield. Although Rice (Oryza sativa) is an Al toxicity tolerant crop, it shows considerable variations among rice genotypes to Al exposure. Therefore, it is pertinent to understand Al toxicity and underlying mechanisms for Al tolerance in Rice. In the present study, 63 rice genotypes screened under Al stress showed significant variations of root growth. Expression stability of endogenous control genes (ECGs) revealed sulphite reductase (SR) as the most stable ECG that can be used as a reference gene for quantitative real-time PCR (qRT-PCR). Expression patterns of Al-responsive genes suggest genes associated with cytoskeletal dynamics, metabolism, and ion transporter could play significant roles in Al adaptation and tolerance in rice. The results showed Motodhan, Vietnam-1, Yimyu and N-861 as Al-toxicity tolerant, while Lespah, RCPL-13, VL-31329, and UPR2919-141-1 as most Al-sensitive genotypes among the studied rice lines cultivated in North-East India.

Metal oxide nanoparticles inhibit nitrogen fixation and rhizosphere colonization by inducing ROS in associative nitrogen-fixing bacteria Pseudomonas stutzeri A1501

The potential effects of engineered metal oxide nanoparticles (MONPs) on bacterial nitrogen fixation are of great concern. Herein, the impact and mechanism of the increasing-used MONPs, including TiO₂, Al₂O₃, and ZnO nanoparticles (TiO₂NP, Al₂O₃NP, and ZnONP, respectively), on nitrogenase activity was studied at the concentrations ranging from 0 to 10 mg L^-1 using associative rhizosphere nitrogen-fixing bacteria Pseudomonas stutzeri A1501. Nitrogen fixation capacity was inhibited by MONPs in an increasing degree of TiO₂NP < Al₂O₃NP < ZnONP. Realtime qPCR analysis showed that the expressions of nitrogenase synthesis-related genes, including nifA and nifH, were inhibited significantly when MONPs were added. MONPs could cause the explosion of intracellular ROS, and ROS not only changed the permeability of the membrane but also inhibited the expression of nifA and biofilm formation on the root surface. The repressed nifA gene could inhibit transcriptional activation of nif-specific genes, and ROS reduced the biofilm formation on the root surface which had a negative effect on resisting environmental stress. This study demonstrated that MONPs, including TiO₂NP, Al₂O₃NP, and ZnONP, inhibited bacterial biofilm formation and nitrogen fixation in the rice rhizosphere, which might have a negative effect on the nitrogen cycle in bacteria-rice system.

Effects of antimony stress on growth, structure, enzyme activity and metabolism of Nipponbare rice (Oryza sativa L.) roots

Some antimony (Sb) contaminated areas are used for rice cultivation in response to economic demands. However, little is known about the effects of Sb stress on the growth and metabolism of rice roots. Thus, a hydroponic experiment was carried out on the growth, root anatomy, enzyme activity, and metabolism of Nipponbare rice (Oryza sativa L. ssp. japonica cv. Nipponbare) under varying levels of Sb (III) stress (0 mg L^-1, 10 mg L^-1, and 50 mg L^-1). With the increase of Sb concentration, rice root length and root fresh weight declined by 67.8 % and 90.5 % for 10 mg L^-1 Sb stress and 94.1 % and 98.4 % for 50 mg L^-1 Sb stress, respectively. Anatomical analysis of cross-sections of Sb-treated roots showed an increase in cell wall thickness and an increase in the number of cell mitochondria. The 10 mg L^-1 and 50 mg L^-1 Sb stress increased the activity of enzyme superoxide dismutase (SOD) in root cells by 1.94 and 2.40 times, respectively. Compared to the control, 10 mg L^-1 Sb treatment increased the activity of catalase (CAT) and peroxidase (POD), as well as the concentrations of antioxidant glutathione (GSH) in the root by 1.46, 1.38, and 0.52 times, respectively. However, 50 mg L^-1 Sb treatment significantly decreased the activity or content of CAT, POD and GSH by 28.1 %, 13.5 % and 28.2 %, respectively. Nontargeted LC/MS-based metabolomics analysis identified 23 and 13 significantly differential metabolites in rice roots exposed to 10 mg L^-1 and 50 mg L^-1 Sb, respectively, compared to the control. These differential metabolites were involved in four main metabolic pathways including the tricarboxylic acid cycle (TCA cycle), butanoate metabolism, alanine, aspartate and glutamate metabolism, and alpha-linolenic acid metabolism. Taken together, these findings indicate that Sb stress destroys the structure of rice roots, changes the activity of enzymes, and affects the metabolic pathway, thereby reducing the growth of rice roots and leading to toxicity.

Metabolome Analysis under Aluminum Toxicity between Aluminum-Tolerant and -Sensitive Rice (Oryza sativa L.)

Aluminum (Al) solubilizes into trivalent ions (Al³⁺) on acidic soils, inhibiting root growth. Since about 13% of global rice cultivation is grown on acidic soils, improving Al tolerance in rice may significantly increase yields. In the present study, metabolome analysis under Al toxicity between the Al-tolerant variety Nipponbare and the Al-sensitive variety H570 were performed. There were 45 and 83 differential metabolites which were specifically detected in Nipponbare and H570 under Al toxicity, respectively. Furthermore, the results showed that 16 lipids out of 45 total metabolites were down-regulated, and 7 phenolic acids as well as 4 alkaloids of 45 metabolites were up-regulated in Nipponbare, while 12 amino acids and their derivatives were specifically detected in H570, of which 11 amino acids increased, including L-homoserine and L-methionine, which are involved in cysteine synthesis, L-ornithine and L-proline, which are associated with putrescine synthesis, and 1-aminocyclopropane-1-carboxylate, which is associated with ethylene synthesis. The contents of cysteine and s-(methyl) glutathione, which were reported to be related to Al detoxification in rice, decreased significantly. Meanwhile, putrescine was accumulated in H570, while there was no significant change in Nipponbare, so we speculated that it might be an intermediate product of Al detoxification in rice. The differential metabolites detected between Al-tolerant and -sensitive rice variants in the present study might play important roles in Al tolerance. These results provide new insights in the mechanisms of Al tolerance in rice.

Alleviating aluminum toxicity in plants: Implications of reactive oxygen species signaling and crosstalk with other signaling pathways

Aluminum (Al) toxicity is a major limiting factor for plant growth and productivity in acidic soil. At pH lower than 5.0 (pH < 5.0), the soluble and toxic form of Al (Al³⁺ ions) enters root cells and inhibits root growth and uptake of water and nutrients. The organic acids malate, citrate, and oxalate are secreted by the roots and chelate Al³⁺ to form a non-toxic Al-OA complex, which decreases the entry of Al³⁺ into the root cells. When Al³⁺ enters, it leads to the production of reactive oxygen species (ROS) in cells, which are toxic and cause damage to biomolecules like lipids, carbohydrates, proteins, and nucleic acids. When ROS levels rise beyond the threshold, plants activate an antioxidant defense system that comprises of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione S-transferase (GST), ascorbic acid (ASA), phenolics and alkaloids etc., which protect plant cells from oxidative damage by scavenging and neutralizing ROS. Besides, ROS also play an important role in signal transduction and influence many molecular and cellular process like hormone signaling, gene expression, cell wall modification, cell cycle, programed cell death (PCD), and development. In the present review, the mechanisms of Al-induced ROS generation, ROS signaling, and crosstalk with other signaling pathways helping to combat Al toxicity have been summarized, which will help researchers to understand the intricacies of Al-induced plant response at cellular level and plan research for developing Al-toxicity tolerant crops for sustainable agriculture in acid soil-affected regions of the world.

Physiological and transcriptomic analyses reveal the roles of secondary metabolism in the adaptive responses of Stylosanthes to manganese toxicity

Background

As a heavy metal, manganese (Mn) can be toxic to plants. Stylo (Stylosanthes) is an important tropical legume that exhibits tolerance to high levels of Mn. However, little is known about the adaptive responses of stylo to Mn toxicity. Thus, this study integrated both physiological and transcriptomic analyses of stylo subjected to Mn toxicity.

Results

Results showed that excess Mn treatments increased malondialdehyde (MDA) levels in leaves of stylo, resulting in the reduction of leaf chlorophyll concentrations and plant dry weight. In contrast, the activities of enzymes, such as peroxidase (POD), phenylalanine ammonia-lyase (PAL) and polyphenol oxidase (PPO), were significantly increased in stylo leaves upon treatment with increasing Mn levels, particularly Mn levels greater than 400 μM. Transcriptome analysis revealed 2471 up-regulated and 1623 down-regulated genes in stylo leaves subjected to Mn toxicity. Among them, a set of excess Mn up-regulated genes, such as genes encoding PAL, cinnamyl-alcohol dehydrogenases (CADs), chalcone isomerase (CHI), chalcone synthase (CHS) and flavonol synthase (FLS), were enriched in secondary metabolic processes based on gene ontology (GO) analysis. Numerous genes associated with transcription factors (TFs), such as genes belonging to the C2H2 zinc finger transcription factor, WRKY and MYB families, were also regulated by Mn in stylo leaves. Furthermore, the C2H2 and MYB transcription factors were predicted to be involved in the transcriptional regulation of genes that participate in secondary metabolism in stylo during Mn exposure. Interestingly, the activation of secondary metabolism-related genes probably resulted in increased levels of secondary metabolites, including total phenols, flavonoids, tannins and anthocyanidins.

Conclusions

Taken together, this study reveals the roles of secondary metabolism in the adaptive responses of stylo to Mn toxicity, which is probably regulated by specific transcription factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07279-2.

Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis

BACKGROUND

The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice.

RESULTS

Genome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting's core collection constructed from 2262 Ting's collections with more than 3.8 million SNPs. Within Ting's core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance.

CONCLUSIONS

The present study provided important information for further using these elite genes existing in Ting's core collection for improvement of rice Al tolerance.