Patterns of stress response and tolerance based on transcriptome profiling of rice crown tissue under zinc deficiency

Micronutrient deficiency-induced oxidative stress in plants

Micronutrients like iron (Fe), zinc (Zn), copper (Cu), manganese (Mn), boron (B), nickel (Ni), and molybdenum (Mo) perform significant roles in the regulation of plant metabolism, growth, and development. Micronutrients, namely Fe, Zn, Cu, Mn, and Ni, are involved in oxidative stress and antioxidant defense as they are cofactors or activators of various antioxidant enzymes, viz., superoxide dismutase (Fe, Cu/Zn, Mn, and Ni), catalase (Fe), and ascorbate peroxidase (Fe). An effort has been made to incorporate recent advances along with classical work done on the micronutrient deficiency-induced oxidative stress and associated antioxidant responses of plants. Deficiency of a micronutrient produces ROS in the cellular compartments. Enzymatic and non-enzymatic antioxidant defense systems are often modulated by micronutrient deficiency to regulate redox balance and scavenge deleterious ROS for the safety of cellular constituents. ROS can strike cellular constituents such as lipids, proteins, and nucleic acids and can destruct cellular membranes and proteins. ROS might act as a signaling molecule and activate the antioxidant proteins by interacting with signaling partners such as respiratory burst oxidase homolog (RBOH), G-proteins, Ca2+, mitogen activated protein kinases (MAPKs), and various transcription factors (TFs). Opinions on probable ROS signaling under micronutrient deficiency have been described in this review. However, further research is required to decipher micronutrient deficiency-induced ROS generation, perception, and associated downstream signaling events, leading to the development of antioxidant responses in plants.

Artemisia argyi allelopathy: a generalist compromises hormone balance, element absorption, and photosynthesis of receptor plants

BACKGROUND

Allelopathy is expressed through the release of plant chemicals and is considered a natural alternative for sustainable weed management. Artemisia argyi (A. argyi) is widely distributed throughout Asia, and often dominates fields due to its strong allelopathy. However, the mechanism of A. argyi allelopathy is largely unknown and need to be elucidated at the physiological and molecular levels.

RESULTS

In this study, we used electron microscopy, ionomics analysis, phytohormone profiling, and transcriptome analysis to investigate the physiological and molecular mechanisms of A. argyi allelopathy using the model plant rice (Oryza sativa) as receptor plants. A. argyi water extract (AAWE)-treated rice plants grow poorly and display root morphological anomalies and leaf yellowing. We found that AAWE significantly inhibits rice growth by destroying the root and leaf system in multiple ways, including the integrity of ultrastructure, reactive oxygen species (ROS) homeostasis, and the accumulation of soluble sugar and chlorophyll synthesis. Further detection of the hormone contents suggests that AAWE leads to indole-3-acetic acid (IAA) accumulation in roots. Moreover, ionomics analysis shows that AAWE inhibits the absorption and transportation of photosynthesis-essential mineral elements, especially Mg, Fe, and Mn. In addition, the results of transcriptome analysis revealed that AAWE affects a series of crucial primary metabolic processes comprising photosynthesis in rice plants.

CONCLUSIONS

This study indicates that A. argyi realizes its strongly allelopathy through comprehensive effects on recipient plants including large-scale IAA synthesis and accumulation, ROS explosion, damaging the membrane system and organelles, and obstructing ion absorption and transport, photosynthesis and other pivotal primary metabolic processes of plants. Therefore, AAWE could potentially be developed as an environmentally friendly botanical herbicide due to its strong allelopathic effects.

Divalent nutrient cations: Friend and foe during zinc stress in rice

Zn deficiency is the most common micronutrient deficit in rice but Zn is also a widespread industrial pollutant. Zn deficiency responses in rice are well documented, but comparative responses to Zn deficiency and excess have not been reported. Therefore, we compared the physiological, transcriptional and biochemical properties of rice subjected to Zn starvation or excess at early and later treatment stages. Both forms of Zn stress inhibited root and shoot growth. Gene ontology analysis of differentially expressed genes highlighted the overrepresentation of Zn transport and antioxidative defense for both Zn stresses, whereas diterpene biosynthesis was solely induced by excess Zn. Divalent cations (Fe, Cu, Ca, Mn and Mg) accumulated in Zn-deficient shoots but Mg and Mn were depleted in the Zn excess shoots, mirroring the gene expression of non-specific Zn transporters and chelators. Ascorbate peroxidase activity was induced after 14 days of Zn starvation, scavenging H₂ O₂ more effectively to prevent leaf chlorosis via the Fe-dependent Fenton reaction. Conversely, excess Zn triggered the expression of genes encoding Mg/Mn-binding proteins (OsCPS2/4 and OsKSL4/7) required for antimicrobial diterpenoid biosynthesis. Our study reveals the potential role of divalent cations in the shoot, driving the unique responses of rice to each form of Zn stress.

Molecular regulation of zinc deficiency responses in plants

Zinc (Zn) is an essential micronutrient for plants and animals. Because of its low availability in arable soils worldwide, Zn deficiency is becoming a serious agricultural problem resulting in decreases of crop yield and nutritional quality. Plants have evolved multiple responses to adapt to low levels of soil Zn supply, involving biochemical and physiological changes to improve Zn acquisition and utilization, and defend against Zn deficiency stress. In this review, we summarize the physiological and biochemical adaptations of plants to Zn deficiency, the roles of transporters and metal-binding compounds in Zn homeostasis regulation, and the recent progresses in understanding the sophisticated regulatory mechanisms of Zn deficiency responses that have been made by molecular and genetic analyses, as well as diverse 'omics' studies. Zn deficiency responses are tightly controlled by multiple layers of regulation, such as transcriptional regulation that is mediated by transcription factors like F-group bZIP proteins, epigenetic regulation at the level of chromatin, and post-transcriptional regulation mediated by small RNAs and alternative splicing. The insights into the regulatory network underlying Zn deficiency responses and the perspective for further understandings of molecular regulation of Zn deficiency responses have been discussed. The understandings of the regulatory mechanisms will be important for improving Zn deficiency tolerance, Zn use efficiency, and Zn biofortification in plants.

Current understanding of plant zinc homeostasis regulation mechanisms

The essential nature of Zn and widespread Zn deficiency in plants under field conditions underlie the great interest of researchers in the regulation of plant Zn homeostasis. Here, the current knowledge of plant Zn homeostasis regulation, mainly in A. thaliana, is reviewed. The plant Zn homeostasis machinery is regulated largely at the transcriptional level. Local regulation in response to changes in cellular Zn status is based on the transcription factors bZIP19 and bZIP23, which sense changes in free Zn²⁺ concentrations in the cell. However, there are likely other unidentified ways to sense cellular free Zn²⁺ concentrations in addition to the well-known bZIP19 and bZIP23 factors. In recent years, the existence of a shoot-derived systemic Zn deficiency signal, which is involved in the upregulation of Zn transport from roots to shoots, was demonstrated. Additionally, rates of mRNA degradation of Zn homeostasis genes are likely regulated by changes in cellular Zn status. In addition to the regulation of Zn transport, other mechanisms for the regulation of plant Zn homeostasis exist. "Zn sparing" mechanisms could be involved in the decrease in plant Zn requirements under Zn deficiency. Additionally, autophagy is probably regulated by local Zn status and involved in Zn reutilization at the cellular level. Current issues related to studying Zn homeostasis regulation are discussed.

Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency

Zinc (Zn) is an indispensable element for rice growth. Zn deficiency results in brown blotches and streaks 2-3 weeks after transplanting, as well as stunting, reduced tillering, and low productivity of rice plants. These processes are controlled by different families of expressed genes. A comparative transcriptome profile analysis was conducted using the roots of two Zn deficiency tolerant varieties (UCP122 and KALIBORO26) and two sensitive varieties (IR26 and IR64) by merging data from untreated control (CK) and Zn deficiency treated samples. Results revealed a total of 4,688 differentially expressed genes (DEGs) between the normal Zn and deficient conditions, with 2,702 and 1,489 unique DEGs upregulated and downregulated, respectively. Functional enrichment analysis identified transcription factors (TFs), such as WRKY, MYB, ERF, and bHLH which are important in the regulation of the Zn deficiency response. Furthermore, chitinases, jasmonic acid, and phenylpropanoid pathways were found to be important in the Zn deficiency response. The metal tolerance protein (MTP) genes also appeared to play an important role in conferring tolerance to Zn deficiency. A heavy metal-associated domain-containing protein 7 was associated with tolerance to Zn deficiency and negatively regulated downstream genes. Collectively, our findings provide valuable expression patterns and candidate genes for the study of molecular mechanisms underlying the response to Zn deficiency and for improvements in breeding for tolerance to Zn deficiency in rice.

Molybdenum induces alterations in the glycerolipidome that confer drought tolerance in wheat

Molybdenum (Mo), which is an essential microelement for plant growth, plays important roles in multiple metabolic and physiological processes, including responses to drought and cold stress in wheat. Lipids also have crucial roles in plant adaptions to abiotic stresses. The aim of this study was to use glycerolipidomic and transcriptomic analyses to determine the changes in lipids induced by Mo that are associated with Mo-enhanced drought tolerance in wheat. Mo treatments increased the transcript levels of genes involved in fatty acid and glycerolipid biosynthesis and desaturation, but suppressed the expression of genes involved in oxylipin production. Wheat plants supplemented with Mo displayed higher contents of monogalactosyldiacyglycerol (MGDG), digalactosyldoacylglycerol (DGDG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and phosphatidylcholine (PC) with increased levels of unsaturation. The levels of MGDG, DGDG, PG, and PC increased under PEG-simulated drought (PSD), and the magnitude of the responses varied in the presence and absence of Mo. Mo increased the accumulation of the most abundant glycerolipid species of C36:6, C34:4, and C34:3 by increasing the expression of genes related to desaturation under PSD, and this contributed to maintaining the fluidity of membranes. In addition, Mo attenuated the decreases in the ratios of DGDG/MGDG and PC/PE that were observed under PSD. These changes in lipids in Mo-treated wheat would contribute to maintaining the integrity of membranes and to protecting the photosynthetic apparatus, thus acting together to enhance drought tolerance.

Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings

BACKGROUND

Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina's high-throughput small RNA sequencing and transcriptome sequencing.

RESULTS

The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results.

CONCLUSION

These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.

Transcriptome profiles of soybean leaves and roots in response to zinc deficiency

Zinc (Zn) deficiency is a widespread agricultural problem in arable soils of the whole world. However, the molecular mechanisms underlying Zn-deficiency response are largely unknown. Here, we analyzed the transcriptomic profilings of soybean leaves and roots in response to Zn deficiency through Illumina's high-throughput RNA sequencing in order to understand the molecular basis of Zn-deficiency response in the plants. A total of 614 and 1011 gene loci were found to be differentially expressed in leaves and roots, respectively, and 88 loci were commonly found in both leaves and roots. Twelve differentially expressed genes (DEGs) were randomly selected for validation by quantitative reverse transcription polymerase chain reaction, and their fold changes were similar to those of RNA-seq. Gene ontology enrichment analysis showed that ion transport, nicotianamine (NA) biosynthetic process and queuosine biosynthetic process were enriched in the upregulated genes, while oxidation-reduction process and defense response were enriched in the downregulated genes. Among the DEGs, 20 DEGs are potentially involved in Zn homeostasis, including seven ZRT, IRT-related protein (ZIP) transporter genes, three NA synthase genes, and seven metallothionein genes; 40 DEGs are possibly involved in diverse hormonal signals such as auxin, cytokinin, ethylene and gibberellin; nine DEGs are putatively involved in calcium signaling; 85 DEGs are putative transcription factor genes. Nine DEGs were found to contain zinc-deficiency-response element in their promoter regions. These results could provide comprehensive insights into the soybean response to Zn deficiency and will be helpful for further elucidation of the molecular mechanisms of Zn-deficiency response and Zn-deficiency tolerance in plants.

The search for candidate genes associated with natural variation of grain Zn accumulation in barley

Combating hidden hunger through molecular breeding of nutritionally enriched crops requires a better understanding of micronutrient accumulation. We studied natural variation in grain micronutrient accumulation in barley (Hordeum vulgare L.) and searched for candidate genes by assessing marker-trait associations (MTAs) and by analyzing transcriptional differences between low and high zinc (Zn) accumulating cultivars during grain filling. A collection of 180 barley lines was grown in three different environments. Our results show a pronounced variation in Zn accumulation, which was under strong genotype influence across different environments. Genome-wide association mapping revealed 13 shared MTAs. Across three environments, the most significantly associated marker was on chromosome 2H at 82.8 cM and in close vicinity to two yellow stripe like (YSL) genes. A subset of two pairs of lines with contrasting Zn accumulation was chosen for detailed analysis. Whole ears and flag leaves were analyzed 15 days after pollination to detect transcriptional differences associated with elevated Zn concentrations in the grain. A putative α-amylase/trypsin inhibitor CMb precursor was decidedly higher expressed in high Zn cultivars in whole ears in all comparisons. Additionally, a gene similar to barley metal tolerance protein 5 (MTP5) was found to be a potential candidate gene.

Transcriptome analysis reveals that barnyard grass exudates increase the allelopathic potential of allelopathic and non-allelopathic rice (Oryza sativa) accessions

BACKGROUND

Allelopathy in rice (Oryza sativa) is a chemically induced response that is elevated by the exogenous application of chemical compounds and barnyard grass root exudates. An in-depth understanding of the response mechanisms of rice to chemical induction is necessary for the identification of target genes for increasing the allelopathic potential of rice. However, no previous studies have evaluated the transcriptomic changes associated with allelopathy in rice in response to barnyard grass exudates treatment. Thus, the aim of the present study was to reveal differentially expressed genes (DEGs) in allelopathic and non-allelopathic rice seedlings treated with barnyard grass exudates to identify target allelopathy genes.

RESULTS

The inhibitory effect of the culture solutions on the allelopathic rice accession PI312777 (PI) and the non-allelopathic rice accession Lemont (LE) significantly increased (P < 0.05) after treatment with barnyard grass root exudates. The RNA sequencing results revealed that 14,891 genes in PI(+B) vs. LE(+B), 12,505 genes in PI(+B) vs. PI(-B), and 5857 genes in LE(+B) vs. LE(-B) were differentially expressed following root exudates treatment. These DEGs were classified into three categories and 32 functional groups, i.e., 12 groups in the biological process category, 12 groups in the cellular component category, and eight groups in the molecular function category. There were 5857 and 2846 upregulated genes and 135 and 50 upregulated Gene Ontology terms (P < 0.05) in the biological process category in PI(+B) vs. PI(-B) and LE(+B) vs. LE(-B), respectively. These results indicated that the allelopathic accession PI is more sensitive than the non-allelopathic accession LE to exogenous root exudates treatment. Genes related to rice allelochemical-related biosynthesis pathways, particularly the shikimic acid and acetic acid pathways, were significantly differentially expressed in both rice accessions. These findings suggested that phenolic acids, fatty acids, and flavonoids, which constitute the downstream metabolites of the shikimic acid and acetic acid pathways, are significantly expressed in response to root exudates of barnyard grass.

CONCLUSIONS

The allelopathic potential of both rice accessions could be significantly enhanced by barnyard grass root exudates application. Furthermore, genes related to the biosynthesis pathways of reported rice allelochemicals were significantly differentially expressed in both accessions. Phenylalanine ammonia lyase was determined to be a potential target for the regulation of chemical induction.

Changes in the Profiles of Yield, Yield Component, Oil Content, and Citral Content in Litsea cubeba (Lour.) Persoon Following Foliar Fertilization with Zinc and Boron

Mountain pepper (Litsea cubeba (Lour.) Persoon) is an important oil plant used as an ingredient in edible oil, cooking condiments, cosmetics, pesticides, and potential biofuels. Zinc and boron are essential micronutrients for plant growth. However, the effects of zinc and boron on the yield, yield component, oil content, and citral content in L. cubeba have not been determined. This study was conducted to evaluate the efficacy of the foliar application of zinc, boron, and multiple micronutrients (zinc + boron) on the yield, yield component, oil content, and citral content of three varieties (Fuyang 1 (FY1), Jianou 2 (JO2), and Jianou 3 (JO3)) of L. cubeba. Zinc sulfate (0.25%), boric acid (0.25%), and zinc sulfate (0.25%) + boric acid (0.25%) were sprayed on selected trees at five different times at full bloom and 28 days before harvest, once every seven days. The results indicated that Zn had a negative effect on the yield, yield component, oil content, and citral content of the FY1, JO2, and JO3 varieties compared to the untreated trees. B had positive effects on the yield, yield component, oil content, and citral content of the JO2 and JO3 varieties but not on those of the FY1 variety when compared to the untreated trees. The highest levels of yield, yield component, oil content, and citral content for all three varieties were obtained with the combined application of zinc sulfate + boric acid. Hence, the foliar application of multiple micronutrients (zinc + boron) is an effective method to improve the yield, oil content, and citral content in L. cubeba. In addition, the 100-fruit weight (HFW) was positively correlated with the yield, oil content, and citral content and could be used as a tool to select new cultivars with high yield, high oil content, and high citral content under zinc sulfate, boric acid, and zinc sulfate + boric acid applications in L. cubeba.