Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

Wang, Meng-qi; Bai, Zhenyu; Xiao, Ya-fang; Li, Yan; Liu, Qinglin; Zhang, Lei; Pan, Yuanzhi; Jiang, Beibei; Fan, Zhengqiu

doi:10.1186/s12864-019-6152-9

Cited by 22 publications

(7 citation statements)

References 63 publications

(61 reference statements)

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“…Differential expression analysis was performed using the DESeq R package (1.10.1) ( Wang et al, 2019 ). A differential expression analysis between treatments was performed using the ratio of FPKM values, and the resulting p-values were corrected for multiplicity using the Benjamini and Hochberg method ( Trapnell et al, 2010 ).…”

Section: Methodsmentioning

confidence: 99%

Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize

Liu

et al. 2022

Front. Genet.

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Stalk lodging, or breakage of the stalk at or below the ear, is one of the vital factors causing substantial yield losses in maize (Zea mays. L). Lodging affects maize plants’ physiological and molecular processes, eventually impacting plant growth and productivity. Despite this known fact, few researchers have investigated the genetic architecture underlying lodging in maize. Herein, through integrated transcriptome, metabolome, and phenotypic analyses of stalks of three diverse hybrid cultivars (highly resistant JNK738, mildly resistant JNK728, and lowly resistant XY335) at the tasseling (10 days to silking, 10 DTS) stage, we identified key genes and metabolic pathways modulating lodging resistance in maize. Based on the RNA-Seq analysis, a total of 10093 differentially expressed genes (DEGs) were identified from the comparison of the three varieties in pairs. Additionally, key lodging resistance–related metabolic pathways were obtained by KEGG enrichment analysis, and the DEGs were found predominantly enriched in phenylpropanoid and secondary metabolites biosynthesis pathways in the L_vs._H and M_vs._H comparison groups. Moreover, K-means analysis clustered the DEGs into clear and distinct expression profiles for each cultivar, with several functional and regulatory genes involved in the cell wall assembly, lignin biosynthetic process and hormone metabolic process being identified in the special clusters related to lodging resistance. Subsequently, integrating metabolome and transcriptome analyses revealed nine key lignin-associated metabolites that showed different expression trends in the three hybrid cultivars, among which L-phenylalanine and p-coumaric acid were regarded as differentially changed metabolites (DCMs). These two DCMs belonged to phenylalanine metabolism and biosynthesis pathways and were also supported by the RNA-Seq data. Furthermore, plant hormone signal transduction pathway–related genes encoding auxin, abscisic acid, jasmonates, and salicylic acid were differentially expressed in the three comparisons of lodging resistance, indicating these DEGs were valuable potential targets for improving maize lodging resistance. Finally, comparative physiological and qRT-PCR analyses results supported our transcriptome-based findings. Our research not only provides a preliminary theoretical basis and experimental ideas for an in-depth study of the regulatory networks involved in maize lodging resistance regulation but also opens up new avenues for molecular maize stalk lodging resistance breeding.

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Section: Methodsmentioning

confidence: 99%

Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize

Liu

et al. 2022

Front. Genet.

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“…Another aspect of this type of analysis is the translocation or accumulation of toxic elements within the different complex cell structures that make up plant roots. Furthermore, the use of technologies such as microarrays, RNAseq, and wide genome analysis has increased the amount of transcriptomic and genomic information available for plants under metal stress [ 135 , 151 , 152 , 153 , 154 , 155 , 156 , 157 , 158 , 159 ]. When analyzing the different plant transcriptomes under conditions of metal/metalloid stress, conserved trends have been observed.…”

Section: Transcriptomes and Metabolic And Functional Characterization Of Metal-toxicity-related Genesmentioning

confidence: 99%

Metal and Metalloid Toxicity in Plants: An Overview on Molecular Aspects

Angulo-Bejarano

Puente-Rivera

Cruz-Ortega

2021

Plants

179

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Worldwide, the effects of metal and metalloid toxicity are increasing, mainly due to anthropogenic causes. Soil contamination ranks among the most important factors, since it affects crop yield, and the metals/metalloids can enter the food chain and undergo biomagnification, having concomitant effects on human health and alterations to the environment. Plants have developed complex mechanisms to overcome these biotic and abiotic stresses during evolution. Metals and metalloids exert several effects on plants generated by elements such as Zn, Cu, Al, Pb, Cd, and As, among others. The main strategies involve hyperaccumulation, tolerance, exclusion, and chelation with organic molecules. Recent studies in the omics era have increased knowledge on the plant genome and transcriptome plasticity to defend against these stimuli. The aim of the present review is to summarize relevant findings on the mechanisms by which plants take up, accumulate, transport, tolerate, and respond to this metal/metalloid stress. We also address some of the potential applications of biotechnology to improve plant tolerance or increase accumulation.

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“…Wang et al [257] studied the adaptability of the ornamental plant Verbena. bonariensis under Cd stress.…”

Section: Transcriptomicsmentioning

confidence: 99%

Phytoremediation of Cadmium: Physiological, Biochemical, and Molecular Mechanisms

Raza

Habib

Najafi-Kakavand

et al. 2020

Biology

167

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Cadmium (Cd) is one of the most toxic metals in the environment, and has noxious effects on plant growth and production. Cd-accumulating plants showed reduced growth and productivity. Therefore, remediation of this non-essential and toxic pollutant is a prerequisite. Plant-based phytoremediation methodology is considered as one a secure, environmentally friendly, and cost-effective approach for toxic metal remediation. Phytoremediating plants transport and accumulate Cd inside their roots, shoots, leaves, and vacuoles. Phytoremediation of Cd-contaminated sites through hyperaccumulator plants proves a ground-breaking and profitable choice to combat the contaminants. Moreover, the efficiency of Cd phytoremediation and Cd bioavailability can be improved by using plant growth-promoting bacteria (PGPB). Emerging modern molecular technologies have augmented our insight into the metabolic processes involved in Cd tolerance in regular cultivated crops and hyperaccumulator plants. Plants’ development via genetic engineering tools, like enhanced metal uptake, metal transport, Cd accumulation, and the overall Cd tolerance, unlocks new directions for phytoremediation. In this review, we outline the physiological, biochemical, and molecular mechanisms involved in Cd phytoremediation. Further, a focus on the potential of omics and genetic engineering strategies has been documented for the efficient remediation of a Cd-contaminated environment.

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Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

Cited by 22 publications

References 63 publications

Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize

Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize

Metal and Metalloid Toxicity in Plants: An Overview on Molecular Aspects

Phytoremediation of Cadmium: Physiological, Biochemical, and Molecular Mechanisms

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