Effects of drought stress and water recovery on physiological responses and gene expression in maize seedlings

Zhang, Xiangbo; Lei, Lei; Lai, Jinsheng; Zhao, Haiming; Song, Weibin

doi:10.1186/s12870-018-1281-x

Cited by 150 publications

(139 citation statements)

References 56 publications

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“…Transcriptome analysis confirms the negative impact of the imposed drought stress on leaf growth and development (Zhang et al, ): among the 2,751 DEGs identified at the end of the stress treatment, the 1,957 stress down‐regulated genes are indeed enriched in functional terms associated to cell cycle regulation, growth and cell wall biosynthesis, indicating the inhibition of both cell division and expansion rates during water deprivation. Many of these genes were previously found down‐regulated in the maize leaf growth zone after mild and severe drought stresses (Avramova et al, ; Granier, Inzé, & Tardieu, ).…”

Section: Discussionmentioning

confidence: 68%

“…However, in studies published so far, osmotic stress has been mostly simulated in vitro by the addition of polyethylene glycol (PEG) or, when plants have been grown in soil, they have been sampled at seedling stage soon after hours of air‐drying or a few days of drought treatment (Ding et al, ; Jia et al, ; Lu et al, ; Opitz et al, ; Shan et al, ; Wu, Ning, Zhang, Wu, & Wang, ). In addition, only a few studies have addressed the genetic and epigenetic regulation of traits for tolerance/susceptibility to drought considering recovery as a real component of environmental challenges in the field (Zhang, Lei, Lai, Zhao, & Song, ).…”

Section: Discussionmentioning

confidence: 99%

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Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

Forestan

Farinati

Zambelli

et al. 2019

Plant Cell & Environment

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During their lifespan, plants respond to a multitude of stressful factors. Dynamic changes in chromatin and concomitant transcriptional variations control stress response and adaptation, with epigenetic memory mechanisms integrating environmental conditions and appropriate developmental programs over the time. Here we analyzed transcriptome and genome‐wide histone modifications of maize plants subjected to a mild and prolonged drought stress just before the flowering transition. Stress was followed by a complete recovery period to evaluate drought memory mechanisms. Three categories of stress‐memory genes were identified: i) “transcriptional memory” genes, with stable transcriptional changes persisting after the recovery; ii) “epigenetic memory candidate” genes in which stress‐induced chromatin changes persist longer than the stimulus, in absence of transcriptional changes; iii) “delayed memory” genes, not immediately affected by the stress, but perceiving and storing stress signal for a delayed response. This last memory mechanism is described for the first time in drought response. In addition, applied drought stress altered floral patterning, possibly by affecting expression and chromatin of flowering regulatory genes. Altogether, we provided a genome‐wide map of the coordination between genes and chromatin marks utilized by plants to adapt to a stressful environment, describing how this serves as a backbone for setting stress memory.

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Section: Discussionmentioning

confidence: 68%

Section: Discussionmentioning

confidence: 99%

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

Forestan

Farinati

Zambelli

et al. 2019

Plant Cell & Environment

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“…Among the enriched GO terms, common drought‐related terms typically recovered in drought stress experiments (Fracasso et al, ; Wu et al, ; Zhang, Lei, Lai, Zhao, & Song, ) were recovered here using both control types. For up‐regulated genes, “response to water deprivation (GO:0009414)” and “response to water (GO:0009415)” were over‐represented on all days before recovery in both species.…”

Section: Resultsmentioning

confidence: 80%

“…For most time points, however, there was considerable overlap in enriched GO terms based on the different control types, and the rank order of these shared GO terms based on FDR was highly similar (Figure ). For up‐regulated genes, for example, shared terms included essential drought‐related terms such as “response to water deprivation (GO:0009414),” “response to abiotic stress (GO:0009628)” and “response to abscisic acid (GO:0009737)” (Fracasso et al, ; Wu et al, ; Zhang et al, ). For nonshared GO terms, when using the TC control type, “secondary metabolic process (GO: 0019748)” was over‐represented on Day 3, Day 4, and Day 5 in P. notatum and “response to external stimulus (GO:0009605)” was over‐represented on Day 3 and Day 4 in P. juergensii .…”

Section: Discussionmentioning

confidence: 99%

Comparing control options for time‐series RNA sequencing experiments in nonmodel organisms: An example from grasses

Qiu

Bachle

Nippert

et al. 2020

Molecular Ecology Resources

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RNA sequencing (RNA‐seq) is a widely used approach to investigate gene expression and increasingly is used in time‐course studies to characterize transcriptomic changes over time. Two primary options are available as controls in time‐course experiments: samples collected at the first sampling time are used as controls (temporal control, TC) and samples collected in parallel at each individual sampling time are used as controls (biological control, BC). While both approaches are used in experimental studies, we know of no analyses performed to date that directly compare effects of control type choices on identifying differentially expressed genes (DEGs) and subsequent functional analysis. In the current study, we compare experimental results using these different control types for time‐course RNA‐seq drought stress experiments in two wild grass species in the genus Paspalum. Our results showed BC assemblies gave a higher number of loci in both species. The number of DEGs increased with increasing stress and then decreased dramatically at the recovery time point using both control types. Expression levels of the same DEGs were highly correlated between control types in both species, ranging from r = .653 to r = .852. We also observed similar rank orders of shared enriched Gene Ontology term lists using the two different control types. Collectively, our findings suggest similar results in differential gene expression and functional annotation between control types. The ultimate choice of control type will rely on the experimental length and organism type, with labour time and sequencing costs as additional factors to be considered.

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“…Previous results showed that boron (B) and silicon (Si) application could induce physiological resistance of oil palm seedlings to drought stress [32]. The genes involved in cellular nitrogen compound metabolic processes and transmembrane transport are differentially expressed during drought treatments [33]. Therefore, we investigated the expression pattern of the amino acid permease genes in the root and leaf tissues in E. guineensis in response to PEG treatment by using qRT-PCR ( Figure 5).…”

Section: Cold Stress Effects On the Expression Profiles Of Amino Acidmentioning

confidence: 99%

Comparative identification and differential expression pattern of amino acid permease genes in Elaeis guineensis

Cao

Liu

et al. 2019

Biotechnology & Biotechnological Equipment

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Elaeis guineensis is a tropical crop with high oil content, and the nutritional value of oil is very high. Amino acids not only affect the growth and development of plants but also act as intermediate metabolites of oils, which determine the final quality of oils. In this study, eleven amino acid permease genes (EgAAPs) in E. guineensis were identified from the amino acid transporter family. Real-time PCR results showed that seven EgAAPs (EgAAP1, EgAAP2, EgAAP3, EgAAP4, EgAAP6 EgAAP9, and EgAAP10) played an important role in vegetative growth because of their higher expression levels in roots and leaves, but EgAAP5, EgAAP7, EgAAP8 and EgAAP11 were also important for their higher expression levels in flowers or fruits. E. guineensis seedlings were treated with 20% PEG-6000 and 4 C to induce drought stress and cold stress, respectively. The expression of six EgAAPs (EgAAP1, EgAAP2, EgAAP4, EgAAP6, EgAAP8 and EgAAP11) was decreased in both roots and leaves during cold treatment, and only the expression of EgAAP5 was increased in both roots and leaves after 6 h of cold treatment. The expression of six EgAAPs (EgAAP2, EgAAP4, EgAAP7, EgAAP8, EgAAP10 and EgAAP11) was decreased in roots but increased in leaves under PEG treatment, indicating an opposite pattern of expression levels of these EgAAPs in roots and leaves. However, only EgAAP5 had a similar pattern of expression levels between roots and leaves under PEG treatment. The findings provide information on how EgAAPs in E. guineensis are regulated during growth and development, and under various environmental stresses.

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Effects of drought stress and water recovery on physiological responses and gene expression in maize seedlings

Cited by 150 publications

References 56 publications

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

Comparing control options for time‐series RNA sequencing experiments in nonmodel organisms: An example from grasses

Comparative identification and differential expression pattern of amino acid permease genes in Elaeis guineensis

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