Transcriptomic Analysis of Drought Stress Responses in Ammopiptanthus mongolicus Leaves Using the RNA-Seq Technique

Abstract Background Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. Results We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. Conclusion Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.

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Drought Stress-Mediated Transcriptome Profile Reveals NCED as a Key Player Modulating Drought Tolerance in Populus davidiana

Frontiers in Plant Science ◽

10.3389/fpls.2021.755539 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sang-Uk Lee ◽

Bong-Gyu Mun ◽

Eun-Kyung Bae ◽

Jae-Young Kim ◽

Hyun-Ho Kim ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Stress Responses ◽

Expression Patterns ◽

Pcr Analysis ◽

Transcriptional Level ◽

Rna Seq ◽

Drought Tolerant ◽

Populus Davidiana ◽

Strict Regulation

Populus trichocarpa has been studied as a model poplar species through biomolecular approaches and was the first tree species to be genome sequenced. In this study, we employed a high throughput RNA-sequencing (RNA-seq) mediated leaf transcriptome analysis to investigate the response of four different Populus davidiana cultivars to drought stress. Following the RNA-seq, we compared the transcriptome profiles and identified two differentially expressed genes (DEGs) with contrasting expression patterns in the drought-sensitive and tolerant groups, i.e., upregulated in the drought-tolerant P. davidiana groups but downregulated in the sensitive group. Both these genes encode a 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme required for abscisic acid (ABA) biosynthesis. The high-performance liquid chromatography (HPLC) measurements showed a significantly higher ABA accumulation in the cultivars of the drought-tolerant group following dehydration. The Arabidopsis nced3 loss-of-function mutants showed a significantly higher sensitivity to drought stress, ~90% of these plants died after 9 days of drought stress treatment. The real-time PCR analysis of several key genes indicated a strict regulation of drought stress at the transcriptional level in the P. davidiana drought-tolerant cultivars. The transgenic P. davidiana NCED3 overexpressing (OE) plants were significantly more tolerant to drought stress as compared with the NCED knock-down RNA interference (RNAi) lines. Further, the NCED OE plants accumulated a significantly higher quantity of ABA and exhibited strict regulation of drought stress at the transcriptional level. Furthermore, we identified several key differences in the amino acid sequence, predicted structure, and co-factor/ligand binding activity of NCED3 between drought-tolerant and susceptible P. davidiana cultivars. Here, we presented the first evidence of the significant role of NCED genes in regulating ABA-dependent drought stress responses in the forest tree P. davidiana and uncovered the molecular basis of NCED3 evolution associated with increased drought tolerance.

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Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima

PLoS ONE ◽

10.1371/journal.pone.0202848 ◽

2018 ◽

Vol 13 (11) ◽

pp. e0202848 ◽

Cited By ~ 3

Author(s):

Heng-Ling Meng ◽

Wei Zhang ◽

Guang-Hui Zhang ◽

Jian-Jun Wang ◽

Zhen-Gui Meng ◽

...

Keyword(s):

Drought Stress ◽

Stress Responses ◽

Rna Seq ◽

Marsdenia Tenacissima

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A lipid-mediated cross-talk between insect defense and drought stress responses

10.1603/ice.2016.94316 ◽

2016 ◽

Author(s):

MIchael Kolomiets

Keyword(s):

Drought Stress ◽

Cross Talk ◽

Stress Responses ◽

Insect Defense

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Current status of microRNA ‐mediated regulation of drought stress responses in cereals

Physiologia Plantarum ◽

10.1111/ppl.13451 ◽

2021 ◽

Author(s):

Garima Singroha ◽

Pradeep Sharma ◽

Ramanjulu Sunkur

Keyword(s):

Drought Stress ◽

Stress Responses ◽

Current Status

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Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽

10.1186/s12864-021-07601-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhiwei Chen ◽

Longhua Zhou ◽

Panpan Jiang ◽

Ruiju Lu ◽

Nigel G. Halford ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Regulatory Elements ◽

Gene Promoters ◽

Related Protein ◽

Rna Seq ◽

Response Elements ◽

Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

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Spermine: Its Emerging Role in Regulating Drought Stress Responses in Plants

Cells ◽

10.3390/cells10020261 ◽

2021 ◽

Vol 10 (2) ◽

pp. 261

Author(s):

Md. Mahadi Hasan ◽

Milan Skalicky ◽

Mohammad Shah Jahan ◽

Md. Nazmul Hossain ◽

Zunaira Anwar ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Stress Responses ◽

Abiotic Stresses ◽

Defense Mechanisms ◽

Antioxidant Defense ◽

Severe Drought ◽

New Information ◽

Effects Of Drought

In recent years, research on spermine (Spm) has turned up a lot of new information about this essential polyamine, especially as it is able to counteract damage from abiotic stresses. Spm has been shown to protect plants from a variety of environmental insults, but whether it can prevent the adverse effects of drought has not yet been reported. Drought stress increases endogenous Spm in plants and exogenous application of Spm improves the plants’ ability to tolerate drought stress. Spm’s role in enhancing antioxidant defense mechanisms, glyoxalase systems, methylglyoxal (MG) detoxification, and creating tolerance for drought-induced oxidative stress is well documented in plants. However, the influences of enzyme activity and osmoregulation on Spm biosynthesis and metabolism are variable. Spm interacts with other molecules like nitric oxide (NO) and phytohormones such as abscisic acid, salicylic acid, brassinosteroids, and ethylene, to coordinate the reactions necessary for developing drought tolerance. This review focuses on the role of Spm in plants under severe drought stress. We have proposed models to explain how Spm interacts with existing defense mechanisms in plants to improve drought tolerance.

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Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes

BMC Plant Biology ◽

10.1186/s12870-021-02859-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhengwen Liu ◽

Xingfen Wang ◽

Zhengwen Sun ◽

Yan Zhang ◽

Chengsheng Meng ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Rapid Evolution ◽

Gene Clusters ◽

Vital Role ◽

Fiber Development ◽

Rna Seq ◽

Evolutionarily Conserved ◽

Cell Wall Development ◽

Tandem Duplications

Abstract Background Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton. Results In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls. Conclusions These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.

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