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Genetic Regulation of Abiotic Stress Responses
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Genetic Regulation of Abiotic Stress Responses

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2017) | Viewed by 93231

Special Issue Editors

Dr. Sarvajeet Singh Gill

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Guest Editor
221/Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak 124 001, Haryana, India
Interests: abiotic stress tolerance; plant molecular biology; ROS; genetic engineering; ncRNA
Dr. Narendra Tuteja

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Co-Guest Editor
Amity Institute of Microbial Technology, Amity University Uttar Pradesh, E-2 Block, 4th Floor, Room # 404A, Sector 125, NOIDA, Uttar Pradesh 201313, India
Dr. Ritu Gill

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Co-Guest Editor
Center for Biotechnology, Maharshi Dayanand University, Rohtak, India
Dr. Juan Francisco Jimenez-Bremont

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Co-Guest Editor
Molecular Biology Division, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosi CP 78216, Mexico
Interests: plant-microbe interactions; polyamines; functional characterization of genes involved in the response to abiotic stress; glycine rich proteins; dehydrins
Special Issues, Collections and Topics in MDPI journals
Dr. Anca Macovei

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Co-Guest Editor
Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
Interests: DNA damage response (DDR); microRNAs; abiotic stress response; systems biology; seed biology
Special Issues, Collections and Topics in MDPI journals
Dr. Naser A. Anjum

E-Mail Website
Co-Guest Editor
Department of Botany, Aligarh Muslim University, Aligarh 202 002, India
Interests: plant-environment adaptation; plant stress physiology and biochemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In order to thrive, plants require optimal environmental conditions. Changes in environmental variables, such as temperature, soil and air quality or light levels, are bound to affect species reproduction and survival. In particular, the predicted increase in temperature, alteration of rain patterns, and extreme weather events across the globe may further impact plant growth and agriculture productivity worldwide. The impact of detrimental environmental conditions on plant growth, productivity and nutrient value are important parameters that are constantly monitored and studied to implement the development of new-generation crops able to feed the world´s burgeoning population.

Though a great deal of research has been done in the field of crop genetics, only limited success in producing abiotic-stress-tolerant cultivars has been achieved thus far. Some of the reasons behind these hardships include the complexity of the traits, as well as the complexity of genetic regulatory networks. The ‘gene regulatory network’ concept refers to sets of interacting genes that contribute to control specific cell functions, crucial in plant development and response to environmental stresses. When considering genes linked to abiotic stress tolerance, several classes can be underlined, mainly (i) genes involved in transcriptional control and signaling cascades, (ii) genes with protective roles at the levels of membranes, (iii) genes involved in the transport of metabolites, etc. However, in addition to the so called ‘regulatory genes’, there are other factors that contribute to the complexity of the regulatory processes, among which the epigenetic modifications, posttranscriptional and posttranslational processing, protein–DNA and protein–protein interactions, are just some of them. In recent years, the study of large-scale gene regulatory networks was made possible due to the development of high-throughput ‘omics’ technologies. The use of high-throughput methods for the study of large numbers of genes, in parallel with the networks of gene regulation, can provide essential clues to their biological functions. In addition, the information on gene profiling can be further integrated with protein expression data to gain a more informative model on how all the parts of a biological system work together. Conclusive information about alterations in gene expression levels can be gained by analyzing the qualitative and quantitative changes of messenger RNAs, proteins and metabolites. Hence, within this complex context, deciphering genetic regulation and genetic regulatory networks in the frame of extreme environmental cues, to further develop plants with drought and temperature tolerance, water-use efficiency, or resistance to pathogens, is crucial from both the agricultural and economic points of view.

This Special Issue focuses on the latest discoveries in the field of genetic regulatory networks and their impact on plant abiotic stress biology. Studies on transgenic plants, aiming to unravel gene functions and regulatory networks are most encouraged. In addition to model species, information retrieved from economically-relevant species is essential to drive agricultural development towards sustainable practices to improve crop performance under adverse environmental conditions. Authors are invited to contribute with original research articles, research notes, as well as review articles with the common aim to illustrate and stimulate the efforts undertaken to decipher the regulatory mechanisms underlying plant resilience to environmental stresses. Contributions to be included in this Special Issue are expected to help potential readers grasp how plants may better cope with abiotic stress conditions.

Potential topics include, but are not limited to:

  • Molecular mechanisms of abiotic stress tolerance in plants, especially modulation of gene networks under various abiotic stresses
  • Genetic engineering approaches and modern genome editing for abiotic stress tolerance
  • Modelling and analysis of regulatory gene networks involved in plant abiotic stress responses
  • Relevance of transcription factors and signaling cascades in abiotic stress response
  • Relevance of posttranscriptional and posttranslational modifications in abiotic stress response
  • Chromatin remodeling, DNA damage, repair and signaling pathways in plants under abiotic stresses
  • Functional genomics, proteomics and metabolomics approaches to study the regulatory aspects of plant abiotic stress responses
  • Epigenetics and the regulation plant’s abiotic stress response
  • Emerging model systems for genetic regulatory networks under abiotic stress response

Dr. Sarvajeet Singh Gill
Dr. Naser A. Anjum
Dr. Anca Macovei
Dr. Juan Francisco Jimenez Bremont
Dr. Ritu Gill
Dr. Narendra Tuteja
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (17 papers)

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Research

22 pages, 16029 KiB  
Article
Genome-Wide Identification and Expression Profiling Analysis of the Xyloglucan Endotransglucosylase/Hydrolase Gene Family in Tobacco (Nicotiana tabacum L.)
by Meng Wang, Zongchang Xu, Anming Ding and Yingzhen Kong
Genes 2018, 9(6), 273; https://doi.org/10.3390/genes9060273 - 24 May 2018
Cited by 47 | Viewed by 6478
Abstract
Xyloglucan endotransglucosylase/hydrolase genes (XTHs) encode enzymes required for the reconstruction and modification of xyloglucan backbones, which will result in changes of cell wall extensibility during growth. A total of 56 NtXTH genes were identified from common tobacco, and 50 cDNA fragments [...] Read more.
Xyloglucan endotransglucosylase/hydrolase genes (XTHs) encode enzymes required for the reconstruction and modification of xyloglucan backbones, which will result in changes of cell wall extensibility during growth. A total of 56 NtXTH genes were identified from common tobacco, and 50 cDNA fragments were verified by PCR amplification. The 56 NtXTH genes could be classified into two subfamilies: Group I/II and Group III according to their phylogenetic relationships. The gene structure, chromosomal localization, conserved protein domains prediction, sub-cellular localization of NtXTH proteins and evolutionary relationships among Nicotiana tabacum, Nicotiana sylvestrisis, Nicotiana tomentosiformis, Arabidopsis, and rice were also analyzed. The NtXTHs expression profiles analyzed by the TobEA database and qRT-PCR revealed that NtXTHs display different expression patterns in different tissues. Notably, the expression patterns of 12 NtXTHs responding to environment stresses, including salinity, alkali, heat, chilling, and plant hormones, including IAA and brassinolide, were characterized. All the results would be useful for the function study of NtXTHs during different growth cycles and stresses. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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16 pages, 4759 KiB  
Article
Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)
by Hong Yue, Duntao Shu, Meng Wang, Guangwei Xing, Haoshuang Zhan, Xianghong Du, Weining Song and Xiaojun Nie
Genes 2018, 9(2), 70; https://doi.org/10.3390/genes9020070 - 01 Feb 2018
Cited by 39 | Viewed by 6587
Abstract
The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been [...] Read more.
The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been studied in wheat, especially those involved in response to abiotic stresses. In this study, 46 wheat HD-Zip genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into four groups, numbered 4, 5, 17 and 20 respectively. In total, only three genes with A, B and D homoeologous copies were identified. Furthermore, the gene interaction networks found that the TaHDZ genes played a critical role in the regulatory pathway of organ development and osmotic stress. Finally, the expression profiles of the wheat HD-Zips in different tissues and under various abiotic stresses were investigated using the available RNA sequencing (RNA-Seq) data and then validated by quantitative real-time polymerase chain reaction (qRT-PCR) to obtain the tissue-specific and stress-responsive candidates. This study systematically identifies the HD-Zip gene family in wheat at the genome-wide level, providing important candidates for further functional analysis and contributing to the better understanding of the molecular basis of development and stress tolerance in wheat. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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3601 KiB  
Article
SlbZIP38, a Tomato bZIP Family Gene Downregulated by Abscisic Acid, Is a Negative Regulator of Drought and Salt Stress Tolerance
by Yanglu Pan, Xin Hu, Chunyan Li, Xing Xu, Chenggang Su, Jinhua Li, Hongyuan Song, Xingguo Zhang and Yu Pan
Genes 2017, 8(12), 402; https://doi.org/10.3390/genes8120402 - 20 Dec 2017
Cited by 34 | Viewed by 5723
Abstract
The basic leucine zipper (bZIP) transcription factors have crucial roles in plant stress responses. In this study, the bZIP family gene SlbZIP38 (GenBank accession No: XM004239373) was isolated from a tomato (Solanum lycopersicum cv. Ailsa Craig) mature leaf cDNA library. The DNA [...] Read more.
The basic leucine zipper (bZIP) transcription factors have crucial roles in plant stress responses. In this study, the bZIP family gene SlbZIP38 (GenBank accession No: XM004239373) was isolated from a tomato (Solanum lycopersicum cv. Ailsa Craig) mature leaf cDNA library. The DNA sequence of SlbZIP38 encodes a protein of 484 amino acids, including a highly conserved bZIP DNA-binding domain in the C-terminal region. We found that SlbZIP38 was differentially expressed in various organs of the tomato plant and was downregulated by drought, salt stress, and abscisic acid (ABA). However, overexpression of SlbZIP38 significantly decreased drought and salt stress tolerance in tomatoes (Ailsa Craig). The findings that SlbZIP38 overexpression reduced the chlorophyll and free proline content in leaves but increased the malondialdehyde content may explain the reduced drought and salt tolerance observed in these lines. These results suggest that SlbZIP38 is a negative regulator of drought and salt resistance that acts by modulating ABA signaling. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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9548 KiB  
Article
Functional Characterization of the Versatile MYB Gene Family Uncovered Their Important Roles in Plant Development and Responses to Drought and Waterlogging in Sesame
by Marie Ali Mmadi, Komivi Dossa, Linhai Wang, Rong Zhou, Yanyan Wang, Ndiaga Cisse, Mame Oureye Sy and Xiurong Zhang
Genes 2017, 8(12), 362; https://doi.org/10.3390/genes8120362 - 12 Dec 2017
Cited by 56 | Viewed by 7285
Abstract
The MYB gene family constitutes one of the largest transcription factors (TFs) modulating various biological processes in plants. Although genome-wide analysis of this gene family has been carried out in some species, only three MYB members have been functionally characterized heretofore in sesame [...] Read more.
The MYB gene family constitutes one of the largest transcription factors (TFs) modulating various biological processes in plants. Although genome-wide analysis of this gene family has been carried out in some species, only three MYB members have been functionally characterized heretofore in sesame (Sesamum indicum L.). Here, we identified a relatively high number (287) of sesame MYB genes (SIMYBs) with an uncommon overrepresentation of the 1R-subfamily. A total of 95% of SIMYBs was mapped unevenly onto the 16 linkage groups of the sesame genome with 55 SIMYBs tandemly duplicated. In addition, molecular characterization, gene structure, and evolutionary relationships of SIMYBs were established. Based on the close relationship between sesame and Arabidopsis thaliana, we uncovered that the functions of SIMYBs are highly diverse. A total of 65% of SIMYBs were commonly detected in five tissues, suggesting that they represent key TFs modulating sesame growth and development. Moreover, we found that SIMYBs regulate sesame responses to drought and waterlogging, which highlights the potential of SIMYBs towards improving stress tolerance in sesame. This work presents a comprehensive picture of the MYB gene family in sesame and paves the way for further functional validation of the members of this versatile gene family. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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4359 KiB  
Article
Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings
by Le Yu, Jianchao Ma, Zhimin Niu, Xiaotao Bai, Wenli Lei, Xuemin Shao, Ningning Chen, Fangfang Zhou and Dongshi Wan
Genes 2017, 8(12), 372; https://doi.org/10.3390/genes8120372 - 08 Dec 2017
Cited by 30 | Viewed by 6528
Abstract
Salt stress is one of the most crucial factors impacting plant growth, development and reproduction. However, information regarding differences in tissue-specific gene expression patterns, which may improve a plant’s tolerance to salt stress, is limited. Here, we investigated the gene expression patterns in [...] Read more.
Salt stress is one of the most crucial factors impacting plant growth, development and reproduction. However, information regarding differences in tissue-specific gene expression patterns, which may improve a plant’s tolerance to salt stress, is limited. Here, we investigated the gene expression patterns in tissues of Populus euphratica Oliv. seedlings using RNA sequencing (RNA-Seq) technology. A total of 109.3 million, 125bp paired-end clean reads were generated, and 6428, 4797, 2335 and 3358 differentially expressed genes (DEGs) were identified in leaf, phloem, xylem and root tissues, respectively. While the tissue-specific DEGs under salt stress had diverse functions, “membrane transporter activity” was the most significant leaf function, whereas “oxidation–reduction process” was the most significant function in root tissue. Further analysis of the tissue-specific DEGs showed that the expression patterns or functions of gene families, such as SOS, NHX, GolS, GPX, APX, RBOHF and CBL, were diverse, suggesting that calcium signaling, reactive oxygen species (ROS) and salt overly sensitive (SOS) pathways are all involved in ionic homeostasis in tissues from P. euphratica seedlings. The DEGs, for example the up-regulated antioxidant genes, contribute to ROS-scavenging induced by salt stress but result in decreased Na+ concentrations in root vasculature cells and in xylem sap, while the down-regulated rbohF leads to the reverse results. These results suggest that the divergence of DEGs expression patterns contribute to maintenance of ionic and ROS homeostasis in tissues and improve plant salinity tolerance. We comprehensively analyzed the response of P. euphratica seedlings to salt stress and provide helpful genetic resources for studying plant-abiotic stress interactions. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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4752 KiB  
Article
Comparative Analysis of Cotton Small RNAs and Their Target Genes in Response to Salt Stress
by Zujun Yin, Xiulan Han, Yan Li, Junjuan Wang, Delong Wang, Shuai Wang, Xiaoqiong Fu and Wuwei Ye
Genes 2017, 8(12), 369; https://doi.org/10.3390/genes8120369 - 05 Dec 2017
Cited by 26 | Viewed by 3976
Abstract
Small RNAs play an important role in regulating plant responses to abiotic stress. Depending on the method of salt application, whether sudden or gradual, plants may experience either salt shock or salt stress, respectively. In this study, small RNA expression in response to [...] Read more.
Small RNAs play an important role in regulating plant responses to abiotic stress. Depending on the method of salt application, whether sudden or gradual, plants may experience either salt shock or salt stress, respectively. In this study, small RNA expression in response to salt shock and long-term salt stress in parallel experiments was described. Cotton small RNA libraries were constructed and sequenced under normal conditions, as well as sudden and gradual salt application. A total of 225 cotton microRNAs (miRNAs) were identified and of these 24 were novel miRNAs. There were 88 and 75 miRNAs with differential expression under the salt shock and long-term salt stress, respectively. Thirty one transcripts were found to be targets of 20 miRNA families. Eight targets showed a negative correlation in expression with their corresponding miRNAs. We also identified two TAS3s with two near-identical 21-nt trans-acting small interfering RNA (tasiRNA)-Auxin Response Factors (ARFs) that coaligned with the phases D7(+) and D8(+) in three Gossypium species. The miR390/tasiRNA-ARFs/ARF4 pathway was identified and showed altered expression under salt stress. The identification of these small RNAs as well as elucidating their functional significance broadens our understanding of post-transcriptional gene regulation in response to salt stress. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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30039 KiB  
Article
Comparative Analysis of Soybean Root Proteome Reveals Molecular Basis of Differential Carboxylate Efflux under Low Phosphorus Stress
by Krishnapriya Vengavasi, Renu Pandey, Gerard Abraham and Ravindra Kumar Yadav
Genes 2017, 8(12), 341; https://doi.org/10.3390/genes8120341 - 30 Nov 2017
Cited by 27 | Viewed by 4210
Abstract
Carboxylate efflux from roots is a crucial and differential response of soybean genotypes to low phosphorus (P) stress. Exudation of carboxylic acids including oxalate, citrate, succinate and fumarate was induced under low P stress, particularly in P-efficient soybean genotypes. Enhancement of root length, [...] Read more.
Carboxylate efflux from roots is a crucial and differential response of soybean genotypes to low phosphorus (P) stress. Exudation of carboxylic acids including oxalate, citrate, succinate and fumarate was induced under low P stress, particularly in P-efficient soybean genotypes. Enhancement of root length, surface area and volume further improved P acquisition under low P stress. To understand the molecular basis of carboxylate efflux under low P stress, the root proteome of contrasting genotypes (P-efficient: EC-232019 and P-inefficient: EC-113396) was compared. Among a total of 325 spots, 105 (32%) were differentially abundant proteins (DAPs) between sufficient (250 µM) and low P (4 µM) levels. Abundance of 44 (14%) proteins decreased by more than two-fold under low P stress, while 61 (19%) proteins increased by more than two-fold. Protein identification and annotation revealed that the DAPs were involved in a myriad of functions including carboxylic acid synthesis, carbohydrate, protein and lipid metabolism. Proteins with significant abundance included malate dehydrogenase, isocitrate dehydrogenase, phosphoglucomutase, phosphoglycerate mutase, fructokinase, enolase, phosphoglycerate kinase, triosephosphate isomerase, alcohol dehydrogenase, glucan water dikinase, glutamine synthetase and argininosuccinate lyase. Inferences from proteomic analysis suggests the crosstalk between various metabolic pathways implicated in conferring superior P acquisition efficiency under stress. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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17089 KiB  
Article
Responsive Proteins in Wheat Cultivars with Contrasting Nitrogen Efficiencies under the Combined Stress of High Temperature and Low Nitrogen
by Peerzada Yasir Yousuf, Elsayed Fathi Abd_Allah, Mohd Nauman, Ambreen Asif, Abeer Hashem, Abdulaziz A. Alqarawi and Altaf Ahmad
Genes 2017, 8(12), 356; https://doi.org/10.3390/genes8120356 - 29 Nov 2017
Cited by 16 | Viewed by 4788
Abstract
Productivity of wheat (Triticum aestivum) is markedly affected by high temperature and nitrogen deficiency. Identifying the functional proteins produced in response to these multiple stresses acting in a coordinated manner can help in developing tolerance in the crop. In this study, [...] Read more.
Productivity of wheat (Triticum aestivum) is markedly affected by high temperature and nitrogen deficiency. Identifying the functional proteins produced in response to these multiple stresses acting in a coordinated manner can help in developing tolerance in the crop. In this study, two wheat cultivars with contrasting nitrogen efficiencies (N-efficient VL616 and N-inefficient UP2382) were grown in control conditions, and under a combined stress of high temperature (32 °C) and low nitrogen (4 mM), and their leaf proteins were analysed in order to identify the responsive proteins. Two-dimensional electrophoresis unravelled sixty-one proteins, which varied in their expression in wheat, and were homologous to known functional proteins involved in biosynthesis, carbohydrate metabolism, energy metabolism, photosynthesis, protein folding, transcription, signalling, oxidative stress, water stress, lipid metabolism, heat stress tolerance, nitrogen metabolism, and protein synthesis. When exposed to high temperature in combination with low nitrogen, wheat plants altered their protein expression as an adaptive means to maintain growth. This response varied with cultivars. Nitrogen-efficient cultivars showed a higher potential of redox homeostasis, protein stability, osmoprotection, and regulation of nitrogen levels. The identified stress-responsive proteins can pave the way for enhancing the multiple-stress tolerance in wheat and developing a better understanding of its mechanism. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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1495 KiB  
Communication
The Tyrosyl-DNA Phosphodiesterase 1β (Tdp1β) Gene Discloses an Early Response to Abiotic Stresses
by Maria Elisa Sabatini, Andrea Pagano, Susana Araùjo, Alma Balestrazzi and Anca Macovei
Genes 2017, 8(11), 305; https://doi.org/10.3390/genes8110305 - 03 Nov 2017
Cited by 7 | Viewed by 3711
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is involved in DNA repair pathways as it mends the topoisomerase I—DNA covalent complexes. In plants, a small Tdp1 gene family, composed by Tdp1α and Tdp1β genes, was identified, but the roles of these genes in abiotic stress responses [...] Read more.
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is involved in DNA repair pathways as it mends the topoisomerase I—DNA covalent complexes. In plants, a small Tdp1 gene family, composed by Tdp1α and Tdp1β genes, was identified, but the roles of these genes in abiotic stress responses are not fully understood. To investigate their specific stress response patterns, the present study made use of bioinformatic and molecular tools to look into the Tdp1β gene function, so far described only in the plant kingdom, and compare it with Tdp1α gene coding for the canonical, highly conserved α isoform. The expression profiles of Tdp1α and Tdp1β genes were examined under abiotic stress conditions (cold, heat, high osmolarity, salt, and UV-B) in two model species, Arabidopsis thaliana and Medicago truncatula. The two isoforms of topoisomerase I (TOP1α and TOP1β) were also taken into consideration in view of their known roles in DNA metabolism and cell proliferation. Data relative to gene expression in Arabidopsis were retrieved from the AtGenExpress microarray dataset, while quantitative Real-Time PCR was carried out to evaluate the stress response in M. truncatula cell cultures. These analyses revealed that Tdp1β gene expression was enhanced during the first hour of treatment, whereas Tdp1α enhanced expression succeeded at subsequent timepoints. In agreement with the gene-specific responses to abiotic stress conditions, the promoter regions of Tdp1α and Tdp1β genes are well equipped with stress-related cis-elements. An in-depth bioinformatic characterization of the HIRAN motif, a distinctive feature of the Tdp1β protein, showed its wide distribution in chromatin remodeling and DNA repair proteins. The reported data suggests that Tdp1β functions in the early response to abiotic stresses. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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3990 KiB  
Article
Expression Profiling of Mitogen-Activated Protein Kinase Genes Reveals Their Evolutionary and Functional Diversity in Different Rubber Tree (Hevea brasiliensis) Cultivars
by Xiang Jin, Liping Zhu, Qi Yao, Xueru Meng, Guohua Ding, Dan Wang, Quanliang Xie, Zheng Tong, Chengcheng Tao, Li Yu, Hongbin Li and Xuchu Wang
Genes 2017, 8(10), 261; https://doi.org/10.3390/genes8100261 - 06 Oct 2017
Cited by 14 | Viewed by 4833
Abstract
Rubber tree (Hevea brasiliensis) is the only commercially cultivated plant for producing natural rubber, one of the most essential industrial raw materials. Knowledge of the evolutionary and functional characteristics of kinases in H. brasiliensis is limited because of the long growth [...] Read more.
Rubber tree (Hevea brasiliensis) is the only commercially cultivated plant for producing natural rubber, one of the most essential industrial raw materials. Knowledge of the evolutionary and functional characteristics of kinases in H. brasiliensis is limited because of the long growth period and lack of well annotated genome information. Here, we reported mitogen-activated protein kinases in H. brasiliensis (HbMPKs) by manually checking and correcting the rubber tree genome. Of the 20 identified HbMPKs, four members were validated by proteomic data. Protein motif and phylogenetic analyses classified these members into four known groups comprising Thr-Glu-Tyr (TEY) and Thr-Asp-Tyr (TDY) domains, respectively. Evolutionary and syntenic analyses suggested four duplication events: HbMPK3/HbMPK6, HbMPK8/HbMPK9/HbMPK15, HbMPK10/HbMPK12 and HbMPK11/HbMPK16/HbMPK19. Expression profiling of the identified HbMPKs in roots, stems, leaves and latex obtained from three cultivars with different latex yield ability revealed tissue- and variety-expression specificity of HbMPK paralogues. Gene expression patterns under osmotic, oxidative, salt and cold stresses, combined with cis-element distribution analyses, indicated different regulation patterns of HbMPK paralogues. Further, Ka/Ks and Tajima analyses suggested an accelerated evolutionary rate in paralogues HbMPK10/12. These results revealed HbMPKs have diverse functions in natural rubber biosynthesis, and highlighted the potential possibility of using MPKs to improve stress tolerance in future rubber tree breeding. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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3657 KiB  
Article
De Novo Assembly and Analysis of Tartary Buckwheat (Fagopyrum tataricum Garetn.) Transcriptome Discloses Key Regulators Involved in Salt-Stress Response
by Qi Wu, Xue Bai, Wei Zhao, Dabing Xiang, Yan Wan, Jun Yan, Liang Zou and Gang Zhao
Genes 2017, 8(10), 255; https://doi.org/10.3390/genes8100255 - 03 Oct 2017
Cited by 41 | Viewed by 5596
Abstract
Soil salinization has been a tremendous obstacle for agriculture production. The regulatory networks underlying salinity adaption in model plants have been extensively explored. However, limited understanding of the salt response mechanisms has hindered the planting and production in Fagopyrum tataricum, an economic [...] Read more.
Soil salinization has been a tremendous obstacle for agriculture production. The regulatory networks underlying salinity adaption in model plants have been extensively explored. However, limited understanding of the salt response mechanisms has hindered the planting and production in Fagopyrum tataricum, an economic and health-beneficial plant mainly distributing in southwest China. In this study, we performed physiological analysis and found that salt stress of 200 mM NaCl solution significantly affected the relative water content (RWC), electrolyte leakage (EL), malondialdehyde (MDA) content, peroxidase (POD) and superoxide dismutase (SOD) activities in tartary buckwheat seedlings. Further, we conducted transcriptome comparison between control and salt treatment to identify potential regulatory components involved in F. tataricum salt responses. A total of 53.15 million clean reads from control and salt-treated libraries were produced via an Illumina sequencing approach. Then we de novo assembled these reads into a transcriptome dataset containing 57,921 unigenes with N50 length of 1400 bp and total length of 44.5 Mb. A total of 36,688 unigenes could find matches in public databases. GO, KEGG and KOG classification suggested the enrichment of these unigenes in 56 sub-categories, 25 KOG, and 273 pathways, respectively. Comparison of the transcriptome expression patterns between control and salt treatment unveiled 455 differentially expressed genes (DEGs). Further, we found the genes encoding for protein kinases, phosphatases, heat shock proteins (HSPs), ATP-binding cassette (ABC) transporters, glutathione S-transferases (GSTs), abiotic-related transcription factors and circadian clock might be relevant to the salinity adaption of this species. Thus, this study offers an insight into salt tolerance mechanisms, and will serve as useful genetic information for tolerant elite breeding programs in future. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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1597 KiB  
Article
Textile Hemp vs. Salinity: Insights from a Targeted Gene Expression Analysis
by Gea Guerriero, Marc Behr, Jean-Francois Hausman and Sylvain Legay
Genes 2017, 8(10), 242; https://doi.org/10.3390/genes8100242 - 26 Sep 2017
Cited by 25 | Viewed by 4354
Abstract
Soil salinity is a serious threat to agriculture, because it compromises biomass production and plant productivity, by negatively affecting the vegetative growth and development of plants. Fiber crops like textile hemp (Cannabis sativa L.) are important natural resources that provide, sustainably, both cellulosic [...] Read more.
Soil salinity is a serious threat to agriculture, because it compromises biomass production and plant productivity, by negatively affecting the vegetative growth and development of plants. Fiber crops like textile hemp (Cannabis sativa L.) are important natural resources that provide, sustainably, both cellulosic and woody fibers for industry. In this work, the response to salinity (200 mM NaCl) of a fiber variety of hemp (Santhica 27) was studied using quantitative real-time PCR. The responses of plantlets aged 15 days were analyzed by microscopy and by measuring the changes in expression of cell wall-related genes, as well as in the general response to exogenous constraints. The results presented here show that a different response is present in the hemp hypocotyls and leaves. In the leaves, genes coding for heat shock proteins were significantly upregulated, together with a phytohormone-related transcript (ethylene-responsive factor 1 ERF1) and genes involved in secondary cell wall biosynthesis (cellulose synthase CesA4, fasciclin-like arabinogalactan proteins FLA10 and FLA8). Moreover, a tendency towards upregulation was also observed in the leaves for genes involved in lignification (4CL, CAD, PAL); a finding that suggests growth arrest. In the hypocotyl, the genes involved in lignification did not show changes in expression, while a gene related to expansion (expansin EXPA8), as well as transcripts coding for calcium-dependent lipid-binding family proteins (CALB), were upregulated. Microscopic analyses on the hypocotyl cross sections revealed changes in the vascular tissues of salt-exposed plantlets, where the lumen of xylem vessels was reduced. The gene expression results show that a different response is present in the hemp hypocotyls and leaves. The data presented contribute to our understanding of the regulatory gene network in response to salinity in different tissues of an important fiber crop. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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5806 KiB  
Article
Genome-Wide Analysis of the Biosynthesis and Deactivation of Gibberellin-Dioxygenases Gene Family in Camellia sinensis (L.) O. Kuntze
by Cheng Pan, Kunhong Tian, Qiuyan Ban, Leigang Wang, Qilu Sun, Yan He, Yuanfei Yang, Yuting Pan, Yeyun Li, Jiayue Jiang and Changjun Jiang
Genes 2017, 8(9), 235; https://doi.org/10.3390/genes8090235 - 19 Sep 2017
Cited by 29 | Viewed by 5239
Abstract
Gibberellins (GAs), a class of diterpenoid phytohormones, play a key role in regulating diverse processes throughout the life cycle of plants. Bioactive GA levels are rapidly regulated by Gibberellin-dioxygenases (GAox), which are involved in the biosynthesis and deactivation of gibberellin. In this manuscript, [...] Read more.
Gibberellins (GAs), a class of diterpenoid phytohormones, play a key role in regulating diverse processes throughout the life cycle of plants. Bioactive GA levels are rapidly regulated by Gibberellin-dioxygenases (GAox), which are involved in the biosynthesis and deactivation of gibberellin. In this manuscript, a comprehensive genome-wide analysis was carried out to find all GAox in Camellia sinensis. For the first time in a tea plant, 14 CsGAox genes, containing two domains, DIOX_N (PF14226) and 2OG-FeII_Oxy, were identified (PF03171). These genes all belong to 2-oxoglutarate-dependent dioxygenases (2-ODD), including four CsGA20ox (EC: 1.14.11.12), three CsGA3ox (EC: 1.14.11.15), and seven CsGA2ox (EC: 1.14.11.13). According to the phylogenetic classification as in Arabidopsis, the CsGAox genes spanned five subgroups. Each CsGAox shows tissue-specific expression patterns, although these vary greatly. Some candidate genes, which may play an important role in response to external abiotic stresses, have been identified with regards to patterns, such as CsGA20ox2, CsGA3ox2, CsGA3ox3, CsGA2ox1, CsGA2ox2, and CsGA2ox4. The bioactive GA levels may be closely related to the GA20ox, GA3ox and GA2ox genes. In addition, the candidate genes could be used as marker genes for abiotic stress resistance breeding in tea plants. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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8531 KiB  
Article
Salt-Stress Response Mechanisms Using de Novo Transcriptome Sequencing of Salt-Tolerant and Sensitive Corchorus spp. Genotypes
by Zemao Yang, Ruike Lu, Zhigang Dai, An Yan, Qing Tang, Chaohua Cheng, Ying Xu, Wenting Yang and Jianguang Su
Genes 2017, 8(9), 226; https://doi.org/10.3390/genes8090226 - 18 Sep 2017
Cited by 27 | Viewed by 5062
Abstract
High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes in leaf and root tissues under salt stress and control conditions. [...] Read more.
High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes in leaf and root tissues under salt stress and control conditions. In total, 68,961 unigenes were identified. Additionally, 11,100 unigenes (including 385 transcription factors (TFs)) exhibited significant differential expression in salt-tolerant or salt-sensitive genotypes. Numerous common and unique differentially expressed unigenes (DEGs) between the two genotypes were discovered. Fewer DEGs were observed in salt-tolerant jute genotypes whether in root or leaf tissues. These DEGs were involved in various pathways, such as ABA signaling, amino acid metabolism, etc. Among the enriched pathways, plant hormone signal transduction (ko04075) and cysteine/methionine metabolism (ko00270) were the most notable. Eight common DEGs across both tissues and genotypes with similar expression profiles were part of the PYL-ABA-PP2C (pyrabactin resistant-like/regulatory components of ABA receptors-abscisic acid-protein phosphatase 2C). The methionine metabolism pathway was only enriched in salt-tolerant jute root tissue. Twenty-three DEGs were involved in methionine metabolism. Overall, numerous common and unique salt-stress response DEGs and pathways between salt-tolerant and salt-sensitive jute have been discovered, which will provide valuable information regarding salt-stress response mechanisms and help improve salt-resistance molecular breeding in jute. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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6153 KiB  
Article
Functional Characterization of Selected Universal Stress Protein from Salvia miltiorrhiza (SmUSP) in Escherichia coli
by Xiao-Fan Wang, Jiao Su, Na Yang, Hui Zhang, Xiao-Yan Cao and Jie-Fang Kang
Genes 2017, 8(9), 224; https://doi.org/10.3390/genes8090224 - 08 Sep 2017
Cited by 21 | Viewed by 4917
Abstract
The multigene universal stress protein (USP) family is evolutionarily conserved. Members play indispensable roles in plant tolerance to abiotic stresses. Although relatively well-characterized in model plants, such as Arabidopsis thaliana and Oryza sativa, this family has not been investigated in Salvia miltiorrhiza [...] Read more.
The multigene universal stress protein (USP) family is evolutionarily conserved. Members play indispensable roles in plant tolerance to abiotic stresses. Although relatively well-characterized in model plants, such as Arabidopsis thaliana and Oryza sativa, this family has not been investigated in Salvia miltiorrhiza, an important herbal plant for which yields can be limited by various abiotic stresses. Here, we identified 32 USP family members in the S. miltiorrhiza genome, and used phylogenetic analysis to sort these SmUSPs into four groups. Groups A and B belong to the ATP-binding class whereas Groups C and D are in the non-ATP-binding class. Motif analysis and multiple sequence alignment hinted that members of group A and B were able to bind ATP. Our qRT-PCR data from different tissues/organs and under salt and heat stresses provided an overall expression pattern for those genes. Three SmUSPs (SmUSP1, SmUSP8, and SmUSP27) were cloned from S. miltiorrhiza and functionally characterized in Escherichia coli. Compared with the control cells, those that expressed SmUSPs exhibited enhanced tolerance to salt, heat, and a combination of the two. This suggested that the protein has a protective role in cells when exposed to single-stress and multiple-stress conditions. Our findings provide valuable information that helps improve our understanding of the evolutionary and functional conservation and diversity associated with the USP gene family in S. miltiorrhiza. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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9293 KiB  
Article
Bacillus amyloliquefaciens SAY09 Increases Cadmium Resistance in Plants by Activation of Auxin-Mediated Signaling Pathways
by Cheng Zhou, Lin Zhu, Zhongyou Ma and Jianfei Wang
Genes 2017, 8(7), 173; https://doi.org/10.3390/genes8070173 - 28 Jun 2017
Cited by 50 | Viewed by 7907
Abstract
Without physical contact with plants, certain plant growth-promoting rhizobacteria (PGPR) can release volatile organic compounds (VOCs) to regulate nutrient acquisition and induce systemic immunity in plants. However, whether the PGPR-emitted VOCs can induce cadmium (Cd) tolerance of plants and the underlying mechanisms remain [...] Read more.
Without physical contact with plants, certain plant growth-promoting rhizobacteria (PGPR) can release volatile organic compounds (VOCs) to regulate nutrient acquisition and induce systemic immunity in plants. However, whether the PGPR-emitted VOCs can induce cadmium (Cd) tolerance of plants and the underlying mechanisms remain elusive. In this study, we probed the effects of Bacillus amyloliquefaciens (strain SAY09)-emitted VOCs on the growth of Arabidopsis plants under Cd stress. SAY09 exposure alleviates Cd toxicity in plants with increased auxin biosynthesis. RNA-Seq analyses revealed that SAY09 exposure provoked iron (Fe) uptake- and cell wall-associated pathways in the Cd-treated plants. However, SAY09 exposure failed to increase Cd resistance of plants after treatment with 1-naphthylphthalamic acid (NPA) or 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (c-PTIO). Under Cd stress, SAY09 exposure markedly promoted Fe absorption in plants with the increased hemicellulose 1 (HC1) content and Cd deposition in root cell wall, whereas these effects were almost abrogated by treatment with NPA or c-PTIO. Moreover, exogenous NPA remarkably repressed the accumulation of nitric oxide (NO) in the SAY09-exposed roots under Cd stress. Taken together, the findings indicated that NO acted as downstream signals of SAY09-induced auxin to regulate Fe acquisition and augment Cd fixation in roots, thereby ameliorating Cd toxicity. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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2879 KiB  
Article
Identification, Characterization and Expression Profiling of Stress-Related Genes in Easter Lily (Lilium formolongi)
by Jewel Howlader, Jong-In Park, Arif Hasan Khan Robin, Kanij Rukshana Sumi and Ill-Sup Nou
Genes 2017, 8(7), 172; https://doi.org/10.3390/genes8070172 - 27 Jun 2017
Cited by 9 | Viewed by 4949
Abstract
Biotic and abiotic stresses are the major causes of crop loss in lily worldwide. In this study, we retrieved 12 defense-related expressed sequence tags (ESTs) from the NCBI database and cloned, characterized, and established seven of these genes as stress-induced genes in Lilium [...] Read more.
Biotic and abiotic stresses are the major causes of crop loss in lily worldwide. In this study, we retrieved 12 defense-related expressed sequence tags (ESTs) from the NCBI database and cloned, characterized, and established seven of these genes as stress-induced genes in Lilium formolongi. Using rapid amplification of cDNA ends PCR (RACE-PCR), we successfully cloned seven full-length mRNA sequences from L. formolongi line Sinnapal lily. Based on the presence of highly conserved characteristic domains and phylogenetic analysis using reference protein sequences, we provided new nomenclature for the seven nucleotide and protein sequences and submitted them to GenBank. The real-time quantitative PCR (qPCR) relative expression analysis of these seven genes, including LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, LfUb, LfCyt-b5, and LfRab, demonstrated that they were differentially expressed in all organs examined, possibly indicating functional redundancy. We also investigated the qPCR relative expression levels under two biotic and four abiotic stress conditions. All seven genes were induced by Botrytis cinerea treatment, and all genes except LfHsp70-3 and LfHsp90 were induced by Botrytis elliptica treatment; these genes might be associated with disease tolerance mechanisms in L. formolongi. In addition, LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, LfUb, and LfCyt-b5 were induced by heat treatment, LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, and LfCyt-b5 were induced by cold treatment, and LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, LfCy-b5, and LfRab were induced by drought and salt stress, indicating their likely association with tolerance to these stress conditions. The stress-induced candidate genes identified in this study provide a basis for further functional analysis and the development of stress-resistant L. formolongi cultivars. Full article
(This article belongs to the Special Issue Genetic Regulation of Abiotic Stress Responses)
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