Omics and Plant Abiotic Stress Tolerance

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National and international regulation of recombinant DNA–modified, or “genetically engineered” (also referred to as “genetically modified,” or GM), plants, including those with enhanced abiotic stress tolerance, is unscientific and illogical, a lamentable illustration of the maxim that bad science makes bad law. Instead of regulatory scrutiny that is proportional to risk – a fundamental principle of regulatory oversight of any product or activity – the degree of oversight of genetically engineered organisms is actually inversely proportional to risk. The current approach to regulation, which captures organisms to be field tested or commercialized according to the techniques used to construct them rather than their properties, flies in the face of scientific consensus. This approach has been costly in terms of economic losses and human suffering. The poorest of the poor have suffered the most because the hugely inflated development costs of genetically engineered plants and food have prevented robust development of new plant varieties with enhanced abiotic stress tolerance and other desirable characteristics. An approach to the regulation of field trials, known as the “Stanford Model,” is designed to assess risks of new agricultural introductions, whether or not the organisms are genetically engineered, and independent of the genetic modification techniques employed. It offers a scientific, rational, risk–based basis for field trial regulations. Using this sort of model for regulatory review would not only better protect human health and the environment but would also permit more expeditious development and more widespread use of innovative, new plants and seeds.

Plant growth and productivity are limited by various types of abiotic stresses. While significant advances have been made in understanding the plant adaptation in stress environments, there are still challenges to translate this acquired knowledge for improved crop performance and productivity under stress environments due to complex genetics involving multitude of genes and stress tolerance mechanisms and interaction with numerous environmental factors pose. Different omics technologies have evolved during the last few decades to systematically analyze and correlate the changes in the genome, transcriptome, proteome, and metabolome to the variability in plant’s response to abiotic stresses. This chapter will provide an overview of various omics technologies and their application to increase the chances of developing abiotic stress tolerant plants. Although, we foresee significant potential of these innovative tools in making genetic improvement, challenges in integrating the vast amount of high throughput omics data should be overcome to understand the genetic network involved in abiotic stress tolerance.

Agriculture using genetically modified crops is emerging as an effective measure to counteract the negative impact of abiotic stresses on crop production. Abiotic stresses mainly salt, drought, cold and heavy metals are the major cause of crop failure which restrict crops to reach their full genetic potential. Salt, drought and heavy metals exert their negative impact essentially by disrupting the ionic and osmotic equilibrium of the cell, whereas, cold causes mechanical constraint to the membrane. Plants respond to abiotic stresses through multifaceted molecular signaling pathways. Therefore, understanding of molecular signaling pathways and identification of key molecules and their specific roles is important for crop improvement. Several genes responsible for abiotic stress tolerance have been identified which code for antioxidants, enzymes that modify lipids in the cell membrane, stress-response transcription factors, proteins that maintain ion homeostasis, heat shock proteins, or enzymes that synthesize important stress-response compounds. Transgenic plants having some of these genes have been produced and found to be abiotic stress tolerant. Present chapter reviews the plant responses to abiotic stresses such as salinity, drought, cold and heavy metal stresses and tolerance mechanisms through omics approaches.

Salinity is one of the most severe environmental stresses affecting plant productivity worldwide. In many plant species, salt sensitivity is associated with the accumulation of sodium (Na+) in photosynthetic tissues. Adaptation of plants to salt stress (i.e. resumption of growth after exposure to high soil salinity) requires cellular ion homeostasis. To prevent the accumulation of Na+ in the cytoplasm, plants have developed three mechanisms that function in a cooperative manner, i.e restriction of Na+ influx, active Na+ extrusion at the root-soil interface, and subsequent vacuolar compartmentalization without toxic ion accumulation in the cytosol. Sodium ions can enter the cell through several low- and high-affinity K+ carriers. Voltage-independent, non selective cation channels (NSCC) provide a pathway for the entry of Na+ into plant cells. Some members of the HKT family (High Affinity K+ transporter) function as sodium transporter and contribute to Na+ removal from the ascending xylem sap and recirculation from the leaves to the roots via the phloem vasculature. Sodium extrusion is presumed to be of critical importance for ion homeostasis and salt tolerance of glycophytes. Na+ sequestration into the vacuole depends on expression and activity of Na+/H+ antiporter that is driven by electrochemical gradient of protons generated by the vacuolar H+-ATPase and the H+-PPase. However, we have a limited molecular understanding of the overall control of Na+ accumulation, the role of each transporter and salt stress tolerance at the whole plant level. Genomics and functional genomics provide a new opportunity in addressing the multigenicity of the plant abiotic stress response through genome sequences, stress-specific transcript collections, protein and metabolite profiles, their dynamic changes and protein interactions. In this review, we analyze available data related to omics and plant abiotic stress responses in order to enhance our understanding about how salinity and other abiotic stresses affect the most fundamental processes of cellular function which have a substantial impact on plant growth development.

During the last forty years, researchers have had the working hypothesis that genes upregulated by low temperatures protect plants from cold stress. When cDNA cloning technologies were developed about twenty years ago, cold-responsive genes such as genes for CBF/DREB transcription factors could be identified in Arabidopsis. The next step was to use microarray technologies to identify cold-regulated genes as a way to improve our understanding of cold tolerance. Unfortunately, there have been several problems with this approach; 1) upregulation of mRNA levels is only one of many mechanisms for the control of gene expression in plants, 2) published microarray results have not always been repeatable by other labs, 3) there has been a heavy emphasis on cold-regulated transcription factor genes to the exclusion of other important determinants, 4) the cold treatments used in several laboratory studies have not always been comparable to natural stress conditions and 5) there has often been a lack of follow-up research, using mutants to prove through functional genomics that specific genes are actually involved in cold tolerance. An alternative transcriptomic approach to identify genes for cold tolerance is chemical genetics based on glycine betaine treatments, using transcriptomics followed by functional studies with mutants. This approach was validated first for the RabA4c GTPase involved in membrane trafficking and has also identified a bZIP transcription factor and FRO2 ferric reductase. In conclusion, although transcriptomics has identified some determinants of cold stress tolerance, there still exists large gaps in our knowledge of this important process.

Polyamines have been proposed to regulate multiple aspects of plant development and stress responses. In most of the cases, they interact with other signaling pathways to exert their action. Here we describe transcriptomic analyses that have lead to the identification of physiologically relevant interactions between polyamines and other hormones, such as abscisic acid, during the response to abiotic stress. Overall, these studies reinforce the premise that polyamines are regulatory signaling molecules which mediate by intricate cross-talks with hormonal pathways in response to different environmental stimuli.

Plants are exposed to various abiotic stresses such as water deficit or ion excess, elevated temperature, high light intensity, salinity, freezing, cold, etc. under field conditions, potentially reducing the yield of crop plants by more than 50%. Investigations of the physiological, biochemical and molecular aspects of stress tolerance have been conducted to unravel the intrinsic mechanisms for mitigation against stress. The new molecular “omic” tools, comprising of genomics, proteomics and metabolomics, have opened up new perspectives in stress biology. Before the advent of genomics era, a gene-by-gene approach was used to decipher the function of genes involved in abiotic stress response. The availability of genome sequences of certain important plant species has enabled the use of strategies like genome-wide expression profiling to identify the genes associated with stress response, followed by the verification of gene function by the analysis of mutants and transgenics. The genomics based approaches provide access to agronomically desirable alleles present at quantitative trait loci (QTLs), thus enabling the improvement of abiotic stress tolerant plants. Marker assisted selection (MAS) is already helping breeders improve drought related traits. The recent upsurge in structural genomics determines the DNA sequence by manual or robotic methods. Further elucidation of the complex networks interacting during stress defenses has been achieved by multi-parallel analysis of transcript levels, microarray analysis, RT-qPCR, Serial analysis of gene expression (SAGE), Massive parallel signature sequencing (MPSS) and more recently oligoarray using the transcriptome of any specie to evaluate abiotic stress response. Analysis of sequence data and gene products would facilitate the identification and cloning of genes at target QTLs and their direct manipulation via genetic engineering. Furthermore, several bioinformatic tools, ESTs and subtractive cDNA libraries have added new dimensions for deciphering the genetic basis of stress tolerance. The current initiatives in functional genomics or proteomic research for the analysis of plant stress tolerance is based on two-dimensional gel electrophoresis (2-DE) and identification of differentially displayed spots by MALDITOF, QTOF MS/MS, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), characterization of separated proteins by mass spectrometer and database searching. In addition, many proteins are modified by post-translational modifications such as phosphorylation, glucosylation, ubiquitinylation, sumoylation and many others. New techniques in gel-based approaches such as difference gel electrophoresis (DIGE) can provide both qualitative and quantitative data about the differential expression of proteins. Proteomics nowadays is also used to study the relationship between gene expression (transcriptomics) and metabolism (metabolomics). Our limited knowledge of stress-associated metabolism remains a major gap in our understanding of the stress response. Therefore comprehensive profiling of stress-associated metabolites is most relevant to the successful molecular breeding of stress-tolerant crop plants. Metabolomic studies, thus along with transcriptomics and proteomics, and their integration with systems biology, will lead to strategies to alter cellular metabolism for adaptation to abiotic stress conditions. The present review will focus on the current development, progress and applications of genomics, proteomics and metabolomic studies, and implementation of systems biology to meet the challenges of abiotic stress and crop improvement program from a practical standpoint. The accumulating information will provide plant researchers to explore new paradigms to address fundamental and practical questions in a multidisciplinary manner.

Epigenome refers to the genomic content of a cell layered with all the covalent/noncovalent modifications on the DNA and histones. Remodeling of the chromatin is induced by these changes in response to environmental or developmental signals without any change in the underlying nucleotide sequence. These modifications are stably inherited through mitotic and meiotic divisions. Every differentiated cell type possesses a characteristic epigenome that is dynamic and differs from the epigenome of neighboring cell type, while the genotype of the cells remains constant. DNA methylation, histone modifications, inclusion of histone variants in the nucleosomes, small RNAs and their effector molecules all contribute towards changing the landscape of the epigenomes. Valuable insights into genomic distribution of methyl groups has been obtained by employing various high throughput technologies. Orchestered changes in the epigenetic landscape also occurs in response to abiotic stress. Plants respond to these stresses by modulating the expression of stress-regulated genes through covalent/noncovalent modifications of chromatin. This chapter highlights the contribution of epigenetic modifications in shaping the epigenome and mediating gene regulation in response to abiotic stress.

Rhizotoxic ions inhibit root growth, resulting in reduced yield of various crop plants. It is thus improvement of tolerance of roots to rhizotoxic ions, one of the most important targets in plant breeding, to improve the productivity of crops in various soil types. Molecular breeding such as marker assisted selection and transgenic breeding would be promising approaches in current plant breeding, while identification of critical genes is needed to realize these approaches. In this chapter, we introduce recent progress of transcriptomics and other -omics studies for complex response of plant roots to rhizotoxic ions, and those that for identifying critical genes for tolerance to rhizotoxic ions.

S-nitrosylation, is a PTM (post translational modification of NO (nitric oxide). Abiotic stress conditions lead to NO evolution and SNO (s-nitosothiols, the cellular NO pool) accumulation. Recently, research on NO and nitrosylation with respect to stress has gained momentum. Partial S-nirosoproteome of Arabidopsis, K. pinata and B.juncea are identified following BST, affinity purification and mass spectometric identification. In this chapter a snapshot of the relevance of NO and nitrosylation in abiotic stress is presented.

Abiotic stresses impair crop production on irrigated land worldwide. Overall, the susceptibility or tolerance to the stress in plants is a coordinated action of multiple stress responsive genes, which also cross-talk with other components of stress signal transduction pathways. Plant responses to abiotic stress can be determined by the severity of the stress and by the metabolic status of the plant. Abscisic acid (ABA) is a phytohormone critical for plant growth and development and plays an important role in integrating various stress signals and controlling downstream stress responses. Plants have to adjust ABA levels constantly in response to changing physiological, metabolic and environmental conditions. To date, the mechanisms for fine-tuning of ABA levels remain elusive. The mechanisms by which plants respond to abiotic stresses include both ABA-dependent and ABA-independent processes. Various transcription factors such as DREB2A/2B, AREB1, RD22BP1 and MYC/MYB are known to regulate the ABA-responsive gene expression by interacting with their corresponding cis-acting elements such as DRE/CRT, ABRE, and MYCRS/MYBRS, respectively. Due to polygenic nature of the trait, it is becoming important to apply genome wide tools for precise understanding of the mechanisms and to ultimately improve stress tolerance in crops plants. This chapter describes the ABA-induced stress response pathway and the application of ‘omics’ technologies to unravel the complex mechanisms governing abiotic stress tolerance in plants.

RNA silencing is an evolutionarily conserved mechanism in eukaryotes that control gene expression through small RNA-guided RNA degradation, translational repression and DNA methylation. Plants have evolved multiple small RNA pathways that have been demonstrated to play an essential role in developmental regulation and defence against invasive nucleic acids such as transposable elements and viruses. Recent studies have provided evidence that the different small RNA pathways play a more diverse role in plant defence against biotic and abiotic stresses. These findings are likely to result in new platforms for engineering stress tolerant crops in the future.

Plant abiotic stress responses are a major yield-limiting factor in agriculture and thereby in the production of food, feed and fibre. Recent technology developments allow studies of such stress responses at a global molecular scale using omics data (metabolome, proteome, transcriptome and more). Significant progress has been made in statistical, mathematical and informatics driven analysis of omics data. Genes, proteins and metabolites can now be classified, categorized and linked at a genomic scale, and network-based analysis of various biological processes is becoming reality. However, in order to gain a complete overview of all processes and active networks in each cell type of the plant at all developmental stages and under all types of environmental variation, data production needs to become feasible at a significantly more massive scale. Systems biology studies the organization of system components and their networks, with the idea that unique properties of a system can only be observed through study of the system as a whole. A system-based analysis can involve multiple scales, ranging from single cells, tissues, organs to whole organisms. One of the foundations of systems biology is the analysis of networks of interacting and interdependent components that produce the system's unique properties. Network analysis provides intuitive ways for omics data visualization, as it reduces the intrinsic complexity of such data. In this chapter we discuss systems biology as a promising tool to study plant stress responses. We list various network and visualization tools available to biologists, to help them analyse high throughput omics data sets.

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