Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches

Environmental constraints that include abiotic stress factors such as salt, drought, cold and extreme temperatures severely limit crop productivity. Improvement of crop plants with traits that confer tolerance to these stresses was practiced using traditional and modern breeding methods. Molecular breeding and genetic engineering contributed substantially to our understanding of the complexity of stress response. Mechanisms that operate signal perception, transduction and downstream regulatory factors are now being examined and an understanding of cellular pathways involved in abiotic stress responses provide valuable information on such responses. This review presents genomic-assisted methods which have helped to reveal complex regulatory networks controlling abiotic stress tolerance mechanisms by high-throughput expression profiling and gene inactivation techniques. Further, an account of stress-inducible regulatory genes which have been transferred into crop plants to enhance stress tolerance is discussed as possible modes of integrating information gained from functional genomics into knowledge-based breeding programs. In addition, we envision an integrative genomic and breeding approach to reveal developmental programs that enhance yield stability and improve grain quality under unfavorable environmental conditions of abiotic stresses.     

Marker assisted selection in crop plants

Genetic mapping of major genes and quantitative traits loci (QTLs) for many important agricultural traits is increasing the integration of biotechnology with the conventional breeding process. Exploitation of the information derived from the map position of traits with agronomical importance and of the linked molecular markers, can be achieved through marker assisted selection (MAS) of the traits during the breeding process. However, empirical applications of this procedure have shown that the success of MAS depends upon several factors, including the genetic base of the trait, the degree of the association between the molecular marker and the target gene, the number of individuals that can be analyzed and the genetic background in which the target gene has to be transferred. MAS for simply inherited traits is gaining increasing importance in breeding programs, allowing an acceleration of the breeding process. Traits related to disease resistance to pathogens and to the quality of some crop products are offering some important examples of a possible routinary application of MAS. For more complex traits, like yield and abiotic stress tolerance, a number of constraints have determined severe limitations on an efficient utilization of MAS in plant breeding, even if there are a few successful applications in improving quantitative traits. Recent advances in genotyping technologies together with comparative and functional genomic approaches are providing useful tools for the selection of genotypes with superior agronomical performancies.     

Genetic and genomic approaches to develop rice germplasm for problem soils

Soils that contain toxic amounts of minerals or are deficient in essential plant nutrients are widespread globally and seriously constrain rice production. New methods are necessary to incorporate the complex adaptive traits associated with tolerance of these abiotic stresses, while simultaneously retaining the high yield potential of rice varieties when conditions are favorable. Significant progress in the genetic characterization of stress response pathways and recent advances in genomics have provided powerful tools for in-depth dissection of tolerance mechanisms. Additionally, tolerance of most of these abiotic stresses in rice is controlled by a few QTLs with large effects despite the intricacy of the numerous traits involved. Genetic dissection of these QTLs and their incorporation into high-yielding varieties will significantly enhance and stabilize rice productivity in these problem soils. Current efforts at IRRI and in rice breeding programs worldwide are seeking to explore diverse germplasm collections and genetically dissect the causal mechanisms of tolerance to facilitate their use in breeding. This review focuses on salinity and P and Zn deficiency as the major problems encountered in rice soils, and examines current understanding of the mechanisms involved and efforts toward germplasm improvement.     

Breeding for Yield Potential and Stress Adaptation in Cereals

The need to accelerate breeding for increased yield potential and better adaptation to drought and other abiotic stresses is an issue of increasing urgency. As the population continues to grow rapidly, the pressure on resources (mainly untouched land and water) is also increasing, and potential climate change poses further challenges. We discuss ways to improve the efficiency of crop breeding through a better physiological understanding by both conventional and molecular methods. Thus the review highlights the physiological basis of crop yield and its response to stresses, with special emphasis on drought. This is not just because physiology forms the basis of proper phenotyping, one of the pillars of breeding, but because a full understanding of physiology is also needed, for example, to design the traits targeted by molecular breeding approaches such as marker-assisted selection (MAS) or plant transformation or the way these traits are evaluated. Most of the information in this review deals with cereals, since they include the world's main crops, however, examples from other crops are also included. Topics covered by the review include the conceptual framework for identifying secondary traits associated with yield potential and stress adaptation, and how to measure these secondary traits in practice. The second part of the review deals with the real role of molecular breeding for complex traits from a physiological perspective. This part examines current developments in MAS and quantitative trait loci (QTL) detection as well as plant transformation. Emphasis is placed on the current limitations of these molecular approaches to improving stress adaptation and yield potential. The essay ends by presenting some ideas regarding future avenues for crop breeding given the current and possible future challenges, and on a multidisciplinary approach where physiological knowledge and proper phenotyping play a major role.     

Enhancing drought tolerance in C(4) crops

Adaptation to abiotic stresses is a quantitative trait controlled by many different genes. Enhancing the tolerance of crop plants to abiotic stresses such as drought has therefore proved to be somewhat elusive in terms of plant breeding. While many C(4) species have significant agronomic importance, most of the research effort on improving drought tolerance has focused on maize. Ideally, drought tolerance has to be achieved without penalties in yield potential. Possibilities for success in this regard are highlighted by studies on maize hybrids performed over the last 70 years that have demonstrated that yield potential and enhanced stress tolerance are associated traits. However, while our understanding of the molecular mechanisms that enable plants to tolerate drought has increased considerably in recent years, there have been relatively few applications of DNA marker technologies in practical C(4) breeding programmes for improved stress tolerance. Moreover, until recently, targeted approaches to drought tolerance have concentrated largely on shoot parameters, particularly those associated with photosynthesis and stay green phenotypes, rather than on root traits such as soil moisture capture for transpiration, root architecture, and improvement of effective use of water. These root traits are now increasingly considered as important targets for yield improvement in C(4) plants under drought stress. Similarly, the molecular mechanisms underpinning heterosis have considerable potential for exploitation in enhancing drought stress tolerance. While current evidence points to the crucial importance of root traits in drought tolerance in C(4) plants, shoot traits may also be important in maintaining high yields during drought.     

Genetic dissection of drought and heat‐responsive agronomic traits in wheat

High yield and wide adaptation are principal targets of wheat breeding but are hindered by limited knowledge on genetic basis of agronomic traits and abiotic stress tolerances. In this study, 277 wheat accessions were phenotyped across 30 environments with non‐stress, drought‐stressed, heat‐stressed, and drought‐heat‐stressed treatments and were subjected to genome‐wide association study using 395 681 single nucleotide polymorphisms. We detected 295 associated loci including consistent loci for agronomic traits across different treatments and eurytopic loci for multiple abiotic stress tolerances. A total of 22 loci overlapped with quantitative trait loci identified by biparental quantitative trait loci mapping. Six loci were simultaneously associated with agronomic traits and abiotic stress tolerance, four of which fell within selective sweep regions. Selection in Chinese wheat has increased the frequency of superior marker alleles controlling yield‐related traits in the four loci during past decades, which conversely diminished favourable genetic variation controlling abiotic stress tolerance in the same loci; two promising candidate paralogous genes colocalized with such loci, thereby providing potential targets for studying the molecular mechanism of stress tolerance–productivity trade‐off. These results uncovering promising alleles controlling agronomic traits and/or multiple abiotic stress tolerances, providing insights into heritable covariation between yield and abiotic stress tolerance, will accelerate future efforts for wheat improvement.     

Breeding for abiotic stresses for sustainable agriculture

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.     

Developing stress tolerant plants through in vitro selection—An overview of the recent progress

Biotic and abiotic stresses impose a major threat to agriculture. Therefore, the efforts to develop stress-tolerant plants are of immense importance to increase crop productivity. In recent years, tissue culture based in vitro selection has emerged as a feasible and cost-effective tool for developing stress-tolerant plants. Plants tolerant to both the biotic and the abiotic stresses can be acquired by applying the selecting agents such as NaCl (for salt tolerance), PEG or mannitol (for drought tolerance) and pathogen culture filtrate, phytotoxin or pathogen itself (for disease resistance) in the culture media. Only the explants capable of sustaining such environments survive in the long run and are selected. In vitro selection is based on the induction of genetic variation among cells, tissues and/or organs in cultured and regenerated plants. The selection of somaclonal variations appearing in the regenerated plants may be genetically stable and useful in crop improvement. This review focuses on the progress made towards the development of stress-tolerant lines through tissue culture based in vitro selection. Plants have evolved many biochemical and molecular mechanisms to survive under stress conditions. The mechanisms of ROS (reaction oxygen species) generation and removal in plants under biotic and abiotic stress conditions have also been reviewed.     

Inducing drought tolerance in plants: Recent advances

Undoubtedly, drought is one of the prime abiotic stresses in the world. Crop yield losses due to drought stress are considerable. Although a variety of approaches have been used to alleviate the problem of drought, plant breeding, either conventional breeding or genetic engineering, seems to be an efficient and economic means of tailoring crops to enable them to grow successfully in drought-prone environments. During the last century, although plant breeders have made ample progress through conventional breeding in developing drought tolerant lines/cultivars of some selected crops, the approach is, in fact, highly time-consuming and labor- and cost-intensive. Alternatively, marker-assisted breeding (MAB) is a more efficient approach, which identifies the usefulness of thousands of genomic regions of a crop under stress conditions, which was, in reality, previously not possible. Quantitative trait loci (QTL) for drought tolerance have been identified for a variety of traits in different crops. With the development of comprehensive molecular linkage maps, marker-assisted selection procedures have led to pyramiding desirable traits to achieve improvements in crop drought tolerance. However, the accuracy and preciseness in QTL identification are problematic. Furthermore, significant genetic × environment interaction, large number of genes encoding yield, and use of wrong mapping populations, have all harmed programs involved in mapping of QTL for high growth and yield under water limited conditions. Under such circumstances, a transgenic approach to the problem seems more convincing and practicable, and it is being pursued vigorously to improve qualitative and quantitative traits including tolerance to biotic and abiotic stresses in different crops. Rapid advance in knowledge on genomics and proteomics will certainly be beneficial to fine-tune the molecular breeding and transformation approaches so as to achieve a significant progress in crop improvement in future. Knowledge of gene regulation and signal transduction to generate drought tolerant crop cultivars/lines has been discussed in the present review. In addition, the advantages and disadvantages as well as future prospects of each breeding approach have also been discussed.     

Research Advances in Mechanisms of Turfgrass Tolerance to Abiotic Stresses: From Physiology to Molecular Biology

Turgrfass used on landscapes, parks, sports fields, and golf courses has significant ecological, environmental, and economic impacts. The economic value of seed production of turfgrasses is second to hybrid corn. The land area cultivated with turfgrass is increasing due to rapid urban development. Turfgrass is often subjected to various abiotic stresses, which cause declines in aesthetic quality, functionality and seed yield. Among abiotic stresses, drought, salinity, heat, and low temperature are the most common detrimental factors for turfgrass growth in various regions. Thorough understanding of mechanisms of turfgrass stress responses is vital for the development of superior stress-tolerant germplasm through breeding and biotechnology. Significant progress has been made in turfgrass stress physiology and molecular biology in recent decades, but research for turfgrasses generally lags behind that of the major Poaceae crops, particularly at the molecular and genomic levels. This review focuses on research advances in turfgrass stress physiology and provides an overview of limited information on gene discovery, genetic transformation, and molecular marker development for improving stress tolerance, with emphasis on drought, salinity, heat, and low temperature stress. Major growth and physiological traits associated with these stresses, as well as metabolic and molecular factors regulating various traits for turfgrass tolerance to each stress are discussed. Future research at the systems biology level and through genomic sequencing is paramount for further insights on fundamental mechanisms of turfgrass stress tolerance and for improving turfgrass tolerance to various environmental stresses.     

Strategies to ameliorate abiotic stress-induced plant senescence

The plant senescence syndrome resembles, in many molecular and phenotypic aspects, plant responses to abiotic stresses. Both processes have an enormous negative global agro-economic impact and endanger food security worldwide. Premature plant senescence is the main cause of losses in grain filling and biomass yield due to leaf yellowing and deteriorated photosynthesis, and is also responsible for the losses resulting from the short shelf life of many vegetables and fruits. Under abiotic stress conditions the yield losses are often even greater. The primary challenge in agricultural sciences today is to develop technologies that will increase food production and sustainability of agriculture especially under environmentally limiting conditions. In this chapter, some of the mechanisms involved in abiotic stress-induced plant senescence are discussed. Recent studies have shown that crop yield and nutritional values can be altered as well as plant stress tolerance through manipulating the timing of senescence. It is often difficult to separate the effects of age-dependent senescence from stress-induced senescence since both share many biochemical processes and ultimately result in plant death. The focus of this review is on abiotic stress-induced senescence. Here, a number of the major approaches that have been developed to ameliorate some of the effects of abiotic stress-induced plant senescence are considered and discussed. Some approaches mimic the mechanisms already used by some plants and soil bacteria whereas others are based on development of new improved transgenic plants. While there may not be one simple strategy that can effectively decrease all losses of crop yield that accrue as a consequence of abiotic stress-induced plant senescence, some of the strategies that are discussed already show great promise.     

Models and tools for studying drought stress responses in peas

The pea (Pisum sativum L.) is an important pulse crop but the growing area is limited because of its relatively low yield stability. In many parts of the world the most important abiotic factor limiting the survival and yield of plants is the restricted water supply, and the crop productivity can only be increased by improving drought tolerance. Development of pea cultivars well adapted to dry conditions has been one of the major tasks in breeding programs. Conventional breeding of new cultivars for dry conditions required extensive selection and testing for yield performance over diverse environments using various biometrical approaches. Several morphological and biochemical traits have been proven to be related to drought resistance, and methods based on physiological attributes can also be used in development of better varieties. Osmoregulation plays a role in the maintenance of turgor pressure under water stress conditions, and information on the behaviour of genotypes under osmotic stress can help selection for drought resistance. Biotechnological approaches including in vitro test, genetic transformation, and the use of molecular markers and mutants could be useful tools in breeding of pea. In this minireview we summarized the present status of different approaches related to drought stress improvement in the pea.     

Retrospective and perspective of rice breeding in China

Breeding is the art and science of selecting and changing crop traits for the benefit of human beings. For several decades, tremendous efforts have been made by Chinese scientists in rice breeding in improving grain yield, nutrition quality, and environmental performance, achieving substantial progress for global food security. Several generations of crop breeding technologies have been developed, for example, selection of better performance in the field among variants (conventional breeding), application of molecular markers for precise selection (molecular marker assisted breeding), and development of molecular design (molecular breeding by rational design). In this review, we briefly summarize the advances in conventional breeding, functional genomics for genes and networks in rice that regulate important agronomic traits, and molecular breeding in China with focuses on high yield, good quality, stress tolerance, and high nutrient-use efficiency. These findings have paved a new avenue for rational design of crops to develop ideal varieties with super performance and productivity.     

Targeting Glycinebetaine for Abiotic Stress Tolerance in Crop Plants: Physiological Mechanism,Molecular Interaction and Signaling

In the era of climate change, abiotic stresses (e.g., salinity, drought, extreme temperature, flooding, metal/metalloid(s), UV radiation, ozone, etc.) are considered as one of the most complex environmental constraints that restricts crop production worldwide. Introduction of stress-tolerant crop cultivars is the most auspicious way of surviving this constraint, and to produce these types of tolerant crops. Several bioengineering mechanisms involved in stress signaling are being adopted in this regard. One example of this kind of manipulation is the osmotic adjustment. The quarternary ammonium compound glycinebetaine (GB), also originally referred to as betaine is a methylated glycine derivative. Among the betaines, GB is the most abundant one in plants, which is mostly produced in response to dehydration caused by different abiotic stresses like drought, salinity, and extreme temperature. Glycinebetaine helps in decreased accumulation and detoxification of ROS, thereby restoring photosynthesis and reducing oxidative stress. It takes part in stabilizing membranes and macromolecules. It is also involved in the stabilization and protection of photosynthetic components, such as ribulose-1, 5-bisphosphate carboxylase/oxygenase, photosystem II and quarternary enzyme and protein complex structures under environmental stresses. Glycinebetaine was found to perform in chaperone-induced protein disaggregation. In addition, GB can confer stress tolerance in very low concentrations, and it acts in activating defense responsive genes with stress protection. Recently, field application of GB has also shown protective effects against environmental adversities increasing crop yield and quality. In this review, we will focus on the role of GB in conferring abiotic stress tolerance and the possible ways to engineer GB biosynthesis in plants.     

miRNAs: Major modulators for crop growth and development under abiotic stresses

Cumulatively, biotic and abiotic stresses of various magnitudes can decrease the production of crops by 70%. miRNAs have emerged as a genetic tool with enormous potential that can be exploited to understand stress tolerance at the molecular level and eventually regulate stress in crops. Plant miRNA targets frequently fit into diverse families of TFs that control the expression of genes related to a certain trait. As key machinery in gene regulatory networks, it is agreed that a broad understanding of miRNAs will greatly increase our understanding of plant responses to environmental stresses. miRNA-led stress regulatory networks are being considered as novel tools for the development of abiotic stress tolerance in crops. At this time, we need to expand our knowledge about the modulatory role of miRNAs during environmental fluctuations. It has become exceedingly clear that with increased understanding of the role of miRNAs during stress, the techniques for using miRNA-mediated gene regulation to enhance plant stress tolerance will become more effective and reliable. In this review we present: (1) miRNAs as a potential avenue for the modulation of abiotic stresses, and (2) summarize the research progress regarding plant responses to stress. Current progress is explained through discussion of the identification and validation of several miRNAs that enhance crop tolerance of salinity, drought, etc., while missing links on different aspects of miRNAs related to abiotic stress tolerance are noted.     

Eco-physiological and Biochemical Responses of Rapeseed (Brassica napus L.) to Abiotic Stresses: Consequences and Mitigation Strategies

Rapeseed yield parameters have been altered due to the increased exposure to abiotic stresses. The changing climatic conditions have reduced biomass production and seed yield, which ultimately affect the success of rapeseed crops. The severity and ability of abiotic stresses to act in tandem are a growing concern for agriculture producers across the globe. Rapeseed is one of the most vital cultivars in the world, serving as a major player in edible oil production. Abiotic stress conditions impose various effects on plant metabolism associated with growth stages, soil water storage capacity and plant physiological aspects. Modern agriculture aims to increased plant productivity to ensure global food security for the future. This can be achieved using quality seed, appropriate agricultural practices, measuring pest reduction techniques and understanding crop production challenges. Important tools, including conventional breeding and biotechnological approaches, can be employed to develop abiotic stress tolerance rapeseed. This review highlights the physiological and biochemical responses of rapeseed to abiotic stresses. The review also addresses conventional and modern stress mitigation strategies for the development of climate-smart rapeseed.

     

The development and application of molecular markers for abiotic stress tolerance in barley

This article represents some current thinking and objectives in the use of molecular markers to abiotic stress tolerance. Barley has been chosen for study as it is an important crop species, as well as a model for genetic and physiological studies. It is an important crop and, because of its well-studied genetics and physiology, is an excellent candidate in which to devise more efficient breeding methods. Abiotic stress work on cultivated gene pools of small grain cereals frequently shows that adaptive and developmental genes are strongly associated with responses. Developmental genes have strong pleiotropic effects on a number of performance traits, not just abiotic stresses. One concern is that much of the genetic variation for improving abiotic stress tolerance has been lost during domestication, selection and modern breeding, leaving pleiotropic effects of the selected genes for development and adaptation. Such genes are critical in matching cultivars to their target agronomic environment, and since there is little leverage in changing these, other sources of variation may be required. In barley, and many other crops, greater variation to abiotic stresses exists in primitive landraces and related wild species gene pools. Wild barley, Hordeum spontaneum C. Koch is the progenitor of cultivated barley, Hordeum vulgare L. and is easily hybridized to H. vulgare. Genetic fingerprinting of H. spontaneum has revealed genetic marker associations with site-of-origin ecogeographic factors and also experimentally imposed stresses. Genotypes and collection sites have been identified which show the desired variation for particular stresses. Doubled haploid and other segregating populations, including landrace derivatives have been used to map genetically the loci involved. These data can be used in molecular breeding approaches to improve the drought tolerance of barley. One strategy involves screening for genetic markers and physiological traits for drought tolerance, and the associated problem of drought relief-induced mildew susceptibility in naturally droughted fields of North Africa.