Gene discovery in cereals through quantitative trait loci and expression analysis in water-use efficiency measured by carbon isotope discrimination

Drought continues to be a major constraint on cereal production in many areas, and the frequency of drought is likely to increase in most arid and semi-arid regions under future climate change scenarios. Considerable research and breeding efforts have been devoted to investigating crop responses to drought at various levels and producing drought-resistant genotypes. Plant physiology has provided new insights to yield improvement in drought-prone environments. Crop performance could be improved through increases in water use, water-use efficiency (WUE) and harvest index. Greater WUE can be achieved by coordination between photosynthesis and transpiration. Carbon isotope discrimination (Δ(13) C) has been demonstrated to be a simple but reliable measure of WUE, and negative correlation between them has been used to indirectly estimate WUE under selected environments. New tools, such as quantitative trait loci (QTL) mapping and gene expression profiling, are playing vital roles in dissecting drought resistance-related traits. The combination of gene expression and association mapping could help identify candidate genes underlying the QTL of interest and complement map-based cloning and marker-assisted selection. Eventually, improved cultivars can be produced through genetic engineering. Future efficient and effective breeding progress in cereals under targeted drought environments will come from the integrated knowledge of physiology and genomics.     

Regulation of Transpiration to Improve Crop Water Use

Decreasing fresh water supplies and increasing agricultural drought threaten sustainable worldwide crop production. Consequently, there is a global priority to develop crops with higher water use efficiency (WUE): biomass production or yield per unit of water used. Water use efficiency varies substantially among species and genotypes within a species, and a major effort is now underway to identify the genetic determinants of WUE. Today, it is known that genotypes in primary gene pools exhibit allelic variation for WUE through mechanisms that regulate transpiration, which is the conductance of water through stomata, the cuticle, and the boundary layer. Because of the differential diffusion properties of water and carbon dioxide (CO₂) through these pathways, it is feasible that WUE could be improved by decreasing transpiration without a concomitant reduction in CO₂ uptake. Since CO₂ uptake and transpirational water loss occur predominantly through stomatal pores, it is not surprising that genes involved in stomatal development and stomatal opening/closing impact WUE. Furthermore, loss- and gain-of-function genetic screens have identified genes that regulate transpiration and WUE by yet undetermined mechanisms. This review will discuss the genetic determinants that regulate transpiration and WUE in the context of the modern agricultural goal of improving WUE while sustaining biomass and yield.     

抗旱相关基因在烟草中的应用研究进展

干旱是影响烟草正常生长、发育、产量和烟叶品质的一个重要逆境因子。在干旱胁迫下,植物体内会通过激发一些抗旱基因的表达来增强植物的抗旱能力。目前,很多抗旱相关的功能蛋白基因和调控蛋白基因已被克隆并在烟草中实现了遗传转化,外源抗旱基因的表达提高了转基因烟草的抗旱能力。抗旱基因的克隆为烟草抗旱新品种的培育奠定了良好的分子基础,系统深入地研究抗旱相关基因在干旱胁迫条件下的表达与调控,可为通过基因工程手段提高烟草的抗旱能力开辟新途径,同时也能为其他农作物的抗旱分子育种和品种改良提供基因资源。     

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.     

Defining selection criteria to improve yield under drought

The many selection criteria that have been proposed to increase drought resistance of our crops have had little, if any, impact on improving crop yields in dry environments. There are several likely reasons for this lack of success. Some of these are: (i) criteria proposed have been related more to survival mechanisms under drought than to productivity, (ii) criteria are inappropriate to the target environment, and (iii) criteria are temporal and are therefore likely to have minimal impact on growth and yield over the entire lifecycle. Another important reason is that breeders have not been convinced the proposed criteria will be successful as they are too difficult to measure. On the other hand, empirical breeding programmes to improve yield under drought have been successful. Surprisingly, some of the greatest successes have been achieved by breeding in environments where water is non-limiting. This paper reviews breeding approaches to improve yield under drought. It focuses on critical factors that must be considered to identify likely plant attributes that can be targeted. These factors, their link with yield, the nature of the target environment, the level of organisation where the trait is expressed are discussed. Three quite different examples are given to emphasize the above considerations and which show substantial promise in targeting traits to improve yield under drought. They are drought at flowering, improving transpiration efficiency and improving early leaf area development.     

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.     

The battle of crops against drought: Genetic dissection and improvement

With ongoing global climate change,water scarcity-induced drought stress remains a major threat to agricultural productivity.Plants undergo a series of physiological and morphological changes to cope with drought stress,including stomatal closure to reduce transpiration and changes in root architecture to optimize water uptake.Combined phenotypic and multi-omics studies have recently identified a number of drought-related genetic resources in different crop species.The functional dissection of t...     

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.     

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.     

Genetic analysis of osmotic adjustment in crop plants

Plant water deficit is a component of several different stresses, including drought, salinity and low temperatures, which severely limit plant growth and crop productivity. Genetic modification of plants to allow growth and yield under unfavourable conditions is an important component of the solution to problems of environmental stress. While disagreement and even confusion may characterize some of the discussions on what constitutes a significant and an effective osmotic adjustment (OA) is receiving increasing recognition as a major mechanism. This paper starts with review of OA functions, genetic variation and inheritance, and theories and principles involved in commonly used protocols for quantifying OA. Emphasis is placed on a summary of current molecular strategies and advanced in the improvement of plant stress resistance through manipulating OA. They include a genetic engineering approach and a QTL mapping approach. Future promising strategies for improving drought resistance lie in molecular technology that allows genes or QTLs controlling OA to be tagged and isolated, these genes to be expressed in transgenic plants, and efficiency of breeding via marker-assisted selection to be improved. Aspects of QTL utilization in plant genetics, breeding and physiology and future research directions are discussed.     

Plant Breeding and Drought in C3 Cereals: What Should We Breed For?

Drought is the main abiotic constraint on cereal yield. Analysingphysiological determinants of yield responses to water may helpin breeding for higher yield and stability under drought conditions.The traits to select (either for stress escape, avoidance ortolerance) and the framework where breeding for drought stressis addressed will depend on the level and timing of stress inthe targeted area. If the stress is severe, breeding under stress-freeconditions may be unsuccessful and traits that confer survivalmay become a priority. However, selecting for yield itself understress-alleviated conditions appears to produce superior cultivars,not only for optimum environments, but also for those characterizedby frequent mild and moderate stress conditions. This impliesthat broad avoidance/tolerance to mild–moderate stressesis given by constitutive traits also expressed under stress-freeconditions. In this paper, we focus on physiological traitsthat contribute to improved productivity under mild–moderatedrought. Increased crop performance may be achieved throughimprovements in water use, water-use efficiency and harvestindex. The first factor is relevant when soil water remainsavailable at maturity or when deep-rooted genotypes access waterin the soil profile that is not normally available; the twolatter conditions become more important when all available wateris exhausted by the end of the crop cycle. Independent of themechanism operating, a canopy able to use more water than anotherwould have more open stomata and therefore higher canopy temperaturedepression, and ¹³C discrimination (¹³C) in plant matter. Thesame traits would also seem to be relevant when breeding forhot, irrigated environments. Where additional water is not availableto the crop, higher water-use efficiency (WUE) appears to bean alternative strategy to improve crop performance. In thiscontext ¹³C constitutes a simple but reliable measure of WUE.However, in contrast to lines performing better because of increasedaccess to water, lines producing greater biomass due to superiorWUE will have lower ¹³C values. WUE may be modified not onlythrough a decrease in stomatal conductance, but also throughan increase in photosynthetic capacity. Harvest index is stronglyreduced by terminal drought (i.e. drought during grain filling).Thus, phenological traits increasing the relative amount ofwater used during grain filling, or adjusting the crop cycleto the seasonal pattern of rainfall may be useful. Augmentingthe contribution of carbohydrate reserves accumulated duringvegetative growth to grain filling may also be worthwhile inharsh environments. Alternatively, extending the duration ofstem elongation without changing the timing of anthesis wouldincrease the number of grains per spike and the harvest indexwithout changing the amount of water utilized by the crop.     

EFFECTS OF ROOT PRUNING AT THE REGREENING STAGE ON DROUGHT TOLERANCE AND WATER USE EFFICIENCY OF WINTER WHEAT IN LATE GROWING STAGE

 通过盆栽试验研究了返青期根修剪对冬小麦(Triticum aestivum)后期耐旱性及水分利用效率的影响。在返青期设置了两个根修剪处理: 1)小剪根, 在植株一侧切去部分侧生根; 2)大剪根, 在主茎四周切去部分侧生根。不剪根者设为对照(CK)。研究结果显示, 两个根修剪处理均显著减少了小麦的根系, 但对根冠比没有显著影响。在花期, 两个根修剪处理的小麦旗叶的叶绿素荧光参数最大光化学效率(The maximum photochemical efficiency of PSⅡ, F_v/F_m)、 PSⅡ潜在活性 (PSⅡ potential activity, F_v/F_o)、实际光化学量子产量(Effective PSⅡ quantum yield, Φ_PSⅡ)、表观光合电子传递速率(Apparent rate of photosynthetic electron transport, ETR)、光化学淬灭系数( Coefficient of photochemical quenching, q_P)和非光化学淬灭系数(Coefficient of non-photochemical quenching, NPQ)值, 在停止供水7 d后, 均显著高于对照, 这表明根修剪小麦的耐旱性强于对照, 因此在干旱胁迫下有较高的光化学活性。小剪根处理在高水条件下对小麦产量无显著影响, 而在中度干旱条件下显著提高了小麦的产量, 因此, 小剪根处理显著提高了小麦的抗旱系数; 小剪根处理在高水分处理(土壤水分含量为田间持水量的85%)和中度干旱胁迫处理(土壤水分含量为田间持水量的55%)条件下, 均显著提高了小麦的水分利用效率。但大剪根处理由于严重影响了群体数量和产量, 水分利用效率和抗旱系数均没有提高。可见, 适当地减少根系有助于小麦的耐旱性和水分利用效率的提高。     

Improving plant drought tolerance and growth under water limitation through combinatorial engineering of signalling networks

Agriculture is by far the biggest water consumer on our planet, accounting for 70 per cent of all freshwater withdrawals. Climate change and a growing world population increase pressure on agriculture to use water more efficiently (‘more crop per drop’). Water‐use efficiency (WUE) and drought tolerance of crops are complex traits that are determined by many physiological processes whose interplay is not well understood. Here, we describe a combinatorial engineering approach to optimize signalling networks involved in the control of stress tolerance. Screening a large population of combinatorially transformed plant lines, we identified a combination of calcium‐dependent protein kinase genes that confers enhanced drought stress tolerance and improved growth under water‐limiting conditions. Targeted introduction of this gene combination into plants increased plant survival under drought and enhanced growth under water‐limited conditions. Our work provides an efficient strategy for engineering complex signalling networks to improve plant performance under adverse environmental conditions, which does not depend on prior understanding of network function.     

Understanding water deficit stress-induced changes in the basic metabolism of higher plants – biotechnologically and sustainably improving agriculture and the ecoenvironment in arid regions of the globe

Water is vital for plant growth, development and productivity. Permanent or temporary water deficit stress limits the growth and distribution of natural and artificial vegetation and the performance of cultivated plants (crops) more than any other environmental factor. Productive and sustainable agriculture necessitates growing plants (crops) in arid and semiarid regions with less input of precious resources such as fresh water. For a better understanding and rapid improvement of soil–water stress tolerance in these regions, especially in the water-wind eroded crossing region, it is very important to link physiological and biochemical studies to molecular work in genetically tractable model plants and important native plants, and further extending them to practical ecological restoration and efficient crop production. Although basic studies and practices aimed at improving soil water stress resistance and plant water use efficiency have been carried out for many years, the mechanisms involved at different scales are still not clear. Further understanding and manipulating soil–plant water relationships and soil–water stress tolerance at the scales of ecology, physiology and molecular biology can significantly improve plant productivity and environmental quality. Currently, post-genomics and metabolomics are very important in exploring anti-drought gene resources in various life forms, but modern agriculturally sustainable development must be combined with plant physiological measures in the field, on the basis of which post-genomics and metabolomics have further practical prospects. In this review, we discuss physiological and molecular insights and effects in basic plant metabolism, drought tolerance strategies under drought conditions in higher plants for sustainable agriculture and ecoenvironments in arid and semiarid areas of the world. We conclude that biological measures are the bases for the solutions to the issues relating to the different types of sustainable development.     

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.     

Advances in Drought Resistance of Rice

Water deficit is a serious environmental stress and the major constraint to rice productivity. Losses in rice yield due to water shortage probably exceed losses from all other causes combined and the extent of the yield loss depends on both the severity and duration of the water stress. Drought affects rice at morphological, physiological, and molecular levels such as delayed flowering, reduced dry matter accumulation and partitioning, and decreased photosynthetic capacity as a result of stomatal closure, metabolic limitations, and oxidative damage to chloroplasts. Small-statured rice plants with reduced leaf area and short growth duration are better able to tolerate drought stress, although the mechanisms are not yet fully understood. Increased water uptake by developing larger and deeper root systems, and the accumulation of osmolytes and osmoprotectants are other important mechanisms for drought resistance. Drought resistance in rice has been improved by using plant growth regulators and osmoprotectants. In addition, several enzymes have been found that act as antioxidants. Silicon has also improved drought resistance in rice by silicification of the root endodermis and improving water uptake. Seed priming improves germination and crop stand establishment under drought. Rice plants expressing HVA1, LEA proteins, MAP kinase, DREB and endo-1, 3-glucanase are better able to withstand drought stress. Polyamines and several enzymes act as antioxidants and reduce adverse effects of drought stress in rice. Drought resistance can be managed by developing and selecting drought-tolerant genotypes. Rice breeding and screening may be based on growth duration, root system, photosynthesis traits, stomatal frequency, specific leaf weight, leaf water potential, and yield in target environments. This review discusses recent developments in integrated approaches, such as genetics, breeding and resource management to increase rice yield and reduce water demand for rice production.     

Genomics-based approaches to improve drought tolerance of crops

The genetic bases of the molecular, cellular and developmental responses to drought involve many gene functions regulated by water availability. Genomics-based approaches provide access to agronomically desirable alleles present at quantitative trait loci (QTLs) that affect such responses, thus enabling us to improve the drought tolerance and yield of crops under water-limited conditions more effectively. Marker-assisted selection is already helping breeders improve drought-related traits. Analysis of sequence data and gene products should facilitate the identification and cloning of genes at target QTLs. Based on such premises, we envision a quick broadening of our understanding of the genetic and functional basis of drought tolerance. Novel opportunities will be generated for tailoring new genotypes "by design". Harnessing the full potential of genomics-assisted breeding will require a multidisciplinary approach and an integrated knowledge of the molecular and physiological processes influencing tolerance to drought.     

Translational research impacting on crop productivity in drought-prone environments

Conventional breeding for drought-prone environments (DPE) has been complemented by using exotic germplasm to extend crop gene pools and physiological approaches that consider water uptake (WU), water-use efficiency (WUE), and harvest index (HI) as drivers of yield. Drivers are associated with proxy genetic markers, such as carbon-isotope discrimination for WUE, canopy temperature for WU, and anthesis-silking interval for HI in maize. Molecular markers associated with relevant quantitative trait loci are being developed. WUE has also been increased through combining understanding of root-to-shoot signaling with deficit irrigation. Impacts in DPE will be accelerated by combining proven technologies with promising new strategies such as marker-assisted selection, and genetic transformation, as well as conservation agriculture that can increase WU while averting soil degradation.     

Functional Genomics of Drought Tolerance in Bioenergy Crops

With predicted global changes in temperature and precipitation, drought will increasingly impose a challenge to biomass production. Most of the bioenergy crops have some degree of drought susceptibility as revealed for example through measures of low water-use efficiency (WUE). It is imperative to improve drought tolerance and WUE in bioenergy crops for sustainable biomass production in arid and semi-arid regions. Genetics and functional genomics can play critical roles in generating knowledge to inform and aid genetic improvement for drought tolerance in bioenergy crops. The molecular aspects of drought response have been extensively investigated in model plants like Arabidopsis, yet our understanding of the molecular mechanisms underlying drought tolerance in bioenergy crops is limited. Plants in general exhibit various responses to drought stress depending on species and genotype. A rational strategy for studying drought tolerance in bioenergy crops is to translate the knowledge from model plants relative to the unique features associated with individual bioenergy species and genotypes. In this review, we summarize the general knowledge concerning drought responsive pathways, with a focus on the identification of commonality and specialty in drought responsive mechanisms among alternate species and genotypes. We describe the genomic resources developed for bioenergy crops and discuss genetic and epigenetic regulation of drought responses. We also examine comparative and evolutionary genomics as a means to leverage the ever-increasing genomics resources and provide new insights beyond what is known from studies on individual species. Finally, we outline future opportunities for studying drought tolerance using the emerging technologies.