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.     

Stress and domestication traits increase the relative fitness of crop-wild hybrids in sunflower

After a decade of transgenic crop production, the dynamics of gene introgression into wild relatives remain unclear. Taking an ecological genetics approach to investigating fitness in crop-wild hybrid zones, we uncovered both conditions and characteristics that may promote introgression. We compared diverse crop-wild hybrid genotypes relative to wild Helianthus annuus under one benign and three stressful agricultural environments. Whereas relative fitness of crop-wild hybrids averaged 0.25 under benign conditions, with herbicide application or competition it reached 0.45 and was more variable. In some instances, hybrid fitness matched wild fitness (approximately 1). Thus, wild populations under agronomic stress may be more susceptible to introgression. Although 'domestication' traits are typically considered unlikely to persist in wild populations, we found some (e.g. rapid growth and early flowering) that may enhance hybrid fitness, especially in stressful environments. Rigorous assessment of how particular genotypes, phenotypes, and environments affect introgression will improve risk assessment for transgenic crops.     

Evolutionary innovations driving abiotic stress tolerance in C4 grasses and cereals

Grasslands dominate the terrestrial landscape, and grasses have evolved complex and elegant strategies to overcome abiotic stresses. The C₄ grasses are particularly stress tolerant and thrive in tropical and dry temperate ecosystems. Growing evidence suggests that the presence of C₄ photosynthesis alone is insufficient to account for drought resilience in grasses, pointing to other adaptations as contributing to tolerance traits. The majority of grasses from the Chloridoideae subfamily are tolerant to drought, salt, and desiccation, making this subfamily a hub of resilience. Here, we discuss the evolutionary innovations that make C₄ grasses so resilient, with a particular emphasis on grasses from the Chloridoideae (chloridoid) and Panicoideae (panicoid) subfamilies. We propose that a baseline level of resilience in chloridoid ancestors allowed them to colonize harsh habitats, and these environments drove selective pressure that enabled the repeated evolution of abiotic stress tolerance traits. Furthermore, we suggest that a lack of evolutionary access to stressful environments is partially responsible for the relatively poor stress resilience of major C₄ crops compared to their wild relatives. We propose that chloridoid crops and the subfamily more broadly represent an untapped reservoir for improving resilience to drought and other abiotic stresses in cereals.

Chloridoid grasses have evolved unique adaptations to adverse environments and represent an untapped reservoir for improving resilience to drought and other abiotic stresses in cereals.     

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.     

Metabolite analysis for the comparison of irrigated and non-irrigated field grown tomato of varying genotype

Every year the consequences of water deficit on crop yield and quality are profound. The observation that many wild species relatives of cultivated crops display a greater stress tolerance and the fact that the cultivated species generally display only a fraction of the allelic diversity available within the tomato clade suggest that crossing of wild species with elite cultivars could improve the stress physiology of modern crops. To assess this from the basis of chemical composition we applied an established GC-MS based metabolite profiling method to fruits from irrigated and non-irrigated tomato plants either of the cultivated tomato (Solanum lycopersicum) or of its hybrid with its wild species relative (Solanum pennellii). Results are discussed in terms of both the metabolic response to drought stress and the potential of utilizing exotic germplasm as a means to improve agronomically important characteristics of crop species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

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.     

Breeding cereals for Mediterranean conditions: ecophysiological clues for biotechnology application

Water stress is the main environmental factor limiting cereal yield in Mediterranean environments. For particular regions, such as the Mediterranean basin, the agroecological conditions are expected to get worse. In response to this challenge attempts are being made to improve crop yield through farm‐ management practices and plant breeding efforts. Here we examine traits that may be used as selection criteria for breeding C3 cereal crops with improved yield and stability in Mediterranean conditions. Emphasis is made on the potential implications of defining proper selection traits and target environments when adopting biotechnology approaches in breeding programmes.     

Cassava biology and physiology

Cassava or manioc (Manihot esculenta Crantz), a perennial shrub of the New World, currently is the sixth world food crop for more than 500 million people in tropical and sub-tropical Africa, Asia and Latin America. It is cultivated mainly by resource-limited small farmers for its starchy roots, which are used as human food either fresh when low in cyanogens or in many processed forms and products, mostly starch, flour, and for animal feed. Because of its inherent tolerance to stressful environments, where other food crops would fail, it is often considered a food-security source against famine, requiring minimal care. Under optimal environmental conditions, it compares favorably in production of energy with most other major staple food crops due to its high yield potential. Recent research at the Centro Internacional de Agricultura Tropical (CIAT) in Colombia has demonstrated the ability of cassava to assimilate carbon at very high rates under high levels of humidity, temperature and solar radiation, which correlates with productivity across all environments whether dry or humid. When grown on very poor soils under prolonged drought for more than 6 months, the crop reduce both its leaf canopy and transpiration water loss, but its attached leaves remain photosynthetically active, though at greatly reduced rates. The main physiological mechanism underlying such a remarkable tolerance to drought was rapid stomatal closure under both atmospheric and edaphic water stress, protecting the leaf against dehydration while the plant depletes available soil water slowly during long dry periods. This drought tolerance mechanism leads to high crop water use efficiency values. Although the cassava fine root system is sparse, compared to other crops, it can penetrate below 2 m soil, thus enabling the crop to exploit deep water if available. Leaves of cassava and wild Manihot possess elevated activities of the C₄ enzyme PEP carboxylase but lack the leaf Kranz anatomy typical of C₄ species, pointing to the need for further research on cultivated and wild Manihot to further improve its photosynthetic potential and yield, particularly under stressful environments. Moreover, a wide range in values of K _m (CO₂) for the C₃ photosynthetic enzyme Rubisco was found among cassava cultivars indicating the possibility of selection for higher affinity to CO₂, and consequently higher leaf photosynthesis. Several plant traits that may be of value in crop breeding and improvement have been identified, such as an extensive fine root system, long leaf life, strong root sink and high leaf photosynthesis. Selection of parental materials for tolerance to drought and infertile soils under representative field conditions have resulted in developing improved cultivars that have high yields in favorable environments while producing reasonable and stable yields under stress.     

Plant domestication: setting biological clocks

Through domestication of wild species, humans have induced large changes in the developmental and circadian clocks of plants. As a result of these changes, modern crops are more productive and adaptive to contrasting environments from the center of origin of their wild ancestors, albeit with low genetic variability and abiotic stress tolerance. Likewise, a complete restructuring of plant metabolic timekeeping probably occurred during crop domestication. Here, we highlight that contrasting timings among organs in wild relatives of crops allowed them to recognize environmental adversities faster. We further propose that connections among biological clocks, which were established during plant domestication, may represent a fundamental source of genetic variation to improve crop resilience and yield.     

Cassava biology and physiology

Cassava or manioc (Manihot esculenta Crantz), a perennial shrub of the New World, currently is the sixth world food crop for more than 500 million people in tropical and sub-tropical Africa, Asia and Latin America. It is cultivated mainly by resource-limited small farmers for its starchy roots, which are used as human food either fresh when low in cyanogens or in many processed forms and products, mostly starch, flour, and for animal feed. Because of its inherent tolerance to stressful environments, where other food crops would fail, it is often considered a food-security source against famine, requiring minimal care. Under optimal environmental conditions, it compares favorably in production of energy with most other major staple food crops due to its high yield potential. Recent research at the Centro Internacional de Agricultura Tropical (CIAT) in Colombia has demonstrated the ability of cassava to assimilate carbon at very high rates under high levels of humidity, temperature and solar radiation, which correlates with productivity across all environments whether dry or humid. When grown on very poor soils under prolonged drought for more than 6 months, the crop reduce both its leaf canopy and transpiration water loss, but its attached leaves remain photosynthetically active, though at greatly reduced rates. The main physiological mechanism underlying such a remarkable tolerance to drought was rapid stomatal closure under both atmospheric and edaphic water stress, protecting the leaf against dehydration while the plant depletes available soil water slowly during long dry periods. This drought tolerance mechanism leads to high crop water use efficiency values. Although the cassava fine root system is sparse, compared to other crops, it can penetrate below 2 m soil, thus enabling the crop to exploit deep water if available. Leaves of cassava and wildManihotpossess elevated activities of the C₄ enzyme PEP carboxylase but lack the leaf Kranz anatomy typical of C₄ species, pointing to the need for further research on cultivated and wild Manihot to further improve its photosynthetic potential and yield, particularly under stressful environments. Moreover, a wide range in values of K _m (CO₂) for the C₃ photosynthetic enzyme Rubisco was found among cassava cultivars indicating the possibility of selection for higher affinity to CO₂, and consequently higher leaf photosynthesis. Several plant traits that may be of value in crop breeding and improvement have been identified, such as an extensive fine root system, long leaf life, strong root sink and high leaf photosynthesis. Selection of parental materials for tolerance to drought and infertile soils under representative field conditions have resulted in developing improved cultivars that have high yields in favorable environments while producing reasonable and stable yields under stress.     

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.     

Cereal flag leaf adaptations for grain yield under drought: knowledge status and gaps

Selection for drought-tolerant cereal varieties has successfully moved to screening for grain yield under stress. Grain yield is the culmination of the process of grain filling, which in turn is closely linked to flag leaf functionalities. For grain filling to occur under drought, either a relatively uncompromised or a favorably reprogrammed functioning of the flag leaf is required. However, knowledge is limited on how effectively flag leaves can function under stress conditions or what adaptations could allow such functioning. The information on rice flag leaf function and/or adaptation under drought is critically limited, while rice continues to be the crop with the highest potential to alleviate hunger and poverty. In fact, other cereal crops are equally important in maintaining regional food baskets and these too suffer intermittently from different intensities and kinds of drought. Patchy information is available on the morpho-anatomical, physiological and biochemical aspects of flag leaves under drought; even this is dispersed within different cereals, with studies predominantly on wheat. Hence, a reasonable understanding of the function of flag leaf under drought is lacking for any cereal. Importantly, very few reports exist on the molecular and mechanistic understanding of any known adaptations of flag leaf function under drought. Here we review the existing information on cereal flag leaf function under drought and highlight the need to better understand its characteristics/adaptations, especially at the molecular level. Novel drought-tolerant breeding material generated through selection for yield under stress can be a useful resource to underpin the mechanistic basis of the contribution of flag leaves to such yield. Improved knowledge can then be used for providing dependable markers (morphological, anatomical, physiological, biochemical and/or molecular) for robust flag leaves, leading to efficient and judicious use of resources for screening broader germplasm collections.     

Striga infestation of cereal crops - an unsolved problem in resource limited agriculture

The parasitic weed Striga causes devastating losses in cereal yields in sub-Saharan Africa. The parasite lifecycle is intimately linked with its host via a complex interchange of signals. Understanding the molecular basis of these interactions and of host resistance to Striga is essential for the identification of genes for improving crop yield via biotechnological or marker assisted breeding strategies. Cloning and sequencing of ESTs from the 'model' parasite Triphysaria versicolor is facilitating the identification of parasitism genes. The identification of resistance to Striga in sorghum and rice germplasm is allowing molecular dissection of these traits using genomic platforms and quantitative trait loci (QTL) analysis. QTL underlying different resistance phenotypes have been identified and the use of advanced backcross populations is allowing the exploitation of sources of resistance in wild relatives of cereals.     

Prospects for utilising plant-adaptive mechanisms to improve wheat and other crops in drought- and salinity-prone environments

Breeding for adaptation to abiotic stress is extremely challenging due to the complexity of the target environments as well as that of the stress‐adaptive mechanisms adopted by plants. While many traits have been reported in the literature, these must be considered with respect to the type of environment for which a cultivar is targeted. In theory, stress‐adaptive traits can be divided into groups whose genes and/or physiological effects are likely to be relatively independent such that when parents with contrasting traits are crossed, adaptive genes will be pyramided. Currently the following groups of candidate traits are being considered for drought adaptation in wheat: traits relating to: (i) pre‐anthesis growth, (ii) water extraction, (iii) water use efficiency, (iv) photo‐protection. A number of mechanisms relating to root function have potential to ameliorate drought stress. Hydraulic redistribution (HR) of water by roots of dryland shrubs enables even relatively small amounts of rainwater to be moved down into the soil profile actively by the root system before it evaporates from the soil surface. Another example is the symbiotic relationship of plants with mycorrhizal fungi that produce a glycoprotein that has a positive effect on soil structure and moisture characteristics. From an agronomic point of view, crop water use efficiency can be increased by exploiting the stress‐adaptive mechanism whereby leaves reduce transpiration rate in response to a chemical root signal in response to drying soil. While there is limited genetic diversity for adaptation to salinity in wheat, tolerance has been found in the ancestral genomes of polyploid wheat and their relatives associated with sodium exclusion into the xylem. Wide crossing techniques such as production of synthetic hexaploids are being exploited to tap into this source of genetic diversity. Looking further into the future, progress is being made into understanding the regulatory mechanisms that are expressed under abiotic stress to maintain cellular homeostasis, as well as in the ability to genetically transform crop plants with genes from alien species.     

北方冬麦区小麦抗旱种质资源遗传多样性分析

遗传多样性分析对于作物资源评价和利用具有重要的意义。本研究以我国北方冬麦区136份小麦抗旱种质资源为材料,分析10个农艺性状及其耐旱指数的相关性,以及抗旱种质的遗传多样性。结果表明:在雨养和灌溉条件下,穗叶距的变异系数最高,分别为42.1%和37.2%,单穗总小穗数的变异系数最低,为6.4%和5.7%;不同水分条件下,植株稳产性主要受单株穗数、有效小穗数及穗下节长的影响;性状耐旱指数的多样性指数在1.95到2.07之间变化,平均值为2.02;根据性状耐旱指数将供试材料分为7个类群,其中第I、第III类群材料表现为对水分条件不敏感,而第II类群材料更适于在干旱条件下种植。材料之间的抗旱性差异可以作为抗旱育种中亲本选配的依据。     

Functional molecular markers for crop improvement

A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as “foundation for twenty-first century crop improvement”, a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as “the holy grail” of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered.     

Combined Role of ACC Deaminase Producing Bacteria and Biochar on Cereals Productivity under Drought

Most of the cereal crops are widely cultivated to fulfil the humans food requirements. Under changing climate scenario, the intensity of drought stress is continuously increasing that is adversely affecting the growth and yield of cereal crops. Although the cereals can tolerate moderate drought to some extent, but mostly they are susceptible to severe drought stress. Higher biosynthesis of ethylene under drought stress has been reported. Many scientists observed that inoculation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing plant growth promoting rhizobacteria (PGPR) is an efficacious tool to overcome this problem. These PGPR secrete ACC deaminase which cleavage the ACC into the compounds, other than ethylene. Furthermore, secretion of growth hormones also play imperative role in enhancing the growth of the cereals under limited availability of water. In addition, the use of biochar has also been recognized as another effective amendment to grant resistance against drought. Biochar application improves the soil physiochemical attributes i.e., porosity, nutrients retention and water holding capacity which decrease the loss of water and increase its bioavailability. In recent era, the idea of coapplication of ACC deaminase producing PGPR and biochar is becoming popular which might be more efficient to use water under drought stress. The aim of current review is to combine the facts and understanding of this novel idea to grant maximum resistance to crops against drought stress. Some scientists have observed significant improvement in yield of cereal crops by combined use of ACC deaminase producing PGPR and biochar. However, more research is suggested for deep understanding of complex synergistic mechanism of ACC deaminase activity in combination with biochar.     

Characterizing drought stress and trait influence on maize yield under current and future conditions

Global climate change is predicted to increase temperatures, alter geographical patterns of rainfall and increase the frequency of extreme climatic events. Such changes are likely to alter the timing and magnitude of drought stresses experienced by crops. This study used new developments in the classification of crop water stress to first characterize the typology and frequency of drought‐stress patterns experienced by European maize crops and their associated distributions of grain yield, and second determine the influence of the breeding traits anthesis‐silking synchrony, maturity and kernel number on yield in different drought‐stress scenarios, under current and future climates. Under historical conditions, a low‐stress scenario occurred most frequently (ca. 40%), and three other stress types exposing crops to late‐season stresses each occurred in ca. 20% of cases. A key revelation shown was that the four patterns will also be the most dominant stress patterns under 2050 conditions. Future frequencies of low drought stress were reduced by ca. 15%, and those of severe water deficit during grain filling increased from 18% to 25%. Despite this, effects of elevated CO₂ on crop growth moderated detrimental effects of climate change on yield. Increasing anthesis‐silking synchrony had the greatest effect on yield in low drought‐stress seasonal patterns, whereas earlier maturity had the greatest effect in crops exposed to severe early‐terminal drought stress. Segregating drought‐stress patterns into key groups allowed greater insight into the effects of trait perturbation on crop yield under different weather conditions. We demonstrate that for crops exposed to the same drought‐stress pattern, trait perturbation under current climates will have a similar impact on yield as that expected in future, even though the frequencies of severe drought stress will increase in future. These results have important ramifications for breeding of maize and have implications for studies examining genetic and physiological crop responses to environmental stresses.