Molecular genetics of disease resistance in cereals

AIMS: This Botanical Briefing attempts to summarize what is currently known about the molecular bases of disease resistance in cereal species and suggests future research directions. SCOPE: An increasing number of resistance (R) genes have been isolated from rice, maize, wheat and barley that encode both structurally related and unique proteins. This R protein diversity may be attributable to the different modus operandi employed by pathogen species in some cases, but it is also a consequence of multiple defence strategies being employed against phytopathogens. Mutational analysis of barley has identified additional genes required for activation of an R gene-mediated defence response upon pathogen infection. In some instances very closely related barley R proteins require different proteins for defence activation, demonstrating that, within a single plant species, multiple resistance signalling pathways and different resistance strategies have evolved to confer protection against a single pathogen species. Despite the apparent diversity of cereal resistance mechanisms, some of the additional molecules required for R protein function are conserved amongst cereal and dicotyledonous species and even other eukaryotic species. Thus the derivation of functional homologues and interacting partner proteins from other species is contributing to the understanding of resistance signalling in cereals. The potential and limit of utilizing the rice genome sequence for further R gene isolation from cereal species is also considered, as are the new biotechnological possibilities for disease control arising from R gene isolation. CONCLUSIONS: Molecular analyses in cereals have further highlighted the complexity of plant-pathogen co-evolution and have shown that numerous active and passive defence strategies are employed by plants against phytopathogens. Many advances in understanding the molecular basis of disease resistance in cereals have focused on monogenic resistance traits. Future research targets are likely to include less experimentally tractable, durable polygenic resistances and nonhost resistance mechanisms.     

Induced disease resistance and gene expression in cereals

Disease resistance strategies reduce chemical input into the environment and are therefore powerful approaches to sustainable agriculture. Induced resistance (IR) has emerged as a potential alternative, or a complementary strategy, for crop protection. IR signifies the control of pathogens and pests by prior activation of plant defence pathways. A molecular understanding of IR in cereals, including the most important global crops wheat and rice, has been largely missing. Evidence indicating that central elements of IR pathways are conserved among Di- and Monocotyledoneae has only recently been presented, although their regulation and interaction with other plant pathways may be quite divergent. We present here a synopsis of current molecular knowledge of cereal IR mechanisms.     

How Can We Use Genomics to Improve Cereals with Rice as a Reference Genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.     

Natural variation in priming of basal resistance: from evolutionary origin to agricultural exploitation

Biotic stress has a major impact on the process of natural selection in plants. As plants have evolved under variable environmental conditions, they have acquired a diverse spectrum of defensive strategies against pathogens and herbivores. Genetic variation in the expression of plant defence offers valuable insights into the evolution of these strategies. The 'zigzag' model, which describes an ongoing arms race between inducible plant defences and their suppression by pathogens, is now a commonly accepted model of plant defence evolution. This review explores additional strategies by which plants have evolved to cope with biotic stress under different selective circumstances. Apart from interactions with plant-beneficial micro-organisms that can antagonize pathogens directly, plants have the ability to prime their immune system in response to selected environmental signals. This defence priming offers disease protection that is effective against a broad spectrum of virulent pathogens, as long as the augmented defence reaction is expressed before the invading pathogen has the opportunity to suppress host defences. Furthermore, priming has been shown to be a cost-efficient defence strategy under relatively hostile environmental conditions. Accordingly, it is possible that selected plant varieties have evolved a constitutively primed immune system to adapt to levels of disease pressure. Here, we examine this hypothesis further by evaluating the evidence for natural variation in the responsiveness of basal defence mechanisms, and discuss how this genetic variation can be exploited in breeding programmes to provide sustainable crop protection against pests and diseases.     

The impact of changing the season in which cereals are sown on the diversity of the weed flora in rotational fields in Denmark

1. Surveys have shown that there has been a dramatic decrease in the weed flora of fields under rotational cultivation during the last 30 years. This trend has been particularly noticeable in winter cereals, a crop of increasing importance in the landscape.
2. The weed flora of spring and winter cereals was compared in 19 unsprayed fields during a 5-year study to test the hypothesis that cereal type exerts no effect on the flora or on the absolute and relative abundance of single species.
3. Plant and species densities, and accumulated species richness, were lower in winter than in spring cereals.
4. Floristic similarity was greater among spring cereal fields and between spring and winter cereals within the same fields than among winter cereal fields.
5. Species that occurred with unequal density in spring and winter cereals occurred at higher densities in the spring cereals; these species germinated mainly in the spring. However, for a few species the relative plant abundance was highest in winter cereals; these species were able to germinate both in the spring and autumn.
6. Some species – on the relative scale – occurred indifferently of season of sowing; all but one of these species were able to germinate both in the spring and autumn.
7. Plant species and taxa that are important food resources for arthropod herbivores occurred at greater densities in spring than in winter cereals and, in addition, occurred with the highest relative abundance in spring cereals.
8. Change in land use from spring to winter cereals involves not only an immediate reduction of more than 25% in the density of plants and species, but also a change and increased uncertainty in the composition of the weed flora. These findings may have serious implications for the ecology of wildlife in the agricultural landscape.     

Differential induction of glutathione transferases and glucosyltransferases in wheat, maize and Arabidopsis thaliana by herbicide safeners

By learning lessons from weed science we have adopted three approaches to make plants more effective in phytoremediation: (1) The application of functional genomics to identify key components involved in the detoxification of, or tolerance to, xenobiotics for use in subsequent genetic engineering/breeding programmes. (2) The rational metabolic engineering of plants through the use of forced evolution of protective enzymes, or alternatively transgenesis of detoxification pathways. (3) The use of chemical treatments which protect plants from herbicide injury. In this paper we examine the regulation of the xenome by herbicide safeners, which are chemicals widely used in crop protection due to their ability to enhance herbicide selectivity in cereals. We demonstrate that these chemicals act to enhance two major groups of phase 2 detoxification enzymes, notably the glutathione transferases and glucosyltransferases, in both cereals and the model plant Arabidopsis thaliana, with the safeners acting in a chemical- and species-specific manner. Our results demonstrate that by choosing the right combination of safener and plant it should be possible to enhance the tolerance of diverse plants to a wide range of xenobiotics including pollutants.     

Informal intercropping of legumes with cereals? A re-assessment of clover abundance in ancient Egyptian cereal processing by-product assemblages: archaeobotanical investigations at Khentkawes town,Giza (2300–2100 <Emphasis Type="SmallCaps">bc</Emphasis>)

The possibility that legumes were specifically cultivated as a separate fodder crop in ancient Egypt has been inferred, usually on the basis of abundance of both legume seeds and or dung in charred macro-botanical samples, combined with a lack of wood charcoal; the implication being that a scarcity of wood led to the use of dung as fuel, and that the legumes in the assemblage derive from livestock which had been fed with cultivated fodder. The archaeobotanical remains from excavations at the Old Kingdom ‘Khentkawes town’ (2300–2100 bc) on the Giza plateau in Egypt contained an abundance of legumes, but also much wood charcoal, and preservation of many fragile and ‘green’ seeds and plant parts. This assemblage has led to questioning of the theory of specific fodder cultivation in Pharaonic Egypt. In this article, alternative interpretations of legume-rich assemblages of cereal processing by-products are investigated. Intercropping of legumes with cereals is one of the most widespread and effective methods of improving crop value and security, and fodder/forage quality. Analysis of this assemblage has led to a hypothesis that Trifolium sp. and other ‘weeds’ may well have been viewed as integral plants within ancient Egyptian cereal fields, due to an awareness of the benefits of intercropping legumes with cereals—as opposed to having been specifically cultivated as a monocrop.     

Infection of cereals by cocksfoot mottle and phleum mottle viruses

Cocksfoot mottle (CFMV) and Phleum mottle (PMV) viruses are both transmitted by the Chrystomelid beetles Ouletna melanopa and O. lichenis. Both viruses are readily inoculated into some cereals but only CFMV has ever been found causing a natural infection, in one wheat crop. The apparent absence of these viruses from cereals in the field results from inefficient transmission by the vectors and the existence of symptomless tolerance in cereals to both viruses, especially after tillering. In cereals symptom expression is related to virus concentration, and both may be influenced by light intensity and ambient temperature. O. melanopa, which is potentially the most important vector of the viruses to cereals, moves to winter-sown cereals only when the virus-tolerant growth stage has been reached, and later to spring-sown cereals when they too have commenced tillering. Whereas the spread of these viruses within grass crops is increased by cutting and grazing, cereal crops are neither cut nor commonly grazed.     

Attracting friends to feast on foes: engineering terpene emission to make crop plants more attractive to herbivore enemies

When attacked by herbivorous insects or mites, some plant species call on other arthropods for help. They emit mixtures of volatile compounds, dominated by terpenes, to attract carnivorous arthropods that prey on or parasitise herbivores and so reduce further damage. This fascinating defence strategy offers a new, environmentally friendly approach to crop protection. Using recent advances in the biochemistry and molecular genetics of terpene biosynthesis, it should now be possible to engineer crop plants that release terpenes for attracting herbivore enemies. By introducing or selectively altering the existing rate of terpene emission and composition, plant breeders could enable attacked plants to attract enemies and reduce additional herbivory, without compromising the effectiveness of other modes of defence.     

Genetic enrichment of cereal crops via alien gene transfer: New challenges

Genetic improvement of crops has traditionally been achieved through sexual hybridization between related species, which has resulted in numerous cultivars with high yields and superior agronomic performance. Conventional plant breeding, sometimes combined with classical cytogenetic techniques, continues to be the main method of cereal crop improvement. More recently, through the introduction of new tools of biotechnology, crossing barriers have been overcome, and genes from unrelated sources have become available to be introduced asexually into plants. Cereal crops were initially difficult to genetically engineer, mainly due to their recalcitrance to in vitro regeneration and their resistance to Agrobacterium infection. Systematic screening of cultivars and explant tissues for regeneration potential, development of various DNA delivery methods and optimization of gene expression cassettes have produced transformation protocols for the major cereals, although some elite cultivars still remain recalcitrant to transformation. Most of the transgenic cereals developed for commercial purpose exhibit herbicide and/or insect resistance; traits that are often controlled by a single gene. In recent years, more complex traits, such as dough functionality in wheat and nutritional quality of rice have been improved by the use of biotechnology. The current challenges for genetic engineering of plants will be to understand and control factors causing transgene silencing, instability and rearrangement, which are often seen in transgenic plants and highly undesirable in lines to be used for crop development. Further improvement of current cereal cultivars is expected to benefit greatly from information emerging from the areas of genomics, proteomics and bioinformatics.     

Brachypodium as an emerging model for cereal–pathogen interactions

Background Cereal diseases cause tens of billions of dollars of losses annually and have devastating humanitarian consequences in the developing world. Increased understanding of the molecular basis of cereal host–pathogen interactions should facilitate development of novel resistance strategies. However, achieving this in most cereals can be challenging due to large and complex genomes, long generation times and large plant size, as well as quarantine and intellectual property issues that may constrain the development and use of community resources. Brachypodium distachyon (brachypodium) with its small, diploid and sequenced genome, short generation time, high transformability and rapidly expanding community resources is emerging as a tractable cereal model.Scope Recent research reviewed here has demonstrated that brachypodium is either susceptible or partially susceptible to many of the major cereal pathogens. Thus, the study of brachypodium–pathogen interactions appears to hold great potential to improve understanding of cereal disease resistance, and to guide approaches to enhance this resistance. This paper reviews brachypodium experimental pathosystems for the study of fungal, bacterial and viral cereal pathogens; the current status of the use of brachypodium for functional analysis of cereal disease resistance; and comparative genomic approaches undertaken using brachypodium to assist characterization of cereal resistance genes. Additionally, it explores future prospects for brachypodium as a model to study cereal–pathogen interactions.Conclusions The study of brachypodium–pathogen interactions appears to be a productive strategy for understanding mechanisms of disease resistance in cereal species. Knowledge obtained from this model interaction has strong potential to be exploited for crop improvement.     

The effect of drought and heat stress on reproductive processes in cereals

As the result of intensive research and breeding efforts over the last 20 years, the yield potential and yield quality of cereals have been greatly improved. Nowadays, yield safety has gained more importance because of the forecasted climatic changes. Drought and high temperature are especially considered as key stress factors with high potential impact on crop yield. Yield safety can only be improved if future breeding attempts will be based on the valuable new knowledge acquired on the processes determining plant development and its responses to stress. Plant stress responses are very complex. Interactions between plant structure, function and the environment need to be investigated at various phases of plant development at the organismal, cellular as well as molecular levels in order to obtain a full picture. The results achieved so far in this field indicate that various plant organs, in a definite hierarchy and in interaction with each other, are involved in determining crop yield under stress. Here we attempt to summarize the currently available information on cereal reproduction under drought and heat stress and to give an outlook towards potential strategies to improve yield safety in cereals.     

Dosage reduction to improve the selectivity of deltamethrin between aphids and coccinellids in cereals

The toxicity of the pyrethroid insecticide deltamethrin to a cereal aphid and a coccinellid beetle predator was assessed. Deltamethrin gave effective aphid control in winter wheat at dose-rates of 6.25, 3.13 and 1.56g a.i./ha. The direct exposure of adultCoccinella septempunctata L. (Coleoptera: Coccinellidae) to spray drops was estimated at a range of positions in a cereal crop canopy from volumetric analysis of fluorescent tracer deposits. These measurements were used to calculate exposure to deltamethrin at the three experimental dose-rates. Observations of coccinellid beetle distribution through a cereal crop canopy permitted a realistic range of direct contact doses tobe calculated and the toxic effects of these levels of exposure to be predicted from laboratory dose-response data. Estimated beetle mortalities from direct exposure were 19, 8 and 3% at the three experimental dose-rates.In situbioassays with adultC. septempunctata which exposed beetles continuously to deltamethrin residues on flag leaves, resulted in 100, 94 and 39% mortality respectively at these dose-rates during the 10 days after spray application. Additionalin situ bioassays exposed beetles to deltamethrin residues on flag leaves for 24 h and then transferred surviving beetles to the soil under the cereal crop canopy for a further 9 days. This resulted in 89, 69 and 29% beetle mortality respectively at the three dose-rates. Mortality predictions combining both direct contact and residual exposure were made for the three dose-rates.to determine the maximum impact of summer sprays of deltamethrin on adult coccinellid populations in cereals. These worst case predictions suggested that a reduction in dose-rate by as much as three quarters of the recommended application rate in UK cereals may be necessary to preserve approximately 60% of adultC. septempunctata in the crop over the 10 days after a deltamethrin spray application. The methodology described may be appropriate for estimating selective dose-rates for key enemies in a range of crops.     

Structure and evolution of cereal genomes

The cereal species, of central importance to our diet, began to diverge 50-70 million years ago. For the past few thousand years, these species have undergone largely parallel selection regimes associated with domestication and improvement. The rice genome sequence provides a platform for organizing information about diverse cereals, and together with genetic maps and sequence samples from other cereals is yielding new insights into both the shared and the independent dimensions of cereal evolution. New data and population-based approaches are identifying genes that have been involved in cereal improvement. Reduced-representation sequencing promises to accelerate gene discovery in many large-genome cereals, and to better link the under-explored genomes of 'orphan' cereals with state-of-the-art knowledge.     

Cereal area and nitrogen use efficiency are drivers of future nitrogen fertilizer consumption

At a global scale, cereal yields and fertilizer N consumption have increased in a near-linear fashion during the past 40 years and are highly correlated with one another. However, large differences exist in historical trends of N fertilizer usage and nitrogen use efficiency (NUE) among regions, countries, and crops. The reasons for these differences must be understood to estimate future N fertilizer requirements. Global nitrogen needs will depend on: (i) changes in cropped cereal area and the associated yield increases required to meet increasing cereal demand from population and income growth, and (ii) changes in NUE at the farm level. Our analysis indicates that the anticipated 38% increase in global cereal demand by 2025 can be met by a 30% increase in N use on cereals, provided that the steady decline in cereal harvest area is halted and the yield response to applied N can be increased by 20%. If losses of cereal cropping area continue at the rate of the past 20 years (?0.33% per year) and NUE cannot be increased substantially, a 60% increase in global N use on cereals would be required to meet cereal demand. Interventions to increase NUE and reduce N losses to the environment must be accomplished at the farm-or field-scale through a combination of improved technologies and carefully crafted local policies that contribute to the adoption of improved N management; uniform regional or national directives are unlikey to be effective at both sustaining yield increases and improving NUE. Examples from several countries show that increases in NUE at rates of 1% per year or more can be achieved if adequate investments are made in research and extension. Failure to arrest the decrease in cereal crop area and to improve NUE in the world’s most important agricultural systems will likely cause severe damage to environmental services at local, regional, and global scales due to a large increase in reactive N load in the environment.     

Cereal area and nitrogen use efficiency are drivers of future nitrogen fertilizer consumption

At a global scale, cereal yields and fertilizer N consumption have increased in a near-linear fashion during the past 40 years and are highly correlated with one another. However,large differences exist in historical trends of N fertilizer usage and nitrogen use efficiency (NUE)among regions, countries, and crops. The reasons for these differences must be understood to estimate future N fertilizer requirements. Global nitrogen needs will depend on: (i) changes in cropped cereal area and the associated yield increases required to meet increasing cereal demand from population and income growth, and (ii) changes in NUE at the farm level. Our analysis indicates that the anticipated 38% increase in global cereal demand by 2025 can be met by a 30% increase in N use on cereals, provided that the steady decline in cereal harvest area is halted and the yield response to applied N can be increased by 20%. If losses of cereal cropping area continue at the rate of the past 20 years (-0.33% per year) and NUE cannot be increased substantially, a 60% increase in global N use on cereals would be required to meet cereal demand. Interventions to increase NUE and reduce N losses to the environment must be accomplished at the farm- or field-scale through a combination of improved technologies and carefully crafted local policies that contribute to the adoption of improved N management; uniform regional or national directives are unlikey to be effective at both sustaining yield increases and improving NUE. Examples from several countries show that increases in NUE at rates of 1% per year or more can be achieved if adequate investments are made in research and extension. Failure to arrest the decrease in cereal crop area and to improve NUE in the world's most important agricultural systems will likely cause severe damage to environmental services at local, regional, and global scales due to a large increase in reactive N load in the environment.     

Cereal area and nitrogen use efficiency are drivers of future nitrogen fertilizer consumption

At a global scale, cereal yields and fertilizer N consumption have increased in a near-linear fashion during the past 40 years and are highly correlated with one another. However, large differences exist in historical trends of N fertilizer usage and nitrogen use efficiency (NUE) among regions, countries, and crops. The reasons for these differences must be understood to estimate future N fertilizer requirements. Global nitrogen needs will depend on: (i) changes in cropped cereal area and the associated yield increases required to meet increasing cereal demand from population and income growth, and (ii) changes in NUE at the farm level. Our analysis indicates that the anticipated 38% increase in global cereal demand by 2025 can be met by a 30% increase in N use on cereals, provided that the steady decline in cereal harvest area is halted and the yield response to applied N can be increased by 20%. If losses of cereal cropping area continue at the rate of the past 20 years (-0.33% per year) and NUE cannot be increased substantially, a 60% increase in global N use on cereals would be required to meet cereal demand. Interventions to increase NUE and reduce N losses to the environment must be accomplished at the farm- or field-scale through a combination of improved technologies and carefully crafted local policies that contribute to the adoption of improved N management; uniform regional or national directives are unlikey to be effective at both sustaining yield increases and improving NUE. Examples from several countries show that increases in NUE at rates of 1% per year or more can be achieved if adequate investments are made in research and extension. Failure to arrest the decrease in cereal crop area and to improve NUE in the world's most important agricultural systems will likely cause severe damage to environmental services at local, regional, and global scales due to a large increase in reactive N load in the environment.     

Architectural evolution and its implications for domestication in grasses

BACKGROUND: The cereal crops domesticated from grasses provide a large percentage of the calories consumed by humans. Domestication and breeding in individual cereals has historically occurred in isolation, although this is rapidly changing with comparative genomics of the sequenced or soon-to-be sequenced genomes of rice, sorghum, maize and Brachypodium. Genetic information transferred through genomic comparisons is helping our understanding of genetically less tractable crops such as the hexaploid wheats and polyploid sugarcane, as well as the approx. 10 000 species of wild grasses. In turn, phylogenetic analysis helps put our knowledge of the morphology of cereal crops into an evolutionary context. GRASS ARCHITECTURE: Domestication often involves a change in the pattern and timing of branching, which affects both vegetative and inflorescence architecture, and ultimately yield. Cereal grasses exhibit two main forms of vegetative architecture: the pooid and erhartoid cereals such as wheat and rice have multiple basal tillers, while panicoid cereals such as maize, sorghum and the millets have few tillers or even only a single main stem. These differences are reflected in the differences between the wild species of pooid and some erhartoid grasses, which emphasize basal branching over axillary branching, and the panicoid grasses, where axillary branching is more frequently found. A combination of phylogenetic and genomic analysis is beginning to reveal the similarities and differences between different cereal crops, and relate these to the diversity of wild grasses to which they are related. Recent work on genes controlling branching emphasizes that developmental genetics needs to be viewed in both an evolutionary and ecological framework, if it is to be useful in understanding how morphology evolves. Increasingly, exploring the phylogenetic context of the crop grasses will suggest new ways to identify and create combinations of morphological traits that will best suit our future needs.     

Cereal weeds variation in middle Egypt: Role of crop family in weed composition

Cereals occupies a major part in the diet of humans globally, participating more to our daily protein and calorie intake than any other crop. The present study highlight the weed flora of cereal crops compared to other crops in middle Egypt and their distribution. Ninety-two weed species were recorded in the all studied crops, cereal and other crops; in the studied area belong to 67 genera and 20 families. Egyptian clover; showed the highest numbers of both weed species and genera followed by wheat, on contrast the lowest weed species and genera numbers were recorded associated with Solanaceous crops tomato and pepper. Wheat crops exhibited the highest number of weed species, among cereals, followed by maize crop, while the lowest weed species number was detected in barley crop. Chenopodium murale, Cynodon dactylon, Convolvulus arvensis and Malva parviflora were the most frequent species in winter cereals, while Echinochloa colona, P. oleraceae were the most frequent weeds in summer cereals. Chorological analysis of the recorded weed species showed that cosmopolitan elements showed the highest numbers in total weed flora Differences in weed species compositions were fundamentally influenced by seasonal priority. Based on TWINSPAN and Ward classifications, crop family showed slightly effect as a factor affecting weed composition.