Breeding for abiotic stresses for sustainable agriculture

Enhanced oxidative stress resistance through activation of a zinc deficiency transcription factor in Brachypodium distachyon

Identification of viable strategies to increase stress resistance of crops will become increasingly important for the goal of global food security as our population increases and our climate changes. Considering that resistance to oxidative stress is oftentimes an indicator of health and longevity in animal systems, characterizing conserved pathways known to increase oxidative stress resistance could prove fruitful for crop improvement strategies. This report argues for the usefulness and practicality of the model organism Brachypodium distachyon for identifying and validating stress resistance factors. Specifically, we focus on a zinc deficiency B. distachyon basic leucine zipper transcription factor, BdbZIP10, and its role in oxidative stress in the model organism B. distachyon. When overexpressed, BdbZIP10 protects plants and callus tissue from oxidative stress insults, most likely through distinct and direct activation of protective oxidative stress genes. Increased oxidative stress resistance and cell viability through the overexpression of BdbZIP10 highlight the utility of investigating conserved stress responses between plant and animal systems.

RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding

RNA interference (RNAi) is a promising gene regulatory approach in functional genomics that has significant impact on crop improvement which permits down-regulation in gene expression with greater precise manner without affecting the expression of other genes. RNAi mechanism is expedited by small molecules of interfering RNA to suppress a gene of interest effectively. RNAi has also been exploited in plants for resistance against pathogens, insect/pest, nematodes, and virus that cause significant economic losses. Keeping beside the significance in the genome integrity maintenance as well as growth and development, RNAi induced gene syntheses are vital in plant stress management. Modifying the genes by the interference of small RNAs is one of the ways through which plants react to the environmental stresses. Hence, investigating the role of small RNAs in regulating gene expression assists the researchers to explore the potentiality of small RNAs in abiotic and biotic stress management. This novel approach opens new avenues for crop improvement by developing disease resistant, abiotic or biotic stress tolerant, and high yielding elite varieties.

Transcriptional behavior of EUL-related rice lectins toward important abiotic and biotic stresses

The rice genome encodes several genes for putative carbohydrate-binding proteins belonging to the family of Euonymus related lectins (EULs). This lectin family was discovered recently and evidence shows that the expression of these proteins is subject to multiple environmental stresses. In this study, quantitative reverse transcription PCR (qRT-PCR) was conducted on rice seedlings exposed to various abiotic (150mM NaCl, 100mM mannitol, and 100μM abscisic acid (ABA)) and biotic (Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae) stresses to compare the transcriptional behavior of the EULs and a known stress related lectin Orysata belonging to the family of jacalin-related lectins. All EUL transcripts were strongly up-regulated after ABA and NaCl treatments in the roots whereas the overall expression level was generally lower and more variable in the shoots. Moreover, all abiotic stresses induced Orysata in both tissues except for mannitol treatment which failed to show an effect in the roots. Orysata also strongly accumulated after X. oryzae pv. oryzae infection, as were various D-type EUL lectins. In contrast, some of the EUL proteins, including OrysaEULS3, OrysaEULD1A and OrysaEULD2, as well as Orysata were significantly down-regulated upon M. oryzae attack, suggesting fungal manipulation of these genes. Collectively, our results clearly show that rice expresses multiple carbohydrate-binding proteins in response to a wide variety of abiotic and biotic stress conditions. We hypothesize that the Euonymus related proteins fulfill a prominent role in sensing and responding to multiple environmental cues.

Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network

Gleditsia sinensis is a genus of deciduous tree in the family Caesalpinioideae, native to China, and is of great economic importance. However, despite its economic value, gene sequence information is strongly lacking. In the present study, transcriptome sequencing of G. sinensis was performed resulting in approximately 75.5 million clean reads assembled into 142155 unique transcripts generating 58583 unigenes. The average length of the unigenes was 900 bp, with an N50 of 549 bp. The obtained unigene sequences were then compared to four protein databases to include NCBI nonredundant protein (NRDB), Swiss-prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Cluster of Orthologous Groups (COG). Using BLAST procedure, 31385 unigenes (53.6%) were generated to have functional annotations. Additionally, sequence homologies between identified unigenes and genes of known species in a protein-protein interaction (PPI) network facilitated G. sinensis PPI network construction. Based on this network construction, new stress resistance genes (including cold, drought, and high salinity) were predicted. The present study is the first investigation of genome-wide gene expression in G. sinensis with the results providing a basis for future functional genomic studies relating to this species.

Abiotic stress QTL in lettuce crop-wild hybrids: comparing greenhouse and field experiments

The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives.

Reliability of ion accumulation and growth components for selecting salt tolerant lines in large populations of rice

Ion accumulation and growth under salt stress was studied in two experiments in a rice mapping population derived from parents CO39 and Moroberekan with 4-fold differences in shoot Na+ accumulation. The 120 recombinant inbred lines (RILs) had differences up to 100-fold in Na+. Measurement of 'salt tolerance' (biomass production of the RILs in 100mM NaCl relative to controls) after 42 days showed a 2-fold variation in 'salt tolerance' between parents, with five RILs being more tolerant than the more tolerant parent CO39. The reliability of various traits for selecting salt tolerance in large populations was explored by measuring Na+, K+ and K+/Na+ ratios in leaf blades and sheaths after 7 or 21 days of exposure to 100mM NaCl, and their correlation with various growth components and with leaf injury. The highest correlations were found for Na+ in the leaf blade on day 21 with injury at day 42 in both experiments (r=0.7). Earlier measurements of Na+ or of injury had lower correlations. The most sensitive growth components were tiller number plant-1 and shoot water content (g water g-1 dry weight), and these were correlated significantly with Na+ and, to a lesser extent, with K+/Na+. These studies showed that exposure for at least 42 days may be needed to clearly demonstrate the beneficial effect of the trait for Na+ exclusion on growth under salinity.

Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Food security: the challenge of increasing wheat yield and the importance of not compromising food safety

Current wheat yield and consumption is considered in the context of the historical development of wheat, from early domestication through to modern plant breeding, the Green Revolution and wheat's place as one of the world's most productive and important crops in the 21st Century. The need for further improvement in the yield potential of wheat in order to meet current and impending challenges is discussed, including rising consumption and the demand for grain for fuel as well as food. Research on the complex genetics underlying wheat yield is described, including the identification of quantitative trait loci and individual genes, and the prospects of biotechnology playing a role in wheat improvement in the future are discussed. The challenge of preparing wheat to meet the problems of drought, high temperature and increasing carbon dioxide concentration that are anticipated to come about as a result of climate change is also reviewed. Wheat yield must be increased while not compromising food safety, and the emerging problem of processing contaminants is reviewed, focussing in particular on acrylamide, a contaminant that forms from free asparagine and reducing sugars during high temperature cooking and processing. Wheat breeders are strongly encouraged to consider the contaminant issue when breeding for yield.

Drought tolerance in modern and wild wheat

The genus Triticum includes bread (Triticum aestivum) and durum wheat (Triticum durum) and constitutes a major source for human food consumption. Drought is currently the leading threat on world's food supply, limiting crop yield, and is complicated since drought tolerance is a quantitative trait with a complex phenotype affected by the plant's developmental stage. Drought tolerance is crucial to stabilize and increase food production since domestication has limited the genetic diversity of crops including wild wheat, leading to cultivated species, adapted to artificial environments, and lost tolerance to drought stress. Improvement for drought tolerance can be achieved by the introduction of drought-grelated genes and QTLs to modern wheat cultivars. Therefore, identification of candidate molecules or loci involved in drought tolerance is necessary, which is undertaken by "omics" studies and QTL mapping. In this sense, wild counterparts of modern varieties, specifically wild emmer wheat (T. dicoccoides), which are highly tolerant to drought, hold a great potential. Prior to their introgression to modern wheat cultivars, drought related candidate genes are first characterized at the molecular level, and their function is confirmed via transgenic studies. After integration of the tolerance loci, specific environment targeted field trials are performed coupled with extensive analysis of morphological and physiological characteristics of developed cultivars, to assess their performance under drought conditions and their possible contributions to yield in certain regions. This paper focuses on recent advances on drought related gene/QTL identification, studies on drought related molecular pathways, and current efforts on improvement of wheat cultivars for drought tolerance.

Repeated evolution of salt-tolerance in grasses

The amount of salt-affected agricultural land is increasing globally, so new crop varieties are needed that can grow in salt-affected soils. Despite concerted effort to develop salt-tolerant cereal crops, few commercially viable salt-tolerant crops have been released. This is puzzling, given the number of naturally salt-tolerant grass species. To better understand why salt-tolerance occurs naturally but is difficult to breed into crop species, we take a novel, biodiversity-based approach to its study, examining the evolutionary lability of salt-tolerance across the grass family. We analyse the phylogenetic distribution of naturally salt-tolerant species on a phylogeny of 2684 grasses, and find that salt-tolerance has evolved over 70 times, in a wide range of grass lineages. These results are confirmed by repeating the analysis at genus level on a phylogeny of over 800 grass genera. While salt-tolerance evolves surprisingly often, we find that its evolution does not often give rise to a large clade of salt-tolerant species. These results suggest that salt-tolerance is an evolutionarily labile trait in grasses.

Dissecting rice polyamine metabolism under controlled long-term drought stress

A selection of 21 rice cultivars (Oryza sativa L. ssp. indica and japonica) was characterized under moderate long-term drought stress by comprehensive physiological analyses and determination of the contents of polyamines and selected metabolites directly related to polyamine metabolism. To investigate the potential regulation of polyamine biosynthesis at the transcriptional level, the expression of 21 genes encoding enzymes involved in these pathways were analyzed by qRT-PCR. Analysis of the genomic loci revealed that 11 of these genes were located in drought-related QTL regions, in agreement with a proposed role of polyamine metabolism in rice drought tolerance. The cultivars differed widely in their drought tolerance and parameters such as biomass and photosynthetic quantum yield were significantly affected by drought treatment. Under optimal irrigation free putrescine was the predominant polyamine followed by free spermidine and spermine. When exposed to drought putrescine levels decreased markedly and spermine became predominant in all cultivars. There were no correlations between polyamine contents and drought tolerance. GC-MS analysis revealed drought-induced changes of the levels of ornithine/arginine (substrate), substrates of polyamine synthesis, proline, product of a competing pathway and GABA, a potential degradation product. Gene expression analysis indicated that ADC-dependent polyamine biosynthesis responded much more strongly to drought than the ODC-dependent pathway. Nevertheless the fold change in transcript abundance of ODC1 under drought stress was linearly correlated with the drought tolerance of the cultivars. Combining metabolite and gene expression data, we propose a model of the coordinate adjustment of polyamine biosynthesis for the accumulation of spermine under drought conditions.

Genomic regions associated with the nitrogen limitation response revealed in a global wheat core collection

Modern wheat (Triticum aestivum L.) varieties in Western Europe have mainly been bred, and selected in conditions where high levels of nitrogen-rich fertilizer are applied. However, high input crop management has greatly increased the risk of nitrates leaching into groundwater with negative impacts on the environment. To investigate wheat nitrogen tolerance characteristics that could be adapted to low input crop management, we supplied 196 accessions of a wheat core collection of old and modern cultivars with high or moderate amounts of nitrogen fertilizer in an experimental network consisting of three sites and 2 years. The main breeding traits were assessed including grain yield and grain protein content. The response to nitrogen level was estimated for grain yield and grain number per m(2) using both the difference and the ratio between performance at the two input levels and the slope of joint regression. A large variability was observed for all the traits studied and the response to nitrogen level. Whole genome association mapping was carried out using 899 molecular markers taking into account the five ancestral group structure of the collection. We identified 54 main regions involving almost all chromosomes that influence yield and its components, plant height, heading date and grain protein concentration. Twenty-three regions, including several genes, spread over 16 chromosomes were involved in the response to nitrogen level. These chromosomal regions may be good candidates to be used in breeding programs to improve the performance of wheat varieties at moderate nitrogen input levels.

Application of selected reaction monitoring mass spectrometry to field-grown crop plants to allow dissection of the molecular mechanisms of abiotic stress tolerance

One major constraint upon the application of molecular crop breeding approaches is the small number of genes linked to agronomically desirable traits through defined biochemical mechanisms. Proteomic investigations of crop plants under abiotic stress treatments have identified many proteins that differ in control versus stress comparisons, however, this broad profiling of cell physiology is poorly suited to ranking the effects and identifying the specific proteins that are causative in agronomically relevant traits. Here we will reason that insights into a protein's function, its biochemical process and links to stress tolerance are more likely to arise through approaches that evaluate these differential abundances of proteins and include varietal comparisons, precise discrimination of protein isoforms, enrichment of functionally related proteins, and integration of proteomic datasets with physiological measurements of both lab and field-grown plants. We will briefly explain how applying the emerging proteomic technology of multiplexed selective reaction monitoring mass spectrometry with its accuracy and throughput can facilitate and enhance these approaches and provide a clear means to rank the growing cohort of stress responsive proteins. We will also highlight the benefit of integrating proteomic analyses with cultivar-specific genetic databases and physiological assessments of cultivar performance in relevant field environments for revealing deeper insights into molecular crop improvement.

Genetic engineering to improve plant performance under drought: physiological evaluation of achievements, limitations, and possibilities

Fully drought-resistant crop plants would be beneficial, but selection breeding has not produced them. Genetic modification of species by introduction of very many genes is claimed, predominantly, to have given drought resistance. This review analyses the physiological responses of genetically modified (GM) plants to water deficits, the mechanisms, and the consequences. The GM literature neglects physiology and is unspecific in definitions, which are considered here, together with methods of assessment and the type of drought resistance resulting. Experiments in soil with cessation of watering demonstrate drought resistance in GM plants as later stress development than in wild-type (WT) plants. This is caused by slower total water loss from the GM plants which have (or may have-morphology is often poorly defined) smaller total leaf area (LA) and/or decreased stomatal conductance (g (s)), associated with thicker laminae (denser mesophyll and smaller cells). Non-linear soil water characteristics result in extreme stress symptoms in WT before GM plants. Then, WT and GM plants are rewatered: faster and better recovery of GM plants is taken to show their greater drought resistance. Mechanisms targeted in genetic modification are then, incorrectly, considered responsible for the drought resistance. However, this is not valid as the initial conditions in WT and GM plants are not comparable. GM plants exhibit a form of 'drought resistance' for which the term 'delayed stress onset' is introduced. Claims that specific alterations to metabolism give drought resistance [for which the term 'constitutive metabolic dehydration tolerance' (CMDT) is suggested] are not critically demonstrated, and experimental tests are suggested. Small LA and g (s) may not decrease productivity in well-watered plants under laboratory conditions but may in the field. Optimization of GM traits to environment has not been analysed critically and is required in field trials, for example of recently released oilseed rape and maize which show 'drought resistance', probably due to delayed stress onset. Current evidence is that GM plants may not be better able to cope with drought than selection-bred cultivars.

Approaches towards nitrogen- and phosphorus-efficient rice

BACKGROUND AND AIMS

Food production has to increase to meet the demand of a growing population. In light of the high energy costs and increasingly scarce resources, future agricultural systems have to be more productive and more efficient in terms of inputs such as fertilizer and water. The development of rice varieties with high yield under low-nutrient conditions has therefore become a breeding priority. The rapid progress made in sequencing and molecular-marker technology is now beginning to change the way breeding is done, providing new opportunities.

SCOPE

Nitrogen (N) and phosphorus (P) are applied to agricultural systems in large quantities and a deficiency of either nutrient leads to yield losses and triggers complex molecular and physiological responses. The underlying genes are now being identified and studied in detail, and an increasing number of quantitative trait loci (QTLs) related to N and P uptake and utilization are being reported. Here, we provide an overview of the different aspects related to N and P in rice production systems, and apply a breeder's perspective on the potential of relevant genes and pathways for breeding applications.

MAIN POINTS

For the development of nutrient-efficient rice, a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very few are actively used in molecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.

Phenotyping for drought tolerance of crops in the genomics era

Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.

Ecophysiological responses to stresses in plants: a general approach

Stress (abiotic and biotic) factors reflect and specify the plant morphology and called as "stress" and have negative effect(s) on growth, development, quality, quantity and can reduce average plant productivity by 65 to 87%, depending on the plants and stage(s) and also give various permanent or temporary damage(s) according to length of exposed period, violence/density, developmental stage, age, etc. Researches have revealed that despite the advanced technology levels the fundamental basis of stress have not been understood comprehensively. Firstly taken response(s) has/have not yet fully understood and secondly any "resistance" or "tolerance level of a variety/species" because of their complex structure(s). But, this point is clear that with the help or assistance of "multi-disciplinary" approaches, it will be able to get promising result(s) in near future. This review focuses some of the ecophysiological responses of plants to biotic and abiotic stresses.

The interaction of plant biotic and abiotic stresses: from genes to the field

Plant responses to different stresses are highly complex and involve changes at the transcriptome, cellular, and physiological levels. Recent evidence shows that plants respond to multiple stresses differently from how they do to individual stresses, activating a specific programme of gene expression relating to the exact environmental conditions encountered. Rather than being additive, the presence of an abiotic stress can have the effect of reducing or enhancing susceptibility to a biotic pest or pathogen, and vice versa. This interaction between biotic and abiotic stresses is orchestrated by hormone signalling pathways that may induce or antagonize one another, in particular that of abscisic acid. Specificity in multiple stress responses is further controlled by a range of molecular mechanisms that act together in a complex regulatory network. Transcription factors, kinase cascades, and reactive oxygen species are key components of this cross-talk, as are heat shock factors and small RNAs. This review aims to characterize the interaction between biotic and abiotic stress responses at a molecular level, focusing on regulatory mechanisms important to both pathways. Identifying master regulators that connect both biotic and abiotic stress response pathways is fundamental in providing opportunities for developing broad-spectrum stress-tolerant crop plants.

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

BACKGROUND

After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency).

RESULTS

Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop.

CONCLUSION

As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.

Amplifying the benefits of agroecology by using the right cultivars

Tropical soils are particularly vulnerable to fertility losses due to their low capacity to retain organic matter and mineral nutrients. This urges the development of new agricultural practices to manage mineral nutrients and organic matter in a more sustainable way while relying less on fertilizer inputs. Two methods pertaining to ecological engineering and agroecology have been tested with some success: (1) the addition of biochar to the soil, and (2) the maintenance of higher earthworm densities. However, modern crop varieties have been selected to be adapted to agricultural practices and to the soil conditions they lead to and common cultivars might not be adapted to new practices. Using rice as a model plant, we compared the responsiveness to biochar and earthworms of five rice cultivars with contrasted selection histories. These cultivars had contrasted responsivenesses to earthworms, biochar, and the combination of both. The mean relative increase in grain biomass, among all treatments and cultivars, was 94% and 32%, respectively, with and without fertilization. Choosing the best combination of cultivar and treatment led to a more than fourfold increase in this mean benefit (a 437% and a 353% relative increase in grain biomass, respectively, with and without fertilization). Besides, the more rustic cultivar, a local landrace adapted to diverse and difficult conditions, responded the best to earthworms in terms of total biomass, while a modern common cultivar responded the best in term of grain biomass. This suggests that cultivars could be selected to amplify the benefit of biochar- and earthworm-based practices. Overall, selecting new cultivars interacting more closely with soil organisms and soil heterogeneity could increase agriculture sustainability, fostering the positive feedback loop between soils and plants that has evolved in natural ecosystems.

Regulation of multiple aquaporin genes in Arabidopsis by a pair of recently duplicated DREB transcription factors

Identifying the transcription factors that mediate responses to abiotic stress is of fundamental importance in plant biology, not least because of their potential utility in crop improvement. The recently duplicated genes RAP2.4B and RAP2.4 encode transcription factors belonging to the abiotic stress-associated DREB A-6 clade in Arabidopsis thaliana. Both proteins localise exclusively to nuclei and show similar DRE-element-binding characteristics. Expression analysis of stressed and non-stressed plants revealed partially overlapping expression patterns. Both genes were highly expressed in stems and roots and were differentially induced in response to cold, dehydration and osmotic stress. RAP2.4B, however, was uniquely expressed at a high level in dry seeds and was induced by heat stress, while RAP2.4 was uniquely induced at a high level by salt stress. Microarray-based transcriptional profiling of double knockout and overexpression lines revealed altered expression of genes associated with adaptation to drought stress. Most strikingly, six aquaporin genes, five of which are members of a recently identified co-expression network, were downregulated in the double knockout line and correspondingly upregulated in the overexpression line, suggesting that these DREBs play a role in the regulation of water homeostasis.

Cytokinin-mediated source/sink modifications improve drought tolerance and increase grain yield in rice under water-stress

Drought is the major environmental factor limiting crop productivity worldwide. We hypothesized that it is possible to enhance drought tolerance by delaying stress-induced senescence through the stress-induced synthesis of cytokinins in crop-plants. We generated transgenic rice (Oryza sativa) plants expressing an isopentenyltransferase (IPT) gene driven by P(SARK) , a stress- and maturation-induced promoter. Plants were tested for drought tolerance at two yield-sensitive developmental stages: pre- and post-anthesis. Under both treatments, the transgenic rice plants exhibited delayed response to stress with significantly higher grain yield (GY) when compared to wild-type plants. Gene expression analysis revealed a significant shift in expression of hormone-associated genes in the transgenic plants. During water-stress (WS), P(SARK)::IPT plants displayed increased expression of brassinosteroid-related genes and repression of jasmonate-related genes. Changes in hormone homeostasis were associated with resource(s) mobilization during stress. The transgenic plants displayed differential expression of genes encoding enzymes associated with hormone synthesis and hormone-regulated pathways. These changes and associated hormonal crosstalk resulted in the modification of source/sink relationships and a stronger sink capacity of the P(SARK)::IPT plants during WS. As a result, the transgenic plants had higher GY with improved quality (nutrients and starch content).

Modelling predicts that heat stress, not drought, will increase vulnerability of wheat in Europe

New crop cultivars will be required for a changing climate characterised by increased summer drought and heat stress in Europe. However, the uncertainty in climate predictions poses a challenge to crop scientists and breeders who have limited time and resources and must select the most appropriate traits for improvement. Modelling is a powerful tool to quantify future threats to crops and hence identify targets for improvement. We have used a wheat simulation model combined with local-scale climate scenarios to predict impacts of heat stress and drought on winter wheat in Europe. Despite the lower summer precipitation projected for 2050s across Europe, relative yield losses from drought is predicted to be smaller in the future, because wheat will mature earlier avoiding severe drought. By contrast, the risk of heat stress around flowering will increase, potentially resulting in substantial yield losses for heat sensitive cultivars commonly grown in northern Europe.

Targeting metabolic pathways for genetic engineering abiotic stress-tolerance in crops

Abiotic stress conditions are the major limitations in modern agriculture. Although many genes associated with plant response(s) to abiotic stresses have been indentified and used to generate stress tolerant plants, the success in producing stress-tolerant crops is limited. New technologies are providing opportunities to generate stress tolerant crops. Biotechnological approaches that emphasize the development of transgenic crops under conditions that mimic the field situation and focus on the plant reproductive stage will significantly improve the opportunities of producing stress tolerant crops. Here, we highlight recent advances and discuss the limitations that hinder the fast integration of transgenic crops into agriculture and suggest possible research directions. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

STARTS--a stable root transformation system for rapid functional analyses of proteins of the monocot model plant barley

Large data sets are generated from plants by the various 'omics platforms. Currently, a limiting step in data analysis is the assessment of protein function and its translation into a biological context. The lack of robust high-throughput transformation systems for monocotyledonous plants, to which the vast majority of crop plants belong, is a major restriction and impedes exploitation of novel traits in agriculture. Here we present a stable root transformation system for barley, termed STARTS, that allows assessment of gene function in root tissues within 6 weeks. The system is based on the finding that a callus, produced on root induction medium from the scutellum of the immature embryo, is able to regenerate roots from single transformed cells by concomitant suppression of shoot development. Using Agrobacterium tumefaciens-mediated transfer of genes involved in root development and pathogenesis, we show that those calli regenerate large amounts of uniformly transformed roots for in situ functional analysis of newly expressed proteins.

Genetic analysis of abiotic stress tolerance in crops

Abiotic stress tolerance is complex, but as phenotyping technologies improve, components that contribute to abiotic stress tolerance can be quantified with increasing ease. In parallel with these phenomics advances, genetic approaches with more complex genomes are becoming increasingly tractable as genomic information in non-model crops increases and even whole crop genomes can be re-sequenced. Thus, genetic approaches to elucidating the molecular basis to abiotic stress tolerance in crops are becoming more easily achievable.

Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance

Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzyme-encoding genes. Drought susceptibility of IR64 was attributable to significant down-regulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis/gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant up-regulation of α-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype. Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.

Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: comparing the early molecular response using time-series transcriptomic and metabolomic analyses

BACKGROUND

In this study, we investigated the individual and combinatorial effect of elevated CO2 conditions and salinity stress on the dynamics of both the transcriptional and metabolic physiology of Arabidopsis thaliana liquid hydroponic cultures over the first 30 hours of continuous treatment. Both perturbations are of particular interest in plant and agro-biotechnological applications. Moreover, within the timeframe of this experiment, they are expected to affect plant growth to opposite directions. Thus, a major objective was to investigate whether this expected "divergence" was valid for the individual perturbations and to study how it is manifested under the combined stress at two molecular levels of cellular function, using high-throughput analyses.

RESULTS

We observed that a) high salinity has stronger effect than elevated CO2 at both the transcriptional and metabolic levels, b) the transcriptional responses to the salinity and combined stresses exhibit strong similarity, implying a robust transcriptional machinery acting to the salinity stress independent of the co-occurrence of elevated CO2, c) the combinatorial effect of the two perturbations on the metabolic physiology is milder than of the salinity stress alone. Metabolomic analysis suggested that the beneficial role of elevated CO2 on salt-stressed plants within the timeframe of this study should be attributed to the provided additional resources; these allow the plants to respond to high salinity without having to forfeit other major metabolic functions, and d) 9 h-12 h and 24 h of treatment coincide with significant changes in the metabolic physiology under any of the investigated stresses. Significant differences between the acute and longer term responses were observed at both molecular levels.

CONCLUSIONS

This study contributes large-scale dynamic omic data from two levels of cellular function for a plant system under various stresses. It provides an additional example of the power of integrated omic analyses for the comprehensive study of the molecular physiology of complex biological systems. Moreover, taking into consideration the particular interest of the two investigated perturbations in plant biotechnology, enhanced understanding of the molecular physiology of the plants under these conditions could lead to the design of novel metabolic engineering strategies to increase the resistance of commercial crops to salinity stress.

Genome-wide analysis of thiourea-modulated salinity stress-responsive transcripts in seeds of Brassica juncea: identification of signalling and effector components of stress tolerance

BACKGROUND AND AIMS

Abiotic stresses including salinity are the major constraints to crop production. In this regard, the use of thiourea (TU) in imparting salinity-stress tolerance to Indian mustard (Brassica juncea) has been demonstrated earlier. To gain an insight into the mechanism of TU action, various molecular and biochemical studies were conducted.

METHODS

Microarray analysis was performed in seeds subjected to distilled water (control), 1 m NaCl, 1 m NaCl + 6·5 mm TU and 6·5 mm TU alone for 1 h. Real-time PCR validation of selected genes and biochemical studies were conducted under similar treatments at 1 h and 6 h.

KEY RESULTS

The microarray analysis revealed a differential expression profile of 33 genes in NaCl- and NaCl + TU-treated seeds, most of which are established markers of stress tolerance. The temporal regulation of eight selected genes by real-time PCR indicated their early and co-ordinated induction at 1 h in NaCl + TU only. Besides, NaCl + TU-treated seeds also maintained a higher level of abscisic acid, reduced to oxidized glutathione (GSH : GSSG) ratio and activities of catalase, phenylalanine ammonia lyase and glutathione-S-transferases, as compared with that of NaCl treatment. The addition of LaCl(3) (a specific calcium-channel blocker) restricted the responses of TU both at molecular and biochemical level suggesting the possible involvement of a cytosolic calcium burst in the TU-mediated response. The TU-alone treatment was comparable to that of the control; however, it reduced the expression of some transcription factors and heat-shock proteins presumably due to the stabilization of the corresponding proteins.

CONCLUSIONS

The TU treatment co-ordinately regulates different signalling and effector mechanisms at an early stage to alleviate stress even under a high degree of salinity. This also indicates the potential of TU to be used as an effective bioregulator to impart salinity tolerance under field conditions.

Genetic engineering for modern agriculture: challenges and perspectives

Abiotic stress conditions such as drought, heat, or salinity cause extensive losses to agricultural production worldwide. Progress in generating transgenic crops with enhanced tolerance to abiotic stresses has nevertheless been slow. The complex field environment with its heterogenic conditions, abiotic stress combinations, and global climatic changes are but a few of the challenges facing modern agriculture. A combination of approaches will likely be needed to significantly improve the abiotic stress tolerance of crops in the field. These will include mechanistic understanding and subsequent utilization of stress response and stress acclimation networks, with careful attention to field growth conditions, extensive testing in the laboratory, greenhouse, and the field; the use of innovative approaches that take into consideration the genetic background and physiology of different crops; the use of enzymes and proteins from other organisms; and the integration of QTL mapping and other genetic and breeding tools.

Stress specific correlated responses in fat content, Hsp70 and dopamine levels in Drosophila melanogaster selected for resistance to environmental stress

Studies of adaptation to stressful environments have frequently encountered cross resistance. This has prompted the hypothesis that certain adaptations confer resistance to multiple stressors. Some of the genes and mechanisms conferring stress resistance have been identified, however, the generality and basis of stress adaptation and cross resistance is still unclear. We investigated several physiological traits that have been previously linked to increased stress resistance: Hsp70 expression, fat content and dopamine levels. Additionally, we studied a behavioural trait, locomotor activity, as a proxy for the physiological state of the organisms. Physiology is the mechanistic link between resistance phenotype and underlying genetic background, and provides insights into the background and generality of cross resistance and correlated responses to selection for stress resistance. We assessed the relationship between the measured traits and stress resistance in a set of lines selected for increased resistance to several environmental stressors. We found that, although all physiological traits displayed significant differentiation among selection regimes, none were consistently associated with increased general stress resistance. This demonstrates that directional changes in Hsp70 expression level, dopamine level and fat content occur in response to the specific requirements of the different stress regimes, rather than as a general response to stress.

Identifying target traits and molecular mechanisms for wheat breeding under a changing climate

Global warming is causing changes in temperature at a rate unmatched by any temperature change over the last 50 million years. Crop cultivars have been selected for optimal performance under the current climatic conditions. With global warming, characterized by shifts in weather patterns and increases in frequency and magnitude of extreme weather events, new ideotypes will be required with a different set of physiological traits. Severe pressure has been placed on breeders to produce new crop cultivars for a future, rapidly-changing environment that can only be predicted with a great degree of uncertainty and is not available in the present day for direct experiments or field trials. Mathematical modelling, therefore, in conjunction with crop genetics, represents a powerful tool to assist in the breeding process. In this review, drought and high temperature are considered as key stress factors with a high potential impact on crop yield that are associated with global warming, focusing on their effects on wheat. Modelling techniques are described which can help to quantify future threats to wheat growth under climate change and simple component traits that are amenable to genetic analysis are identified. This approach could be used to support breeding programmes for new wheat cultivars suitable for future environments brought about by the changing climate.

Impacts of climate change on wheat in England and Wales

The frequency and magnitude of extreme weather events are likely to increase with global warming. However, it is not clear how these events might affect agricultural crops and whether yield losses resulting from severe droughts or heat stress will increase in the future. The aim of this paper is to analyse changes in the magnitude and spatial patterns of two impact indices for wheat: the probability of heat stress around flowering and the severity of drought stress. To compute these indices, we used a wheat simulation model combined with high-resolution climate scenarios based on the output from the Hadley Centre regional climate model at 18 sites in England and Wales. Despite higher temperature and lower summer precipitation predicted in the UK for the 2050s, the impact of drought stress on simulated wheat yield is predicted to be smaller than that at present, because wheat will mature earlier in a warmer climate and avoid severe summer drought. However, the probability of heat stress around flowering that might result in considerable yield losses is predicted to increase significantly. Breeding strategies for the future climate might need to focus on wheat varieties tolerant to high temperature rather than to drought.

Agricultural sustainability: concepts, principles and evidence

Concerns about sustainability in agricultural systems centre on the need to develop technologies and practices that do not have adverse effects on environmental goods and services, are accessible to and effective for farmers, and lead to improvements in food productivity. Despite great progress in agricultural productivity in the past half-century, with crop and livestock productivity strongly driven by increased use of fertilizers, irrigation water, agricultural machinery, pesticides and land, it would be over-optimistic to assume that these relationships will remain linear in the future. New approaches are needed that will integrate biological and ecological processes into food production, minimize the use of those non-renewable inputs that cause harm to the environment or to the health of farmers and consumers, make productive use of the knowledge and skills of farmers, so substituting human capital for costly external inputs, and make productive use of people's collective capacities to work together to solve common agricultural and natural resource problems, such as for pest, watershed, irrigation, forest and credit management. These principles help to build important capital assets for agricultural systems: natural; social; human; physical; and financial capital. Improving natural capital is a central aim, and dividends can come from making the best use of the genotypes of crops and animals and the ecological conditions under which they are grown or raised. Agricultural sustainability suggests a focus on both genotype improvements through the full range of modern biological approaches and improved understanding of the benefits of ecological and agronomic management, manipulation and redesign. The ecological management of agroecosystems that addresses energy flows, nutrient cycling, population-regulating mechanisms and system resilience can lead to the redesign of agriculture at a landscape scale. Sustainable agriculture outcomes can be positive for food productivity, reduced pesticide use and carbon balances. Significant challenges, however, remain to develop national and international policies to support the wider emergence of more sustainable forms of agricultural production across both industrialized and developing countries.