Breeding technologies to increase crop production in a changing world

Agricultural biotechnology for crop improvement in a variable climate: hope or hype?

Developing crops that are better adapted to abiotic stresses is important for food production in many parts of the world today. Anticipated changes in climate and its variability, particularly extreme temperatures and changes in rainfall, are expected to make crop improvement even more crucial for food production. Here, we review two key biotechnology approaches, molecular breeding and genetic engineering, and their integration with conventional breeding to develop crops that are more tolerant of abiotic stresses. In addition to a multidisciplinary approach, we also examine some constraints that need to be overcome to realize the full potential of agricultural biotechnology for sustainable crop production to meet the demands of a projected world population of nine billion in 2050.

Functions and application of the AP2/ERF transcription factor family in crop improvement

Plants have acquired sophisticated stress response systems to adapt to changing environments. It is important to understand plants' stress response mechanisms in the effort to improve crop productivity under stressful conditions. The AP2/ERF transcription factors are known to regulate diverse processes of plant development and stress responses. In this study, the molecular characteristics and biological functions of AP2/ERFs in a variety of plant species were analyzed. AP2/ERFs, especially those in DREB and ERF subfamilies, are ideal candidates for crop improvement because their overexpression enhances tolerances to drought, salt, freezing, as well as resistances to multiple diseases in the transgenic plants. The comprehensive analysis of physiological functions is useful in elucidating the biological roles of AP2/ERF family genes in gene interaction, pathway regulation, and defense response under stress environments, which should provide new opportunities for the crop tolerance engineering.

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.

A rice phenolic efflux transporter is essential for solubilizing precipitated apoplasmic iron in the plant stele

Iron deficiency is one of the major agricultural problems, as 30% of the arable land of the world is too alkaline for optimal crop production, rendering plants short of available iron despite its abundance. To take up apoplasmic precipitated iron, plants secrete phenolics such as protocatechuic acid (PCA) and caffeic acid. The molecular pathways and genes of iron uptake strategies are already characterized, whereas the molecular mechanisms of phenolics synthesis and secretion have not been clarified, and no phenolics efflux transporters have been identified in plants yet. Here we describe the identification of a phenolics efflux transporter in rice. We identified a cadmium-accumulating rice mutant in which the amount of PCA and caffeic acid in the xylem sap was dramatically reduced and hence named it phenolics efflux zero 1 (pez1). PEZ1 localized to the plasma membrane and transported PCA when expressed in Xenopus laevis oocytes. PEZ1 localized mainly in the stele of roots. In the roots of pez1, precipitated apoplasmic iron increased. The growth of PEZ1 overexpression lines was severely restricted, and these lines accumulated more iron as a result of the high solubilization of precipitated apoplasmic iron in the stele. We show that PEZ1 is responsible for an increase of PCA concentration in the xylem sap and is essential for the utilization of apoplasmic precipitated iron in the stele.

Strategies for engineering a two-celled C(4) photosynthetic pathway into rice

Every day almost one billion people suffer from chronic hunger, and the situation is expected to deteriorate with a projected population growth to 9 billion worldwide by 2050. In order to provide adequate nutrition into the future, rice yields in Asia need to increase by 60%, a change that may be achieved by introduction of the C(4) photosynthetic cycle into rice. The international C(4) Rice Consortium was founded in order to test the feasibility of installing the C(4) engine into rice. This review provides an update on two of the many approaches employed by the C(4) Rice Consortium: namely, metabolic C(4) engineering and identification of determinants of leaf anatomy by mutant screens. The aim of the metabolic C(4) engineering approach is to generate a two-celled C(4) shuttle in rice by expressing the classical enzymes of the NADP-ME C(4) cycle in a cell-appropriate manner. The aim is also to restrict RuBisCO and glycine decarboxylase expression to the bundle sheath (BS) cells of rice in a C(4)-like fashion by specifically down-regulating their expression in rice mesophyll (M) cells. In addition to the changes in biochemistry, two-celled C(4) species show a convergence in leaf anatomy that include increased vein density and reduced numbers of M cells between veins. By screening rice activation-tagged lines and loss-of-function sorghum mutants we endeavour to identify genes controlling these key traits.

Role of RNA interference in plant improvement

Research to alter crops for their better performance involving modern technology is underway in numerous plants, and achievements in transgenic plants are impacting crop improvements in unparalleled ways. Striking progress has been made using genetic engineering technology over the past two decades in manipulating genes from diverse and exotic sources, and inserting them into crop plants for inducing desirable characteristics. RNA interference (RNAi) has recently been identified as a natural mechanism for regulation of gene expression in all higher organisms from plants to humans and promises greater accuracy and precision to plant improvement. The expression of any gene can be down-regulated in a highly explicit manner exclusive of affecting the expression of any other gene by using RNAi technologies. Additional research in this field has been focused on a number of other areas including microRNAs, hairpin RNA, and promoter methylation. Manipulating new RNAi pathways, which generate small RNA molecules to amend gene expression in crops, can produce new quality traits and having better potentiality of protection against abiotic and biotic stresses. Nutritional improvement, change in morphology, or enhanced secondary metabolite synthesis are some of the other advantages of RNAi technology. In addition to its roles in regulating gene expression, RNAi is also used as a natural defense mechanism against molecular parasites such as jumping genes and viral genetic elements that affect genome stability. Even though much advancement has been made on the field of RNAi over the preceding few years, the full prospective of RNAi for crop improvement remains to be fully realized. The intricacy of RNAi pathway, the molecular machineries, and how it relates to plant development are still to be explained.

Integrated soil-crop system management for food security

China and other rapidly developing economies face the dual challenge of substantially increasing yields of cereal grains while at the same time reducing the very substantial environmental impacts of intensive agriculture. We used a model-driven integrated soil-crop system management approach to develop a maize production system that achieved mean maize yields of 13.0 t ha(-1) on 66 on-farm experimental plots--nearly twice the yield of current farmers' practices--with no increase in N fertilizer use. Such integrated soil-crop system management systems represent a priority for agricultural research and implementation, especially in rapidly growing economies.

The impact of the EU regulatory constraint of transgenic crops on farm income

World population and the need for nutritious food continue to grow. For 14 years farmers from a range of countries across the globe have been accessing transgenic technologies either to reduce crop production costs, increase yield and/or to exploit a range of rotational benefits. In 2009 134 Mha of transgenic crops was grown. The arable area of the EU 27 is approximately 102 Mha; however, only about 0.1 Mha of transgenic crops, mainly maize in Spain, is grown in the EU. This is in part due to limited approvals before the establishment of a moratorium on the cultivation of transgenic crops. In this paper we estimate the revenue foregone by EU farmers, based on the potential hectarages of IR and HT transgenic crops that have been economically successful elsewhere if they were to be grown in areas of the EU where farmers could expect an overall financial benefit. This benefit would accrue primarily from reduced input costs. We estimate that if the areas of transgenic maize, cotton, soya, oil seed rape and sugar beet were to be grown where there is agronomic need or benefit then farmer margins would increase by between €443 and €929 M/year. It is noted that this margin of revenue foregone is likely to increase if the current level of approval and growth remains low, as new transgenic events come to market and are rapidly taken up by farmers in other parts of the world.

Raising yield potential of wheat. I. Overview of a consortium approach and breeding strategies

Theoretical considerations suggest that wheat yield potential could be increased by up to 50% through the genetic improvement of radiation use efficiency (RUE). However, to achieve agronomic impacts, structural and reproductive aspects of the crop must be improved in parallel. A Wheat Yield Consortium (WYC) has been convened that fosters linkage between ongoing research platforms in order to develop a cohesive portfolio of activities that will maximize the probability of impact in farmers' fields. Attempts to increase RUE will focus on improving the performance and regulation of Rubisco, introduction of C(4)-like traits such as CO(2)-concentrating mechanisms, improvement of light interception, and improvement of photosynthesis at the spike and whole canopy levels. For extra photo-assimilates to translate into increased grain yield, reproductive aspects of growth must be tailored to a range of agro-ecosystems to ensure that stable expression of a high harvest index (HI) is achieved. Adequate partitioning among plant organs will be critical to achieve favourable expression of HI, and to ensure that plants with heavier grain have strong enough stems and roots to avoid lodging. Trait-based hybridization strategies will aim to achieve their simultaneous expression in elite agronomic backgrounds, and wide crossing will be employed to augment genetic diversity where needed; for example, to introduce traits for improving RUE from wild species or C(4) crops. Genomic selection approaches will be employed, especially for difficult-to-phenotype traits. Genome-wide selection will be evaluated and is likely to complement crossing of complex but complementary traits by identifying favourable allele combinations among progeny. Products will be delivered to national wheat programmes worldwide via well-established international nursery systems and are expected to make a significant contribution to global food security.

A stress-free walk from Arabidopsis to crops

Global concerns such as food security and climate change have highlighted an urgent need for improved crop yield. Breakthroughs in Arabidopsis research provide fresh application routes to achieve novel crop varieties that can withstand or avoid stresses imposed by a changing growth environment. This review features advances in CBF-stress signalling that expand opportunities to produce super hardy crops that can withstand multiple abiotic stresses. It examines molecular external coincidence mechanisms that avoid abiotic stresses by confining plant growth and reproduction to favourable times of the year. The potential value of mathematical modelling approaches is discussed in relation to improving crop-stress resistance or avoidance, and forecasting crop performance.

Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

BACKGROUND

Arabidopsis thaliana is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (Oryza sativa). To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation.

RESULTS

Organ specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence of cis-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis.

CONCLUSIONS

These results reveal significant divergence between Arabidopsis and rice, in terms of the abiotic stress response and its regulation. Both plants are shown to employ unique combinations of genes to achieve growth and stress responses. Comparison of these networks provides a more rational approach to translational studies that is based on the response observed in these two diverse plant models.

The evolution and future of Earth's nitrogen cycle

Atmospheric reactions and slow geological processes controlled Earth's earliest nitrogen cycle, and by ~2.7 billion years ago, a linked suite of microbial processes evolved to form the modern nitrogen cycle with robust natural feedbacks and controls. Over the past century, however, the development of new agricultural practices to satisfy a growing global demand for food has drastically disrupted the nitrogen cycle. This has led to extensive eutrophication of fresh waters and coastal zones as well as increased inventories of the potent greenhouse gas nitrous oxide (N(2)O). Microbial processes will ultimately restore balance to the nitrogen cycle, but the damage done by humans to the nitrogen economy of the planet will persist for decades, possibly centuries, if active intervention and careful management strategies are not initiated.

More genomic resources for less-studied crops

Many of the crop species considered to be minor on a global scale, yet are important locally for food security in the developing world, have remained less-studied crops. Recent years have witnessed the development of large-scale genomic and genetic resources, including simple sequence repeat, single nucleotide polymorphism and diversity array technology markers, expressed sequence tags or transcript reads, bacterial artificial chromosome libraries, genetic and physical maps, and genetic stocks with rich genetic diversity, such as core reference sets and introgression lines in these crops. These resources have the potential to accelerate gene discovery and initiate molecular breeding in these crops, thereby enhancing crop productivity to ensure food security in developing countries.

High-throughput shoot imaging to study drought responses

Drought is a complex stress which elicits a wide variety of plant responses. As such, genetic studies of drought are particularly difficult. Elucidation of the genetic basis of components contributing to drought tolerance is likely to be more tractable than that of overall drought tolerance. Certain of the traits which contribute to drought tolerance in plants and the high-throughput phenotyping techniques available to measure those traits are described in this paper. On the basis of the dynamic nature of drought, plant development, and the resulting stress response, the focus is on non-destructive imaging techniques which allow a temporal resolution and monitoring of the same plants throughout the experiment. Information on the physiological changes in response to drought over time is vital in order to identify and characterize different drought-tolerance mechanisms. High-throughput imaging provides a valuable new tool which allows the dissection of plant responses to drought into a series of component traits.

Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales

Arabidopsis thaliana is the model plant and is grown worldwide by plant biologists seeking to dissect the molecular underpinning of plant growth and development. Gene copy number variation (CNV) is a common form of genome natural diversity that is currently poorly studied in plants and may have broad implications for model organism research, evolutionary biology, and crop science. Herein, comparative genomic hybridization (CGH) was used to identify and interrogate regions of gene CNV across the A. thaliana genome. A common temperature condition used for growth of A. thaliana in our laboratory and many around the globe is 22 degrees C. The current study sought to test whether A. thaliana, grown under different temperature (16 and 28 degrees C) and stress regimes (salicylic acid spray) for five generations, selecting for fecundity at each generation, displayed any differences in CNV relative to a plant lineage growing under normal conditions. Three siblings from each alternative temperature or stress lineage were also compared with the reference genome (22 degrees C) by CGH to determine repetitive and nonrepetitive CNVs. Findings document exceptional rates of CNV in the genome of A. thaliana over immediate family generational scales. A propensity for duplication and nonrepetitive CNVs was documented in 28 degrees C CGH, which was correlated with the greatest plant stress and infers a potential CNV-environmental interaction. A broad diversity of gene species were observed within CNVs, but transposable elements and biotic stress response genes were notably overrepresented as a proportion of total genes and genes initiating CNVs. Results support a model whereby segmental CNV and the genes encoded within these regions contribute to adaptive capacity of plants through natural genome variation.

Genetic and genomic tools to improve drought tolerance in wheat

Tolerance to drought is a quantitative trait, with a complex phenotype, often confounded by plant phenology. Breeding for drought tolerance is further complicated since several types of abiotic stress, such as high temperatures, high irradiance, and nutrient toxicities or deficiencies can challenge crop plants simultaneously. Although marker-assisted selection is now widely deployed in wheat, it has not contributed significantly to cultivar improvement for adaptation to low-yielding environments and breeding has relied largely on direct phenotypic selection for improved performance in these difficult environments. The limited success of the physiological and molecular breeding approaches now suggests that a careful rethink is needed of our strategies in order to understand better and breed for drought tolerance. A research programme for increasing drought tolerance of wheat should tackle the problem in a multi-disciplinary approach, considering interaction between multiple stresses and plant phenology, and integrating the physiological dissection of drought-tolerance traits and the genetic and genomics tools, such as quantitative trait loci (QTL), microarrays, and transgenic crops. In this paper, recent advances in the genetics and genomics of drought tolerance in wheat and barley are reviewed and used as a base for revisiting approaches to analyse drought tolerance in wheat. A strategy is then described where a specific environment is targeted and appropriate germplasm adapted to the chosen environment is selected, based on extensive definition of the morpho-physiological and molecular mechanisms of tolerance of the parents. This information was used to create structured populations and develop models for QTL analysis and positional cloning.

Improving the use of modelling for projections of climate change impacts on crops and pastures

Projections of climate change impacts on global food supply are largely based on crop and pasture modelling. The consistency of these models with experimental data and their ability to simulate the effects of elevated CO(2) and of increased climate variability has been debated. The effects of high temperatures, of increased climate variability and of several limiting factors which interact with elevated CO(2) such as soil nutrients, pests and weeds are neither fully understood nor well implemented in leading models. Targeted model developments will be required based on experimental data concerning: (i) the role of extreme climatic events, (ii) the interactions between abiotic factors and elevated CO(2), (iii) the genetic variability in plant CO(2) and temperature responses, (iv) the interactions with biotic factors, and (v) the effects on harvest quality. To help make better use of the available knowledge, it is envisioned that future crop and pasture modelling studies will need to use a risk assessment approach by combining an ensemble of greenhouse gas emission (or stabilization) scenarios, of regional climate models and of crop and pasture models, as well as an ensemble of adaptation options concerning both management practices and species/varieties.