The dichotomy of yield and drought resistance: Translation challenges from basic research to crop adaptation to climate change

Global climate change and the increasing human population require crop varieties with higher yield and draught resistance. But meeting both goals is not an easy task for breeders and plant science.

The human population is increasing and so does the demand on food production. The Food and Agriculture Organization of the United Nations (FAO) predicts that in order to meet the global food demands by 2050, the production of staple cereal crops must be doubled at least (FAO, 2017), which means that the current rate of yield improvement needs to increase by at least 40%. Crop breeders are expected to cope with this challenge and come up with novel high‐yield varieties, but the prospects of even maintaining the current rate of yield improvement in light of climate change are unclear. To meet the growing demand for food and increase the yield of staple crops, we need a better understanding of how plants adapt to environmental factors that limit their productivity in terms of turning sunlight and CO₂ into tissues and seeds.

To meet the growing demand for food and increase the yield of staple crops, we need a better understanding of how plants adapt to environmental factors that limit their productivity…

Although nature provides many examples of how plants adapt to harsh environments, these are rarely suitable for use in an agronomic environment, mainly owing to the economics: Any stress‐tolerance variety must also be profitable for the farmer. If a stress response mechanism enables the plant to survive but reduces yield, it will not be economical and, therefore, not be used by farmers. Thus, understanding the key parameters limiting crop yield—plant‒environment interactions, in particular—will help us to cope with the food security challenges presented by changing environmental conditions. In particular, this knowledge helps to inform breeding programmes to more efficiently create and screen for crop varieties to meet the challenges of population growth and climate change. This is not an easy task.Plants are autotrophic; sessile organisms and their productivity completely depends on the temperature, light levels, and the availability of inorganic substances in the soil. Terrestrial plants are further, and primarily, limited by the availability of water, as the absorption of CO₂ from the air requires water: A few hundred water molecules are lost for each CO₂ molecule absorbed. Therefore, understanding the mechanisms that maintain water balance is critical for optimizing crop growth and fruit production in any given environment.     

Molecular approaches for improvement of medicinal and aromatic plants

Medicinal and aromatic plants (MAPs) are important sources for plant secondary metabolites, which are important for human healthcare. Improvement of the yield and quality of these natural plant products through conventional breeding is still a challenge. However, recent advances in plant genomics research has generated knowledge leading to a better understanding of the complex genetics and biochemistry involved in biosynthesis of these plant secondary metabolites. This genomics research also concerned identification and isolation of genes involved in different steps of a number of metabolic pathways. Progress has also been made in the development of functional genomics resources (EST databases and micro-arrays) in several medicinal plant species, which offer new opportunities for improvement of genotypes using perfect markers or genetic transformation. This review article presents an overview of the recent developments and future possibilities in genetics and genomics of MAP species including use of transgenic approach for their improvement.     

Phenomics--technologies to relieve the phenotyping bottleneck

Global agriculture is facing major challenges to ensure global food security, such as the need to breed high-yielding crops adapted to future climates and the identification of dedicated feedstock crops for biofuel production (biofuel feedstocks). Plant phenomics offers a suite of new technologies to accelerate progress in understanding gene function and environmental responses. This will enable breeders to develop new agricultural germplasm to support future agricultural production. In this review we present plant physiology in an 'omics' perspective, review some of the new high-throughput and high-resolution phenotyping tools and discuss their application to plant biology, functional genomics and crop breeding.     

Anther and pollen development:A conserved developmental pathway

Pollen development is a critical step in plant development that is needed for successful breeding and seed formation.Manipulation of male fertility has proved a useful trait for hybrid breeding and increased crop yield.However,although there is a good understanding developing of the molecular mechanisms of anther and pollen anther development in model species,such as Arabidopsis and rice,little is known about the equivalent processes in important crops.Nevertheless the onset of increased genomic information and genetic tools is facilitating translation of information from the models to crops,such as barley and wheat;this will enable increased understanding and manipulation of these pathways for agricultural improvement.     

Holoparasitic plant–host interactions and their impact on Mediterranean ecosystems

Although photosynthesis is essential to sustain life on Earth, not all plants use sunlight to synthesize nutrients from carbon dioxide and water. Holoparasitic plants, which are important in agricultural and natural ecosystems, are dependent on other plants for nutrients. Phytohormones are crucial in holoparasitic plant–host interactions, from seed germination to senescence, not only because they act as growth and developmental regulators, but also because of their central role in the regulation of host photosynthesis and source–sink relations between the host and the holoparasitic plant. Here, we compile and discuss current knowledge on the impact and ecophysiology of holoparasitic plants (such as the broomrapes Orobanche sp. and Phelipanche sp.) that infest economically important dicotyledonous crops in Mediterranean agroecosystems (legumes [Fabaceae], sunflowers [Helianthus sp.], or tomato [Solanum lycopersicum] plants). We also highlight the role of holoparasitic plant–host interactions (such as those between Cytinus hypocistis and various shrubs of the genus Cistus) in shaping natural Mediterranean ecosystems. The roles of phytohormones in controlling plant–host interactions, abiotic factors in parasitism, and the biological significance of natural seed banks and how dormancy and germination are regulated, will all be discussed. Holoparasitic plants are unique organisms; improving our understanding of their interaction with hosts as study models will help us to better manage parasitic plants, both in agricultural and natural ecosystems.

Advances

• Mediterranean ecosystems represent unique environments to study holoparasitic plant-host interactions
• Holoparasitic plants cause severe reductions in productivity, but can also exert positive effects on diversity in natural ecosystems
• A bidirectional flux of phytohormones occurs in holoparasitic plant-host interactions
• The establishment of seed banks is essential for the success of both Orobanche and Cytinus infection in Mediterranean ecosystems

     

Multiple models for Rosaceae genomics

The plant family Rosaceae consists of over 100 genera and 3,000 species that include many important fruit, nut, ornamental, and wood crops. Members of this family provide high-value nutritional foods and contribute desirable aesthetic and industrial products. Most rosaceous crops have been enhanced by human intervention through sexual hybridization, asexual propagation, and genetic improvement since ancient times, 4,000 to 5,000 B.C. Modern breeding programs have contributed to the selection and release of numerous cultivars having significant economic impact on the U.S. and world markets. In recent years, the Rosaceae community, both in the United States and internationally, has benefited from newfound organization and collaboration that have hastened progress in developing genetic and genomic resources for representative crops such as apple (Malus spp.), peach (Prunus spp.), and strawberry (Fragaria spp.). These resources, including expressed sequence tags, bacterial artificial chromosome libraries, physical and genetic maps, and molecular markers, combined with genetic transformation protocols and bioinformatics tools, have rendered various rosaceous crops highly amenable to comparative and functional genomics studies. This report serves as a synopsis of the resources and initiatives of the Rosaceae community, recent developments in Rosaceae genomics, and plans to apply newly accumulated knowledge and resources toward breeding and crop improvement.     

Potential for the environmental impact of transgenic crops

In recent years, there has been increasing interest in how changes in agricultural practice associated with the introduction of particular genetically modified (GM) crops might indirectly impact the environment. There is also interest in any effects that might be associated with recombinant and novel combinations of DNA passing into the environment, and the possibility that they may be taken up by microorganisms or other live biological material. From the current state of knowledge, the impact of free DNA of transgenic origin is likely to be negligible compared with the large amount of total free DNA. We can find no compelling scientific arguments to demonstrate that GM crops are innately different from non-GM crops. The kinds of potential impacts of GM crops fall into classes familiar from the cultivation of non-GM crops (e.g., invasiveness, weediness, toxicity, or biodiversity). It is likely, however, that the novelty of some of the products of GM crop improvement will present new challenges and perhaps opportunities to manage particular crops in creative ways.     

Diverse approaches to achieving grain yield in wheat

Artificial selection (domestication and breeding) leaves a strong footprint in plant genomes. Second generation high throughput DNA sequencing technologies make it possible to sequence the gene complement of a plant genome within 3 to 5 months, and the costs of doing so are declining very quickly. This makes it practical to identify genomic regions that have undergone very strong selection. Available reference sequences of important crops such as rice, maize, and sorghum will promote the wide use of re-sequencing strategies in these crops. Marker/trait associations, especially haplotype (or haplotype block) association analyses, will help the precise mapping of important genomic regions and location of favored alleles or haplotypes for breeding. This mini-review examines a genomics approach to defining yield traits in wheat.     

Evidence for the evolution of native plant response to mycorrhizal fungi in post‐agricultural grasslands

Plant–microbe interactions play an important role in structuring plant communities. Arbuscular mycorrhizal fungi (AMF) are particularly important. Nonetheless, increasing anthropogenic disturbance will lead to novel plant–AMF interactions, altering longstanding co‐evolutionary trajectories between plants and their associated AMF. Although emerging work shows that plant–AMF response can evolve over relatively short time scales due to anthropogenic change, little work has evaluated how plant AMF response specificity may evolve due to novel plant–mycorrhizal interactions. Here, we examine changes in plant–AMF interactions in novel grassland systems by comparing the mycorrhizal response of plant populations from unplowed native prairies with populations from post‐agricultural grasslands to inoculation with both native prairie AMF and non‐native novel AMF. Across four plant species, we find support for evolution of differential responses to mycorrhizal inocula types, that is, mycorrhizal response specificity, consistent with expectations of local adaptation, with plants from native populations responding most to native AMF and plants from post‐agricultural populations responding most to non‐native AMF. We also find evidence of evolution of mycorrhizal response in two of the four plant species, as overall responsiveness to AMF changed from native to post‐agricultural populations. Finally, across all four plant species, roots from native prairie populations had lower levels of mycorrhizal colonization than those of post‐agricultural populations. Our results report on one of the first multispecies assessment of local adaptation to AMF. The consistency of the responses in our experiment among four species provides evidence that anthropogenic disturbance may have unintended impacts on native plant species'' association with AMF, causing evolutionary change in the benefit native plant species gain from native symbioses.     

Inducing drought tolerance in plants: Recent advances

Undoubtedly, drought is one of the prime abiotic stresses in the world. Crop yield losses due to drought stress are considerable. Although a variety of approaches have been used to alleviate the problem of drought, plant breeding, either conventional breeding or genetic engineering, seems to be an efficient and economic means of tailoring crops to enable them to grow successfully in drought-prone environments. During the last century, although plant breeders have made ample progress through conventional breeding in developing drought tolerant lines/cultivars of some selected crops, the approach is, in fact, highly time-consuming and labor- and cost-intensive. Alternatively, marker-assisted breeding (MAB) is a more efficient approach, which identifies the usefulness of thousands of genomic regions of a crop under stress conditions, which was, in reality, previously not possible. Quantitative trait loci (QTL) for drought tolerance have been identified for a variety of traits in different crops. With the development of comprehensive molecular linkage maps, marker-assisted selection procedures have led to pyramiding desirable traits to achieve improvements in crop drought tolerance. However, the accuracy and preciseness in QTL identification are problematic. Furthermore, significant genetic × environment interaction, large number of genes encoding yield, and use of wrong mapping populations, have all harmed programs involved in mapping of QTL for high growth and yield under water limited conditions. Under such circumstances, a transgenic approach to the problem seems more convincing and practicable, and it is being pursued vigorously to improve qualitative and quantitative traits including tolerance to biotic and abiotic stresses in different crops. Rapid advance in knowledge on genomics and proteomics will certainly be beneficial to fine-tune the molecular breeding and transformation approaches so as to achieve a significant progress in crop improvement in future. Knowledge of gene regulation and signal transduction to generate drought tolerant crop cultivars/lines has been discussed in the present review. In addition, the advantages and disadvantages as well as future prospects of each breeding approach have also been discussed.     

Genome Elimination: Translating Basic Research into a Future Tool for Plant Breeding

During the course of our history, humankind has been through different periods of agricultural improvement aimed at enhancing our food supply and the performance of food crops. In recent years, it has become apparent that future crop improvement efforts will require new approaches to address the local challenges of farmers while empowering discovery across industry and academia. New plant breeding approaches are needed to meet this challenge to help feed a growing world population. Here I discuss how a basic research discovery is being translated into a potential future tool for plant breeding, and share the story of researcher Simon Chan, who recognized the potential application of this new approach—genome elimination—for the breeding of staple food crops in Africa and South America.

This article is part of the PLOS Biology Collection “The Promise of Plant Translational Research.”

     

Natural genetic variation for improving crop quality

The narrow genetic basis of many crops combined with restrictions on the commercial use of genetically modified plants, has led to a surge of interest in exploring natural biodiversity as a source of novel alleles to improve the productivity, adaptation, quality and nutritional value of crops. Genetic methodologies have been applied to natural variation to improve quality aspects that are associated with the chemical composition of agricultural products. A future challenge in this emerging field is to integrate metabolic, phenotypic and genomic databases to allow a wider view of the plant metabolome and the application of this knowledge within genomics-assisted breeding.     

Antibody-mediated resistance against plant pathogens

Plant diseases have a significant impact on the yield and quality of crops. Many strategies have been developed to combat plant diseases, including the transfer of resistance genes to crops by conventional breeding. However, resistance genes can only be introgressed from sexually-compatible species, so breeders need alternative measures to introduce resistance traits from more distant sources. In this context, genetic engineering provides an opportunity to exploit diverse and novel forms of resistance, e.g. the use of recombinant antibodies targeting plant pathogens. Native antibodies, as a part of the vertebrate adaptive immune system, can bind to foreign antigens and eliminate them from the body. The ectopic expression of antibodies in plants can also interfere with pathogen activity to confer disease resistance. With sufficient knowledge of the pathogen life cycle, it is possible to counter any disease by designing expression constructs so that pathogen-specific antibodies accumulate at high levels in appropriate sub-cellular compartments. Although first developed to tackle plant viruses and still used predominantly for this purpose, antibodies have been targeted against a diverse range of pathogens as well as proteins involved in plant–pathogen interactions. Here we comprehensively review the development and implementation of antibody-mediated disease resistance in plants.     

Role of glucosinolates in plant invasiveness

Many plants have been intentionally or accidentally introduced to new habitats where some of them now cause major ecological and economic threats to natural and agricultural ecosystems. The potential to become invasive might depend on plant characteristics, as well as on specific interactions with other organisms acting as symbionts or antagonists, including other plants, microbes, herbivores, or pollinators. The invasion potential furthermore depends on abiotic conditions in the habitat. Several species of the Brassicaceae, well known for their glucosinolate–myrosinase defence system, are invasive species. Various factors are reviewed here that might explain why these species were so successful in colonising new areas. Specific emphasis is laid on the role of glucosinolates and their hydrolysis products in the invasion potential. This particular defence system is involved specifically in plant–plant, plant–microbe and plant–insect interactions. Most research has been done on the mechanisms underlying invasion success of Alliaria petiolata and Brassica spp., followed by Bunias orientalis and Lepidium draba. Some examples are also given for plants that are not necessarily considered as invasives, but which were well investigated with respect to their interference potential with their biotic environment. For each species, most likely a combination of different plant characteristics enhanced the competitive abilities and led to diverse invasive phenotypes.     

Plant genomics in Africa: present and prospects

Plants are the world’s most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population’s increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving next-generation sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine.     

Gametic embryogenesis and haploid technology as valuable support to plant breeding

Plant breeding is focused on continuously increasing crop production to meet the needs of an ever-growing world population, improving food quality to ensure a long and healthy life and address the problems of global warming and environment pollution, together with the challenges of developing novel sources of biofuels. The breeders’ search for novel genetic combinations, with which to select plants with improved traits to satisfy both farmers and consumers, is endless. About half of the dramatic increase in crop yield obtained in the second half of the last century has been achieved thanks to the results of genetic improvement, while the residual advance has been due to the enhanced management techniques (pest and disease control, fertilization, and irrigation). Biotechnologies provide powerful tools for plant breeding, and among these ones, tissue culture, particularly haploid and doubled haploid technology, can effectively help to select superior plants. In fact, haploids (Hs), which are plants with gametophytic chromosome number, and doubled haploids (DHs), which are haploids that have undergone chromosome duplication, represent a particularly attractive biotechnological method to accelerate plant breeding. Currently, haploid technology, making possible through gametic embryogenesis the single-step development of complete homozygous lines from heterozygous parents, has already had a huge impact on agricultural systems of many agronomically important crops, representing an integral part in their improvement programmes. The aim of this review was to provide some background, recent advances, and future prospective on the employment of haploid technology through gametic embryogenesis as a powerful tool to support plant breeding.     

Progress and Challenges in Agricultural Applications of Arbuscular Mycorrhizal Fungi

Arbuscular mycorrhiza is a widespread interaction between plant roots and mutualistic fungi that both promotes plant mineral nutrition and supports stability in many natural ecosystems. Given the demand in current agriculture for these ecosystem services, it appears desirable to further integrate this interaction in current management schemes. While two different approaches can be identified in this regard, a number of problems have limited the agricultural application of mycorrhiza to date. In this review, the sensitivity of arbuscular mycorrhizal fungi to certain agricultural management methods, the functional variability of arbuscular mycorrhizal fungi, and the variability of plant responsiveness will be discussed in particular. In addition we will focus on recent advances in the study of mycorrhiza in natural ecosystems, and illustrate how such knowledge might be used to further the integration of arbuscular mycorrhizal fungi in agricultural regimes, and so increase the sustainability and robustness of current practice.     

Transgenic Populus Trees for Forest Products,Bioenergy, and Functional Genomics

Species within the genus Populus are among the fastest growing trees in regions with a temperate climate. Not only are they an integral component of ecosystems, but they are also grown commercially for fuel, fiber, and forest products in rural areas of the world. In the late 1970s, they were designated as a bioenergy crop by the U.S. Department of Energy, as a result of research following the oil embargo. Populus species also serve as model trees for plant molecular biology research. In this article, we will review recent progress in the genetic improvement of Populus, considering both classical breeding and genetic engineering for bioenergy, as well as in using transgenics to elucidate gene functionality. A perspective for future improvement of Populus via functional genomics will also be presented.     

Molecular Genetics and Developmental Physiology: Implications for Designing Better Forest Crops

Current tree biology related to tree genetics and breeding has two important developments that have not well been integrated in the literature. The first is the physiological and biochemical dissection of plant yield, whereas the second is the genetic mapping based on molecular markers, such as RFLPs, RAPDs, AFLPs, and microsatellites. Genetic mapping has revolutionized traditional quantitative genetic analysis by which the genetic variation of a character is described in terms of its mean and (co)variance without the knowledge of the underlying genes. By integrating physiological and developmental studies of yield traits, genetic mapping can provide a unique means for detecting key QTL that play important roles in affecting tree growth and metabolism. The incorporation of these QTL into commercial populations through gene transformation or marker-assisted selection will move current breeding programs strictly based on an empirism to an approach that is mechanistically oriented. In this review, we discuss how plant physiology and development are merged with genetic mapping to formulate the strategy of molecular breeding in which superior forest crops are selected at the gene level. It is anticipated that this novel breeding strategy can potentially provide major breakthroughs for tree breeding.