More Food: Road to Survival

During the Green Revolution both the yield and the global production significantly increased. The yield increase was achieved, for some main crops, thanks to the so called high yielding varieties. Higher global production was also due to the increase of the crop production surface which took place especially in some areas of the planet. In the current scenario of rapid human population increase, with a sharp increase of livestock, the challenge is to achieve efficient, productive, sustainable and resilient land use, while conserving biodiversity and assuring, everywhere, food security inside a framework of sustainable diets. The paper, after a discussion on the meanings of such concepts as yield, yield gap, production and global production describes some of the main issues related to increased intensification of food security and global productivity in the current discussions on the potential of the Green Revolution approach and the agro-ecological paradigm.

One fundamental problem in plant breeding is the relationships between selection and target environments. Selection theory shows that response to selection (genetic gains) depends on this relationship because of genotype x environment interactions. Therefore, response to selection can be increased by making the selection environment as similar as possible to the target environment (decentralized breeding). However, this does not yet guarantee farmers’ acceptance of the new variety, which we argue is a more correct way of measuring plant breeding efficiency than variety release as usually done by public breeding programs. Using selection theory, the chapter shows that the probability that a new variety is accepted by farmers, thus impacting their livelihood, increases by selecting in the target environment (decentralized selection) in collaboration with farmers. Decentralized-participatory plant breeding also increases agrobiodiversity and makes plant breeding more cost-effective. The proclaimed efficiency of private breeding program, which can claim a wide farmers’ adoption, is actually driven by a seed market monopoly, which severely limits farmers’ choice of which seed to buy. However, the weak point of decentralized-participatory plant breeding is the unreliability and unpredictability of Institutional participation. Evolutionary-participatory plant breeding may overcome the limitations of participatory plant breeding, because farmers can handle evolutionary populations independently from Institution, yet without excluding them from participating. Because in evolutionary-participatory plant breeding the unit of selection becomes the individual plant rather than a plot, a much higher selection intensity is possible, thus increasing even further the efficiency.

To respond to the contemporary increasing demand for food, feed, and feedstocks for bioenergy and bio-factory applications, there is an urgent need to improve agricultural plant production and quality-related features. Genetics and plant breeding are powerful strategies for increasing crop productivity. The objectives of this chapter are devoted to summarize i) historical developments of applied plant genetics or plant breeding, ii) fundamental principles affecting the current methods of molecular plant breeding, and iii) key factors that will affect the use of molecular breeding in crop improvement procedures. Additionally, the chapter takes a close look at the current exploitation of molecular plant breeding for the discovery of genes and their functions. These topics would disclose new perspectives for crucial plant biology research that will be beneficial to ensure food security to the rapidly growing world population and to sustainable agricultural systems. Moreover, they would open new doors to improve feedstocks to sustain non-food applications for the synthesis of high-added value products.

It is time to start to take into consideration the role of epigenetics in breeding programs. So far, various authors have reported hereditable gene silencing phenomena generally affecting qualitative traits. Usually the genes involved in these phenomena determine characters which can easily be scored by visual inspection, such as modifications in the plant architecture and pigment accumulation, or characters like the loss of antibiotic resistance. But we have to take into account that the majority of genes are involved in the determination of quantitative characters, and the phenotypic modifications caused by QTL silencing will result in subtle variations which are difficult to detect. For this reason it would be very hard to find silencing phenomena involving quantitative traits. Therefore, assuming that epigenetics concerns not only the qualitative but also the quantitative traits, this phenomenon must be taken into account in breeding programs. In particular, the transcriptional state of the different epialleles should be considered. This chapter will start by defining what we mean by epigenetics, as numerous definitions are now used, starting from the original definition of Waddington and adapting the definition to the different fields of study. We will then describe the epigenetics marks, before going into more detail of the epigenomic studies on two model plants, arabidopsis and rice. Then we will present data concerning the interaction of epigenetics and the environment and the role of the epigenetic phenomena on crops and in particular, on yield improvement. A brief paragraph on the epigenetic phenomenon called paramutation will conclude the chapter.

Doubling agricultural production will be essential by 2050 to satisfy the demand of food of a constantly growing population, but climate change brings a lot of uncertainty and complexity to this challenge for agriculture. One of the most important changes that must be addressed is the increase in atmospheric [CO2], which has increased from approximately 280 ppm in pre-industrial times to about 400 ppm nowadays and will further increase to values of 470–570 ppm by 2050 depending on the climate scenario (IPCC Synthesis report, Climate Change 2007). Although this increase in [CO2] is expected to have a positive and significant effect on C3 crops production, it is counteracted by the rise in temperature and the higher evaporative demand, with the increased risks for drought and heat likely to be progressive in all regions of our planet. As a matter of fact, the average stimulation of C3 leaf photosynthesis under field conditions at elevated [CO2] has been reported to be only 14% on average across FACE (550–600 ppm in Free Air CO2 Enrichment) experiments, much lower than the expected increase of 38%. Down-regulation of photosynthesis can be ascribe to multiple factors. These include the limited sink strength of the plants and the consequent accumulation of inhibitory photo-assimilates, the “hysterical” behavior of photosynthetic organisms to excess illumination, by either triggering EED (Excess Energy Dissipation) beyond the level effective for photo-protection or retaining a relevant fraction of quenching for extended periods after return to limiting light conditions, and the complex and multi-factorial network that controls CO2 fixation and carbon allocation. Here we describe the genetic constraints that limit yield potential and prevent it from being realized on the farm, in order to improve the understanding of plant responses under elevated [CO2], and provide tentative biotechnological solutions to overcome the crop yield limitations. It is worth noting that the huge improvements in agricultural production gained during the ‘Green Revolution’ were not directly related to manipulation of photosynthesis, therefore its modification remains an unexplored target for crop improvement.

Grain yield in cereals is considered one of the most important traits in the perspective of global food supply. It largely depends on several components including grain size and grain number. Several studies have been conducted to understand the genetic and molecular basis of these two traits. In this article we review the information so far obtained on the mechanisms governing seed size in crop plants particularly in cereals and discuss the potential uses of this information to improve the productivity of seeds in cereal crops.

Embryogenesis, germination and the early phases of seedling growth represent critical phases in the plant life cycle and are probably the most important events in determining the success of an annual plant. In the perspective of a more sustainable agriculture, we aim to achieve a robust seedling phase with improved resistance to abiotic as well as biotic environmental stress. Genetic improvement has forced the developmental pathway of crop plants toward the realization of highly productive species in which resource allocation processes are optimized at the expense of defense processes. In this context the discovery of key factors underlying the developmental process and at the same time playing an important role in the interplay between the young individuals and the environment is crucial for designing future gene manipulation approaches. Among the different aspects affecting seedling development, the two that will be analyzed in this chapter also play an important role in the interplay with the environment. Hormones are endogenous signals governing seedling growth and architecture establishment but at the same time are able to induce plant responses to environmental stress. Wax deposition is required for determining correct embryo and seedling development, and provides, besides that, a protective barrier that plants produce in their early developmental phases to defend themselves from pathogens as well as from variation in environmental abiotic components, such as temperature and water availability. We will explore the genetic, biochemical and physiological factors implicated and highlight the most significant aspects that might be taken into consideration in future breeding programs.

With the human population expected to exceed 9 billion by 2050, food production will need to increase significantly in the coming years. In particular the forecast doubling in cereal demands requires improvement of yields of the top four cereal crops, maize, rice, wheat and barley. This goal is made more challenging by global environmental changes and the connected abiotic and biotic stresses. In this chapter we briefly discuss two different breeding strategies to increase cereal yield: the heterosis approach in maize and the ideotype approach based on knowledge of the genes controlling yield components in rice. We further discuss the importance of crop genetic diversity in connection to studies of the domestication history of maize, rice, wheat and barley. We present examples of how crop genetic resources including landraces and wild relatives have been used in genetic improvement of yield and adaptation to biotic and abiotic stresses. More extensive deployment of such resources to face future challenges is now empowered by new genomic tools enabling efficient exploration of genetic variability and innovative approaches to direct collection and conservation of genetic resources for food and agriculture.

Domestication is the process through which a wild plant becomes a crop. The process is the result of the selection, either deliberate or as a byproduct of agricultural practices, of characteristics favorable to human beings. The sum of such characteristics is usually described as the ‘domestication syndrome’ because the types of traits selected are often shared among many different species. The most commonly selected traits are loss of seed dispersal, reduced seed dormancy, changes in growth habit, flowering time, and gigantism, all of which have an impact on morphology, reproductive strategies and, most importantly, production (yield and harvest index). Depending on the plant and its use, other traits could be selected, such as reduction or loss of toxic compounds, winter hardiness, nutritional quality, etc. Most domestication took place in ancient times, but there are a few examples of recent and accelerated domestication, for instance sugar beet. It is now possible to achieve the domestication of new species, based on the deliberate induction and combination of traits, using a set of approaches: classical plant breeding via hybridization and selection (including wide area crosses, hybrid seeds and plant cell culture), coupled with molecular tools such as Marker Assisted Selection, transgenesis, and site directed mutagenesis. Examples of interesting traits as well as candidate crops are discussed. Thus, we have the means to repeat the achievements of the early domestication wave and do even better, but this requires drastic changes in international and national regulations impacting on plant biotechnology and novel breeding techniques.

Most cropping environments worldwide are suboptimal for plant growth and reproduction. Unfavorable environmental conditions prevent crops from attaining their full yield potential. Abiotic stresses including heat, cold, drought, salinity, and flooding have a major impact on world agriculture, reducing by 50% the average yield for most crop plants. Among these, water scarcity is the major factor limiting the expansion of agriculture and the single leading cause of crop losses worldwide. With the impact of climate change and demographic growth looming, stress-tolerant varieties and climateresilient crops emerge as relevant and necessary targets to ensure global food security and to improve sustainability in agriculture. Breeding of crops with enhanced stresses tolerance has been particularly compelling, as the related agronomic traits are complex and quantitative in nature, often associated to several loci exhibiting additive effects. Advances in plant genomics have greatly contributed to dissect such complex traits, unraveling the mechanisms underlying the plant response to stress, and opening unprecedented avenues in breeding improved varieties against unfavorable environmental conditions. This chapter will focus on recent successful stories in molecular breeding and biotechnological strategies for crop improvement against abiotic stress, with particular emphasis on drought tolerance.

The long-term target of improving crops resistance to biotic stresses is a familiar goal for breeders. Plants ought to constantly protect themselves versus aggressions from a wide spectrum of organisms that include viruses, bacteria, oomycetes, fungi, insects and other herbivores, and weeds. In this chapter attention will be given to depict a picture on the genetic and molecular mechanisms that plants have promoted to recognize and react to invasion by numerous parasites (pathogens and pests). These topics include non-host resistance, constitutive barriers, and race-specific resistance. The chapter also examines current progresses in clarifying the structure and molecular devices developed by plants to neutralize pathogen and pest aggressions. Moreover, it takes a look with aspects experienced in breeding for resistance to relevant biotic stress factors. Major considerations in breeding for resistance to pathogens, insect pests, and weeds, traditional sources of resistance or other possible strategies, such as mutation breeding, genetic manipulations, and molecular strategies to develop crops more resistant to parasites are also explored.

Apomixis is a naturally occurring reproduction mode in flowering plants that results in embryo formation in absence of both meiosis and eggcell fertilization. Apomixis results from the combination of two processes: apomeiosis (unreduced embryosac formation due to diplospory or apospory) and parthenogenesis (development of an embryo without fertilization). Seed-derived progenies of an apomictic plant are genetically identical to the maternal parent, i.e., they are clonal in origin. The impact on agriculture of the introgression of apomixis into sexual crops, will be revolutionary. In fact, apomixis will allow clonal seed production and thus enable efficient and consistent yields of high quality seeds, fruits and vegetables at lower costs. The development of apomixis technology will reduce cost and breeding time also avoiding the complications typical of sexual reproduction (e.g., incompatibility barriers) and vegetative propagation (e.g., viral transfer). Progresses in the search for apomixis genes obtained by several groups could allow the manipulation of apomixis and its transfer to crop species where the apomixis system is not present and to revolutionize modern agriculture. Moreover, when coupled with male-sterility systems, apomictic reproduction (with no need for male contribution) could help in addressing issues related to transgene escape from GM crops to organic or conventional crops, and thereby allow for better coexistence systems.

The steadily increasing world population and the concurrent reduction in cultivated lands are two major threats to food security, especially in the underdeveloped countries. Among the many strategies that can mitigate this situation modern biotechnologies play a central role. Many tools are available to scientists to face the challenges of increased production needs and sustainable agriculture. Among these, genetic modification and molecular breeding appear to be the most promising. Both of these approaches require the combined use of technologies such as genome sequencing, genotyping and phenotyping and large-scale data analysis and mining to determine genes and functions amenable to manipulation in the target species. Molecular markers, used in both target gene studies and assisted breeding, represent a powerful tool. This chapter deals with their nature and applications, and also describes some case studies where their use in marker-assisted selection has positively affected some target crop species.

By genetic engineering, one or a few genes are typically introduced into plants, so major direct improvements on complex quantitative traits such as yield are not easily realized. However, yield can be, and has been indirectly increased by reducing the gap between potential and actual crop yield, introducing resistance to diseases, pests, abiotic stresses, or herbicides, alone or combined. New traits are appearing on the market and many others are in the pipeline, which promise to contribute to global food production, such as tolerance to drought, to acid or saline soil, and nutrient use efficiency. The possibility to boost the photosynthetic potential by genetic engineering is also attractive. In this chapter, after an brief presentation of plant engineering techniques, I provide an overview of the actual contribution and potentialities of genetic engineering for enhancing crop yield.

Next generation sequencing (NGS) refers to a set of technologies based on massive parallel sequencing. NGS technologies can be included in three main groups: sequencing by synthesis, by ligation, and single-molecule sequencing. NGS technologies are improving at a fast pace and the cost of sequencing per base is decreasing, thus allowing to use NGS to approach a variety of biological questions as impossible before. In plants, tools based on genome decoding, building on NGS, contribute to increase the rate of genetic gain during selection and the precision when choosing superior genotypes. The tools used to facilitate the process leading to genomes drafts is described. The chapter also presents new methods, such as genomic selection or genome-wide association mapping, which are based on NGS to disclose an unprecedented amount of genetic variability made available to plant breeding. In addition, the use of NGS to decode the epigenome and the transcriptome is reported, as well as its power, when combined with appropriate genetic designs, to map and clone quantitative trait loci. It is out of scope of this review to provide a comprehensive repertory of sequencing efforts and techniques that are rapidly evolving and quickly becoming obsolete. The paper, moreover, does not provide a comprehensive list of all the too numerous experiments conducted in the field, but rather it describes rationales and examples of possible applications of plant genome sequencing.

The possibility to feed an increasing world population will largely depend on the capacity to increase yield and the nutritional value of crops. Breeding has played a pivotal role so far but more is to be done to meet the challenging objective of feeding 9 billion people by 2050. Applied plant genetics is facing the dawn of a new era, in which novel genome editing technologies are opening unexpected horizons in basic and applied research. The study of DNA nucleases that can be engineered to land on specific loci of the DNA and alter its sequence is providing incredible tools for plant geneticists. This Chapter will describe genome editing technologies and the molecular bases that govern their function. Application to plant species is recent but advancing fast. Several traits of interest have already been successfully introduced or modified in crops and the first applications are starting to leave the lab and enter the path leading to commercial approval. This process is raising issues related to the regulation of genome-edited crops that governments all over the world will soon be called to rule.

Small grain cereals (here including durum wheat, bread wheat, barley and oats) have been crucial to the development of mankind providing a regular staple source of food compounds – carbohydrates, proteins, fat and secondary metabolites – since their domestication 10,000 years ago. Historically, genetic studies have their foundations in Mendelian mutants, characterized by altered physiology and/or morphology. In this regard there are examples of morphological mutations described in the past for which the gene/genes responsible have been recently cloned, characterized and used. An example is the Rht-B1b gene that controls plant height in wheat, which induces semidwarf plants due to the effect of a single nucleotide mutation capable of converting the majority of sugar into grain starch. With this model the source-sink relationship has been studied in depth and new varieties based on the concept of “Improved Harvest Index” have been released with an impressive grain yield enhancement in a wide range of environments. The question is: “Can we produce and supply sufficient food in the next 40 years without consuming more land?” On the basis of modern plant science, the answer is positive. Selection is specifically directed to create highly tolerant and/or resistant genotypes to increase the “High Yield Potential and Stability of Yield” and to reduce the gap between high yield potential and the actual yield also in very poor small farms (low or zero input). In fact the interaction between private and public pre-breeding-/breeding programmes, allowing the introduction of modern varieties which are very well adapted in fertile as well as in severe stress conditions, represents the modern vision to improve not only grain yield but even the quality of life of all farmers.