Groundnut is an important nutrient-dense crop grown in over 100 countries. Breeding for improved varieties is critical for increasing yields and enhancing quality. This chapter describes the genetic resources of groundnut and their potential for mining desirable traits, potential breeding targets and ways to maximise groundnut oil quantity and quality. The chapter provides a detailed case study of groundnut production in Uganda, and outlines the potential benefits of improved groundnut varieties, including disease resistance, as well as suggesting future directions for groundnut research.

Cowpea is an important source of nutritious food and fodder and it is grown as an integral component of various cropping systems in the semi-arid tropics and sub-tropics covering over 65 countries. This chapter describes existing cowpea programs and past challenges, with a particular focus on cowpea breeding at the International Institute for Tropical Agriculture (IITA). The chapter gives an account of the most important examples of progress made to date, including cowpea international trials, and suggests future lines of research for the future.

Abiotic stresses namely drought, salinity, high or low temperature, submergence, nutrient deficiency and so forth have an impact on potato yields. These suboptimal conditions restrict potato plant performance so that the plants do not reach their full genetic potential. This chapter examines different abiotic stress improvement targets in the potato as well as the variety of tools and techniques being developed and used for crop improvement for abiotic stresses. The chapter reviews technological advances to develop abiotic stress resistance in potatoes and tolerant varieties, especially through genetic engineering, and looks ahead to future trends in this area.

The sweetpotato (Ipomoea batatas (L.) Lam.) is the sixth most important food crop on a global scale. While China accounts for about 80% of global production, Nigeria, Uganda, Indonesia and Tanzania are also large producers of sweetpotato. The chapter examines the origin and dispersal of sweetpotato, including archaeological data for the early distribution of the crop, before moving on to considering its general botany. The chapter considers in vitro germplasm storage in sweetpotato genebanks, as well as issues of quality control. The chapter looks at the importance of managing sweetpotato crop wild relatives (CWR) and examines plant quarantine and phytosanitary issues and the status of genebanks under international treaties. The chapter considers a number of specific issues associated with sweetpotato germplasm. Finally, the chapter looks at the application of next-generation sequencing to sweetpotato and its CWR, before looking ahead to future trends in this area.

Crop improvement depends on fast and continuous scientific progress. Recent technological advances have led to remarkable breakthroughs in barley genomics and grain physiology. This chapter aims to highlight the progress in our understanding of barley grain, its functional architecture, and energy metabolism shaped by the constraints of internal hypoxia. The authors provide a current view on the relevance of programmed cell death for grain development, and mechanisms regulating sugar intake. Finally, the authors discuss the outcome of multiscale metabolic modeling studies and how they have advanced our understanding of grain physiology. This provides an insider’s view on the life of the developing barley grain and raises new questions, which remain to be answered by applying the most advanced approaches, including nuclear magnetic resonance imaging.

Barley breeders cross complementary parents for desirable characters and use suitable screening systems to select superior recombinant lines. The advent of molecular markers, especially high throughput genome-wide systems, means that selection for characters, e.g. quality can be conducted indirectly earlier in the breeding cycle. Genome wide association studies (GWAS) have been applied to elite germplasm collections to identify the genomic regions that control key characters and hence markers for use in selection. This chapter shows how GWAS has highlighted contrasts between different breeding germplasm groups, revealing where crossing between groups can produce greater advance than continuing to cross within. GWAS can also be used as training populations for genomic selection but will remain a key R&D technology as it provides a route to candidate gene identification and hence to suitable sources of genetic diversity to maintain breeding progress. Integration of multi-environment GWAS with climatic variables is essential to breed for adaptation to climate change.

Understanding the ways in which apples grow and develop is crucial for achieving sustainable apple cultivation, which means a regulated crop of apples that provides as high a yield as possible of desired quality while allowing the development of a good and consistent return bloom and cropping in subsequent years. This chapter examines how apples grow and ripen (basic structure, growth habit and physiology), some of the factors that support or limit growth, why fruit abscise and how growers can manipulate fruit growth and abscission to optimize cropping. Among other topics, the chapter explores in detail seasonal growth patterns, the chemical composition of apples in different seasons, the role of hormones in abscission and seasonal ripening patterns. The chapter suggests ways to model and prevent apple thinning, and suggests future trends for research in this area

The foundations of a productive and healthy orchard are the rootstocks that provide anchorage, water and nutrients essential to the above-ground portions of the trees. Utilization of composite trees has increased the efficiency of breeding productive apple trees by dividing the selection of scion traits and rootstock traits into two genetically (and functionally) different specimens, which are then brought together through grafting. As part of the tree, the rootstock influences many factors in addition to tree size, particularly productivity, fruit quality, pest resistance, stress tolerance and ultimately profitability. Understanding how scion properties are modulated by rootstocks allows targeting of traits that may be selected to improve whole tree performance by improving rootstock performance. This chapter examines apple-breeding methods and explores how rootstocks affect scion traits, before addressing the impact of rootstocks on disease and pest resistance.

This book chapter describes key issues regarding genetic diversity of tomatoes, including taxonomy and mating system. Figures on global ex situ conservation of tomato germplasm are provided and the world’s largest collection in the public domain, held by AVRDC – The World Vegetable Center, is described in some detail. This chapter also deals with the policy framework for the conservation, access and benefit-sharing mechanisms of plant genetic resources (PGR). It describes how the policy framework and stricter phytosanitary requirements affect the exchange and use of PGR. Ways to strengthen sharing of PGR for food and nutrition security and climate change adaptation are discussed.

Tomato (Solanum lycopersicum L.) is an excellent plant model for unravelling physiological processes, fruit quality and shelf-life determinants, such as stress-responsive signalling, pathogenicity and ripening in climacteric fruits. Consumer awareness of tomato as a phytonutrient source of lycopene, β-carotene, flavonoids and vitamin C has intensified tomato research. The genome of inbred tomato Heinz 1706 cultivar has already been deciphered, genetic linkages for fruit quality have been characterized and tomatoes have been genetically engineered to enhance fruit quality and abiotic/biotic stress tolerance. Furthermore, tomato is a model for vaccine production. This chapter shows how genetic dissection using fruit-ripening mutants, new transgenic plants and molecular breeding has created a road map for the further unravelling of the regulation of genes governing fruit quality attributes as well as fundamental metabolic processes. Precision in engineering plant genomes has enabled development of novel tomatoes with marketable traits beneficial to human health.

Tomato fruit quality is a complex trait involving a number of components, including appearance, flavour, aroma and texture. There is a large range of genetic diversity in tomato for fruit quality components. Although a few major mutations may have a huge effect on fruit quality (notably the rin mutation), most of the components have a quantitative inheritance. Several Quantitative Trait Loci (QTL) mapping experiments have been performed, mostly on interspecific progeny. Many loci and QTL have thus been detected, revealing some QTL cluster regions. Tomato is a model plant for fruit development and composition, and knowledge about its physiology is rapidly increasing. This chapter examines the use of QTL to identify and determine favourable sensory characteristics, exploring current technologies and suggesting future trends for research in this area.

As in other crops, the development of molecular tools is allowing significant progress in understanding different aspects of mango biology. This chapter reviews advances made in the use of different molecular tools in mango in the last decades, including biochemical markers and DNA research. The chapter looks ahead to current and future developments in the field, including next-generation sequencing and localization of genes of interest for breeding purposes. The chapter offers suggestions for further reading on the subject.

The availability of true-to-type, pest- and disease-free planting material is fundamental to successful banana cultivation. It ensures that crops will not succumb to pathogens introduced at planting. This chapter examines the key issues in the selection, establishment and management of a field germplasm collection, with a focus on how best to provide a reliable source of quality banana planting stock. The chapter discusses characterisation strategies for variety selection and includes a case study of banana cultivation in Queensland, Australia. The chapter addresses the sourcing of material for the germplasm collection and strategies to ensure freedom from pests and disease. Finally, the chapter suggests future trends in research and offers guidance on where to look for further information on the subject.

Crop models have been instrumental in predicting yields in wide ranges of current and future environmental conditions. However, they encounter problems in representing spatial heterogeneity of a plant stand and the associated plant responses to local conditions, as well as in simulating the effects of specific plant traits, management choices that influence plant architecture and lighting regimes such as those in greenhouses. For such purposes, functional–structural plant (FSP) models have been developed, which simulate individual plants that interact with each other in 3D, with the changes in plant architecture feeding back on the distribution of environmental drivers that make them grow and develop (light, water, nutrients). In this chapter, the authors outline the purposes of FSP models, the components they need to have in order to serve the purposes mentioned above and give an account of recent applications of such models.

Efficient artificial insemination (AI) is essential for future challenges in the pig industry. Core business for AI companies worldwide is diluting semen from high fertile breeding boars, and by that inseminating many sows. Efficient use of AI boars with high genetic merit is important to maximise dissemination of the genetic progress made in the breeding nucleus. An overview of factors affecting the reproductive efficiency of boars is presented. Boar semen is the most important carrier of genetic progress.

Winter wheat is planted in the autumn and must survive the winter months before being harvested the following summer. Winterhardiness is therefore of paramount importance to the survival of the crop. This chapter reviews recent advances in our understanding of the transcriptomic and genetic basis of the wheat plants’ response to low, above-freezing temperatures and to sub-freezing temperatures. We show that wheat plants enact numerous transcriptomic and metabolic networks in response to low temperatures, and that the response is exquisitely tied to the nature of the cold stress, the developmental status of the plant, the part of the plant and the time of day of the onset of low temperature.

The faba bean is an important cool-season food legume crop grown under different cropping systems for dry grain and green pods, animal feed and a green manure worldwide. This chapter presents the major research achievements in producing new varieties of faba bean tolerant of heat, drought and herbicides and resistant to broomrape, disease and high nitrogen fixation. The chapter looks ahead to future trends in research in this area.

Sugarcane is considered one of the most efficient plants on the planet given its capacity to transform solar energy into chemical energy with high carbon fixation rates. It has traditionally been exploited for sucrose production, but has now also gained importance for energy and ethanol production from bagasse and molasses, two major co-products from sugar processing. This chapter provides an overview of the history of sugarcane and the variety of species, as well as a description of the features of the plant. The chapter introduces breeding, agronomic practices in sugarcane and milling. Finally, the chapter examines types of sugarcane cultivated today and looks ahead to future research and development in this area, and provides suggestions for further reading on this subject.

The majority of cultivars in current commercial sugarcane breeding programmes trace back to a few key interspecific hybrids that were developed during the early 1900s. Sugarcane breeders have expressed concerns about the narrow sampling of ancestral clones in modern sugarcane breeding programmes, and this concern has prompted periodic attempts at so-called ‘base-broadening’ programmes. This chapter begins by providing an overview of sugarcane germplasm collections and then describes introgression-related research and breeding efforts focused on the use of Saccharum spontaneum, Erianthus and other species. It emphasizes the difficulties and challenges that need to be overcome in order to achieve successful outcomes from introgression breeding. Finally, a few possible future directions are considered.

Sugarcane breeding has until very recently been based solely on phenotype, and marker-assisted breeding of sugarcane remains in its infancy compared with that of row crops such as maize and soybean. A major reason for this is the complex genetics of sugarcane. This chapter reviews the uses of DNA marker technology in fingerprinting and diversity analysis of sugarcane. This is followed by a review of the development of linkage maps and initial trait/QTL mapping, including the Bru1 locus for resistance to brown rust (Puccinia melanocephala). Finally, the chapter reviews the use of newer next-generation sequencing–based technologies in sugarcane, including genome-wide association analysis and genomic selection.

The physiological quality of seed tubers is very important for the performance of the crop grown from them, and interacts strongly with seed tuber size. Physiological quality consists of two components: dormancy and physiological age. This chapter reviews the conditions which influence both dormancy and physiological age, and the effects of seed quality on various aspects of crop performance. Future research should aim for a reliable, cheap indicator of physiological age that can predict the performance of the crop grown from the seed under different conditions and for different outlets.

Preserving genetic diversity lies at the heart of improvements in breeding and resilience in potato cultivation. This chapter discusses the challenges, opportunities and recent accomplishments of potato gene banks in the areas of acquisition, classification, preservation, evaluation and distribution of genetic stocks and information, as well as offering a legal perspective on access to genetic materials. The chapter reviews routes for acquisition of potato genetic material, together with methods for its classification and preservation. The chapter also discusses the evaluation and enhancement of potato genetic material, before looking at issues of control and assess to minimise problems such as transmission of disease.

Potato is highly heterozygous. In order to maintain productivity, improved potato varieties are therefore developed by inter-mating desired parental lines and selecting superior clones from the progeny. Since potato is vegetatively propagated, any selected genotype can be fixed with all its intra- and inter-locus interactions responsible for phenotypic expression, and multiplied for commercial cultivation if desired. Recent advances in molecular breeding provide opportunities for rapid genetic gain (Slater et al. 2014a). Nevertheless, phenotypic selection remains the common practice in conventional potato-breeding programmes. Nearly all new varieties of potato still emerge from a process free from use of molecular technologies. This chapter reviews the progress and advances made in phenotypic selection techniques of conventional potato breeding. The role of molecular approaches in improving phenotypic selection is also described briefly.

This chapter provides a review of key developments in experimental design in barley breeding. After a brief history to set the scene, the chapter covers the background of experimental design for field trials, highlighting the key principles that are still fundamental for modern comparative experiments, including model-based design. The following section explores the quantification of genetic relationships through either pedigree or molecular marker information. Finally, the chapter presents the principles of multi-phase experiments for testing material both in the field and in the laboratory. Three case studies are included to highlight non-standard experimental designs that should be in the toolkit of every agricultural scientist and which are essential for modern plant breeding programs.

Fruit production of apples is a two-year process, beginning with the transition of a bud from vegetative to a floral state during the summer. The bud differentiates, overwinters and emerges as a flower the following spring. Flowers are then pollinated, fertilized and the fruit grows first by cell division and later by cell enlargement. All of these processes are vital to the development of high-quality fruit. Suboptimal environmental, biological or cultural conditions during any of these stages can reduce both productivity and fruit quality. Here we discuss the biological processes and genetic controls of these developmental stages. We also highlight some of the key environmental effects and how these processes can be manipulated by cultural management.