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.

<p>High laying performance and simultaneous high fattening performance in chicken breeding are mutually exclusive due to negative correlations. Currently, roosters from laying lines can only be raised and marketed economically to a very limited extent. Generally, the majority of male offspring are culled immediately after hatching and marketed as animal feed for carnivorous animals. Several methods of in ovo sex determination have been developed to avoid the routine killing of day-old male chicks. Methods such as hyperspectral imaging and analysis of certain components in the allantoic fluid have successfully followed development to practical application in Europe and are already used in commercial hatcheries. Other techniques of in ovo sex determination, e.g. spectroscopic methods, have the potential to end the culling of day-old male chicks. However, to meet industry requirements regarding precision and speed, full automation of the process is required to make these technologies applicable in hatcheries.</p>

<p>This chapter will discuss these two aspects of the hatching phase. First, the hatcher phase will be described from an embryonic point of view, focusing on the developmental and physiological changes during the final days of the incubation process. Second, the hatcher phase will be described from an incubator point of view, discussing the influence of the main environmental conditions – temperature, relative humidity and CO2 concentration – in relation to survival and chick quality at hatch and in later life. This chapter will focus mainly on broiler and layer chickens (Gallus gallus domesticus).</p>

Plant root system architecture (RSA), the spatial configuration of a root system in the soil, is critical for water and nutrient acquisition. Rice generates a root system consisting of seminal, lateral, and crown/adventitious roots, whose growth and development are regulated by plant hormones and can be fine-tuned to meet adverse environmental conditions. A broad range of studies have been carried out in the past to decipher the underlying molecular and genetic mechanisms. This chapter summarizes original and more recent findings on genes and molecules identified so far to be involved in rice root development. It also discusses the cellular organization and function of rice roots, as well as the responses of RSA to the availability of water and nutrients.

In this chapter we review strategies to capture benefits from deeper rooting, taking the example of the semi-arid southern Australian wheat belt. The chapter focusses on the theme of better capturing deep subsoil water with deeper and more effective root systems. The chapter looks at ways of increasing root depth, the role of agronomic techniques as well as genetic improvement methods.

This chapter reviews genetic diversity in barley and its role in improving varieties, including adaptation to abiotic stresses. Sulphur is an essential macronutrient required in plants for normal growth and development. Its deficiency in agricultural soils reduces grain yield and grain quality traits. Studies conducted with barley and wheat varieties demonstrate substantial variations among crops and varieties in their response to application of different levels of sulphur. The chapter looks at factors affecting sulphur nutrition in barley and the potential role of genetic differences in breeding more resilient varieties.

Modelling predicts that temperature and precipitation are the abiotic factors that have the biggest impact on banana production. It is clear that banana needs tropical temperatures and that it responds very early to a reduced soil water content. The stomata of banana plants also respond very sensitively to an increased Vapour Pressure Deficit even when the soil water potential is non-limiting. This sensitivity causes considerable yield losses. This chapter discusses banana physiology in relation to its agro-ecological environment and the phenotyping of traits such as sub-optimal temperature tolerance and water deficit tolerance. A workflow where the biodiversity is phenotyped in a high throughput fashion in a controlled environment and linked to molecular analysis is presented. Once interesting traits are identified, strategies are required to identify potential genetic markers that are correlated to these traits. Methods to identify the genetics behind these traits, such as genome-wide association study (GWAS), associative transcriptomics and proteomics are briefly discussed. The identification of correlations between phenotype and genetic markers will speed up future banana breeding.

Genetic engineering plays a key role in plant functional research and genetic improvement. A novel and powerful gene editing technique, CRISPR/Cas9, which was developed from a type II bacterial immune system, opened up a new era in precision genetic engineering in plants. This technique is based on a non-permanent transgene system and is starting to be adopted for precise gene editing in major cereal crops. It offers tremendous potential to accelerate crop improvement in a way that potentially reduces or eliminates the cumbersome and expensive regulatory processes associated with traditional transgenic crops. This chapter describes the advance of gene editing applied to sorghum, a drought tolerant C4 crop, and a successful strategy of CRISPR/Cas9 mediated gene family editing to improve sorghum digestibility and protein quality. It also discusses future prospects of CRISPR/Cas9 gene editing for sorghum genetic improvement.

Hybrid potato breeding promises to create new cultivars within a few years. This would facilitate the introgression of genes by marker-assisted selection. In addition, hybrid cultivars can be made available as true seeds, free of soil-borne pathogens, quick to multiply and easy to transport and store. Self-incompatibility and inbreeding depression were previously thought to be prohibiting factors for hybrid potato breeding but have recently been overcome: nearly homozygous diploid inbred lines have been generated and the first experimental hybrids have been evaluated in the field. In this chapter, we review the scientific basis for hybrid potato breeding and highlight the features of our strategy for creating a hybrid breeding system in potato including propagation through seed. We discuss the recent progress made towards the development of useful hybrid varieties, and consider how the hybrid potato breeding technology platform will need to be adapted and optimized for different production systems.

Asian countries with a cereal-based cropping system face a tremendous food security challenge to feed their 4.3 billion people. Potato, being a complete food, can be a valid alternative. This chapter describes the selection of germplasm and traits for breeding early-maturing varieties of potato, exploring genetic aspects of earliness and breeding strategy. The chapter looks at early tuber initiation, high dry matter partitioning efficiency and basic factors that need to be taken into account when breeding for earliness in the potato. The chapter suggests breeding strategies for earliness and stress resistance and considers the genetic aspects. The chapter incorporates a detailed case study of developing an early-maturing, moderately late-blight-resistant Kufri Khyati potato variety for Indian plains. Finally, the chapter looks ahead to future research trends in this area.

By reducing the number of seedlings using marker-assisted selection (MAS), field breeders of cassava can allocate their limited phenotyping resources to a smaller number of selection candidates for further phenotypic evaluation of complex traits such as yield and drought tolerance. This chapter describes the strengths and limitations of MAS, the resources that are required, and outlines the practical considerations for its implementation. The chapter also describes the contribution of genome-wide studies (GWAS), summarizes the published quantitative trait loci (QTL) studies in cassava and looks ahead to future research and developments in this area.

For the last two decades, marker-assisted selection has reshaped breeding programmes and facilitated gains from selection. Recent developments in genomic technologies, including the advent of high-throughput DNA sequencing technologies and cost-effective genotyping platforms, are effecting shifts in the prevailing framework of plant breeding towards a more precise utilization of genetic variation for crop improvement. This chapter describes the importance of selection and hybridization in crop improvement. It gives a detailed account of current trends in rice molecular breeding, including QTL mapping and marker-assisted selection, and presents a case study of gene Sub1A to illustrate how these techniques increased breeding efficiency and precision for target traits. Finally, it analyses the emerging tools in genomics-based breeding that promise to increase the efficiency of modern rice breeding towards a more rapid varietal development and release.

This chapter examines three different major strategies designed to break the ‘yield barrier’ so that rice production keeps up with population growth: new ideotype breeding, heterosis and green super rice. The chapter shows that exploring the genetic diversity of wild Oryza species may lead to identification of novel and superior alleles, which may have been ignored during the process of crop domestication. The chapter describes the traits determining rice yield: number of grains per panicle, panicle size and branching, and grain weight. It shows that by deploying a particular gene or gene combinations in the breeding programmes, desired phenotype and yield enhancement of rice can be achieved. Molecular markers for marker-assisted selection processes to pyramid yield-related genes are also discussed in this chapter, which suggests future trends for research to enable a second ‘green revolution’.

Soybean is one of the world’s most widely grown and economically significant crops, having an extensive range of end uses. Understanding soybean growth and physiology is paramount to maximising its productivity and optimising its yield. This chapter highlights recent advances in understanding soybean development, and the genetic factors underpinning the molecular mechanisms that drive it. The main physiological, molecular and bioinformatic approaches used to progress this rapidly growing research area are also outlined. Outcomes that improve the understanding of soybean growth and development could aid in the targeted selection of superior varieties, helping to maximise yields in an array of environmental conditions. Moreover, using soybean as a model species can assist in improving food security, soil health and agricultural sustainability via the enhanced understanding of legume nodulation and nitrogen fixation. Optimising these processes can help in reducing the use of expensive, often polluting, nitrogen-based fertilisers in agriculture.

This chapter provides an overview of the basic principles and processes involved in the breeding of sorghum. A number of standard field operations are described, such as crossing, emasculation and harvesting, followed by a discussion of various methods of selection and topcrossing. After describing these classical breeding methodologies, there follows an evaluation of new directions in sorghum breeding, such as the use of molecular markers and high-throughput means of phenotyping plants. These techniques are discussed in terms of the availability of technology and their economic viability. It is concluded that although classical breeding methodologies will continue to be a requirement in future, sorghum breeders will need to make use of evolving technologies if they are to be successful.

A thorough understanding of how grain sorghum develops is essential in determining how best to manage this crop. Grain sorghum has three predictable phases of growth: vegetative (planting to panicle initiation); reproductive (panicle initiation to flowering) and grain filling (after flowering to maturity). This chapter describes each of the phases in detail, observing how each stage is affected by factors such as genotype, temperature and photoperiod. Climatic conditions for optimal growth, as well as the effects and physiological basis of drought, high temperature and elevated carbon dioxide tolerance, are discussed. Due to climate change, sorghum-producing areas are facing increased exposure to water deficits and extreme temperatures, making comprehension of plant response to environmental stresses even more necessary. It is concluded that the use of high-yielding varieties and proper management practices will be essential to the future of this crop.

The challenge of grain legume production is to continue increasing productivity while reducing the significant seed yield gap between developed and developing countries/regions. Advanced breeding techniques play an important role in the era of genomics. This chapter describes the main grain legume breeding programmes, including breeding targets such as stressors and phenotypes. The chapter examines grain legume reference-genome sequences, legume common lineages and synteny and describes the use of whole-genome and reduced representation resequencing and SNP chips.

Lentil is a popular pulse consumed primarily in Asia. It has a protein content of approx. 28% and also contains high amounts of macro- and micro-nutrients. Lentils are cropped under rainfed conditions and on residual/conserved soil moisture, and their inclusion in rotation benefits succeeding crops as a result of biological nitrogen fixation. This chapter reviews the reviews global production of lentils, and shows how the breeding and use of new varieties with higher yield potential and improved disease resistance has led to increased productivity in many countries. It discusses successful attempts to broaden the genetic base of lentil in South Asia and to cross domestic varieties with wild relatives to access new disease resistance genes. Finally, it considers the scope for breeding new climate-smart varieties of lentil in response to emerging climate changes and variability.

Pigeonpea [Cajanus cajan (L.) Millsp.] is a high protein pulse crop which grows well under biotic and abiotic stress situations. It could play a significant role in meeting the challenges of food security in the tropics and sub-tropics, under the looming threat of drought, warm climate, and rising production costs. This chapter examines the role of pigeonpea in global nutritional security for humans and animals, and addresses the physical, environmental and genetic factors that may affect the sustainability of pigeonpea production. The chapter examines four ways of enhancing pigeonpea production: through crop modeling, an efficient seed system, plant breeding and hybridization. Finally, the chapter considers the latest trends in pigeonpea breeding and production.

Sugarcane (Saccharum spp.) is one of the most important crops for producing sugar and bioethanol, and breeding for superior sugarcane cultivars would benefit significantly from available genetic and genomic resources. This chapter explains the difficulties of sequencing and mapping the genome of sugarcane and strategies to overcome these difficulties. The chapter outlines progress on sugarcane sequencing, genetic mapping of simply inherited and complex traits. The chapter then focuses on the mapping of a gene controlling sugarcane brown rust resistance, Bru1, which exemplifies the concepts of marker-assisted selection. Finally, the chapter discusses prospects for future research in sugarcane genome sequencing and genetic mapping.

All sugarcane cultivars currently grown throughout the world arise from breeding programmes which have used a reasonably similar approach sustained over many decades. This comprises a continuous pipeline of operations of regular (usually annual) crossing among selected parent clones to produce large populations of seedling clones, followed by selection of these clones in successive stages of field trials for usually 9–12 years for important traits. This chapter outlines the history and structure of sugarcane breeding programmes as context for considering efforts to advance rates of progress. It reviews studies conducted in the last 30 years to improve many specific aspects of operations in sugarcane breeding programmes. Finally, it describes emerging concerns about whether current rates of genetic gain in sugarcane are optimal, and suggests some avenues for faster gains.

Due to its botanical characteristics, genetic improvement of tea is slow. Its high gestation period, the difficulty of producing homozygous lines, and the non-availability of mutant genotypes and a mapping population are all hindrances to development. This chapter describes and evaluates the potential of genetic transformation as an alternative for varietal improvement of tea, via the deployment of agrobacterium and particle bombardment. The chapter describes in detail progress global progress on research into transgenic tea.

Theobroma cacao is one of the most important cash crops in the world and is native to the tropical, humid forests of South America. This chapter discusses its origin and the taxonomy and classification of the varieties of Theobroma. It then reviews the characteristics of the three general groups of Theobroma: criollo, forastero and trinitario.

This chapter explores the main developments in cacao breeding programmes in Trinidad, Brazil, Ecuador and Costa Rica in the Americas; and Ghana, Ivory Coast, Nigeria and Cameroon in Africa. The different types of commercial cacao cultivars and breeding programme objectives are described. Heterosis and heterotic groups in cacao, and the contrast between ‘traditional’ and new cacao breeding methods are explored. Finally, the issue of breeding cacao for organoleptic quality is examined and future developments in this area are discussed.

Over a long period of more than a century, breeding and improvements in cropping systems have led to a constant increase in grain yield in barley. Due to its autogamous propagation, commercial barley varieties are normally true inbred lines or doubled haploid lines normally having completely homozygous genomes. Hybrid breeding in autogamous cereals such as barley, however, is still in its infancy. This chapter describes the principles of heterosis in barley and its potential for yield enhancement. The chapter explains the potential of hybrid breeding in winter barley and examines the challenges associated with broadening the genetic basis for heterosis in winter barley. The chapter describes the cytoplasmic male sterility system for hybrid seed production in barley and looks at the environmental and genetic effects of hybrid breeding on the stability of cytoplasmic male sterility.