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>

<p>To meet the global demand poultry meat, poultry should be produced efficiently and sustainably. Feed constitutes 70% of the cost of poultry production, meaning improvements in feed efficiency would be beneficial to producers, consumers and the environment. Feed conversion ratio (FCR) is an economic trait preferred by producers because it is directly related to profitability. Different combinations of feed intake and body weight gain can provide the same FCR value and may have the same economic outcome but with different underlying biological causes. Residual feed intake (RFI) breaks down feed efficiency into efficiencies of feed intake for maintenance and growth, respectively. Feed efficiency is affected by ambient factors, animal factors and output factors and is an aggregate of several complex traits with several interacting components. Identification of a major driver, e.g. reduction in maintenance requirement, efficiency of digestion, efficiency of protein retention and efficiency of growth can significantly improve the trait.</p>

<p>This chapter discusses challenges and options for developing dedicated organic dairy breeding programmes with a focus on developing cows best suited to low-input production in particular local contexts. It reviews ways of identifying target traits and establishing breeding goals as well as when to develop separate organic breeding lines and how best to integrate phenotypic and genomic data in breeding. The chapter also discusses options for optimising organic breeding programmes such as the potential multiple ovulation and embryo transfer (MOET) and the role of crossbreeding.</p>

<p>Survivability of piglets during the neonatal period has been decreasing as genetic selection for highly prolific animals continues across the swine industry. Piglets considered medium weight at birth (1.0-1.3kg) provide the greatest opportunity to improve survival. Colostrum consumption by the neonate after birth aids in thermoregulation and improves survival to weaning as well as provides passive immunity to the piglet from the dam to aid in health pre- and post-weaning. Researchers have studied supplementing piglets with porcine and bovine colostrum or with colostrum-like products rich in energy, protein and immunoglobulins. This chapter reviews current research on a range of types of supplementation to young piglets prior to weaning on growth, immune status and survival.</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.

<p>Genetic selection for higher ovulation rate has increased the number of piglets born per litter. The increase in litter size has been accompanied by an increased proportion of low birthweight piglets and piglets with signs of intra uterine growth restriction (IUGR), Conception rates have increased substantially over the years due to genetic selection for ovulation rate and the application of advanced reproductive biotechnologies and nutritional management. Using genome-wide association studies (GWAS) and other methodologies, a number of genes have been identified that influence litter size and teat number. To overcome problems associated with low birth weight and IUGR piglets, selection for uterine capacity appears to be necessary. Finally, selection for favourable maternal behaviour also is required to reduce piglet mortality in large litters. Genetic selection efforts should be directed towards increasing litter quality and reducing post-natal piglet mortality.</p>

<p>The preservation of genetic diversity is particularly important because human selection processes have resulted in a small number of commercial breeds and a large number of small, residual populations. This chapter looks at ways of analyzing pig genetic diversity. It then reviews what these techniques show about the current state of genetic diversity in traditional, local breeds. As the chapter suggests, optimal contribution selection (OCS), genomic selection (GS), and next-generation sequencing (NGS) techniques represent valid strategies for maintaining genetic diversity. In the future, strategies in swine epigenomics and microbiomics will play an important role, especially in improving animal resilience.</p>

<p>Fertility of the swine breeding is high when considering measures for estrus, farrowing and litter sizes. The success in reproduction is a result of an array of factors that involve genetics, health, environment, and reproductive technologies. The population of females in the breeding herd is managed to optimize parity, sow retention, and gilt replacement. Key elements to fertility include selection and management of gilts for early puberty and managing body condition in gestating sows to optimize feed intake during lactation. Artificial insemination technologies are evolving to facilitate gene transfer from high indexing sires through use of lower number of sperm per litter produced. Changes in breeding herd size, housing systems, labor, and litter size, place emphasis on efficiency and throughput. In these intense systems, infertility can create issues in animal flow throughout the production chain and management will need to anticipate and adapt to prevent these problems in the future.</p>

<p>A well-functioning digestive tract is key to a sustainable poultry production. Significant progress in our understanding of the digestive tract functionality has allowed for further improvements, and will continue to do so. Feed intake is a prerequisite for a high performance, where feed particle size is a key element. Although crop retention would potentially improve the digestion process, the practice of ad libitum feeding does not fully stimulate to its maximal use. The gizzard plays a very important role due to its very effective fine grinding and its role as a feed-flow regulator, but structural components need to be included in the diet. As material passes into the relatively short small intestine, it is remarkably quickly digested and absorbed. Fermentation in the caeca may contribute to some energy for the bird, but its major role seems to be water reabsorption, including from urine being refluxed into the caeca from the cloaca.</p>

<p>To meet the food demand of the growing population, there's a need to increase the amount of protein produced from animals. Pork is the second largest contributor of global meat consumption. Identifying ways to increase the efficiency of pig production is pivotal to meeting the US and global demand for nutrients and maintaining resilient supply chains. Genome editing technology can accelerate genetic improvements by introgressing novel traits, decreasing the number of generations required to incorporate the desired allele(s), providing solutions to animal welfare concerns, maximizing nutrient yield, and reducing the use of resources. The technology provides scientists a tool to incorporate multiple genetic traits into a line of livestock species or introduce novel traits. This review highlights the methods for generating genetically engineered pigs beginning with the production of embryos and ending with techniques for performing the genetic modifications. Available swine models designed to benefit production agriculture are highlighted.</p>

<p>This chapter summarizes the basic physiology of porcine female reproduction, including: ovarian structure and function, ovarian follicle development (folliculogenesis), the role of the corpus luteum in the establishment and maintenance of pregnancy, biosynthesis of steroid hormones (steroidogenesis) and the role of the hypothalamic-pituitary-gonadal (HPG) axis in regulating reproduction. It also describes stages of the porcine estrous cycle as well as puberty and gilt development. The chapter goes on to discuss a range of environmental factors which can impair reproductive performance, including the effects of pesticide residues and mycotoxins. Finally, the chapter reviews research on the way heat stress can affect porcine female reproductive function.</p>

Solving problems associated with reproductive failure in sow herds can be a challenge. It is critical to meet breeding targets on a routine basis, and to achieve the appropriate farrowing rates and litter sizes. Reproductive failure interferes with the consistent production of pigs, which ultimately results in the suboptimal number of pigs for market. This chapter will highlight some of the factors affecting reproductive efficiency, including gilt development, litter size, control of the weaning to oestrus interval and seasonal infertility. Attention is given to various management strategies which help producers to continue to be profitable.

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.

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 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.

Soil reserves of potassium are generally large, but most of it is not plant-available. On crop farms, negative potassium balance is common due to greater removal of potassium in hay, straw and grain than fertilizer potassium. Consequently, soil potassium depletion is increasing the prevalence of crop potassium deficiency. Crops require adequate levels of potassium for high yields, and global demand for potassium fertilisers is expected to increase significantly, particularly in developing countries. In this chapter, various aspects relating to the potassium cycle in crop production are discussed, including the use of potassium fertilizer in rain-fed and irrigated agriculture with the focus on soil potassium input and output, crop potassium residue and removal, soil potassium sorption and leaching. A good understanding of the potassium cycle in cropping systems would improve decision making for optimal use of soil potassium reserves and for better management of potassium fertiliser particularly on low potassium soils.

In this chapter root anatomical traits and trait states, and nutrient acquisition mechanisms, along with the environmental issues affecting nutrient acquisition are summarized. Then, the whole range of adaptations of root anatomical traits, and its impact on nutrient acquisition are discussed. Combinations of anatomical traits lead to suggestions of root ideotypes potentially capable of supporting agricultural productivity under different edaphic constraints. Spatiotemporal aerenchyma formation in the various root types of maize under nitrate, phosphate or sulfate deprivation is discussed in a case study.

At a global scale, phosphorus (P) deficiency comprises a large area of cropland, while P has also been used in excess of crop requirements in many other regions. Improved crop P-acquisition efficiency would allow lower target critical soil P values and provide savings in P-fertiliser use. At the same time, it would reduce P lost through erosion, leaching and/or soil sorption. This chapter summarises the progress in research on root traits associated with P acquisition, including root morphology, architecture, biochemistry, colonisation by arbuscular mycorrhizal fungi, and fine root endophytes, and the trade-offs among all these traits. Farming-management practices to improve P acquisition under current intensive agricultural systems are also discussed. The chapter summarises breeding progress in improving P-acquisition efficiency. In the face of soil P deficiency or legacy P globally, the chapter suggests future directions to improve P acquisition in five key areas.

Plant roots have evolved with the presence of rhizobacteria that can colonise the surface or interior of the plant. Some of these rhizobacteria are actively recruited by the plant and carry out particular functions, in particular in nutrient acquisition. Nitrogen-fixing bacteria form associations with many plant species, either as external associations or as symbiotic endophytes. The symbiosis between legumes and nitrogen-fixing rhizobia has been studied in most detail and is the most important contributor to nitrogen fixation in agriculture. This chapter highlights our current understanding of the molecular determinants of legume nodulation as well as challenges for improvements of biological nitrogen fixation in legumes and non-legumes. There is a need for connecting out knowledge of the molecular regulation of nodulation with field-based studies that take into account the interaction of nodulation with biotic and abiotic constraints. In addition, current approaches for engineering new symbioses are discussed.

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.