The rumen is a complex ecosystem essential for the health and productivity of ruminants. Metabolomics is an emerging technology, with rumen metabolomics research generating important data offering insights into the metabolites present in the rumen, and the factors affecting the rumen microbiome and metabolome. The importance this virtual organ plays in whole animal function is profound. With this, a greater understanding of the factors that impact the rumen composition and its functionality will be key to maximising health, productivity and sustainability of ruminants in the future. This chapter provides an overview of metabolomic analysis, the importance of the rumen metabolome and the factors that affect its composition and function.

Feed utilization efficiency is a trait of high economic importance in livestock production. In poultry meat and egg production, feed accounts for over 70% of the total production costs. Consequently, improving feed utilization efficiency has been a major goal in the poultry industry. The efficient use of feed for livestock production also positively impacts environment. After a brief history of broiler breeding, this chapter summarizes the quantitative genetic properties (heritability and genetic correlation estimates) of feed efficiency and discusses some of its main contributing factors: basal metabolism, protein turnover, body composition, and digestive efficiency. Contribution of metabolic systems (liver, adipose tissue and skeletal muscle) and relevant genomic studies are also discussed. The chapter also includes a section on unfavorable meat quality consequences of improving feed efficiency and ends with discussion on future considerations.

Although barley is of great importance for the brewing and animal feed industries and is regarded as a model for small grain cereals, only a few results on targeted gene modification using CRISPR/Cas endonuclease technology have been published to date. In this chapter, the frontiers and achievements of the currently used techniques in barley genome modification are discussed.

Non-timber forest products (NTFPs) were hailed as a “silver bullet” to provide the economic incentives to conserve standing forests, while contributing to local livelihoods. While the livelihood benefits of NTFPs have been widely acknowledged, the contribution of the NTFP sector to biodiversity conservation is less certain. Despite increasing skepticism of the ability of NTFPs to contribute to conservation, their promotion and development remains a readily implemented tool for many site level conservation projects. However, this chapter dispels certain assumptions related to NTFP sustainability and the links between NTFP extraction systems and conservation. We conclude that the links are generally tenuous to say the least and suggest that, despite the value of NTFP-based systems to rural livelihoods, our perceptions of the relative value of NTFPs in terms of biodiversity conservation need to be revised.

This chapter reviews the particular challenges of developing improved breeds of chicken for small-scale backyard poultry farming on which many smallholder families depend for a balanced diet and income. It reviews issues such as genetic resources for indigenous breeds, breeding strategies and the management strategies needed to optimize the potential of improved breeds. The chapter discusses how new breeds can improve smallholder livelihoods.

Impaired skeletal function occurs in both meat-type and layer poultry, with different aetiologies. This chapter reviews the literature on quantitative genetics and genetic mapping of skeletal traits in both types of poultry. Both skeletal defects and bone quality traits in poultry are lowly to moderately heritable. Skeletal defects are only modestly unfavourably correlated with production traits, relatively easy to measure, and consequently show evidence of reduction in commercial breeding programs. Bone quality traits are more difficult to deal with, due largely to more involved phenotyping. There are also potentially unfavourable correlations with egg traits, but this is less well explored. Linkage mapping and genome-wide association studies have identified numerous loci associated with bone traits. The genomic resolution to identify individual causative genes and variants is lacking. However, several studies have identified plausible candidate genes located close to loci with strong association signals.

Single-step genomic BLUP (ssGBLUP) aims to eliminate the bias in BLUP by considering phenotypic, pedigree, and genomic information jointly. In ssGBLUP this is done by combining pedigree and genomic relationships into a single relationship matrix. ssGLBLUP has become a tool of choice because of high accuracy and ability to utilize existing software. The purpose of this chapter is to review formulas for ssGBLUP, discuss key issues in implementation, and assess lessons from analyses with ssGBLUP.

For decades, the method of choice the prediction of breeding values in poultry breeding programs was the Best Linear Unbiased Prediction (BLUP). More recently, genomic selection is quickly becoming the standard tool for genetic evaluation. One of the main challenges in the implementation of genomic selection is that the number of variants, mainly Single Nucleotide Polymorphisms (SNPs), in the association model are far greater that the number of phenotypic records leading the well know large p, small n problem. Bayesian inference provides powerful tools to circumvent this problem through the assumption of appropriate prior distributions for the unknown parameters in the association model. In this chapter, the most frequently used prior distributions in the implementation of genomic selection using regression models are reviewed. Additionally, Bayesian strategies to accommodate non-additive effects and non-parametric approaches to predict future performance for purebred and crossbred individuals are discussed.

Landscape genomics has become an important tool to study the neutral genetic structure of populations and to identify loci and genomic regions under natural or artificial selection. The understanding of the actions of selection on the genome and their association with specific environmental and landscape factors provides an excellent opportunity to further understand the mechanisms involved in natural selection and the possibility for using identified adaptive loci and genome segments in the enhancement of genetic improvement programs of livestock species. This is especially the case for backyard chickens in several developing countries. These local ecotypes are well adapted to their local environmental conditions and landscape genomics could be used to identify and integrate these adaptive loci into sustainable and efficient breeding programs. Continuous decrease in the economic and logistic costs associated with the collection of genomic and environmental information will further favor the implementation of the landscape genomics approach.

This chapter discusses some of the different aspects of physiological limitations of concern in poultry breeding and production. It then covers research to map the genetic determinants of ascites, including recent successes in identifying the genetic determinants of ascites. The chapter shows how this approach could be applied to a multitude of physiological, multi-genic traits.

Forests in Africa, if managed sustainably, are important for providing livelihood support to millions of people by delivering environmental, economic and social values. However, high deforestation and forest degradation, undefined policies on land and forest tenure, and associated benefit sharing contribute to the unsustainable forest management in Africa. This chapter highlights some of the concept of Sustainable Forest Management (SFM) as a way of presenting opportunities to stakeholders and communities, as well as contributing to sustainability of forest resources. Furthermore, opportunities for using SFM are highlighted using the Participatory Forest Management (PFM) approaches as a case study.

This chapter examines the relationship between cereal grains during storage and approaches which have been used to minimise fungal spoilage and mycotoxin contamination. The role of abiotic factors such as water availability and temperature and their interactions on ecology of spoilage and mycotoxigenic fungi are discussed. The use of volatile organic compounds (VOCs) as an early indicator of spoilage is also reviewed. The potential for the early detection of initiation of fungal spoilage moulds in stored grain by using CO2 as an early warning is examined in combination with predictive modelling of boundary conditions for growth and toxin production as tools for the development of DSS systems. Control measures including abiotic factors, use of natural preservatives, biocontrol agents, and physical methods such as irradiation, cold plasma treatments, hermetic bag systems and fumigation with ozone (O3) are considered. Finally, the potential of developing real time approaches for better post-harvest management of stored cereals and other commodities are discussed.

Post-harvest losses by rodents are estimated to be similar as for pre-harvest losses; somewhere from 0.25% to 25% or more, but generally considered to average around 5-10%, which is similar to the level of post-harvest losses caused by insects. There have been very few studies measuring post-harvest rodent damage and losses. The main pests are the widespread commensal rodent species. Rodents cause direct losses by consuming grain, but they also spoil grain (contamination with hair, urine and faeces), and expose grains to further mould or insect damage. There is a risk of transfer of diseases and zoonoses to humans and livestock. Rodents damage infrastructure such as the warehouses and stores themselves, but also cables and water pipes. There is little information about the ecology of the main rodent pest species in grain stores. Therefore, this remains an important research topic to improve management recommendations about the timing and location of control strategies.

Smallholder farmers constitute the bulk of staple grain producers in developing countries but there is inadequate support in the postharvest management (PHM) phase of the food supply chain. Several effective PHM technologies have been developed to tackle food grain losses. However, minimum impact has been realised mainly because the technologies have not been widely adopted for various reasons. This chapter analyses PHM practices, available technologies and delivery models, and examines factors causing non- or poor adoption of the technologies in developing countries. Missing parts of the PHM jigsaw puzzle are identified and possible practical solutions offered. The chapter proposes strategies to support smallholders in building sustainable and robust PHM interventions to enhance technology uptake for effective reduction of postharvest loss in quantity and quality. There is no “silver bullet” in addressing the diverse and complex grain postharvest challenges faced by smallholder farmers, and associated service-providers in developing countries.

Understanding the genetics underlying quantitative traits and identifying the causal genes and polymorphisms that are causal to these traits is hard at the best of times, but in the case of behaviour, the more modest heritabilities and repeatabilities involved make these tasks even more challenging. Understanding the genetics of behavioural traits can have large ramifications for not only welfare (to try and reduce maladaptive stress responses to the domestic environment) but also production (where certain behavioural traits are associated with either an increase or decrease in productivity). Traditionally, linkage and linkage disequilibrium based techniques have been used to identify the genetic architecture of behavioural traits in poultry. More recently, more advanced transcriptomic tools such as expression QTL mapping and even transgenic birds have increased both the potential for identifying causal genes and polymorphisms that underpin variation in these traits.

This chapter discusses the role of ecosystem services (ESS) in enhancing recreational and amenity services of tropical forests. It outlines the relationship between forests, recreation and tourism, including the concepts and issues involved in policy making. This chapter discusses the challenges involved and examples of failures in managing ESS sustainably in relation to recreation to show how they might be better managed in the future.

This chapter discusses definitions of SFM to promote clarity about the avoidable and unavoidable tradeoffs associated with SFM. The chapter reviews about spatial scales for SFM and for the expansion of the scale at which sustainability is considered from stands up to forested landscapes. We review expanding the scope of SFM from individual stands, to which many definitions of SFM pertain, to the scale of forested landscapes, in keeping with other efforts towards comprehensiveness of land use planning.

This chapter reviews the status and trends of tropical forest governance, how it is manifested in sustainable forest management (SFM), and what can improve it. The chapter starts by drawing attention to the development ambitions which provide a context for efforts to preserve or sustainably manage tropical forests. It then reviews a range of research on the state of governance in tropical forests, initiatives to strengthen governance, and evidence of progress or otherwise. It discusses drivers behind favoured approaches to governance, as well as limitations to fulfilment of governance ambitions, including capacity constraints and lack of integration into the fabric of tropical societies. It ends with key messages on possible ways forward.

This chapter reviews recent developments in assessing and mapping tropical forests. It discusses the planning of inventories, assessment procedures and statistical evaluation. It discusses the use of remote sensing techniques to identify changes in land use such logging and deforestation. It also looks at the role of in-situ assessment and how this data can be integrated with remote sensing data. Particular attention is paid to cost efficiency and quantification of uncertainty in inventories.

This chapter reviews some of the main pressures on tropical forests, starting with an overview of recent rates of deforestation. The drivers of this loss of tropical forests are summarised, and the main ones – clearance of forests for agriculture, often linked to global trade flows, and, to a lesser extent, logging for timber – are analysed in more detail. The key underlying problems of weaknesses in forest governance and law enforcement are discussed, and the chapter concludes with a summary of international efforts to tackle these and to eliminate deforestation from global supply chains.

Secure tenure rights are fundamental to the sustainable management of the world’s tropical forests. By determining the depth of rights and consequent decisions actors can make, tenure regimes allow present-day considerations of future values, thus incentivising investments in the sustainable use and management of forests, including their conservation and restoration. While legally recognized community forests tend to have lower rates of deforestation, store more carbon and benefit more people than forests managed by either public or private entities, over two-thirds of forestlands remain locked in the hands of governments—a significant portion of which is contested by the communities that traditionally use, govern and protect these ecosystems. Using longitudinal tenure data and analysis of global trends in forest ownership developed by the Rights and Resources Initiative, this chapter details the distribution of statutory forest rights across the world’s most forested low- and middle-income countries in Asia, Africa and Latin America.

Bananas were among the first crops cultivated by man and continue to be important for the livelihoods of millions of people throughout the tropics and subtropics. Yet many cultivars and landraces are susceptible to biotic and abiotic stresses. Genetic resistance to diseases and pests is the best form of crop protection and it is imperative to develop new cultivars that perform well across a variety of changing environments. Currently, the production of improved cultivars with relevant gains in resistance to diseases and pests and other preferred agronomic traits has been accomplished through both conventional and non-conventional breeding. This chapter reviews the various genetic improvement strategies used to develop new banana cultivars and discusses the strategies that have been employed over the last one hundred years. They include hybridization approaches, mutation breeding, genetic transformation and marker assisted selection. The role of genomics and more recent molecular breeding approaches are also discussed.

The value of Crop Wild Relatives as sources of new genes that can help secure crop production is increasingly recognized. In banana (Musa spp.), past collecting and conservation efforts focused mainly on the two direct ancestors of cultivated bananas, M. acuminata Colla and M. balbisiana Colla. However, more than 70 taxa of wild Musa species exist in the wild and hold through their diversity and the different habitats they occupy high capacity for adaptation. This chapter presents how much wild banana diversity has been underexplored in the past and how the clonal propagation of the banana crop has prevented the efficient collecting and conservation of wild Musa species. The change in focus from the collection of single clonal individuals to seed populations are presented and practical issues linked to collecting populations are discussed within the scope of wild Musa species reproductive biology.

Sustainable agriculture is possible when smallholder farmers overcome economic barriers to establish profitable farm businesses. This chapter outlines key economic factors of land, labour, capital and inputs which impact the production costs. Access to markets influences the farmer’s ability to effectively sell their products and affects both the distribution costs and the revenue. These economic factors are combined as inter-related constraints in the farmers mind as decisions about what crops to produce, how to optimize production and where to sell it. Solutions to these barriers that smallholder farmers face within these economic factors are context dependent and may include policy changes, adoption of new technologies, temporary incentives to stimulate market growth and building capacity of actors that results in structural changes. A case study is presented based on the authors’ work with smallholder farmers building a cassava seed system in Tanzania.

Sub-Saharan Africa (SSA) continues to experience food insecurity underpinned by low crop productivity. Yields for cereal crops in smallholder farming systems are typically less than 30% of attainable yields and low use of fertilizer and other nutrient resources are recognized as the one of the major limiting factors. Improved crop nutrition depends fundamentally on optimizing soil health. This chapter review the principles and use of integrated soil fertility management (ISFM) as a path towards sustainable intensification. It addresses the challenges of improving uptake and accounting for the huge variability in smallholder systems.