Maria Hilda Pérez-Barraza and Jorge Alberto Osuna-Gracia, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Mexico
Advances in understanding flowering, pollination and fruit development in mangoes
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The number of flowers produced by a mango plant is determined a year before production via induction, initiation and floral differentiation processes. The number of fruits will depend the success of the pollination, fecundation and fruit set processes. This chapter addresses flowering, pollination and mango fruit development, beginning with vegetative shoot formation and then the plant’s induction, initiation and floral differentiation. The chapter analyses the genes governing the flowering process and the processes of pollination and fertilisation. It suggests future research trends in this area and recommends further reading on the subject.
C. Michael Deom, University of Georgia, USA; and David Kalule Okello, National Semi-Arid Resources Research Institute, Uganda
Developing improved varieties of groundnut
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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.
Heng Ye, Babu Valliyodan, Li Song, J. Grover Shannon, Pengyin Chen and Henry T. Nguyen, University of Missouri, USA
Advances in the drought and heat resistance of soybean
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Drought combined with heat is the major abiotic stress that threatens crop production. Climate changes are anticipated to intensify the occurrence of irregular precipitation patterns worldwide, which will further negatively affect crop production and food security. The success of soybean improvement under drought and heat stress depends on the discovery and utilization of genetic variations present in the germplasm. Identification of genetic diversities for traits related to drought and heat tolerance have helped identify genetic resources in soybean. In this chapter, advances in drought and heat tolerance in soybean are summarized by highlighting the genetic diversity and quantitative trait loci (QTL) associated with the traits contributing to drought and heat tolerance. In addition, genomic resources that can facilitate a better understanding of phenotype-genotype association and formulate genomic-assisted breeding strategies are discussed.
Julius van der Werf, School of Environmental & Rural Science, University of New England, Australia; and Andrew Swan and Robert Banks, Animal Genetics and Breeding Unit, University of New England, Australia
Advances in sheep breeding
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This chapter summarises early developments in sheep breeding programmes, with the main emphasis on the Australian industry. It will examine common current breeding practices such as objective trait measurement, flock genetic evaluation and the development of breeding objectives based on rational economic analysis. The chapter shows that breeding programmes for dairy, meat and wool sheep differ in how well the main breeding objective traits can be measured on breeding animals. This has a major impact on the rate of genetic progress that can be achieved as well as on the economic sustainability of technologies such as progeny testing, artificial insemination and genomic selection. The chapter mainly focuses on wool and meat sheep breeding programmes, with a discussion on the implementation and adoption of genetic evaluation systems, the development of breeding objectives and the recent developments towards uptake of genomic selection.
Y.-C. Lee, R. Lemes Hamawaki, V. Colantonio, M. J. Iqbal and D. A. Lightfoot, Southern Illinois University, USA
The use of marker-assisted selection in developing improved varieties of soybean
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Marker-assisted selection (MAS) for soybean improvement is based on over two thousand mapped loci. In genetics databases there are thousands of mapped loci that underlie quantitative traits, oligogenic traits and simple traits. This chapter describes examples of methods for developing and using DNA markers derived from genomic sequences for monogeneic, oligogeneic and polygeneic traits, together with examples of successful mapping, fine mapping and gene isolation. The chapter examines ways in which marker-assisted selection can be used to isolate and select desirable traits in soybeans.
John O. Ojiem, Kenya Agricultural and Livestock Research Organization, Kenya
Improving cultivation practices for common beans
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The common bean (Phaseolus vulgaris L.) is perhaps the world’s most important, and the most widely cultivated grain legume. It serves as a food security crop and meets more than 50% of household dietary protein requirements, especially in sub-Saharan Africa. In addition, common bean contributes to household cash income, and is believed to play a significant role in the management of human health, particularly reduction of blood cholesterol levels and combating heart diseases, cancers and diabetes. However, its productivity is poor in most of the major growing regions. This chapter examines the major production constraints and how these can be addressed to improve productivity, from an integrated crop management (ICM) perspective. In particular, cropping system, integrated pest management, major pests and diseases and control strategies, water management, integrated nutrient management, liming, and foliar fertilization are discussed.
K. K. Jena and G. Ramkumar, International Rice Research Institute, The Philippines
Breeding strategies to improve rice yields: an overview
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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’.
T. Vuong, University of Missouri, USA; and D. Walker, USDA-ARS and University of Illinois, USA
Advances in marker-assisted breeding of soybeans
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This chapter reviews key developments in marker-assisted breeding of soybean. It begins by discussing types of molecular markers such as simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs). It then discusses marker assays and genotyping platforms for marker-assisted selection, including SSR marker genotyping and developments in high-throughput genotyping. The chapter then reviews applications of marker-assisted selection in soybean breeding to deal with biotic threats such as nematodes, rusts and aphids, abiotic threats such as salinity, as well as aspects of quality such as fatty acid composition. The chapter concludes by looking at developments in genomic selection.
Dr Laurent Bedoussac
Grain legume–cereal intercropping systems
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There is currently renewed interest in intercropping in Europe in order to achieve sustainable, ecological or eco-functional intensification of agricultural production, particularly in organic farming. This chapter summarises data from over 50 field experiments undertaken since 2001 on cereal–grain legume intercropping in 13 sites in Southern and Western France as well as in Denmark using spring and winter cereal–grain legume intercrops. The chapter addresses the effects of intercropping on yields and quality, the agronomical performance of intercropping and cultivation practices in intercropping.
Elizabeth Ryan, Colorado State University, USA; Indi Trehan, Kristie Smith and Mark Manary, Washington University, USA
Dietary health benefits, phytochemicals and anti-nutritional factors in grain legumes
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Legumes are a significant source of essential nutrients including dietary fibres, proteins, dietary minerals, and carbohydrates. Abundant in both soluble and insoluble fibre, legumes support colonic and overall health. The chapter describes the impact of grain legume consumption on inflammation, the health benefits of dietary fibre, and possible connections between dry grain legume consumption and carcinogenesis. The chapter explores the relationship between grain legume consumption and gut health, analysing the phytochemical content of grain legumes as well as possible chemical toxicant exposures from grain legume consumption.
Junming Li, Institute of Vegetables and Flowers – Chinese Academy of Agricultural Sciences (CAAS), China
Advances in marker-assisted breeding of tomatoes
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Tomato is one of the most important vegetable crops in the world. This chapter describes the process of marker development and how this can be used to improve tomato breeding. The chapter discusses the techniques of marker-assisted selection (MAS) and genomic selection (GS) to identify and exploit specific traits in tomato.
Dr Barbara Frűh
Organic pig farming: key characteristics, opportunities, advantages and challenges
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Organic pig production strives to provide housing and management conditions that guarantee a high level of animal health and welfare, sustainability, a closed soil–plant–animal cycle and produce high-quality products. This chapter discusses how housing of organic pigs affects welfare and the environment, and outlines how organic production systems are desperately in need of alternatives to feedstuffs that are in direct competition with human nutrition. The chapter examines why certain breeding goals should be adapted to organic conditions, and which health problems are typical for organic housing systems. Finally, the chapter shows how waiving of castration could be a challenge but also a chance for organic pig production and looks ahead to future research trends in this area.
Pekka Huhtanen, Swedish University of Agricultural Sciences, Sweden
Advances in feeding grass silage
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Grass silage is the main forage source during indoor feeding periods in many temperate regions. The digestibility and energy concentration of silage are mainly determined by the maturity at harvest, but changes in carbohydrate and nitrogen fractions during fermentation process can markedly modify the profile of nutrients absorbed from the digestive tract and also influence intake potential. This chapter reviews research on factors affecting nutrient supply from the digestive tract in animals fed a grass silage–based diet. The chapter examines the effects of energy and protein supplementation on production responses, taking into account nitrogen and methane emissions. The chapter highlights recent developments in the big bale system that has become popular especially in Northern Europe and looks ahead to future trends in this area.
Prof. P. Zhang
Advances in genetic modification of cassava
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Until recently, hybridization was used to breed new varieties of the common tropical and subtropical crop cassava, but changes in global climate, food security and industrialization have accelerated the breeding of new cassava varieties with increased nutrition, high stress resistance and starch content. Genetic engineering shows great potential for cassava, particularly for enhancing starchy storage root development, starch accumulation, health-promoting components, and stress response and regulation. This chapter describes recent progress relating to transgenic modification of cassava. As a vital component of an integrated breeding system, genetic engineering, together with functional genomics, proteomics, marker-assisted selection and traditional hybridization, has greatly promoted the efficiency of cassava production. The chapter also addresses how future research on cassava can strengthen food security, commercialization and bioenergy development.
Don W. Morishita, University of Idaho, USA
Weed management in grain legume cultivation
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The importance of managing weeds in a grain legume crop is critical for obtaining optimum yield. All grain legumes are relatively poor competitors with weeds and thus are prone to yield reductions when grown in the presence of weeds. This chapter outlines the nature and challenges of weed interference and methods of weed control, as well as offering two detailed case studies. The chapter demonstrates that a combination of practices, such as cultivar selection, planting date, tillage system, in-crop tillage or cultivation, and/or herbicides are needed to increase the likelihood of successful weed control.
Stephen Roderick, Duchy College, UK
Pastoralism and organic animal farming: are they complementary?
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A general absence of reliance on purchased inputs as well as a focus on natural pastures and free-ranging animals prompts comparison between pastoralism and organic farming. Pastoralism frequently occurs in the marginal lands that can be found where humans and herds of domesticated animals living in a form of symbiotic relationship, utilising nutritional resources that would otherwise be unavailable for other forms of food production. This chapter discusses some of the key characteristics of pastoralism and explores in detail how these systems complement and conflict with the traditional view of what constitutes organic animal production. The chapter examines pastoral management strategies, compares pastoralism with commercial ranching and contrasts breeding strategies. The chapter looks at the opportunities for animal health promotion and considers the question of whether pastoralism provides good animal welfare. Finally, the chapter examines opportunities for integrated systems, impacts of pastoralism on biodiversity and provides guidance on further reading on the subject.
S. Adjei-Nsiah , International Institute of Tropical Agriculture (CIAT), Ghana ; and B.D.K. Ahiabor , CSIR-Savanna Agricultural Research Institute, Ghana
Soil and nutrient management in grain legume cultivation
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Due to their role in improving soil fertility, grain legumes can be integrated into farming systems as part of soil fertility management. This offers a potential pathway towards sustainable intensification. In this chapter we focus on how to maximize biological nitrogen fixation and yields of grain legumes through soil and nutrient management options. We review existing literature on optimal conditions for legume cultivation and biological nitrogen fixation in grain legumes, and then discuss recent studies in biological nitrogen fixation in the Guinea Savanna zone of Ghana. We conclude by considering future trends in grain legume research.
Z. A. Pretorius, University of the Free State, South Africa; M. Ayliffe, CSIRO Agriculture and Food, Australia; R. L. Bowden, ARS-USDA, USA; L. A. Boyd, National Institute of Agricultural Botany, UK; R. M. DePauw, Advancing Wheat Technologies, Canada; Y.
Advances in control of wheat rust
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Rusts are feared diseases of wheat. Despite the many resources invested into genetics of rust resistance, the lack of durability of resistance in wheat and the availability of low-cost fungicides have led to widespread reliance on chemical control. This reliance is unsustainable in the long term and requires continued research in the management of wheat rusts. This chapter describes advances in wheat rust control. Critical concepts involved in studying the wheat rusts are pathogen and host genetics, host–pathogen interactions, epidemiology and management strategies. The overarching goal of research is to use collective knowledge of these aspects to achieve durable rust resistance through application in selection and breeding.
Dr Dr Jean Claude Rubyogo
Variety selection and seed quality management in grain legume cultivation
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A key aspect of grain legume crop cultivation is selecting and being able to access the seed of the right type and quality. This is becoming more challenging as grain legumes become cash crops and smallholder farmers transition from subsistence farming to market-oriented production. This chapter discusses the challenges of legume variety selection and seed quality management as well as how they can be addressed, for example through participatory varietal selection (PVS). It includes case studies on improving seed selection and quality management in practice in sub-Saharan Africa.
Phillip Jackson, CSIRO, Australia
Advances in conventional sugarcane breeding programmes
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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.
P. J. Bramel and H. D. Upadhyaya, Global Crop Diversity, Germany and International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
Conserving and characterizing the genetic diversity of grain legumes
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An increase in the production and marketing of grain legumes would help to diversify diets and improve human nutrition, as well as contributing to the sustainability of cropping systems and long- term soil health. However, the projected impacts of climate change and the current local adaptation and use of these crops pose challenges to increasing production. One of the key resources for meeting these challenges through crop improvement will be the genetic diversity conserved ex situ in genebanks and in situ with farmers or in protected areas. This chapter reviews global strategies to assess the status of the major grain legume genetic resources held in ex situ collections, develop a vision of a more secure global system of conservation, and identify high- priority actions to facilitate the establishment of this global system. As an example, we focus on the characterization and exploitation of the genetic resources of chickpeas and pigeon peas.
Shoba Sivasankar, Former Director, CGIAR Research Program on Grain Legumes
Developing drought- and heat-tolerant varieties of grain legumes
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Despite the complexity imposed by the polygenic nature of plant tolerance to drought and to heat, significant strides have been made in understanding the underlying response and adaptation of plants to these stresses. Together with advanced and accessible technologies such as next-generation sequencing and precision phenotyping, this has enabled the assembly of molecular and physiological tools in grain legumes that would support the development of tolerance through traditional and molecular breeding. This chapter provides an overview of physiological, biochemical and molecular responses and adaptation mechanisms to drought, and to heat, with specific examples from grain legumes. The chapter examines the challenge of developing tolerance to drought and to heat, examining traditional breeding and the utilization of natural genetic diversity, and efforts towards molecular breeding including the identification of genetic associations and quantitative trait loci. Finally, the chapter considers functional genomics studies on stress-relevant candidate genes or gene families and suggests further reading on the topic.
Velmurugu Ravindran and Mohammad R. Abdollahi, Massey University, New Zealand
Advances and future directions in poultry feeding: an overview
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The poultry industry has witnessed remarkable advancements in recent years. This chapter provides a discussion of the advances and future directions in the poultry feeding. Advancements include defining nutrient requirements, composition and ingredient quality, better feed formulation and the advent of additives. It also discusses the developments in feed processing and phase feeding. Future directions include sustainability, ingredient quality, antibiotic-free nutrition, crystalline and synthetic amino acids, feed enzymes, chick nutrition and growth models. Optimal feed processing and the related hygiene practices are discussed briefly. The chapter then discusses future trends in poultry feeding. The chapter concludes with a section dedicated to further information on these topics, in order for the readers to expand their knowledge.
Roger L. Monk, formerly DuPont Pioneer, USA
Advanced testing, multiplication and release of new sorghum varieties
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The release of a new sorghum variety or hybrid is the culmination of many years of breeding and evaluation. This chapter describes the hybrid advancement process, including ways of increasing the parent lines for hybrid production and the guidelines that must be followed to ensure high-quality seed. The chapter also examines procedures for registration, certification, plant variety protection and plant patenting. This chapter focuses especially on hybrid evaluation and release.
Sastia P. Putri and Eiichiro Fukusaki, Osaka University, Japan
Metabolomics as a powerful tool for coffee authentication
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Detecting fraudulent adulteration of coffee is essential for both the industry and legislative authorities. Both parties are accountable for establishing quality standards through labelling, composition regulations and routine evaluation protocols to circumvent unfair competition among manufacturers as well as to ensure the safety, quality and authenticity of the product for consumers. This chapter addresses current issues in the area of adulteration of coffee as well as describes recent progress on coffee quality evaluation and authentication using the metabolomics approach. The chapter includes a detailed case study on the application of metabolomics to authenticate Asian palm civet coffee and looks ahead to future research trends in this area.
Noël Durand, CIRAD, France; and Angélique Fontana, University of Montpellier, France
Harmful compounds in coffee
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In recent years, public health issues in the food industry have led to regulations concerning contaminants in foodstuffs, including coffee. Four main types of compound are known to contaminate coffee. First, pesticides come from agricultural treatments, transport and storage. Ochratoxin A is the main mycotoxin found in coffee and is linked to environmental conditions and post-harvest processing. Polycyclic aromatic hydrocarbon contamination can be of exogenous (during drying) or endogenous (during roasting) origin. Finally, acrylamide appears during roasting. This chapter discusses each of these compounds, reviewing our current state of knowledge, regulations for avoiding or dealing with contamination and effective ways of limiting contamination.
Dugald C. Close and Sally A. Bound , University of Tasmania, Australia
Advances in understanding apple tree growth: the manipulation of tree growth and development
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Recent research and development has investigated the factors influencing apple tree growth, with the ultimate aim of helping apple growers provide the market with fruit which is consistent in quality and which exhibits the features that consumers value, such as firmness, juiciness, colour and appropriate sugar–acid balance. This chapter offers a detailed review of how different interventions after planting allow the manipulation of apple tree growth and development. It then provides discussion of two case studies which show the importance of this factor, and illustrates how it can interact with choice of rootstock and planting system to optimize yield.
Nutrient sources and their application in cassava cultivation
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This chapter discusses various sources of nutrients to be applied to prevent soil nutrient depletion, as well as the optimum rates, times and methods of their application. It also describes how computer models can predict site-specific nutrient requirements and balanced fertilizer rates to maximize nutrient use efficiency, increase farmers’ profits and prevent waste and potential pollution of the environment. It ends by considering the variation among cassava genetic resources in nutrient use efficiency in order to breed new varieties with greater tolerance to low soil fertility.
Dr Claudine Campa
Beneficial compounds from coffee leaves
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Leaves are the leading source of carbon for plant growth and reproduction, and possess a wide range of protection systems against environmental stress. The leaves of the coffee plant, characterized by a high antioxidant potential, have a significant impact on fruit quality, and identifying markers in leaves for plant adaptability to environmental stress provides an indication of the quality of future fruits. This chapter provides an inventory of molecules identified to date in the leaves of cultivated coffee trees. It describes the beneficial effects of the molecules exclusively found in leaves on both plant physiology and human health, and suggests where future trends of research in this area may lead.
Dr Dr Stephen Roderick
Improving organic animal farming for the future
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This chapter reviews key issues and approaches in improving organic animal farming for the future. It emphasises the value of developing diverse solutions suited to local conditions as well as the importance of understanding and working in harmony with the natural resource base. The chapter highlights the need for a more holistic concept of health as resilience together with the importance of locally adapted and more resilient breeds. It discusses the role of skills and better communication between different partners and the importance of an ethical framework underpinning all aspects of organic farming operations.
Timo Stadtlander, Research Institute of Organic Agriculture (FiBL), Switzerland
The development of organic aquaculture
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This chapter offers a general overview of global aquaculture production, explaining some of the key drivers (such as environmental, health and welfare issues with intensive conventional aquaculture) which led to the development of organic aquaculture more than two decades ago. The chapter looks at negative environmental impacts of aquaculture, general rules and regulations governing aquaculture, and the concept of trophic levels. The chapter offers a brief history of organic aquaculture and examines culture and production systems. Finally, the chapter looks ahead to future research trends in this field and the prospects of sustainable organic aquaculture.
Michael N. Clifford
Chemical composition of coffee beans: an overview
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This chapter provides an overview of the composition of green coffee beans and the changes associated with roasting and beverage production. The chapter focusses principally, but not exclusively, on more recent advances related to the major chemical components of coffee such as the chlorogenic acids, the alkaloids (caffeine and trigonelline), the diterpenes (cafestol and kahweol), volatile aromatics and the poorly characterized melanoidins.
Alan Carvalho Andrade, Embrapa Café/Inovacafé, Brazil
Developments in molecular breeding techniques in Robusta coffee
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As a perennial crop, faster breeding methods are needed for coffee to be able to cope with the challenges of climate change that lie ahead. This chapter focuses on the state of the art of developed molecular tools, characterized traits, quantitative trait loci and candidate genes already described for Coffea canephora (Robusta coffee), which accounts for a third of the worldwide coffee production. The chapter examines coffee’s molecular markers, genetic diversity and the current state of molecular breeding, as well as looks ahead to future developments in this area.
K. Ellis, Scottish Centre for Production Animal Health and Food Safety, University of Glasgow, UK
Biosecurity and safety for humans and animals in organic animal farming
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‘Biosecurity’ describes methods of reducing the risk of disease spread. Two defining aspects of organic farming are the requirement to allow animals outside access and the aim to nurture animal health without reliance on veterinary medicines. These measures create differences in risks of disease and access to environmental pollutants compared to non-organic animals. This chapter summarises some of the biosecurity issues particular to organic farming and discusses their significance to human health. Particular focus is given to organic animal rearing and the unique challenges of this sector. A number of strategies for reducing risk of infectious disease are discussed, and two case studies are presented to show how biosecurity has been addressed in practice. It is concluded that applying bespoke biosecurity plans on farms can reduce animal disease risk, thereby increasing the health and welfare of farmed animals and contributing to high standards of food quality.
Dr Dr Isabel Blanco-Penedo
Organic beef farming: key characteristics, opportunities, advantages, and challenges
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This chapter offers an overview of the current status of organic beef production systems and emphasizes the need for more data to better characterize this farm system. It also offers an overview of the course of farm conversion, together with the available resources and options to determine the conditions required for the farm to be competitive in the market. The chapter focuses on the challenges, advantages and opportunities of organic beef farming as an important provider of ecosystem services. It also examines the nature of consumer demand and current preferences and looks ahead to future trends in the area of organic beef farming.
Dr Dr Mette Vaarst
Organic poultry farming: opportunities and challenges
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Poultry constitute a fascinating and diverse group of animals with huge potentials to adapt to many local conditions and to be integrated into a wide variety of organic farming systems throughout the world. Poultry herds fit into many different farm settings throughout the world, including the diverse farming environments in Europe. However, at the other end of the range of organic poultry production, we see increasingly industrial farms based on a complete separation between organic egg and broiler breeds, some with the same welfare and disease problems as the non-organic systems. This chapter looks at organic poultry production through the lenses of the four organic IFOAM principles, and discusses current options and challenges such as genetic material and breeds, and possible future developments with a focus on animal welfare and health, beyond existing systems, for example agroforestry and mobile housing systems, and integration into peri-urban and urban system.
Fábio M. DaMatta, Universidade Federal de Viçosa, Brazil
Coffee tree growth and environmental acclimation
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In this chapter, some aspects of coffee growth and development as well as the recent advances in the environmental physiology of growth and production are reviewed. The information deals with both Coffea arabica and C. canephora, which together account for 99% of coffee bean production worldwide. This chapter is organized into sections dealing with vegetative growth, flowering and fruiting, competition between vegetative and reproductive growth, and physiological acclimation to environmental factors including light, water and temperature.
Prof. Raphael Wahome
Smallholder integrated organic farming: how can it work in the tropics?
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Organic animal farming in the tropics varies considerably across countries and regions, and comprises many different types of systems with significant variation in the degree to which animals are integrated into the systems. The chapter focuses on the issues associated with keeping animals on organic farms in the tropical regions of the world where smallholder systems dominate and will draw specifically on experiences from smallholder dairy farms in East Africa to unfold some of the challenges and opportunities that these systems can face. After giving an overview of tropical animal production and organic and smallholder farming, the chapter describes organic standards for animal husbandry in the tropics and challenges faced by tropical organic animal farmers.
Lindsay K. Whistance, The Organic Research Centre, UK
Enhancing naturalness and human care in organic animal farming
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Organic farming aims to produce food in a way that respects the environment, the people and the animals involved. These aims are covered by the principles of Health, Ecology, Fairness and Care. Naturalness and human care are integral components of welfare for farm animals that are managed under organic systems. Naturalness includes allowing animals to interact with nature and so develop resilience to potential health threats. It also includes animals being able to perform natural behaviour patterns that allow them to fulfil wants and needs when motivated to do so. Physiological health and emotional well being are integral to the welfare of the animals as individuals and as a group. Human care ranges from the provision of appropriate environment and management practices, where stockpersons are a friendly ally to the animals, to more intimate care when health and welfare are compromised. Support networks including advisors and veterinarians are important.
K. B. Saxena, United Arab Emirates; Y. S. Chauhan, Department of Agriculture and Fisheries, Australia; C. V. S. Kumar, A. J. Hingane, R. V. Kumar, R. K. Saxena and G. V. R. Rao, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), I
Developing improved varieties of pigeonpea
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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.
Herbert A. M. van der Vossen, Coffee Breeding Consultant, The Netherlands
Developing varieties of Arabica coffee
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About 60% of the annual world coffee production is harvested from Arabica (Coffea arabica) coffee, with the remainder harvested from Robusta (C. canephora) coffee. The former is superior in beverage quality, but more expensive to cultivate. The demand for quality coffees is steadily increasing, but anticipated climate change may jeopardize the sustainability of Arabica coffee production. This chapter reviews the achievements of several coffee research centres in conserving and evaluating genetic resources and variety development in Arabica coffee. It then discusses the main preconditions for successful next-generation variety development. These are related to genetic variation, disease and pest resistances, tolerance to abiotic stress factors, beverage quality and cost-effective mass propagation of hybrid cultivars. Breeders will have to combine classic selection methods with advanced genetic and genomic technologies in order to meet the challenge of developing resilient (hybrid) cultivars for sustainable, climate-change-tolerant Arabica coffee production.
Eduardo Somarriba, CATIE, Costa Rica; Luis Orozco-Aguilar, University of Melbourne, Australia; Rolando Cerda, CATIE, Costa Rica; and Arlene López-Sampson, James Cook University, Australia
Analysis and design of the shade canopy of cocoa-based agroforestry systems
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Cocoa-based agroforestry (AF) systems are a conspicuous element of agricultural landscapes worldwide. Shade canopy analysis and design is a key component of crop husbandry, and requires a good understanding of the interactions, synergies and trade-offs between shade, yield and environmental services. In this chapter we provide a guide and some principles to analyse and design an optimal shade canopy that provides a diverse, resilient AF system. We first review the different cocoa system typologies described in the literature, placing special emphasis on cocoa–timber systems. We present a guide for the analysis of the shade canopy of shaded cocoa systems, and then investigate the optimal design for cocoa shade canopies, with emphasis on the analysis of trade-offs and synergies between carbon storage and cocoa yields. Finally, we consider critical issues in applying AF science/knowledge to cocoa cultivation programmes.
Susanne Padel, The Organic Research Centre, UK
The principles of organic livestock farming
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Organic animal farming is guided by considerations of naturalness, systems thinking and sustainability, and the four IFOAM principles of health, ecology, fairness and care. The principle of health emphasises the connectedness of different parts of the system and seeks high animal health status through system design. The principle of ecology relates to the integration of livestock with cropping for feeding and nutrient recycling within the farm or region. The principle of fairness encourages respect for animal rights, whilst the principle of care places a responsibility for humane treatment of animals on those working with them. This chapter presents a range of current issues relating to these principles, and illustrates how achieving high animal health and welfare requires active engagement from the whole sector, including farmers, consumers, regulators, advisers and researchers.
Dr Pooja Bhatnagar-Mathur
Genetic modification of grain legumes
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Grain legumes constitute a number of important oilseeds and food crops of the world. Most of these grow predominantly in the low-input production systems in the developing countries of Asia and Africa and are subject to several production constraints. This chapter addresses progress in and prospects for transgenic interventions in the improvement of grain legumes, concentrating on chickpea, pigeonpea, cowpea, lentils, peas, peanuts and other grain legumes. The chapter shows how these technological interventions provide opportunities for enhancing efficiency and effectiveness of breeding programmes for complex traits, as well as increasing the rate of genetic gains in these nutritious grain legumes. The chapter looks ahead to future trends in this area and provides detailed guidance on further reading.
Dr Jorge Teodoro De Souza
Cocoa diseases: witches' broom
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Witches' broom, caused by the hemibiotrophic basidiomycete Moniliophthora perniciosa, is one of the most important cocoa diseases. The pathogen co-evolved with cocoa in the Amazon River basin and is currently restricted to South and Central America. Other cocoa-producing regions of the world are at risk because the introduction of the pathogen would greatly impact cocoa production. In the last few years new technologies such as NGS, bioinformatics, transformation, and the establishment of a model host-plant interaction accelerated the gain of information and have enabled significant advances in our knowledge of witches’ broom. In this chapter, we review the information on witches' broom, including the latest information on disease physiology, genomics and transcriptomics, diversity, and management practices.
R. Redden, RJR Agricultural Consultants, Australia; X. Zong, Chinese Academy of Agricultural Sciences (CAAS), China; R. M. Norton, International Plant Nutrition Institute and The University of Melbourne, Australia; F. L. Stoddard, University of Helsinki,
Efficient and sustainable production of faba bean
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Faba bean is mainly grown under rain-fed conditions, although irrigated production is important in Egypt, parts of China and central Asia. China is the leading producer with a wide range of intensive rotation and inter-crop holistic cropping systems. The main focus of this chapter is faba bean cultivation under rain-fed growing conditions. We cover faba bean production in China and in West Asia, North and East Africa Regions, including discussion of the diseases, weeds and pests affecting this crop. We also review faba bean breeding, genetic resources and markers for breeding, water deficit management, tillage systems, biological nitrogen fixation (BNF) and mineral nutrient requirements.
David Jordan, Rick Brandenburg and Gary Payne, North Carolina State University, USA; David Hoisington, Nick Magnan and James Rhoads, The University of Georgia, USA; Mumuni Abudulai, Savanna Agricultural Research Institute, Ghana; Koushik Adhikari and Jinr
Preventing mycotoxin contamination in groundnut cultivation
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Aflatoxin contamination of crops and food poses a substantial threat to humans and livestock worldwide. Preventing various Aspergillus species from becoming established and growing on peanuts (groundnut, Arachis hypogaea L.) can reduce aflatoxin contamination. This chapter describes factors that affect the growth of A. flavus and A. parasiticus on peanut, as well as models predicting contamination, cultural and biological control measures designed to minimize contamination, challenges associated with research and quantification of aflatoxin. The chapter also features three case studies from current value chain projects in Ghana, Haiti, and Malawi. The chapter argues the need for a more focused and concerted effort to address the issue of aflatoxin contamination in peanut.
Dr Alpha Y. Kamara
Improving cultivation of cowpea in West Africa
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Cowpea [Vigna unguiculata (L.) Walp.] is a legume crop of vital importance to the livelihoods of millions of people in West and Central Africa, providing a nutritious grain and an inexpensive source of protein for both rural poor and urban consumers. This chapter examines what constitutes an optimal cowpea plant population and explains plant configuration in intercropping systems in West Africa. The chapter explores how planting dates can be manipulated to improve cowpea productivity, and how nutrient management can be used to increase cowpea yields. Finally, the chapter examines the application of Integrated Pest Management (IPM) in cowpea production and looks ahead to future trends in this area.
Paul Macek, World Cocoa Foundation, USA; Upoma Husain and Krystal Werner, Georgetown University, USA
Supporting smallholders in achieving more sustainable cocoa cultivation: the case of West Africa
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Sustainability initiatives, including associations, platforms and networks, voluntary sustainability standards, corporate and non-governmental and civil society initiatives, have all been developed as solutions to the multiple, long-running challenges facing cocoa growers and producers. Largely implemented by cocoa farmers and groups, these initiatives are often supported by traders, government agencies, certification organisations and other not-for-profit organisations. This chapter examines the different sustainability initiatives and their social, economic and environmental impacts on cocoa farmers, farms and ecosystems. The chapter provides detailed case studies of impacts in Ghana and Ivory Coast. The chapter also looks ahead to future research trends in this area and provides detailed guidance for further reading on the topic.
Dr Christian Cilas
Advances in pest- and disease-resistant cocoa varieties
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Plant-parasitic nematodes cause cocoa yield losses, a sudden death of trees and retardation of seedling growth in nurseries. This chapter explains the hidden nature and the masking effects of these nematodes and how these have led to erroneous control measures. The chapter describes the nematode pests associated with cocoa and the symptoms of damage. It also addresses several available control options and outlines how nematode management is essential in order to reduce crop losses and to ensure self-sufficiency for food and industrial raw materials. The chapter finally looks ahead to future research in this area and provides additional reading for those interested in researching further.
S. N. Nigam
Improving cultivation of groundnuts
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Genetic and management options are available to realize an optimal pod yield and quality of groundnut production that meets the needs of the processors and consumers, as well as ensuring food safety standards. This chapter discusses various options for groundnut cultivation, from the choice of the variety to methods of storage available or are in use to achieve improved pod yield and quality. It discusses advanced groundnut farming practices such as conservation tillage in the USA, polythene mulch technology in China, and precision farming in developed countries. The chapter addresses the limitations of current agronomic recommendations for groundnut, assesses the available varieties and cultivars, and examines methods of field preparation and soil resources management. The chapter explores groundnut seed preparation, planting and weed and water management, as well as plant protection practices and harvesting, drying, curing, and storage methods. Finally, the chapter focuses on precision cultivation and groundnut seed systems.
Frederick P. Baijukya and Harun M. Murithi, International Institute of Tropical Agriculture (IITA), Tanzania; and Fred Kanampiu, International Institute of Tropical Agriculture (IITA), Kenya
Improving cultivation practices for soybeans in sub-Saharan Africa
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Soybean production in sub-Saharan Africa (SSA) has significantly increased due to the surge in demand arising from increasing populations and improved incomes. Analysis across SSA revealed an increase in soybean consumption of 7.4% between 1990 and 2011 with more than 50% of the production gap filled by importation. There is therefore an urgent need to improve the production of this important legume in SSA. In this chapter, we present the best practices for soybean cultivation together with evidence for their effectiveness in improving soybean yields. These best practices include the use of improved varieties; correct plant population; and nutrient, disease and pest management. We discuss the importance of supporting these practices with good input delivery and financing systems, agricultural advisory services and functioning output markets.
Darin A. Sukha and Naailah A. Ali, The University of the West Indies, Trinidad and Tobago
Analysing sensory and processing quality of cocoa
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Flavour is a critical facet of cocoa quality, impacting to a large extent the value and end use of traded cocoa beans. This chapter provides a road map towards bridging the knowledge gap that currently exists between industry and cocoa producers by defining approaches for analysing sensory and processing quality of cocoa. The chapter describes the quality criteria for cocoa being developed and communicated to cocoa farmers around the world with varying levels of depth, clarity and consistency into one harmonised and pragmatic approach. It links quality with the genetic expression of flavour potential and is informed by existing recognised international standards, experiences and recent research output. The chapter also highlights the evolution of sensory evaluation as a science and the use of physical and sensory evaluation as a tool to drive improvements in the cocoa value chain.
James D. Kelly, Michigan State University, USA
Developing improved varieties of common bean
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The genetic improvement of common bean (Phaseolus vulgaris) has been a century old endeavor at institutions in North America and Mexico. This chapter describes Improvement programs focussing on a wide range of biotic and abiotic production constraints, traits for local adaptation, and consumer quality, with yield being the overriding challenge for most bean breeding programs. The chapter assesses the wide range of breeding procedures used to improve bean yields, from ideotype breeding to Quantitative Trait Analysis (QTL) of yield traits. The chapter discusses the impact of these procedures on yield gains and the future role of genomic research on yield improvement of the common bean.
Prof. William Erskine
Developing improved varieties of lentil
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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.
Fred J. Muehlbauer, Washington State University, USA; and Ashutosh Sarker, International Center for Agricultural Research in the Dry Areas (ICARDA), India
Improving cultivation of lentil
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Lentil is an important food legume in the semi-arid regions of the world where it can be grown successfully on limited soil moisture and in relatively poor soils. This chapter describes agronomic practices used in lentil-producing countries, addressing methods of land preparation, sowing, harvesting, threshing and cleaning. Procedures used in developed countries where the crop is entirely mechanized are also included. The chapter suggests improvements to seed supply systems, seed varieties, planting methods, weed control, and harvesting methods.
L. L. Murdock and D. Baributsa, Purdue University, USA
Grain legume storage in developing nations
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Grain legume grain stored after harvest is subject to catastrophic qualitative and quantitative loss. The major cause of loss is storage insects and mycotoxin-producing organisms, which reduce the monetary value of the grain as well as its food value. This chapter describes the various insect control approaches and technologies, both ancient and modern, that have the potential to help low-resource farmers. The chapter specifies the features such technologies must have if they are to be sustainably adopted by low-resource farmers.
Dr Leila Bagny Beilhe
Insect pests affecting cacao
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Pests have a major impact on cacao production: estimates of losses due to pest and disease range from 30% to 40%. The use of chemical inputs, for example, pesticides and fertilizers, for pest and disease control and production enhancement, respectively, can have numerous negative impacts on the environment and human health. An integrated and holistic approach is therefore required to enhance and sustain crop production. This chapter presents the main insect pests attacking cacao in each of the three principal production regions: the Americas, Africa and Asia, and provides general information on control measures adopted for each of the main insect pests. The chapter also presents case studies that showcase how research can help to develop more sustainable and environmentally friendly control measures. Finally, the chapter discusses some of the non-traditional areas in which research should focus to overcome the challenges posed by insect pests.
C.B. Singh, University of South Australia, Australia; and D.S. Jayas, University of Manitoba, Canada
Drying, handling, storing and quality monitoring of pulses
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Pulses are an affordable, vegetarian source of protein. They are low in fat, high in carbohydrates and a rich source of micronutrients, amino acids and vitamins. This chapter discusses on how drying, storing and handling of pulses can adversely affect their quality. It reviews how pulse quality is assessed and discusses strategies for drying, handling and storing pulses in order to maintain quality. A technology for grain monitoring and automated aeration control system, as well as non-destructive techniques for quality assessment of pulses, is described.
Alan de Brauw, International Food Policy Research Institute, USA
The nutritional potential of grain legumes: an economic perspective
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Present-day food systems leave a substantial share of the world’s population malnourished. Though rates of undernutrition have been falling, many people continue to suffer from micronutrient malnutrition and rates of overnutrition are rapidly increasing. This chapter argues that the increased role of pulses in the diet could help alleviate the latter two forms of malnutrition. First, it discusses the evidence in the nutrition literature on the role pulses can potentially play in increasing dietary iron, particularly among vulnerable groups. It then discusses economic reasons behind inadequate pulse production, and constraints, which act as barriers to increased production, faced by smallholders. Finally, the chapter discusses the types of consumer interventions that could also lead to increased pulse demand and an increased role in the diet.
Chris Johansen and Kadambot H.M. Siddique, The University of Western Australia, Australia
Grain legumes in integrated crop management systems
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This chapter focuses on integrated crop management strategies to increase grain legume production in rainfed, resource-poor farming systems. Generally, grain legumes fail to reach even half of their potential yields in these systems. For rainfed grain legumes the major contributor to the yield gap is sub-optimal soil moisture, along with a suite of nutrient, pest and disease constraints. The challenge is to identify remedial action within the means of resource-poor farmers. This requires greater emphasis on farmer-participatory research to identify local constraints, and engaging farmers in trialling locally feasible solutions. Examples of this approach are documented. Particular areas in need of intensive on-farm research include adapting grain legume farming to conservation agriculture and exploring means to increase cropping intensity of grain legumes in cereal-dominated cropping systems. It is suggested that a concerted shift in international and national efforts to support farmer-participatory approaches is needed.
Keith Thomas, University of Sunderland, UK
Diseases affecting grain legumes and their management
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Legume plants are peculiarly susceptible to diseases due to their association with Rhizobium bacteria, their large seeds and stress intolerance. Specific and generalist disease species are well documented, but pathogen virulence evolves rapidly making management a continual challenge. This challenge can no longer rely on pesticide applications as many chemicals become unavailable through regulatory changes. Instead, integrated disease management (IDM) is now promoted as a more suitable and sustainable approach. Integration of disease control has many elements, a number of which are traditional and well developed such as field and crop management. In addition, advanced monitoring methods, modelling and molecular methods of detection are becoming essential features to assist precision in prediction and control. Rapid responses to new disease varieties require development of ever more sophisticated techniques which can, ideally, be applied on site. Local management is likely to incorporate all these elements and be increasingly integrated to global coordination.
Juan M. Osorno and Phillip E. McClean, North Dakota State University, USA; and Timothy Close, University of California (Riverside), USA
Advanced breeding techniques for grain legumes in the genomics era
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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.
Tolulope A. Agunbiade, Yale University, USA; Weilin Sun, Michigan State University, USA; Brad S. Coates, USDA-ARS, USA; Fousséni Traore, Institut de l ’ Environnement et de Recherches Agricoles, Burkina Faso; James A. Ojo, Kwara State University, Niger
Insect pests and integrated pest management techniques in grain legume cultivation
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Cowpea is a major staple legume food crop grown and consumed in the dry savanna regions of sub-Saharan West Africa. Cowpea provides much-needed income to both farmers and traders; cowpea grain is also a major source of protein for the growing human populations, particularly, women, infants and children in West Africa. This chapter describes the pests that attack cowpea at every stage of its development, including aphids, thrips, pod-sucking bugs and lepidopteran pod borers. The chapter explains current control measures and their limitations, and advocates development of an integrated pest management strategy by exploiting knowledge of pest biology, host plant resistance (including Bt cowpea) and biocontrol, as well as incorporating research utilizing recent advances in ’omics’ research technologies. The chapter also emphasizes the importance of disseminating new information to farmers via Scientific Animations Without Borders, which uses cell phones to distribute freely downloadable video media.
Diego Rubiales, Institute for Sustainable Agriculture, Spain
Developing pest- and disease-resistant cultivars of grain legumes
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Average yields of most grain legumes are still relatively low due to limited adaptability of available cultivars to a broad range of environmental conditions, and susceptibility to pests and diseases. This chapter explores current knowledge of pest- and disease-resistant cultivars of a variety of grain legume crops, including faba beans, peas, lentils, chickpeas, grass peas and common beans. The chapter considers cultivars less susceptible to foliar diseases incited either by biotrophic or necrotrophic pathogens, soil-borne diseases, as well as nematodes, bacteria, insect pests and parasitic weeds. Finally, the chapter looks ahead to future research trends in this area and provides extensive further reading on the subject.
Ningjian Liang
Bioactive compounds in coffee beans with beneficial health properties
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In recent years, the health benefits of coffee beverage consumption have received considerable interest. This chapter describes the latest research on the potential health benefits of coffee components including caffeine, phenolics, trigonelline, cafestol and kahweol. The chapter pays particular attention to the antioxidant, anti-inflammatory and antimicrobial properties of these compounds, and evaluates the results of clinical studies on the effects of coffee beverage consumption on human health.
Richard Asare, International Institute of Tropical Agriculture (IITA), Ghana; Victor Afari-Sefa, World Vegetable Center, Benin; Sander Muilerman, Wageningen University, The Netherlands; and Gilbert J. Anim-Kwapong, Cocoa Research Institute of Ghana, Ghana
Good agronomic practices in cocoa cultivation: rehabilitating cocoa farms
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Cocoa cultivation covers a total area of about 5.9 million ha worldwide with around 73% of this area found in the four large cocoa-producing countries in West Africa namely Cameroon, Côte d’Ivoire, Ghana and Nigeria. Adoption of good agronomic practices is crucial for the sustainability of cocoa cultivation and this chapter describes good practices at both the pre- and post-planting stages. The chapter focuses on the challenge of rehabilitating cocoa farms, and includes a detailed case study on rehabilitation of farms in Ghana. The chapter looks forward to future developments in this area and provides further reading on the subject.
Mario R. Fernández-Alduenda, Coffee Quality Institute, USA
Flavour as the common thread for coffee quality along the value chain
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Quality, in the case of coffee, ultimately means flavour, as this is the aspect of coffee perceived by consumers as valuable. The assessment of coffee flavour quality is therefore the key tool for quality assurance in coffee, and is essential in strategies for achieving higher-value coffee. In this chapter, we discuss the definition of ‘quality’ as applied to commercial and speciality coffee, and then argue that despite many interesting advancements in the prediction of coffee flavour using instrumental, analytical methods, nevertheless the only practical way to analyse coffee flavour is still through sensory assessment. This usually means cupping, the process of grading coffee quality based on tasting performed by an expert using a specific protocol. We review how cupping has evolved, the protocols involved and how it can be used as a tool to reach consensus about quality. Finally, we consider other meaningful quality parameters related to coffee processing.
Dr Louis Bockel
Life cycle analysis and the carbon footprint of coffee value chains
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This chapter presents concepts and tools around the life cycle assessment (LCA) and carbon footprint (CFP) with their applications to the coffee value chain. Coffee is characterised by a particularly complex value chain with multiple actors involved along every step, from production to consumers. This chapter explains the concepts of life cycle analysis and the coffee value chain, and describes in detail how carbon footprint performances can be used to upgrade coffee value chains. The chapter includes a case study on use of the EX-ACT value chain tool in Haiti.
Dário Ahnert, Universidade Estadual de Santa Cruz, Brazil; and Albertus Bernardus Eskes, formerly CIRAD and Bioversity International, France
Developments in cacao breeding programmes in Africa and the Americas
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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.
Lambert A. Motilal, The University of the West Indies, Trinidad and Tobago
The role of gene banks in preserving the genetic diversity of cacao
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Cacao (Theobroma cacao L.) is an important tree crop for millions of farmers and for the multi-billion dollar chocolate industry but is derived from a limited genetic diversity. The centre of diversity of cacao is being deforested, thereby increasing genetic erosion, but fortunately a wealth of genetic diversity exists in global cacao collections. This chapter discusses the role and types of gene banks to capture genetic diversity. The chapter deals with the distinction between cacao gene banks and other gene banks and examines how this affects the management and estimation of genetic diversity. The chapter advocates an SNP panel for fingerprinting and addresses molecular marker-assisted management with the objective of comparing global collections and formulating a core collection.
Bodo Raatz, International Center for Tropical Agriculture (CIAT), Colombia
Biofortification of grain legumes
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Micronutrient malnutrition (MNM) is one of the world’s major health threats. Fe and Zn deficiencies affect more than a third of the world’s population, most severely women and children. Biofortified legume crops are being developed with higher levels of bioavailable Fe and Zn to alleviate MNM and improve the nutritional status of affected populations. In this chapter, we review the genetic variability of Fe and Zn content in many legume crops, and show how this is being used to guide breeding efforts through both transgenic approaches and agronomic management. We also consider the importance of factors that influence the bioavailability of microminerals. We review current breeding activities and releases, and so demonstrate an active research field, with progress in all stages of development.
Adriana Farah, Federal University of Rio de Janeiro, Brazil
Nutritional and health effects of coffee
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An increasing number of studies have shown that, in spite of its nutritional limitations, coffee is a complex mixture of bioactive substances that may act together to help prevent diseases when consumed in a proper way. This chapter reviews the literature on the nutritional and health-related aspects of regular coffee consumption, then examines the potential side effects, and looks ahead to future research in this area.
N. Surya Prakash, Central Coffee Research Institute, India
Developing varieties of Robusta coffee
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Coffee is one of the important agricultural commodities, contributing substantially to the national exchequers of growing countries. Coffee is generally obtained from two types of coffee plants, namely Arabica and Robusta; the two species differ from each other in their centre of origin, breeding behaviour, growth habit, adaptability, production potential and quality attributes, but together produce unique blends for the consumer. This chapter offers a comprehensive review of various topics related to the development of Robusta coffee varieties, including the growth habits and agronomical characteristics of Robusta coffee, its breeding behaviour and genetic resources. The chapter describes the genetic structure of Robusta base populations and their phenotypic variability and initial efforts in the development of improved varieties. The chapter finally addresses the factors limiting sustained breeding initiatives and looks ahead to pragmatic strategies for the future.
Dr Enrique Troyo-Dieguez
Advances in understanding grain legume physiology: stomatal behaviour and response to abiotic stress
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Grain legumes can fulfill several roles: they can be an immediate seed crop for consumption or marketing, a means to increase soil fertility as a result of their nutrient-rich residues and a key component of livestock feed. They are therefore likely to have an increasing role in agriculture in both less developed and developed regions of the world. However, a potential constraint on their use is their response to drought in the more arid conditions predicted in some parts of the world due to climate change. This chapter will review the responses of various grain legumes to water-deficit conditions, and then will discuss how grain legumes can be bred for the stomatal characteristics most appropriate for water-scarce environments.
Dr Chifumi Nagai
Breeding caffeine-free coffee beans
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Regular Arabica coffee contains about 1.2% caffeine. ‘Decaffeinated’ (less than 0.1%) and ‘low caffeine’ (0.2–0.8%) coffee can be obtained by removing the caffeine. However, this can compromise the flavour, and may lead to consumers viewing the product as less ‘natural’. Over the past 25 yrs, efforts have been made to develop naturally non- or low-caffeinated varieties, and some coffee beans with reduced caffeine content are now commercially available. In this chapter, we first review the process of caffeine biosynthesis and the economic significance of naturally decaffeinated and low-caffeine coffee. We consider the varying levels of caffeine in different coffee species, the production and characteristics of non- and low-caffeine coffee and the challenges of moving to large-scale cultivation for new varieties.
Frans Wielemaker, Consultant (formerly Director of Research at Dole Fresh Fruit International), Costa Rica
Organic banana cultivation and sustainability
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The cultivation of conventional bananas of the commercial Cavendish variety for export markets in the wet tropics requires a substantial amount of synthetic agrochemical input. Over the last 25 years, organic banana production has soared in Latin America. This chapter describes organic banana production, identifying the key requirements for success: growing location, soil quality and the use of rotation. The chapter examines the importance of soil fertility and fertilization, disease management and managing nematode and insect pests. The chapter also focuses on weed management, and offers suggestions for further reading in this subject area.
Louis Bockel, Laure-Sophie Schiettecatte and Orane Debrune, Food and Agriculture Organization (FAO), Italy
Life cycle assessment and carbon footprint of banana cultivation
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This chapter presents concepts and tools around the life cycle assessment (LCA) and carbon footprint (CFP) of the banana value chain. Bananas are the world’s most exported fresh fruit in volume and value and a key crop for millions of households in developing countries providing food, nutrition and income. As one of the most traded fruit, including transoceanic transportation, more attention is being paid to the social and environmental impact along the whole value-chain of bananas. LCA and CFP give farmers, individuals and multinationals the opportunity to identify GHG hotspots along the banana value chain and adopt practices reducing or offsetting the CFP. The FAO tailored the EX-Ante Carbon-balance Tool for value chain tool (EX-ACT VC) to the banana value chain (EX-ACT BVC) allowing analysis of its CFP, resilience and socio-economic factors. The present chapter gives an example of an Ecuadorian and Peruvian banana value chain analysis with EX-ACT BVC.
Dr Dr Philippe Lashermes
Diversity and genome evolution in coffee
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While the worldwide production of coffee relies on a small number of cultivars with reduced diversity, wild coffee trees represent huge reserves of genetic diversity that could help to mitigate the effects of unstable climate and plant diseases, as well as modify the wealth of health-related chemicals present in the coffee seeds. This chapter describes the results of studies of coffee tree species distribution and characterization, phylogenetic relationships among coffee species and the molecular bases of coffee species diversification, as well as looking ahead to future developments in this area.
Dr Thierry Joët
Environmental and genetic effects on coffee seed biochemical composition and quality
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Reserve compounds that accumulate in coffee seeds contribute to a large extent– directly or through roasting-induced chemical reactions – to the broad spectrum of aromas and flavours of the coffee cup. Coffee seed reserves are mainly composed of cell wall polysaccharides, lipids, proteins, sucrose and secondary metabolites including chlorogenic acids, caffeine and trigonelline. Understanding coffee quality requires a detailed characterization of the metabolic pathways dedicated to the synthesis of these aroma/flavour precursors. This chapter describes the current state of knowledge on the relationships between coffee quality, seed chemical composition, and genetic and environmental effects, with a special focus on environmental regulations of coffee seed metabolic pathways. It includes a case study on coffee production on La Réunion Island and provides suggestions for further reading as well as looking ahead to future developments in coffee seed chemical composition research.
Dr Dr Christian Bunn
Climate change and cocoa cultivation
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Climate change has been projected to impact cocoa production unless cultivation practices are adapted. Guiding effective adaptation is a challenging task because of the high model uncertainty for precipitation which is a vital consideration for cocoa producers. We focus on identifying preconditions for forward-looking, proactive adaptation, describing global climatic changes at current cocoa production locations and demonstrating that impacts are spatially differentiated with the example of Ivory Coast. Temperatures were found to rise beyond historically experienced levels with high certainty. In Ivory Coast, at the frontier along the Savanna, dry season conditions may become too severe for cocoa growing. In order to effectively guide adaptation strategies, cocoa research will need to close important knowledge gaps regarding the interaction of cocoa genotypes, high growing season temperatures and reductions in bean quality, the effect of combined heat and drought events for plant survival, and likely changes of pest and disease threats.
Roberto Buffo, National University of Tucumán, Argentina
Advances in research on coffee flavour compounds
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Coffee’s global appeal is related to its unique flavour, taste and mouthfeel. Coffee is the second-most traded global commodity after petroleum, and a thorough understanding of the chemical dynamics associated with its aroma is essential for the enhancement and permanence of its popularity. This chapter covers the chemical composition of green coffee beans, the process of roasting, the profile of volatile and non-volatile compounds generated by roasting and the chemical reactions responsible for their formation. We use research from the 1990s to the present to discuss the presence of incidental compounds in roasted coffee, the influence of coffee processing on aroma profile and the central issue of key volatiles in the determination of coffee aroma. Finally, we provide insights regarding future directions in the elucidation of coffee flavour.
Jetse J. Stoorvogel, Wageningen University, The Netherlands; and Rafael A. Segura, CORBANA S.A., Costa Rica
Nutrition and soil management in banana cultivation
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There is significant variation in banana production systems across the world, particularly at the level of soil management. However, research on plant nutrition and soil management in relation to bananas has been limited for a number of reasons: bananas are unusual in their physiology and management, and the characteristics of the crop make it difficult to carry out standard fertilizer response experiments. Given the considerable investment in soil management, the scarcity of fertilization studies in bananas is surprising. This chapter provides an overview of general aspects of crop nutrition in the broader context of soil management. Focusing mostly on intensively managed systems where fertilizer use is the highest, the chapter discusses a number of strategies for soil nutrition as well as advantages and disadvantages of each approach.
Charles Staver, Bioversity International, France
Good agricultural practices: an end point or a starting point for more sustainable banana production?
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Bananas, a longstanding export crop, have not been immune from consumer concerns about food safety and the environmental and human health impacts of production. About half of export banana production is certified under four labels – GlobalGap, Organic, FairTrade and Rainforest – based on Good Agricultural Practices (GAPs). GAP certification is a short-term guarantee to marketers and consumers, but GAPs have also been proposed as indicators of sustainability. Our review of the effectiveness of GAP suggests that they could become more useful by incorporating more ecological intensification indicators with economic implications. The present chapter illustrates the application of this approach in smallholder organic export banana to address not only the yield gap, but also improved synchronization between ecological processes, production routines and cost efficiency. While GAPs are an imperfect tool, they are also dynamic and open to new knowledge and practices, to make the extensive tracking and monitoring required of banana growers more effective, enabling as well better understanding of sustainable banana production.
Dr Charles Lambot
Disseminating improved coffee varieties for sustainable production
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Although coffee is one of the most valuable agricultural commodities of the world, it is an orphan crop in relation to investment in plant breeding. An efficient system to develop, introduce and propagate improved coffee varieties is required to place productive, attractive and affordable plants at farmers’ disposal. The chapter describes the rationale of developing and propagating new coffee varieties, presenting a strategy to increase efficiency of coffee production without compromising the quality of results. The chapter considers the physiological constraints of coffee variety development, the legal aspects of plant or seed shipments and the protection of the breeder’s rights within national or international systems. The chapter also includes case studies on statistical methods applied to multi-location trials. The chapter presents some trends for the future and recent initiatives that may be able to accelerate the development and deployment of genetic innovation at farmer level.
Amanda Berlan, De Montfort University, UK
Organic cocoa cultivation
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The last two decades have witnessed a dramatically increased demand for organically produced goods. As a crop, cocoa can be grown successfully using organic methods, and demand for organic chocolate has risen in line with the overall growth in the organic market. This chapter offers a summary of current issues in the production of organic cocoa. I discuss production trends, acknowledging some of the challenges in accurately monitoring such trends, before considering some of the issues surrounding different cultivation methods, and the certification and pricing of organic cocoa. Finally, the chapter considers different techniques for controlling pests and diseases without the use of chemical inputs. A number of conclusions are presented, such as the importance of farmer acceptance of methods, the need for integrated pest management strategies and the challenges of highly variable markets.
Samuel Orisajo, Cocoa Research Institute of Nigeria, Nigeria
Nematode pests of cocoa
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Plant-parasitic nematodes cause cocoa yield losses, a sudden death of trees and retardation of seedling growth in nurseries. This chapter explains the hidden nature and the masking effects of these nematodes and how these have led to erroneous control measures. The chapter describes the nematode pests associated with cocoa and the symptoms of damage. It also addresses several available control options and outlines how nematode management is essential in order to reduce crop losses and to ensure self-sufficiency for food and industrial raw materials. The chapter finally looks ahead to future research in this area and provides additional reading for those interested in researching further.
Sarada Krishnan, Denver Botanic Gardens, USA
Ensuring the genetic diversity of coffee
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Developing adaptation strategies will be critical in sustaining the coffee economy and livelihoods in many countries, owing to continued rises in production costs, as well as problems related to negative impacts of climate change and higher incidence of pests and diseases. Utilizing the varied genetic resources of coffee to develop varieties with drought stress tolerances, pest and disease resistances, high cup quality and increased production will ensure the future sustainability of the crop. This chapter examines the genetic resources of coffee in both ex situ collections and in situ situations and provides a detailed case study of the conservation of wild coffee species in Madagascar. In the context of the development of a Global Conservation Strategy for Coffee Genetic Resources, the chapter looks ahead to future developments in this area.
Prof Prof David W. Turner
A functional approach to bunch formation in banana
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Sustainable management of bananas requires knowledge of development, especially the pivotal processes of bunch formation. This chapter presents a functional analysis of the formation of the inflorescence up to flowering (bunch emergence), emphasising interaction of the plant with the environment. We discuss the role of cool temperature in shortening the juvenile phase and long photoperiod in shortening the mid-vegetative phase of development. We examine differentiation of functionally female flowers that form fruit and subsequently male flowers that do not form fruit. We conclude that hand formation and fruit number per hand are independent but coordinated processes. Genotype and environment determine the relationship between the number of hands per bunch and flowers per hand along the female peduncle. Further research is needed to quantify relationships that underpin new genotypes and management practices for sustainable banana production.
M. A. Rutherford, J. Crozier and J. Flood, CABI, UK; and S. Sastroutomo, CABI-SEA, Malaysia
Improving best practice with regard to pesticide use in cocoa
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Consumer concerns about food safety have been translated into policy in consuming countries, including pesticide residues in cocoa. Such policy changes have an impact on cocoa producers and other supply chain stakeholders, as they have to comply with legislation or risk losing lucrative markets. Consequently, development and implementation of best practice for pesticide use is critical, but major challenges exist in-country. The chapter provides an overview of pesticide use in cocoa-producing countries and the challenge of improving pesticide regulation, before moving on to consider the development of best practice for pesticide use. The chapter provides detailed case studies on establishing baselines, promoting awareness and developing a holistic approach. Finally, the chapter looks ahead to future research trends and provides guidance for further reading in this area.
Didier Snoeck and Bernard Dubos, CIRAD, UR Systèmes de pérennes, France
Improving soil and nutrient management for cacao cultivation
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The results of early fertiliser trials on cacao showed that phosphorus (P) and potassium (K) always had positive effects, along with variable effects from calcium (Ca) and magnesium (Mg). The variability of yield responses to nutrients pointed to the need to link the nutrients with each other or with other factors, in particular with soil, climate, and topography. This chapter outlines an approach to nutrition management based on correcting the soil so that the cacao can find the nutrients it needs in optimal quantities and balances. Through two detailed case studies, the chapter discusses the determination of fertiliser formula by physical-chemical analyses of a sample of soil taken from each plot to be corrected. Finally, the chapter looks ahead to future trends in this area and suggests further reading on the subject.
W. K. Tushemereirwe and J. Kubiriba, National Agricultural Research Laboratories, Uganda
Banana cultivation in Africa
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Banana is important as a food, cash and climate-resilient crop in Africa. However, its productivity has declined tremendously to less than 10 t/ha compared with a potential 60–100 t/ha and plantation longevity has also severely reduced. This chapter examines the composition and distribution of banana cultivars, assesses banana production systems and focuses particularly on banana production in Uganda. The chapter addresses the challenges of banana production, including nutrient deficiencies, moisture stress and pests and diseases that affect them. It examines the ways in which banana varieties might be improved for management of pests and diseases and shows how marketing acts as a constraint to banana production in Uganda. Finally, the chapter looks ahead to future research trends in this area.
Verina Ingram, Yuca Waarts and Fedes van Rijn, Wageningen University, The Netherlands
Cocoa sustainability initiatives: the impacts of cocoa sustainability initiatives in West Africa
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Sustainability initiatives, including associations, platforms and networks, voluntary sustainability standards, corporate and non-governmental and civil society initiatives, have all been developed as solutions to the multiple, long-running challenges facing cocoa growers and producers. Largely implemented by cocoa farmers and groups, these initiatives are often supported by traders, government agencies, certification organisations and other not-for-profit organisations. This chapter examines the different sustainability initiatives and their social, economic and environmental impacts on cocoa farmers, farms and ecosystems. The chapter provides detailed case studies of impacts in Ghana and Ivory Coast. The chapter also looks ahead to future research trends in this area and provides detailed guidance for further reading on the topic.
Ulrike Krauss, Palm Integrated Services and Solutions (PISS) Ltd., Costa Rica
Frosty pod rot, caused by Moniliophthora roreri
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Frosty pod rot (FPR) of cacao (Theobroma cacao) is caused by Moniliophthora roreri. FPR commonly can reduce yields by over 80% and is extremely difficult to manage. This chapter reviews the origins, spread and impact of Moniliophthora roreri. It also discusses methods for managing FPR, from strategies for prevention, early detection and rapid response (EDRR), to impact mitigation using integrated approaches. These include cultural control, supplemented by chemical, biological and genetic approaches.
Andrew Daymond, University of Reading, UK
Safe handling and movement of cocoa germplasm for breeding
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Cocoa (Theobroma cacao L.) originated in South America, but is now cultivated in various parts of the tropics. Movement of cocoa germplasm is often required in breeding programmes to increase the genetic diversity pool or to test clones/progeny in the field. However, such movement brings with it the risks of spread of pests and diseases, many of which are confined to particular geographical locations. Thus, it is critical that movement of germplasm is conducted within a quarantine framework. This chapter reviews the risks associated with the movement of cocoa germplasm. It considers international governance of plant movement and discusses the International Cocoa Quarantine Centre at the University of Reading (ICQC,R) as a hub for safe handling and movement of cocoa germplasm.
Mary A. Egbuta, Southern Cross University, Australia
Mycotoxins in cocoa: causes, detection and control
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Mycotoxins are produced as secondary metabolites by various species of filamentous fungi, and may affect many agricultural crops and products. The potential health risks associated with these chemical compounds mean that significant attention has been given to their detection and control. However, most study has so far been dedicated to mycotoxin contamination of agricultural crops such as cereals, with less attention given to cocoa. This chapter presents an overview of the current understanding of mycotoxin contamination of cocoa. The main groups of mycotoxins are discussed, followed by a summary of three methods of detection. There follows an explanation of various methods of controlling mycotoxins in cocoa, including recommendations at the stages of production, processing and fermentation and discussion of attempts to decontaminate infected crops. It is concluded that there is a need for more research into the different mycotoxins affecting cocoa and methods of reducing their presence and impact.
Dr Sietze Vellema
Sustainable banana cultivation: from standards to multiple solutions
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There is no single recipe for sustainable banana cultivation. Pest and disease management has been central to sustainability efforts, particularly in the export industry. The global and local spread of pathogens make the capacity to manage such threats a shared concern for leading banana exporters and smallholders. This chapter addresses the gap between implementation of global sustainability standards in the export industry based on a single banana variety, Cavendish, and the overwhelming diversity of varieties, uses and production environments related to local food security and rural livelihoods. This gap between ecologically and socially diverse production systems and management strategies relying on standardisation of a package of practices complicates coordinated action working towards multiple solutions. The chapter includes a case study of a major banana-producing region in the Philippines, representing variety in banana production systems, which shows the importance of working towards a territorial approach that has the capacity to accommodate and connect multiple solutions for making banana cultivation sustainable.
Navreet K. Bhullar, ETH Zurich, Switzerland
Development of rice varieties with improved iron content in grain
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Iron deficiency constitutes one of the most prevalent forms of micronutrient deficiencies affecting human health. Biofortification of food crops is suggested as a suitable approach to address iron deficiency in a sustainable and cost-effective manner. Rice, a staple food for over half of the world’s population, is an important target crop for iron enrichment. Due to limited germplasm variability for endosperm iron content, conventional breeding has not met much success in developing high-iron rice lines. Genetic engineering approaches have demonstrated varied degrees of success in enriching rice endosperm with iron. This chapter reviews the studies focused on iron enhancement in the rice endosperm.
Chuan Tong and Jinsong Bao, Zhejiang University, China
Agronomic and environmental factors affecting rice grain quality
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Recent research has shown the importance of both cultivation practices and environmental factors in determining the yield and quality of rice crops. These aspects of rice production are increasingly important given the need to develop sustainable production techniques which will provide food security despite a changing climate. This chapter begins by considering the effects of cultivation practices such as sowing, transplantation and harvesting dates, irrigation and fertilizer application on rice production. It then discusses the effects of elevated temperatures, elevated atmospheric levels of CO2 and O3, and water availability. Changes in yield, milling performance and appearance, nutritional quality and cooking properties are all reviewed. Organic rice cultivation is then considered as an effective, sustainable technique for producing high-quality rice..
Siela N. Maximova and Mark J. Guiltinan, The Pennsylvania State University, USA
The potential of somatic embryogenesis for commercial-scale propagation of elite cacao varieties
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Plant tissue culture can be used to speed up the development and deployment of genetically improved genotypes. Research conducted by multiple groups for over 25 years has led to the development of protocols for efficient somatic embryogenesis (SE) of cacao. This chapter provides a synthesis of publically available information and literature describing the research and development activities on cacao tissue culture and of field-test evaluations of SE-derived plants. The chapter also reviews current activities in cacao-producing countries involving adoption and scale-up for large-scale propagation of important genotypes, providing a number of field studies from Africa, Asia and the Americas.
