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2. What is agricultural biotechnology?

Broadly speaking, biotechnology is any technique that uses living organisms or substances from these organisms to make or modify a product for a practical purpose (Box 2). Biotechnology can be applied to all classes of organism - from viruses and bacteria to plants and animals - and it is becoming a major feature of modern medicine, agriculture and industry. Modern agricultural biotechnology includes a range of tools that scientists employ to understand and manipulate the genetic make-up of organisms for use in the production or processing of agricultural products.

Some applications of biotechnology, such as fermentation and brewing, have been used for millennia. Other applications are newer but also well established. For example, micro-organisms have been used for decades as living factories for the production of life-saving antibiotics including penicillin, from the fungus Penicillium, and streptomycin from the bacterium Streptomyces. Modern detergents rely on enzymes produced via biotechnology, hard cheese production largely relies on rennet produced by biotech yeast and human insulin for diabetics is now produced using biotechnology.

Biotechnology is being used to address problems in all areas of agricultural production and processing. This includes plant breeding to raise and stabilize yields; to improve resistance to pests, diseases and abiotic stresses such as drought and cold; and to enhance the nutritional content of foods. Biotechnology is being used to develop low-cost disease-free planting materials for crops such as cassava, banana and potato and is creating new tools for the diagnosis and treatment of plant and animal diseases and for the measurement and conservation of genetic resources. Biotechnology is being used to speed up breeding programmes for plants, livestock and fish and to extend the range of traits that can be addressed. Animal feeds and feeding practices are being changed by biotechnology to improve animal nutrition and to reduce environmental waste. Biotechnology is used in disease diagnostics and for the production of vaccines against animal diseases.

Clearly, biotechnology is more than genetic engineering. Indeed, some of the least controversial aspects of agricultural biotechnology are potentially the most powerful and the most beneficial for the poor. Genomics, for example, is revolutionizing our understanding of the ways genes, cells, organisms and ecosystems function and is opening new horizons for marker-assisted breeding and genetic resource management. At the same time, genetic engineering is a very powerful tool whose role should be carefully evaluated. It is important to understand how biotechnology - particularly genetic engineering - complements and extends other approaches if sensible decisions are to be made about its use.

This chapter provides a brief description of current and emerging uses of biotechnology in crops, livestock, fisheries and forestry with a view to understanding the technologies themselves and the ways they complement and extend other approaches. It should be emphasized that the tools of biotechnology are just that: tools, not ends in themselves. As with any tool, they must be assessed within the context in which they are being used.

Defining agricultural biotechnology

The Convention on Biological Diversity (CBD) defines biotechnology as: “any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products for specific use” (Secretariat of the Convention on Biological Diversity, 1992). This definition includes medical and industrial applications as well as many of the tools and techniques that are commonplace in agriculture and food production.

The Cartagena Protocol on Biosafety defines “modern biotechnology” more narrowly as the application of:

  1. (a) In vitro nucleic acid techniques, including recombinant deoxyribonucleic acid (DNA) and direct injection of nucleic acid into cells or organelles, or
  2. (b) Fusion of cells beyond the taxonomic family, that overcome natural physiological reproductive or recombination barriers and that are not techniques used in traditional breeding and selection.

(Secretariat of the Convention on Biological Diversity, 2000)

The FAO Glossary of biotechnology defines biotechnology broadly as in the CBD and narrowly as “a range of different molecular technologies such as gene manipulation and gene transfer, DNA typing and cloning of plants and animals” (FAO, 2001a).

Recombinant DNA techniques, also known as genetic engineering or (more familiarly but less accurately) genetic modification, refer to the modification of an organism's genetic make-up using transgenesis, in which DNA from one organism or cell (the transgene) is transferred to another without sexual reproduction. Genetically modified organisms (GMOs) are modified by the application of transgenesis or recombinant DNA technology, in which a transgene is incorporated into the host genome or a gene in the host is modified to change its level of expression. The terms “GMO”, “transgenic organism” and “genetically engineered organism (GEO)” are often used interchangeably although they are not technically identical. For the purposes of this report they are used as synonyms.

Understanding, characterizing and managing genetic resources

Farmers and pastoralists have manipulated the genetic make-up of plants and animals since agriculture began more than 10 000 years ago. Farmers managed the process of domestication over millennia, through many cycles of selection of the best adapted individuals. This exploitation of the natural variation in biological organisms has given us the crops, plantation trees, farm animals and farmed fish of today, which often differ radically from their early ancestors (see Table 1).

The aim of modern breeders is the same as that of early farmers - to produce superior crops or animals. Conventional breeding, relying on the application of classic genetic principles based on the phenotype or physical characteristics of the organism concerned, has been very successful in introducing desirable traits into crop cultivars or livestock breeds from domesticated or wild relatives or mutants (Box 3). In a conventional cross, whereby each parent donates half the genetic make-up of the progeny, undesirable traits may be passed on along with the desirable ones, and these undesirable traits may then have to be eliminated through successive generations of breeding. With each generation, the progeny must be tested for its growth characteristics as well as its nutritional and processing traits. Many generations may be required before the desired combination of traits is found, and time lags may be very long, especially for perennial crops such as trees and some species of livestock. Such phenotype-based selection is thus a slow, demanding process and is expensive in terms of both time and money. Biotechnology can make the application of conventional breeding methods more efficient.

An agricultural technology timeline



Genetic interventions


About 10 000 years BC

Civilizations harvested from natural biological diversity, domesticated crops and animals, began to select plant materials for propagation and animals for breeding

About 3 000 years BC

Beer brewing, cheese making and wine fermentation


Late nineteenth century

Identification of principles of inheritance by Gregor Mendel in 1865, laying the foundation for classical breeding methods


Development of commercial hybrid crops

1940s to 1960s

Use of mutagenesis, tissue culture, plant regeneration. Discovery of transformation and transduction. Discovery by Watson and Crick of the structure of DNA in 1953. Identification of genes that detach and move (transposons)



Advent of gene transfer through recombinant DNA techniques. Use of embryo rescue and protoplast fusion in plant breeding and artificial insemination in animal reproduction


Insulin as first commercial product from gene transfer. Tissue culture for mass propagation in plants and embryo transfer in animal production


Extensive genetic fingerprinting of a wide range of organisms. First field trials of genetically engineered plant varieties in 1990 followed by the first commercial release in 1992. Genetically engineered vaccines and hormones and cloning of animals


Bioinformatics, genomics, proteomics, metabolomics

Source: Adapted from van der Walt (2000) and FAO (2002a).

Induced mutation-assisted breeding

Spontaneous mutations are the “natural” motor of evolution, and the resource into which breeders tap to domesticate crops and to “create” better varieties. Without mutations, there would be no rice, or maize or any other crop.

Starting in the 1970s, the International Atomic Energy Agency (IAEA) and FAO sponsored research on mutation induction to enhance genetic improvement of food and industrial crops for breeding new improved varieties. Induced mutations are brought about by treating plant parts with chemical or physical mutagens and then selecting for desirable changes - in effect, to mimic spontaneous mutations and artificially broaden genetic diversity. The precise nature of the mutations induced has generally not been a concern irrespective of whether the mutant lines were used directly or as sources of new variation in cross-breeding programmes.

Induced mutation to assist breeding has resulted in the introduction of new varieties of many crops such as rice, wheat, barley, apples, citrus, sugar cane and banana (the FAO/IAEA Mutant Varieties Database lists more than 2 300 officially released varieties1). The application of mutation induction to crop breeding has translated into a tremendous economic impact on agriculture and food production that is currently valued in billions of US dollars and millions of hectares of cultivated land. Recently, mutation techniques have undergone a renaissance, expanding beyond their direct use in breeding into novel applications such as gene discovery and reverse genetics.

1 Available at


The most significant breakthroughs in agricultural biotechnology are coming from research into the structure of genomes and the genetic mechanisms behind economically important traits (Box 4). The rapidly progressing discipline of genomics is providing information on the identity, location, impact and function of genes affecting such traits - knowledge that will increasingly drive the application of biotechnology in all agricultural sectors. Genomics sets the foundation for post-genomics activities, including new disciplines such as proteomics and metabolomics to generate knowledge on gene and protein structure, as well as their functions and interactions. These disciplines seek to understand systematically the molecular biology of organisms for their practical use.

A vast range of new and rapidly advancing technologies and equipment has also been developed to generate and process information about the structure and function of biological systems. The use and organization of this information is called bioinformatics. Advances in bioinformatics may allow the prediction of gene function from gene sequence data: from a listing of an organism's genes, it will become possible to build a theoretical framework of its biology. The comparison across organisms of physical and genetic maps and DNA sequences will significantly reduce the time needed to identify and select potentially useful genes.

Through the production of genetic maps that provide the precise location and sequences of genes, it is apparent that even distantly related genomes share common features (Box 5). Comparative genomics assists in the understanding of many genomes based on the intensive study of just a few. For instance, the rice genome sequence is useful for studying the genomes of other cereals with which it shares features according to its degree of relatedness, and the mouse and malaria genomes provide models for livestock and some of the diseases that affect them. There are now model species for most types of crops, livestock and diseases and knowledge of their genomes is accumulating rapidly.

DNA from the beginning

All living things are made up of cells that are programmed by genetic material called deoxyribonucleic acid (DNA). Only a small fraction of the DNA chain actually makes up genes, which in turn code for proteins, and the remaining share of the DNA represents non-coding sequences whose role is not yet clearly understood. The genetic material is organized into pairs of chromosomes. For example, there are five chromosome pairs in the much-studied mustard species Arabidopsis thaliana. An organism's entire set of chromosomes is called the genome. The Human Genome Sequencing Project has provided the agricultural research community not only with many spin-off technologies that can be applied across the board for all living organisms but also with a model for international collaboration in tackling large genome-sequencing projects for model plants such as Arabidopsis and rice.

For a refresher course in DNA, genetics and heredity, see the interactive Web site developed by the Cold Spring Harbor Laboratory in the United States, where much of the pioneering work in genetics and genetic engineering has been performed.

Synteny is life!

Mike Gale1

Synteny describes the conservation or consistency of gene content and gene order along the chromosomes of different plant genomes. Until well into the 1980s we imagined that each crop plant had its own genetic map. Only when we were able to make the first molecular maps, using a technique called “restriction fragment length polymorphism” (RFLP), did it begin to dawn on us that related species had remarkably similar gene maps. The early experiments demonstrated conservation over a few million years of evolution in syntenous relationships between potato and tomato in the broad-leafed plants and between the three genomes of bread wheat in the grasses. Later we were able to show that the same similarities held over the rice, wheat and maize genomes, which were separated by some 60 million years of evolution. The diagram summarizes this research and shows 70 percent of the world's food linked in a single map. The 12 chromosomes of rice can be aligned with the ten chromosomes of maize and the basic seven chromosomes of wheat and barley in such a way that any radius drawn around the circles will pass through different versions, known as alleles, of the same genes.

The discovery of synteny has had an enormous impact on the way we think about plant genetics. There are obvious applications for evolutionary studies; for example, the white arrows on the wheat and maize circles describe evolutionary chromosomal translocations that describe Pooideae and Panicoideae groups of grasses. There are great opportunities to predict the presence and location of a gene in one species from what we know from another. Now that we have the complete DNA sequence of rice we are able to identify and isolate key genes from large genome intractable species such as wheat and barley by predicting that the same genes will be present in the same order as in rice. Key genes for disease resistance and tolerance to acid soils have recently been isolated from barley and rye in this way. For practical plant breeding, knowledge of synteny allows breeders access to all alleles in, for example, all cereals rather than just the species on which they are working. A key first example of this is the transfer to rice of the wheat dwarfing genes that made the Green Revolution possible. In these experiments the gene was located in rice by synteny and then isolated and engineered with the alteration in DNA sequence that characterized the wheat genes before replacing the engineered gene in rice. This approach can be applied to any gene in any cereal, including the so-called “orphan crops” that have not attracted the research dollars that the big three - wheat, rice and maize - have over the past century. The main significance is, however, that we can now pool our knowledge of biochemistry, physiology and genetics and transfer it between crops via synteny.

1 Professor Gale is Deputy Director of the John Innes Centre, Norwich, United Kingdom.

Molecular markers

Reliable information on the distribution of genetic variation is a prerequisite for sound selection, breeding and conservation programmes. Genetic variation of a species or population can be assessed in the field or by studying molecular and other markers in the laboratory. A combination of the two approaches is required for reliable results. Molecular markers are identifiable DNA sequences, found at specific locations of the genome and associated with the inheritance of a trait or linked gene. Molecular markers can be used for (a) marker-assisted breeding, (b) understanding and conserving genetic resources and (c) genotype verification. These activities are critical for the genetic improvement of crops, forest trees, livestock and fish.

Marker-assisted breeding

Genetic linkage maps can be used to locate and select for genes affecting traits of economic importance in plants or animals. The potential benefits of marker-assisted selection (MAS) are greatest for traits that are controlled by many genes, such as fruit yield, wood quality, disease resistance, milk and meat production, or body fat, and that are difficult, time-consuming or expensive to measure. Markers can also be used to increase the speed or efficiency of introducing new genes from one population to another, for example when wishing to introduce genes from wild relatives into modern plant varieties. When the desired trait is found within the same species (such as two varieties of millet - Box 6), it may be transferred with traditional breeding methods, with molecular markers being used to track the desired gene.

Molecular markers and marker-assisted
selection for pearl millet in India

Tom Hash1

Pearl millet is a cereal grown for foodgrain and straw in the hottest, driest areas of Africa and Asia where rainfed and dryland agriculture are practised. It is similar to maize in its breeding behaviour. Traditional farmers' varieties are open-pollinated and out-breeding and thus continuously changing. Genetically uniform hybrid varieties have been developed that offer higher yield potential but are more vulnerable to a plant disease called downy mildew. In India, pearl millet is grown on about 9 million ha and more than 70 percent of this is sown to such hybrid cultivars. Since pearl millet hybrids first reached farmers' fields in India in the late 1960s, every variety that has become popular with farmers has ultimately succumbed to a downy mildew epidemic. Unfortunately, by the time the poorer farmers in a given region decide to adopt a particular variety, its days are usually numbered.

The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) wanted to reduce the risks associated with adoption of higher-yielding pearl millet hybrids and extend the useful economic life of these varieties, especially for poorer producers. Biotechnology helped us to achieve this. With tools from the John Innes Centre and support from the Plant Sciences Research Programme of the Department for International Development (DFID), we developed and applied molecular genetic tools for pearl millet. We mapped the genomic regions of pearl millet that control downy mildew resistance, straw yield potential, and grain and straw yield under drought stress conditions. Then our millet breeders used conventional breeding and marker-assisted selection (MAS) to transfer several genomic regions conferring improved downy mildew resistance to the two elite inbred parental lines of popular hybrid HHB 67. We then used MAS to derive two new varieties - ICMR 01004 and ICMR 01007 - with two different downy mildew resistance gene blocks.

These varieties have performed as well or better than their parent lines for grain and straw yield, and are markedly improved for downy mildew resistance. They also retain several favourable traits, including 1 000-grain mass, panicle length, plant height and rust resistance. Hybrids based on crosses involving ICMR 01004 and ICMR 01007 have recently advanced to trials in the Indian states of Gujarat, Rajasthan and Haryana under the All India Coordinated Pearl Millet Improvement Project. This follows their successful evaluation in 2002, in which they exhibited marginal grain yield superiority and substantially better downy mildew resistance than HHB 67, while maintaining the early maturity that contributes to its popularity.

At least one of these two hybrids could be released as a replacement for HHB 67 before the latter succumbs (as it surely will) to a downy mildew epidemic. Because HHB 67 is so widely grown by poor farmers in India, if its timely replacement could prevent such an epidemic for even one year, the losses avoided would exceed the total value of research-funding support by DFID for the development and application of the molecular genetic tool kit for pearl millet (£3.1 million to date). All future benefits from this research by ICRISAT, its DFID-supported partners in the United Kingdom, and collaborating national programme partners in India can then be considered profits to society.

1 Tom Hash is Principal Scientist (Molecular Breeding) at ICRISAT, Patancheru, Andhra Pradesh, India.

Measuring and conserving genetic diversity

The use of molecular markers to measure the extent of variation at the genetic level, within and among populations, is of value in guiding genetic conservation activities and in the development of breeding populations in crops, livestock, forestry and fisheries. Studies carried out using these technologies in fish and forest tree species have revealed high levels of genetic variation both among and within populations. Livestock species are characterized by a high degree of genetic variation within populations, whereas crops exhibit a higher degree of variation across species. Data from other approaches, for example field observation, often cannot provide such information or are extremely difficult to collect.

Molecular markers are increasingly used to study the distribution and patterns of genetic diversity. Global surveys indicate, for example, that 40 percent of the remaining domestic livestock breeds are at risk of extinction. Most of these breeds are found only in developing countries, and there is often little knowledge about them or of their potential for improvement. They may contain valuable genes that confer adaptation or resilience to stresses, such as heat tolerance or disease resistance, that may be of use for future generations. Modern biotechnologies can help to counteract trends of genetic erosion in all food and agriculture sectors.

Genotype verification

Molecular markers have been widely used for identifying genotypes and for “genetic fingerprinting” of organisms. Genetic fingerprinting has been used in advanced tree-breeding programmes in which the correct identification of clones for large-scale propagation programmes is essential. Molecular markers have been used to identify endangered marine species that are either inadvertently captured in wild fisheries or that are purposefully taken illegally. Genotype verification is used intensively in parentage testing of domestic animals and for tracing livestock products in the food chain back to the farm and animal of origin.

Breeding and reproducing crops and trees

In addition to MAS, described above, a number of biotechnologies are used in breeding and reproducing crops and trees. Often these technologies are used in combination with each other and with conventional breeding approaches.

Cell and tissue culture and micropropagation

Micropropagation involves taking small sections of plant tissue, or entire structures such as buds, and culturing them under artificial conditions to regenerate complete plants. Micropropagation is particularly useful for maintaining valuable plants, breeding otherwise difficult-to-breed species (e.g. many trees), speeding up plant breeding and providing abundant plant material for research. For crop and horticultural species, micropropagation is now the basis of a large commercial industry involving hundreds of laboratories around the world. In addition to its rapid propagation advantages, micropropagation can also be used to generate disease-free planting material (Box 7), especially if combined with the use of disease-detection diagnostic kits. There have been some attempts to use micropropagation more widely in forestry. Compared with vegetative propagation through cuttings, the higher multiplication rates available through micropropagation offer a more rapid dissemination of planting stock, although limited availability of desirable clones is an impediment to its wider adoption in forestry.

Micropropagation of disease-free banana in Kenya

Banana is generally grown in developing countries where it is a source of employment, income and food. Banana production is in decline in many regions because of pest and disease problems that cannot be addressed successfully through agrochemical control for reasons of cost and negative environmental effects. The problem is exacerbated because banana is reproduced clonally; the use of diseased mother plants therefore gives rise to diseased offspring.

Micropropagation represents a means of regenerating disease-free banana plantlets from healthy tissue. In Kenya, banana shoot tips have been successfully tissue-cultured. An original shoot tip is heat-treated to destroy infective organisms and then used through many cycles of regeneration to produce daughter plants. A single section of tissue can be used to produce as many as 1 500 new plants through ten cycles of regeneration.

Micropropagation of banana has had a tremendous impact in Kenya, among many other countries, contributing to improved food security and income generation. It has all the advantages of being a relatively cheap and easily applied technology and one that brings significant environmental benefits.

In vitro selection

In vitro selection refers to the selection of germplasm by applying specific selection pressure to tissue culture under laboratory conditions. Many recent publications have reported useful correlations between in vitro responses and the expression of desirable field traits for crop plants, most commonly disease resistance. Positive results are available also for tolerance to herbicides, metals, salt and low temperatures. For the selection criteria of major general importance in forest trees (in particular vigour, stem form and wood quality), poor correlations with field responses still limit the usefulness of in vitro selection. However, this method may be of interest in forestry programmes for screening disease resistance and tolerance to salt, frost and drought.

Genetic engineering

When the desired trait is found in an organism that is not sexually compatible with the host, it may be transferred using genetic engineering. In plants, the most common method for genetic engineering uses the soil bacterium Agrobacterium tumefasciens as a vector. Researchers insert the desired gene or genes into the bacterium and then infect the host plant. The desired genes are transmitted to the host along with the infection. This method is used mainly with dicot species such as tomato and potato. Some crops, particularly monocot species such as wheat and rye, are not naturally susceptible to transformation via A. tumefasciens, although the method has recently been successfully used to transform wheat and other cereals. In the most common transformation technique for these crops, the desired gene is coated on gold or tungsten particles and a “gene gun” is used literally to shoot the gene into the host at high velocity.

Three distinctive types of genetically modified crops exist: (a) “distant transfer”, in which genes are transferred between organisms of different kingdoms (e.g. bacteria into plants); (b) “close transfer”, in which genes are transferred from one species to another of the same kingdom (e.g. from one plant to another); and (c) “tweaking”, in which genes already present in the organism's genome are manipulated to change the level or pattern of expression. Once the gene has been transferred, the crop must be tested to ensure that the gene is expressed properly and is stable over several generations of breeding. This screening can usually be performed more efficiently than for conventional crosses because the nature of the gene is known, molecular methods are available to determine its localization in the genome and fewer genetic changes are involved.

Most of the transgenic crops planted so far have incorporated only a very limited number of genes aimed at conferring insect resistance and/or herbicide tolerance (see Chapter 3 for more information regarding the transgenic crops that are currently being researched and grown commercially). However, some transgenic crops and traits of greater potential interest for developing countries have been developed but have not yet been released commercially. Box 8 describes one research project to improve the tolerance of wheat to aluminium, a problem that affects acid soils in much of Africa and Latin America. Similar work is being performed to improve the tolerance of plants to other stresses such as drought, saline soils and temperature extremes.

Nutritionally enhanced crops could make a significant contribution to the reduction of micronutrient malnutrition in developing countries. Biofortification (the development of nutritionally enhanced foods) can be advanced through the application of several biotechnologies in combination. Genomic analysis and genetic linkage mapping are needed to identify the genes responsible for natural variation in nutrient levels of common foods (Table 2). These genes can then be transferred into familiar cultivars through conventional breeding and MAS or, if sufficient natural variation does not occur within a single species, through genetic engineering. Non-transgenic approaches are being used, for example, to enhance the protein content in maize, iron in rice, and carotene in sweet potato and cassava.

Genetic variation in concentrations of iron,
zinc, beta-carotene and ascorbic acid found in germplasm of five
staple foods, dry weight basis






Ascorbic acid








































1 Range for total carotenoids is much greater.
2 Fresh weight basis.
3 Including wild relatives.
Source: International Center for Tropical Agriculture (CIAT), 2002.

Genetic engineering can be used when insufficient natural variation in the desired nutrient exists within a species. Box 9 describes the debate surrounding a project to enhance the protein content of potato using genetic engineering. The well-known transgenic Golden Rice contains three foreign genes - two from the daffodil and one from a bacterium - that produce provitamin A (see Box 13 on page 42). Scientists are well on their way to developing transgenic “nutritionally optimized”' rice that would contain genes producing provitamin A, iron and more protein (Potrykus, 2003). Other nutritionally enhanced foods are under development, such as oils with reduced levels of undesirable fatty acids. In addition, foods that are commonly allergenic (shrimp, peanuts, soybean, rice, etc.) are being modified to contain lower levels of allergenic compounds.

A major technical factor limiting the application of genetic modification to forest trees is the current low level of knowledge regarding the molecular control of traits that are of most interest. One of the first reported trials with genetically modified forest trees was initiated in Belgium in 1988 using poplars. Since then, there have been more than 100 reported trials involving at least 24 tree species, primarily timber-producing species. Traits for which genetic modification has been contemplated for forest trees include insect and virus resistance, herbicide tolerance and lignin content. Reduction of lignin is a valuable objective for species producing pulp for the paper industry because it would enable a reduction in the use of chemicals in the process.

Agriculture on acid soils:
improving aluminium tolerance in cereals

Miftahudin,1,2 M.A. Rodriguez Milla,2 K. Ross3 and J.P. Gustafson3

Aluminium in acid soils limits plant growth on more than 30 percent of all arable land, primarily in developing countries. There are two approaches to increasing crop production on acid soils. Lime can be added to the soil to increase the pH, but this is a costly, temporary measure. Alternatively, genetically improved cultivars, tolerant to aluminium, can be developed. Existing wheat cultivars do not contain significant genetic variation for increasing aluminium tolerance. Improved tolerance will have to be introduced into wheat from the gene pools of related, more tolerant species. A genetic linkage map of wheat was developed using available markers for the existing aluminium-tolerance gene.

Rye exhibits a fourfold increase in aluminium tolerance over wheat. Therefore, a rye gene controlling aluminium tolerance was characterized. Markers from wheat, barley and rice were used to establish a tight linkage, flanking the rye gene, and to construct a high-resolution genetic map. A potential candidate gene was used for root-gene-expression, time-course studies that showed expression in rye roots only under aluminium stress.

Targeting the aluminium tolerance gene is one example of using problem-based approaches to integrate molecular and breeding tools to improve wheat production. Using the genetic relationship (synteny) among the cereals to supply markers to identify and characterize value-added traits, complementary approaches for improved wheat production emerge. Breeders can use the markers flanking the rye gene in marker-assisted breeding programmes in areas where GMOs cannot be grown or where only conventional breeding tools are available. In addition, these markers can be used for map-based cloning to isolate the gene in question for transgenic approaches to wheat improvement. Finally, the use of syntenous relationships offers the technology to manipulate many value-added traits for crop improvement in other species.

1 Department of Agronomy, University of Missouri, Columbia, United States.
2 Department of Biology, Bogor Agricultural University, Bogor, Indonesia.
3 United States Department of Agriculture Agricultural Research Service, Plant Genetics Research Unit, and Department of Agronomy, University of Missouri, Columbia, United States.

The “protato”: help for the poor or a Trojan horse?

Researchers at Jawaharlal Nehru University in India have developed a genetically engineered potato that produces about one-third to one-half more protein than usual, including substantial amounts of all the essential amino acids such as lysine and methionine. Protein deficiency is widespread in India and potato is the staple food of the poorest people.

The “protato” was developed by a coalition of Indian charities, scientists, government institutes and industry as part of a 15-year campaign against childhood mortality. The campaign aims to eliminate childhood mortality by providing children with clean water, better food and vaccines.

The protato includes a gene from the amaranth plant, a high-protein grain that is native to South America and widely sold in Western health-food stores. The protato has passed preliminary field trials and tests for allergens and toxins. Final approval from the Indian Government is probably at least five years away.

Supporters such as Govindarajan Padmanaban, a biochemist at the Indian Institute of Science, argue that the protato can provide an important nutritional boost to children with little danger of allergy because potatoes and amaranth are both already widely consumed. There is also little threat to the environment because neither potatoes nor amaranth have wild relatives in India, and the protato does not involve any change in normal potato production practices. Furthermore, because the protato was developed by public-sector scientists in India, there are no concerns about foreign corporate control of the technology. Given these benefits, Padmanaban commented: “I think it would be morally indefensible to oppose it” (Coghlan, 2003).

Opponents such as Charlie Kronick of Greenpeace argue that potatoes are naturally quite low in protein (about 2 percent), so even a doubling of the protein content would make only a minute contribution to India's malnutrition problem. He claims that the effort to develop the protato was aimed more at gaining public acceptance of genetic engineering than at addressing the problem of malnutrition: “The cause of hunger isn't lack of food. It's lack of cash and of access to the food. Creating these GM crops is something to make them look attractive when actually the utility of eating them is very, very low. It's very difficult to see how this on its own will change the face of poverty” (Charles, 2003).

Breeding and reproducing livestock and fish

Biotechnology has long been a source of innovation in livestock and aquaculture production and processing and has had a profound impact on both sectors. Rapid advances in molecular biology and further developments in reproductive biology provide new and powerful tools for further innovation. Technologies such as genomics and molecular markers, as described above, are valuable in understanding, characterizing and managing genetic resources in livestock and fisheries as well as in crops and forestry (Box 10). Genetic engineering is also relevant in livestock and fisheries, although the techniques differ, and additional reproductive technologies are available in these sectors. This section describes the reproductive biotechnologies that are specific to the livestock and fisheries sectors.

The main objective of reproductive biotechnologies for livestock is to increase reproductive efficiency and rates of animal genetic improvement. The genetic improvement of locally adapted breeds will be important in realizing sustainable production systems within the broad spectrum of developing country production environments, and will probably best be realized by the strategic use of both non-genetic and genetic interventions. Reproductive biotechnology in fisheries presents opportunities to increase growth rates and improve the management of farmed species and to limit the reproductive potential of genetically engineered species.

BOX 10
State of the World's Animal Genetic Resources

FAO has been requested by its member countries to develop and implement the Global Strategy for the Management of Farm Animal Genetic Resources. As part of this country-driven strategy for the management of farm animal genetic resources, FAO invited 188 countries to participate in preparing the First Report on the State of the World's Animal Genetic Resources, to be completed before 2006. To date, 145 countries have agreed to submit country reports and 30 country reports have been received and analysed (Cardellino, Hoffmann and Templeman, 2003). It is clear from these reports that artificial insemination (AI) is the most common biotechnology used by developing countries in the livestock sector. Many countries have requested training for the expansion of AI use, while expressing concerns that it has often been introduced without proper planning and may pose a potential threat to the conservation of local breeds. Although the use of multiple ovulation followed by embryo transfer (MOET) is mentioned and the desire for its introduction or expansion expressed, no clear objectives for this technique are mentioned. All countries have expressed the wish to introduce and develop molecular techniques, often as a complement to phenotypic breed characterization. Cryoconservation was identified as a priority by all countries and gene banks were recommended, but funding remains a major constraint. When animal GMOs are mentioned it is mainly to express the lack of proper regulations and guidelines for their eventual production, use and exchange. Some countries have expressed concerns that biotechnologies in the livestock sector should be, but are not always, pursued as an integral part of an overall genetic improvement strategy.

Artificial insemination and multiple ovulation/embryo transfer

Advances in artificial insemination (AI) and multiple ovulation followed by embryo transfer (MOET) have already had a major impact on livestock improvement programmes in developed countries and many developing countries because they speed up the process of genetic improvement, reduce the risk of disease transmission and expand the number of animals that can be bred from a superior parent - the male in the case of AI and the female in the case of MOET. They also increase the incentives for private research in animal breeding and significantly expand the market for improved parent stock.

The number of AIs performed globally during 1998 was over 100 million in cattle (primarily dairy cattle, including buffalo), 40 million in pigs, 3.3 million in sheep and 0.5 million in goats. These figures illustrate both the higher economic returns in dairy cattle and the fact that cattle semen is much easier to deep-freeze than semen from other animals. Although over 60 million cattle AIs were performed in South and Southeast Asia, fewer than 1 million were performed in Africa.

AI is only effective when the farm sector has access to considerably greater technical and institutional and other organizational capacity than when male animals are used directly for breeding purposes. On the positive side, farmers employing AI do not have to face the costs or hazards of rearing breeding males and can have access to semen from any part of the world.

Despite the widespread use of AI in developed countries and in many developing countries, including within more advanced smallholder systems, it is applied only on farms that practise intensive livestock management with high-value animals. This is clearly not because of technical problems with semen production and storage, as most procedures are now fully standardized and proven to be effective under tropical developing-country conditions. Rather, it is because of the many organizational, logistical and farmer-training constraints that influence the quality and efficiency of the technology.

MOET takes AI one step further, both in terms of genetic gains possible and level of technical capacity and organization required. MOET is one of the basic technologies for the application of more advanced reproductive biotechnologies such as cloning and transgenics. During 2001 the number of embryos transferred globally was 450 000, mainly in dairy cattle, with North America and Europe accounting for 62 percent, followed by South America (16 percent) and Asia (11 percent). About 80 percent of the bulls used in AI are derived from MOET. The main potential advantage of MOET for developing countries will be in the possibility of importing frozen embryos instead of live animals, for example in the establishment of nucleus breeding stocks of locally adapted genetic resources, with the related lower sanitary risks.

Chromosome-set manipulation and sex reversal in fish

Controlling the sex and reproductive capacity of fish can be important for commercial and environmental reasons. One sex is often more desirable than the other; for example, only female sturgeon produce caviar and male tilapia grow faster than females. Sterility may be desirable when reproduction affects the taste of the product (e.g. oysters) or when farmed species (transgenic or not) might breed with wild populations. Chromosome-set manipulation and sex reversal are well-established techniques to control these factors. In chromosome-set manipulation, temperature, chemical and pressure shocks applied to fish eggs can be used to produce individuals that have three sets of chromosomes rather than the usual two. These triploid organisms generally do not channel energy into reproduction and thus are functionally sterile. Sex reversal can be accomplished by several methods including administering appropriate hormones. For example, genetically male tilapia can be turned into females through oestrogen treatments. These genetic males, when mated with normal males, produce a group of all-male tilapia.

Genetic engineering in livestock and fish

Genetic engineering in animals can be used to introduce foreign genes into the animal genome or, alternatively, to “knock-out” selected genes. The method most used at present involves direct microinjection of DNA into the pronuclei of fertilized eggs, but progress is being made with new approaches such as nuclear transfer and the use of lentiviruses as DNA vectors.

In the first genetic engineering experiments with farm animals, genes responsible for growth were introduced into pigs to increase growth and improve carcass quality. Current research efforts include engineering resistance to animal diseases, such as Marek's disease in poultry, scrapie in sheep and mastitis in cattle, and diseases that affect human health such as Salmonella in poultry. Other examples include increasing the casein content of milk and inducing the production of pharmaceutical or industrial chemicals in the milk or semen of animals. Although conceptually simple, the methods used to genetically engineer livestock require special equipment and considerable dexterity, and no agricultural applications have proved commercially successful thus far. Applications in the near future therefore seem to be limited to the production of transgenic animals for use in the production of industrial or pharmaceutical products.

Genetic engineering is an active area of research and development in aquaculture. The large size and hardy nature of many fish eggs allow them to be manipulated easily and facilitate gene transfer by direct injection of a foreign gene or by electroporation, in which an electric field assists gene transfer. Gene transfer in fish has usually involved genes that produce growth hormone and has been shown to increase growth rates dramatically in carp, salmon, tilapia and other species. In addition, a gene from the winter flounder that produces an antifreeze protein was put into salmon in the hope of extending the farming range of the fish. The gene did not produce enough of the protein to extend the salmon's range into colder waters, but it did allow the salmon to continue growing during cold months when non-transgenic salmon would not grow. These applications are still in the research and development stage, and no transgenic aquatic animals are currently available to the consumer.

Other biotechnologies

Diagnostics and epidemiology

Plant and animal diseases are difficult to diagnose because the signs may be misleading or even entirely absent until serious damage has occurred. Advanced biotechnology-based diagnostic tests make it possible to identify disease-causing agents and to monitor the impact of disease control programmes to a degree of precision not previously possible. Molecular epidemiology characterizes pathogens (viruses, bacteria, parasites and fungi) by nucleotide sequencing, which enables their origin to be traced. This is particularly important for epidemic diseases, in which the possibility of pinpointing the source of infection can significantly contribute to improved disease control. For example, the molecular analysis of rinderpest viruses has been vital for determining the lineages circulating in the world and instrumental in aiding the Global Rinderpest Eradication Programme (GREP) (Box 11). Enzyme-linked immunosorbent assay (ELISA) tests have become the standard methodology for the diagnosis and surveillance of many animal and fish diseases worldwide, and the polymerase chain reaction (PCR) technique is especially useful in diagnosing plant diseases and is proving increasingly so also for livestock and fish diseases. The effectiveness of plant and animal health programmes is also being considerably enhanced by the development of genetic probes that allow specific pathogens to be distinguished and detected in tissue, whole animals and even in water and soil samples.

BOX 11
Biotechnology: ridding the world of rinderpest

Rinderpest, one of the world's most devastating livestock diseases, is a serious threat to millions of small-scale farmers and pastoralists who depend on cattle for their food and livelihoods. This viral disease, which affects cattle including buffalo, yak and related wildlife species, destroyed nearly 90 percent of all cattle in sub-Saharan Africa in the 1890s. An epidemic between 1979 and 1983 killed more than 100 million head of cattle in Africa - more than 500 000 in Nigeria alone - causing estimated losses of $1.9 billion. Asia and the Near East have also been badly affected by this disease.

Today, the world is almost free of rinderpest: Asia and the Near East are believed to be free of the virus and strenuous efforts are being made to ensure that it does not break out of its last possible focus - believed to be the Somali pastoral ecosystem that encompasses northeastern Kenya and southern Somalia. The goal of complete freedom from rinderpest is within our grasp. Rinderpest would be only the second disease to be eradicated worldwide, after smallpox.

The progress seen so far has been a remarkable triumph for veterinary science, and a powerful example of what can be achieved when the international community and individual countries, their veterinary services and farming communities, cooperate to develop and implement results-based policies and strategies for seeing them through. The Pan African Rinderpest Eradication Campaign (PARC), overseen by the African Union, and the Global Rinderpest Eradication Programme (GREP), overseen by FAO, are the key coordinating institutions in the battle against rinderpest.

Biotechnology is at the heart of this effort. First, it enabled the development and large-scale production of the vaccines used to protect many millions of animals through national mass vaccination campaigns. The initial vaccine, which was developed by Dr Walter Plowright and colleagues in Kenya with support from the United Kingdom, was based on a virus that was attenuated by successive passages in tissue culture. Dr Plowright was awarded the World Food Prize in 1999 for this work. Although highly effective and safe, this vaccine lost some of its potency when exposed to heat. Further research was therefore directed at developing a thermostable vaccine for use in remote areas. Success was achieved through research in Ethiopia by Dr Jeffery Mariner supported by the United States Agency for International Development (USAID).

Secondly, biotechnology provided the technological platform (ELISA, chromatographic pen-side systems and molecular tests) to detect and identify viruses and monitor the effectiveness of vaccination campaigns. Before these techniques and the necessary sampling and testing strategies, which were developed by FAO and the International Atomic Energy Agency (IAEA) with support from the Swedish International Development Cooperation Agency (SIDA), vaccinated animals could not be distinguished from infected ones, so countries could not demonstrate that they were free of rinderpest. As a result, they had to conduct costly annual vaccination programmes indefinitely while they continued to suffer from restrictions on animal movement and trade that were imposed to avoid the spread of the disease.

The economic impact of these efforts is already clearly apparent. Although the cost of vaccination and blood sampling and testing has been high for both developing and developed nations, the effectiveness of national campaigns and regional and global coordination is demonstrated by the fact that there is only one small focus of disease outbreaks still occurring around the world. By contrast, in 1987, for example, the disease was present in 14 African countries as well as in Pakistan and some countries in the Near East.

Although costs and benefits vary considerably from country to country, the figures for Africa illustrate the cost-effectiveness of PARC and GREP. Major outbreaks of rinderpest normally last for five years and result in a total mortality of 30 percent. With a total cattle population of 120 million in sub-Saharan Africa, this represents about 8 million head of cattle per year. At an estimated value per head of $120, the cost of another major rinderpest outbreak would be around $960 million. Under PARC, about 45 million head of cattle were vaccinated each year at a cost of $36 million, and the costs of serological monitoring and surveillance were around $2 million. This gives an annual cost-benefit ratio of around 22 : 1 and a net annual economic benefit to the region of at least $920 million.

PARC and GREP have also provided other significant benefits. Not least of these is that through the policies, strategies and institutional arrangements put in place to tackle rinderpest, and that have enabled effective linkages to be established among farmers, field and laboratory personnel and national authorities, they have opened up opportunities for countries to move on and tackle the challenges of controlling or eradicating other diseases affecting livestock and food security in the world.

Vaccine development

Genetically engineered vaccines are being developed to protect fish and livestock against pathogens and parasites. Although vaccines developed using traditional approaches have had a major impact on the control of foot-and-mouth and tick-borne diseases, rinderpest and other diseases affecting livestock, recombinant vaccines can offer various advantages over conventional vaccines in terms of safety, specificity and stability. Importantly, such vaccines, coupled with the appropriate diagnostic test, allow the distinction between vaccinated and naturally infected animals. This is important in disease control programmes as it enables continued vaccination even when the shift from the control to the eradication stage is contemplated.

Today, quality improved vaccines are available for, for example, Newcastle disease, classical swine fever and rinderpest. In addition to the technical improvements, advances in biotechnology will make vaccine production cheaper, and therefore improve supply and availability for smallholders.

Animal nutrition

Biotechnologies have already resulted in animal nutrition aids such as enzymes, probiotics, single-cell proteins and antibiotic feed additives that are already widely used in intensive production systems worldwide to improve the availability of nutrients from feeds and the productivity of livestock and aquaculture. Gene-based technologies are being increasingly employed to improve animal nutrition, either through modifying the feeds to make them more digestible or through modifying the digestive and metabolic systems of animals to enable them to make better use of the available feeds. Although progress in the latter approach is likely to be slow because of gaps in our current understanding of the underlying genetics, physiology and biochemistry, one example of commercial success in high-input, intensively managed systems is the use of recombinant somatotropin, a hormone that results in increased milk production in dairy cows and accelerated growth and leaner carcasses in meat animals.


Biotechnology is a complement - not a substitute - for many areas of conventional agricultural research. It offers a range of tools to improve our understanding and management of genetic resources for food and agriculture. These tools are already making a contribution to breeding and conservation programmes and to facilitating the diagnosis, treatment and prevention of plant and animal diseases. The application of biotechnology provides the researcher with new knowledge and tools that make the job more efficient and effective. In this way, biotechnology-based research programmes can be seen as a more precise extension of conventional approaches (Dreher et al., 2000). At the same time, genetic engineering can be seen as a dramatic departure from conventional breeding because it gives scientists the power to move genetic material between organisms that could not be bred through classical means.

Agricultural biotechnology is cross-sectoral and interdisciplinary. Most of the molecular techniques and their applications are common across all sectors of food and agriculture, but biotechnology cannot stand on its own. Genetic engineering in crops, for example, cannot proceed without knowledge derived from genomics and it is of little practical use in the absence of an effective plant-breeding programme. Any single research objective requires mastery of a bundle of technological elements. Biotechnology should be part of a comprehensive, integrated agricultural research programme that takes advantage of work in other sectoral, disciplinary and national programmes. This has broad implications for developing countries and their development partners as they design and implement national research policies, institutions and capacity-building programmes (see Chapter 8).

Agricultural biotechnology is international. Although most of the basic research in molecular biology is taking place in developed countries (see Chapter 3), this research can be beneficial for developing countries because it provides insight into the physiology of all plants and animals. The findings of the human and the mice genome projects provide direct benefits for farm animals, and vice versa, whereas studies of maize and rice can provide parallels for applications in subsistence crops such as sorghum and tef. However, specific work is needed on the breeds and species of importance in developing countries. Developing countries are host to the greatest array of agricultural biodiversity in the world, but little work has been done on characterizing these plant and animal species at the molecular level to assess their production potential and their ability to resist disease and environmental stresses or to ensure their long-term conservation.

The application of new molecular biotechnologies and new breeding strategies to the crops and livestock breeds of specific relevance to smallholder production systems in developing countries will probably be constrained in the near future for a number of reasons (see Chapters 3 and 7). These include lack of reliable longer-term research funding, inadequate technical and operational capacity, the low commercial value of the crops and breeds, lack of adequate conventional breeding programmes and the need to select in the relevant production environments. Nevertheless, developing countries are already faced with the need to evaluate genetically modified (GM) crops (see Chapters 4-6) and they will one day also need to evaluate the possible use of GM trees, livestock and fish. These innovations may offer opportunities for increased production, productivity, product quality and adaptive fitness, but they will certainly create challenges for the research and regulatory capacity of developing countries.

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