Chapter 13: Genetic engineering and biotechnology.
After completing this chapter, you should be able to:
* Define biotechnology, genetic engineering, and related terms
* Understand the basic processes of biotechnology research
* Recognize the degree of progress made in biotechnology research up to this point
* Identify the latest developments or applications resulting from biotechnology research in plant science
* Describe future impacts of biotechnology research and genetic engineering
* Discuss environmental, ethical, control, and conflict of interest concerns brought about by biotechnology research
* Name five plants altered by genetic engineering
* List four goals of genetic engineering in plants
* Describe the process of genetic engineering
* Explain how DNA controls formation of proteins
* Describe a transgenetic plant
* Diagram how the genetic code is translated
* Give three advantages of genetic engineering over traditional selective breeding
messenger RNA (mRNA)
recombinant DNA (rDNA)
The term biotechnology refers to an array of related basic sciences that have as their centerpiece the use of new methods for the manipulation of the fundamental building blocks of genetic information to create life forms that might not ever emerge in nature--life forms that can expand and enhance the well-being of humans.
The American Association for the Advancement of Science called genetic engineering one of the four major scientific revolutions of this century, on a level with unlocking the atom, escaping the earth's gravity, and the computer revolution. The newfound ability to manipulate cellular machinery has been termed a biotechnology revolution. It could have as profound effect on our society as has the information revolution occurring alongside it. Many believe that the impact of biotechnology will be as great or greater in agriculture as in medicine.
The biotechnology revolution in agriculture is a part of an overall increasing sophistication of biological techniques for improving the production, processing, and marketing of food and fiber. Biotechnology, for instance, allows an acceleration of the process of selection and breeding that has been under way for over 100 years.
In the case of agriculture, as shown in Figure 13-1, biotechnology is built on a broad base of existing and ongoing scientific research that supports and enhances the use of the new methods in genetic engineering and related techniques. This science base helps define what should be genetically engineered and enables the products of fundamental research in the laboratory to be practically applied in the field.
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Every cell in plants, animals, and microbes contains the genetic information to allow perpetuation of that cell or organism. The study of the structure, chemistry, and function of this genetic material has been the basis of understanding that has enabled the biotechnology revolution to come of age.
Genetic engineering, or manipulation, involves taking genes from their normal location in one organism and either transferring them elsewhere or putting them back into the original organism in different combinations. Its value to biotechnology is twofold.
First, scientists can take useful genes from plant and animal cells and transfer them to microorganisms such as yeasts and bacteria that are easy to grow in large quantities. Products that once were available only in small amounts from an animal or plant are then available in large quantities from rapidly growing microbes. One example is the use of genetically engineered bacteria to produce human insulin for treating diabetes.
The second benefit holds particular promise for plant and animal breeders. Genetic engineering allows desirable genes from one plant, animal, or microorganism to be incorporated into an unrelated species, thus avoiding the constraints of normal crossbreeding. A wider range of traits is available to the breeder, and these traits can be incorporated more quickly and more reliably into target species than possible with conventional methods.
Genetic material is arranged in helical strands that contain the code for triggering the characteristic functions of that organism in succeeding generations. The discovery of the structure of the DNA helix in the 1950s (see Table 13-1), the unraveling of genetic code in the 1960s, and the development and refinement of the tools of genetic engineering in the 1970s has caused something fundamentally different to happen in biotechnology science. Using enzymes as "genetic scissors," the genetic structure of cells can be snipped apart and reconstructed in combinations impossible to achieve by natural reproduction (see Figure 13-2). Scientists can not only alter existing genes, but construct totally synthetic genes to cause the organism to perform a desired function.
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To make genetic engineering work, methods are being developed to transfer genetic material into plants and animals and to make sure that the function that has been engineered is expressed at the right place and at the right time. But genetic engineering is only a part of biotechnology. The total picture includes understanding the physiology and biochemistry of the function of interest and knowledge of the existing genetic codes that regulate the process. This allows scientists to understand what to genetically engineer to produce a more desirable organism. Once such product has been created in the laboratory, a variety of techniques such as tissue culture (see Figure 13-3) are often needed to recreate an organism that can compete in a practical ecosystem. The techniques of plant breeding and development are used to take the final product back to the field.
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The Genetic Code
Before scientists could undertake such genetic manipulation, they had to unravel the secrets of the genetic code. They discovered that DNA is a long double-stranded molecule wound in a spiral called a helix, as shown in Figure 13-4. Each gene is a segment of the DNA strand that usually codes for a particular protein. Proteins, like DNA, are also long, chainlike molecules. They are constructed from 20 different amino acid building blocks. They are extremely versatile molecules, anywhere from a few dozen to several hundred amino acids long. Unlike the regular spiral formed by DNA strands, proteins fold and twist into an enormous variety of three-dimensional shapes. The plant and animal bodies possess thousands of different kinds of protein and each plays a specific role in life. That role can be structural or physiological--for example, the proteins involved in the photosynthetic processes.
The DNA code is translated into amino acid sequences in proteins, through an intermediary called messenger RNA (mRNA)--a single-stranded molecule similar to one side of the double-stranded DNA. To be able to control the protein manufacturing process, scientists needed to understand the detail of the DNA coding system.
The DNA Jigsaw
The DNA molecule contains subunits called nucleotides. Each nucleotide comprises a sugar component (deoxyribose), a phosphate component, and one of four different bases--adenine (A), guanine (G), thymine (T), and cytosine (C). Scientists discovered
that DNA was formed from two strands of nucleotides, held together by the bonds between the bases on opposite strands. The entire structure is like a ladder. The sides are formed by the sugar and phosphate groups, and the rungs are the bases. The bases in the "rungs" are matched in pairs like pieces in a jigsaw. The two strands forming the ladder are then wound around one another to form the helix (see Figure 13-4).
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These DNA molecules contain the blueprint for all proteins made in a cell. Each sequence of three bases along the DNA strand is a chemical code for 1 of the 20 amino acids--the building blocks of proteins.
Translating the Code
To make the proteins, the DNA molecule is unraveled, the strands separate, and the cell makes a copy of the relevant part, in the form of single-stranded messenger RNA. The mRNA then moves to the cell's "factories" called ribosomes, where it acts as a template for protein manufacture. The code for the protein is read off the base sequence on the mRNA, and the appropriate amino acids are added to the protein one by one, aligned against the mRNA code by small segments of RNA called transfer RNA (tRNA) (refer to Figure 13-2).
The coding system is universal. It is basically the same in all animals, plants, and microorganisms. A piece of DNA from a plant inserted into the chromosome of a bacterium makes perfect sense to the bacterial cell.
Scientists have known the detailed amino acid sequence of many key proteins for a long time. Once they also understood which base sequences in DNA were represented by which amino acids, they could identify the genes in the chromosome that coded for particular proteins.
Recombinant DNA Technology
Identifying the genes is not enough. The next step is to be able to copy the gene and insert it into other cells--cells that can be grown easily using existing microbiological techniques, or cells of other plants or animals where the protein is required (see Figure 13-5). To do this, scientists used new biochemical techniques, involving special enzymes, to break the DNA strand at chosen points, insert new segments, and "stitch" the strand back together again. The result, known as recombinant DNA (rDNA), is DNA that incorporates extra segments bearing genes it had not previously contained.
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Insertion of genes into different organisms is made much easier by the existence of bacterial plasmids--small circles of DNA that are much smaller than the bacterial chromosome. Some of these plasmids can pass readily from one cell to another, even when the cells are far apart on the evolutionary scale. Using the special "cut and paste" enzymes mentioned earlier, scientists can insert genes from one organism into a bacterial plasmid, then insert the recombinant plasmid into a living microorganism, where it will direct the synthesis of the desired proteins. Human insulin for treating diabetes can now be produced in this way.
So far, scientists have used genetic engineering to produce the following:
* Improved vaccines against animal diseases such as foot rot and pig scours
* Pure human products such as insulin and human growth hormone in commercial quantities
* Existing antibiotics by more economical methods
* New kinds of antibiotics not otherwise available
* Plants with resistance to some pesticides, insects, and diseases * Plants with improved nutritional qualities to enhance livestock productivity
In the past, agriculture has been an energy and labor intensive industry. Biotechnology offers the opportunity to reduce both these costs in future operations. Inherent resistance to pests and disease can reduce the use of chemical pesticides, reducing the cost of production and the potentially harmful environmental effects of such practices. The possible uses of biotechnology for agriculture are limited only by imagination and initiative, such as the peach and apple orchards in Figure 13-6.
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The total system for food and fiber production is extremely diverse and multifaceted, providing a broad range of potential applications of biotechnology. Biotechnology is not only enhancing the traditional enterprises in food and fiber production, it also is producing new high technology industries that are providing new jobs and producing new goods and services. Sometimes thinking of biotechnological applications is limited to production agriculture, where an exciting new array of scientific breakthroughs is being developed. Other exciting areas related to production agriculture include: the new application of biotechnology to food processing and manufacturing, to new methods for ecologically sound disposal of wastes, and to biochemical engineering where totally new products are being produced from agricultural residues using biotechnological tools.
One of the early uses of biotechnology has been to use simple organisms such as bacteria and yeast as so-called biological factories to produce biologically active compounds. Genetic codes for these compounds are inserted into the genetic makeup of these simple organisms along with genetic instructions that cause the production of the desired material.
Through these techniques, for instance, human insulin is now produced and is replacing insulin from animal sources for treatment of diabetes in humans, as shown in Figure 13-7.
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Interferon, a biological anticancer treatment and antiviral material previously available in only minute quantities, can now be produced inexpensively and in large quantities using biological factories. Hormones, such as bovine growth hormone, have been manufactured using this method. The product is being injected in dairy cattle to enhance milk production by some 20% to 30%. Diagnostic reagents and improved vaccines for animal and human disease are being produced using these techniques. Early progress has been rapid in this area because the genetics of these organisms is relatively simple.
In many parts of the world, water is the limiting factor in food production. Biotechnology is being used to greatly enhance the production of plants with high drought-stress tolerance. These plants will maintain yields in environments with much less water, and there is the promise of developing plants that can use brackish water. These developments could have a profound effect on stretching water resources and will be crucial as water for irrigation becomes less available and more expensive.
Plant growth and development has been the subject of investigation for decades, but until recently remained poorly understood. Biotechnology makes it possible to isolate, characterize, and manipulate specifc genes. This new technology provides a powerful tool to understand plant growth and development and a way to directly manipulate the process. Opportunities in this field include altering chemical composition of the plant product, improving processing quality, producing plants resistant to stress or herbicides, altering plant size, changing the ratio of grain to stalk, and making an annual plant a perennial (see Figure 13-8).
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The transfer of nitrogen-fixing genes to plants is possible with the techniques of biotechnology. Nitrogen-fixing genes might be transferred to plants that do not now have this nitrogen-fixing capacity. These genes would have to be in a form that could be incorporated into the plant genome, replicated, and expressed. The genes would have to be expressed in an environment amenable to nitrogen fixation where the enzyme, nitrogenase, could be protected from oxygen and where the enzyme system could tap into the sources of reductant and energy from the plant.
The full complement of nitrogen-fixing genes has been cloned from Klebsiella pneumoniae and transferred to and expressed in another bacterium, Escherichia coli.
Plant Disease Resistance
Genetic engineering offers an exciting and environmentally sound way of reducing the cost and increasing the effectiveness of plant pest control, through the development of genetic resistance to disease. Because disease resistance is controlled by relatively few genes, this area is among the most favorable candidates for early application of biotechnology to plants.
The search for resistant genes involves screening cultivars or species of plants to identify individuals that exhibit resistance to infection, replication, or spread of a pathogen. If the resistance trait is the result of expression of a single gene or genetic locus, plant breeders begin the task of introducing the resistance trait into a cultivar having desirable agroeconomic traits that will ultimately be released to the farmer. The plant-breeding process (see Figure 13-9) usually requires more than five years and considerable evaluation of progeny to eliminate plants that contain undesirable traits in addition to the disease-resistance trait.
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Tobacco Mosaic Virus
Tobacco mosaic virus (TMV) causes the leaves of some important crop plants, including the tomato, to wither and die. Scientists have incorporated into the tomato plant a gene that protects it from infection. It has the same effect as a vaccine for humans. This approach is now being applied to other viral diseases in crops.
Plant microbes affect agriculture both detrimentally and beneficially. Economic losses and human suffering result from plant diseases caused by microbes, so much ecological research deals with plant pathogens (disease-producing agents). Unfortunately, with so many important crops, diseases, and agroecosystems, only a small proportion can be investigated intensively.
Scientists focus on microbial influences that maintain plant health. One of the successful applications involves cross-protection, in which the infection of plant tissues by one virus suppresses the disease caused by another closely related strain of the virus. The protecting strain must have negligible impact on the host. Such strains have been found naturally, but also can be created in the laboratory via biotechnology. Cross-protection has been used successfully in protecting citrus trees from severe strains of Citrus tristeza virus.
Another successful example involves the bacterium that causes crown gall of stone fruits and other plants: A nonpathogenic (or "friendly") strain produces an antibiotic that inhibits the pathogenic strain. Because the two strains are closely related, the nonpathogen survives in the same niches as the pathogen, and responds similarly to environmental fluctuations. Consequently, upon deliberate release of the biocontrol agent, close association of the two bacteria is assured. For crown gall, the biocontrol agent was naturally occurring, but with biotechnology it will be possible to engineer normal resident nonpathogenic microbes into biocontrol agents.
Some microbes can be used as biocontrol agents for weeds. For example, a fungus is used to control northern jointvetch in rice and soybean fields. Knowledge of the ecology and epidemiology of this fungus contributed to the development of a rational, effective biological control (biocontrol) approach. Even though the genetic and biochemical bases of pathogenicity are unknown for this pathogen, it is so specific in its actions and is relatively unable to be dispersed widely that it makes a desirable biocontrol agent. With biotechnology, other pathogens of weeds can be altered for use in biocontrol. The ecology of specific candidates will have to be well described to assure selection of those with the greatest potential for safe, effective use.
DARWIN DAY Darwin Day is the anniversary of the birthday of Charles Darwin on February 12, 1809. Science and people in general have been deeply affected by Darwin's work. Now with over 200 years of evidence supporting his initial findings, modification and refinement continue to this day. For his contributions to the body of scientific knowledge and his commitment to scientific methodology, his birthday is celebrated globally. These celebrations of Darwin's work, and tributes to his life, have been organized since his death in 1882. Darwin provided the first coherent theory of evolution by means of natural selection. His theory has had far-reaching implications in almost all disciplines--rocking the foundation of our knowledge base. Charles Darwin's Origin of Species (published in 1859) is a key work in scientific literature and in evolutionary biology. The book's full title is On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. It introduced the theory that populations evolve over the course of generations through a process of natural selection. It was controversial because it contradicted religious beliefs of biology. Darwin's book was the result of evidence he had accumulated on the voyage of the Beagle in the 1830s and added to through continuing investigations and experiments after returning. The book is readable and attracted widespread interest on publication. It also was controversial, generating much discussion on scientific, philosophical, and religious grounds. Here is how Darwin described natural selection in his book: As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form. Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring.... I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man's power of selection. The scientific theory of evolution has evolved since Darwin first presented it, but natural selection remains the most widely accepted scientific model of how species evolve. Some advocates would like to have a public holiday declared for February 12, 2009. The year 2009 will mark an important year for Darwin Day celebrations. It will be the 200th anniversary of Darwin's birth, and will also mark the 150th anniversary of the publication of Darwin's On the Origin of Species.
Mobile or transposable elements provide an opportunity to isolate and identify genes that would enhance crop quality and productivity. These mobile elements provide a direct link between plant characteristics, for example, disease resistance, plant height, organ shapes, and the DNA molecules that control the particular traits.
Transposable elements provide one way of physically isolating genes that control complex plant traits because they provide a direct connection between the observable trait and the DNA molecule that controls it. Even though all the intermediate steps in the process (the messenger RNA, the proteins produced by the genes, and the pathways) may be unknown, the gene responsible for the trait can be identified and physically isolated using a tagging procedure.
Nutritional Quality of Plants
Many plant foods are deficient in nutrients or lose nutritional value during storage. Some plants have other features that are not optimum for human or animal health. Genetic engineering can be used to both improve and retain nutritive value as well as to modify undesirable properties of plant products. For instance, through genetic engineering, the composition of dietary fats can be modified to reduce their possible contribution to cardiovascular disease.
Scientists are working to develop a sulfur-rich feed plant for sheep. Research has shown that sulfur supplements in the diet help sheep produce better quality wool fiber. Scientists believe it would be more cost effective to feed the sheep on pasture that was naturally sulfur-rich. Using biotechnology, scientists have developed alfalfa strains that produce a sulfur-rich protein in their leaves. They now plan to develop pasture grasses with the same characteristics.
Biological Control of Pests
Biological control exploits natural factors in the life cycle of harmful insects as a means of control. Some possibilities include use of highly specific insect pathogens (bacteria, viruses, fungi) to produce insect disease or death or to use unique viruses that interfere with the insect immune system, making it more vulnerable to disease. Also, insect chromosomes or genes with some ability to control population growth are under study as well as methods that interfere with normal growth and maturation. All these processes of biological control are potentially capable of being enhanced through the use of genetic engineering to improve the effectiveness of the crop insect's natural enemy. These processes are highly specific to single insect species and so are highly desirable environmentally as alternatives to chemical pesticides (see Figure 13-10).
For example, an insecticidal protein has been successfully incorporated into tomato plants to provide protection from some leafeating insects. The protein comes originally from Bacillus thuringiensis, a naturally occurring bacterium that lives in the ground. Using genetic engineering techniques, scientists have inserted the gene for this protein into the plant's genetic material. When an insect eats the modified plant, the protein is released and the insect dies.
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Another example is glyphosate, which is an environmentally friendly, widely used broad spectrum herbicide. It is easily degraded in the agricultural environment and works by interfering with an enzyme system that is present only in plants. Unfortunately, the herbicide kills crop plants as well as weeds, but scientists have now used genetic engineering methods to breed crop plants that are glyphosate resistant. By planting these modified crops, farmers can control weeds by spraying with glyphosate alone.
Transgenic plants and animals result from genetic engineering experiments in which genetic material is moved from one organism to another, so that the latter will exhibit a desired characteristic. Scientists, farmers, and business corporations hope that transgenic techniques will allow more precise and cost-effective animal and plant breeding programs. They also hope to use these new methods to produce animals and plants with desirable characteristics that are not available using current breeding technology. Table 13-2 lists genetically modified plants.
In traditional breeding programs, only closely related species can be crossbred, but transgenic techniques allow genetic material to be transferred between completely unrelated organisms, so that breeders can incorporate characteristics that are not normally available to them. The modified organisms exhibit properties that would be impossible to obtain by conventional breeding techniques.
Although the basic coding system is the same in all organisms, the fine details of gene control often differ. A gene from a bacterium will often not work correctly if it is introduced unmodified into a plant or animal cell. The genetic engineer must first construct a transgene--the gene to be introduced. This is a segment of DNA containing the gene of interest and some extra material that correctly controls the gene's function in its new organism. The transgene must then be inserted into the second organism.
Making a Transgene
All genes are controlled by a special segment of DNA found on the chromosome next to the gene and called a promoter sequence. When making a transgene, scientists generally substitute the organism's own promoter sequence with a specially designed one that ensures that the gene will function in the correct tissues of the animal or plant and also allows them to turn the gene on or off as needed. Figure 13-11 shows a common transgenetic plant. For example, a promoter sequence that requires a light "trigger" can be used to turn on genes for important growth regulators (hormones) in plants. The plant would not produce the new hormone unless provided the appropriate trigger.
Inserting the Transgene
Unlike animals, plants do not have a separate germ line (eggs and sperm), and all cells of a plant retain the capacity to develop into a whole plant. This makes inserting the transgene much simpler. The transgene can be introduced into a single cell by a variety of physical or biological techniques, including using viruses or derivatives to carry the new gene into the plant cells.
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Tissue culture techniques can then be used to propagate that cell and encourage its development into a transgenic plant, all of whose cells contain the transgene. Once the plant is produced, nature takes over and increases plant numbers by normal seed production.
Uses of Transgenic Techniques
Transgenic methods have now been developed for a number of important crop plants such as rice, cotton, soybean, and oilseed rape and a variety of vegetable crops like tomato, potato, cabbage, and lettuce. New plant varieties have been produced using bacterial or viral genes that confer tolerance to insect or disease pests and allow plants to tolerate herbicides, making the herbicide more selective in its action against weeds and allowing farmers to use less herbicide.
For example, a new variety of cotton has been developed that uses a gene from the bacterium Bacillus thuringiensis to produce a protein that is specifically toxic to certain insect pests including bollworm, but not to animals or humans. (This protein has been used as a pesticide spray for many years.) These transgenic plants should help reduce the use of chemical pesticides in cotton production, as well as in the production of many other crops that could be engineered to contain the Bacillus thuringiensis gene. In another case, a gene from the potato leaf roll virus has been introduced into a potato plant, giving the plant resistance to this serious potato disease.
Transgenic technologies are now being used to modify other important characteristics of plants such as the nutritional value of pasture crops or the oil quality of oilseed plants like linseed or sunflower.
With techniques similar to those used to make insulin-producing bacteria, it may be possible to develop animals that produce other useful biopharmaceuticals--drugs produced by living tissues. For example, researchers have developed transgenic animals such as cows and sheep that secrete economic quantities of medically important chemicals in their milk. The cost of these drugs may be much less than for those produced using conventional techniques.
Eventually it may also be possible to develop crops for nonfood uses by modifying the starches and oils they produce to make them more suitable for industrial purposes, or to use plants rather than animals to make antibodies for medical and agricultural diagnostic purposes. In the cut flower industry, transgenic research may yield products such as blue carnations as novelty items.
Advantages over Selective Breeding
Transgenic technology is an extension of agricultural practices that have been used for centuries--selective breeding and special feeding or fertilizing programs. It may reduce or even replace the large-scale use of pesticides and long-lasting herbicides. Transgenic technology is still experimental and is still very expensive. If it could be made commercially viable, it would offer a number of advantages over traditional methods.
Compared with traditional methods, transgenic breeding is:
* More specific--scientists can choose with greater accuracy the trait they want to establish. The number of additional unwanted traits can be kept to a minimum.
* Faster--establishing the trait takes only one generation compared with the many generations often needed for traditional selective breeding, where much is left to chance.
* More flexible--traits that would otherwise be unavailable in some animals or plants may be achievable using transgenic methods.
* Less costly--much of the cost and labor involved in administering feed supplements and chemical treatments to animals and crops could be avoided.
Micropropagation (Tissue Culture)
Plant breeders already use micropropagation techniques in which whole plants are grown from single cells or from small plant parts for rapid multiplication of identical, disease-free plants, such as the papaya plantlets in Figure 13-12. If necessary, genetic engineering can be used to incorporate desired characteristics from other species into the cell prior to propagation.
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Current research will see the improvement and development of crops for specific purposes. Plants that require less water could be developed for countries with arid climates. Crop plants engineered to be tolerant to salt could be farmed in salt-damaged farmland or could be irrigated with salty water. Crops with higher yields and higher protein values are also possible. Biotechnology will help to do the following:
* Improve farming productivity
* Protect our environment by allowing reduced and more effective use of chemical pesticides and herbicides
* Reduce food costs
Table 13-3 summarizes the long-term goals of plant biotechnology.
Following biotechnology and genetic engineering has been the development of three new fields of study: genomics, bioinformatics, and proteomics. This "omics" revolution in science has been very fast and, in many cases, borders on overwhelming.
The term genome originated in 1930 and was used to denote the totality of genes on all chromosomes in the nucleus of a cell. Incredibly, DNA was not identified as the genetic material of all living organisms until 1944. The genetic code was elucidated in 1961; with these fundamental insights in hand, it was possible to contemplate the concept that biological organisms had a blueprint consisting of finite numbers of genes. The sequence of these genes encoded all the information required to specify the reproduction, development, and adult function of an individual organism.
Genomics is operationally defined as investigations into the structure and function of very large numbers of genes undertaken in a simultaneous fashion. Because all modern genomics have arisen from common ancestral genomes, the relationships between genomes can be studied with this fact in mind. The study of all the nucleotide sequences, including structural genes, regulatory sequences, and noncoding DNA segments, in the chromosomes of an organism plant or animal is called genomics. The massive interest and commitment to genomics flows from the generally held perception that genomics will be the single most fruitful approach to the acquisition of new information in basic and applied biology in the next several decades.
Despite the importance of plants, much basic research on plant functions still needs to be done. For example, scientists need to learn more about how plants grow, how they protect themselves from disease or insects, and how they respond to their environment. One of the best ways to do this is to study the information encoded in a plant's DNA, the material which makes up its genes.
An understanding of genomics means that information gained in one organism can have application in other even distantly related organisms. Comparative genomics enables the application of information gained from facile model systems to agricultural or nonmodel taxa. The nature and significance of differences between genomes also provides a powerful tool for determining the relationship between genotype and phenotype. Plant genomics hold the promise of describing the entire genetic repertoire of plants. Ultimately, plant genomics may lead to the genetic modification of plants for optimal performance in different biological, ecological, and cultural environments for the benefit of humans and the environment.
Recent scientific advances through private and public investments in studying DNA structure and function not only in humans but in other organisms such as plants can extend a new biological paradigm to improving the useful properties of plants that are important to humanity. Solutions to many of the world's greatest challenges can be met through the application of plant-based technologies. For example, the revitalization of rural America will come from a more robust agriculture sector; reductions in greenhouses gasses can be achieved from the production of plant biofuels for energy; chemically contaminated sites can be rehabilitated economically using selected plants; and worldwide malnutrition can be greatly reduced through the development of higher yielding and more nutritious crops that can be grown on marginal soil.
Molecular plant breeding efforts have received a boost in the past decade from massive amounts of gene and genome sequence information (genomics), which have been used in parts to generate molecular markers for marker-assisted breeding in species such as alfalfa--the number one forage crop--white clover, and tall fescue.
Functional genomics can produce massive amounts of data on the majority of genes of a sequenced organism. Functional genomics includes transcriptomics, proteomics, and metablolmics, which identify and quantify thousands to tens of thousands of gene transcripts (RNA), proteins, and metabolites, respectively, in cells, tissues, or organs. By revealing concerted changes in RNA, proteins, and metabolites during plant development, under optimal or stressed conditions genes determine important plant characteristics or traits.
Other disciplines involved in plant genomics are genetics, biochemistry, biophysics, molecular and cell biology, and physiology. They are also used to elucidate the precise biological function(s) of specific gene products. Ultimately by combining genomics, functional genomics, and other approaches, the aim is to identify genes with key roles in plant metabolism, growth, development, and response to the environment, which will be of value to plant breeding efforts to improve plant performance, yield, and quality.
Genomics and functional genomics approaches are used to identify genes and process that enable plants to respond and adapt to environmental challenges, such as pathogen attack (bacterial, fungal, or viruses), intensive grazing, or abiotic stress such as drought and soil acidity/aluminum toxicity. Another target of this type of research is plant secondary metabolism, which yields an amazing array of compounds of industrial and medicinal value. Secondary metabolism is crucial for the production of structural compounds in plants such as lignin, which affects digestibility of plant material.
The part of the "omics revolution" that has made it possible to analyze and interpret all the genomics data is bioinformatics; for example, genomics generates data, bioinformatics provides the analytical tools enabling those data to be interpreted.
Bioinformatics is the study of the inherent structure of biological information and biological systems. It puts together the ever increasing avalanche of systematic biological data with the analytic theory and practical tools of computer science and mathematics.
Genomics data can be viewed as the greatest encoding problem of all time. These bioinformatics problems open the way for biologists to collaborate with mathematicians and computer scientists, because it aims to translate "biology problems" into new challenges that are interesting to theoreticians: problems of information content, structure, and encoding, which inherently interest theorists. By contrast, the common view and practice of bioinformatics, as simply an application of existing mathematical and computer science to biological problems, translates biological questions into the language of information content, structure, and encoding, so the mathematicians and computer scientists are needed to help solve these problems.
Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology.
Included in the "omics" revolution are a number of powerful tools including variations on the theme of proteomics. Proteomics aims to identify and characterize the expression pattern, cellular location, activity, regulation, posttranslational modifications, molecular interactions, three-dimensional structures, and functions of each protein in a biological system.
The potential of proteomics for plant improvements is outstanding considering that the developments in robotics and nanotechnology achieved in the last 10 years allow for the genome sequencing of many organisms. The new genomics science highlights our ignorance of the newly discovered sequenced genes.
In plant science, the number of proteome studies is rapidly expanding after the completion of the Arabidopsis thaliana genome sequence and proteome analysis of other important or emerging model systems. This analysis of plants is subject to many obstacles and limitations as in other organisms, but the nature of plant tissue, with their ridged cell walls and complex variety of secondary metabolites, means that extra challenges are involved that may not be faced when analyzing other organisms.
Proteomics is a complementary approach to solve many problems; from mutant characterization to genetic variability estimates, from the establishment of genetic relationship to the identification of the genes involved in the response to biotic or abiotic stresses, from the definition of genes coregulated or coaffected by a given molecule to the quantification of their amounts, proteomics, with its recent development in mass spectrometry and database management is today a very powerful new tool to deal with the global approaches of modern biology.
Proteomics is a promise of a great revolution. If genomes and microarrays gave us a glimpse into the blueprint of life, proteomics was going to unravel the working end of the cell: the protein machinery. But, it has rapidly become apparent that proteins were not going to give up their secrets without a fight. Proteins are much more diverse in their properties than nucleic acids, a single protocol for example preparation or analysis is unlikely. There is no PCR for proteins, so the amount of starting tissue and detection sensitivity are critical limitations. Protein concentrations extend over a far greater dynamic range than nucleic acids. Proteomics must deal with differences in abundance of six to eight orders of magnitude, meaning that the few most abundant proteins often interfere with detection of low-level proteins. None of these problems are insurmountable, but they have slowed the appearance of the expected biological results as each problem needed to be solved individually.
With the sequencing of the Arabidopsis genome, there is a mature proteomics technology platform. Now is the time to bring the resources and tools together. Proteomics gives us the molecular mechanisms that will fill in the gaps that have existed in the defined genetic pathways. Proteomics will blend perfectly and powerfully with genetics. The revolution has begun and it continues at a rapid pace.
Biotechnology Policy, Public Perception, and the Law
While the opportunities for using biotechnology in agriculture are truly fantastic, they have triggered public concern and a corresponding need to develop methods to assure that biotechnology is used in an environmentally sound manner. Some people fear that widespread use of plants and animals with altered genetic characteristics may threaten the environment by disturbing the existing balance between organisms. This balance is a dynamic one. Since gene mutation and changes in gene position within chromosomes are normal events in all living organisms, organisms with new properties are constantly emerging. However, transgenic technology does expand the scope of these events. Careful examination of the properties of the transgenic organism is essential before it is studied outside the closed environment of the laboratory.
Agricultural researchers are enhancing traditional methods of manipulating plant and animal germplasm used for over 100 years as well as using the guidelines in recombinant DNA studies directed by human applications. In both cases, there is a sound track record of safety associated with research and its products. Recombinant DNA techniques have been safely employed since the mid-1970s through an essentially self-imposed series of safety guidelines and reviews within the scientific community. Formerly under the control of the National Institutes of Health, these safety procedures are now the responsibility of the U.S. Department of Agriculture. Methods and procedures are being completed to assure continued safety in applying recombinant DNA techniques for agricultural research and in producing biotechnology products.
1. Success in biotechnology and genetic engineering is based on our increasing understanding of the genetic code. Biotechnology research benefits agriculture, forestry, and industrial processing by diversifying crops and crop products, with increasing concern and care for the environment. Some plants have already benefited from genetic engineering.
2. Much current research focuses on understanding and developing useful promoter sequences to control transgenes and establishing more precise ways to insert and place the transgene in the recipient. Much still needs to be done to improve our knowledge of specific genes and their actions and of the potential side effects of adding foreign DNA and of manipulating genes within an organism.
3. Following biotechnology and genetic engineering has been the development of three new fields of study: genomics, bioinformatics, and proteomics. The "omics" revolution in science continues at a rapid pace.
4. A formal regulatory system exists to examine areas of risk or uncertainty before field testing is approved. The government, industry, and other interested groups are also considering more general questions on the uses of this new technology, including ethical questions and sociological consequences.
Something to Think About
1. Explain why to a cell, DNA is DNA whether it came from a plant or animal, or from a different species.
2. Name the four bases found in DNA.
3. List five crops that have been genetically engineered.
4. Name four of the goals of biotechnology.
5. Identify the role of the following: DNA, rDNA, tRNA, and mRNA.
6. Explain how DNA controls the formation of proteins.
7. Why are people concerned about biotechnology and genetic engineering?
8. What future impacts could genetic engineering have on agriculture?
9. Define genetic engineering, biotechnology, and transgenetic.
10. Describe the advantages that genetic engineering has over traditional selective breeding.
11. Do the benefits of genetic engineering and biotechnology outweigh the risks?
Halford, N., Ed. 2006. Plant biotechnology: Current and future applications of genetically modified crops. New York: Wiley.
United States Department of Agriculture. 1986. Research for tomorrow. The yearbook of agriculture. Washington, DC: USDA.
United States Department of Agriculture. 1992. New crops, new uses, new markets. 1992 yearbook of agriculture. Washington, DC: USDA.
United States Department of Agriculture. 1994. Biotechnology and sustainable agriculture: A bibliography. Washington, DC: USDA.
Vasil, I. K., Ed. 1990. Biotechnology: Science, education and commercialization. An international symposium. New York: Elsevier Publishing Company.
Internet sites represent a vast resource of information. The URLs for Web sites can change. Using one of the search engines on the internet, such as Google, Yahoo!, Ask.com, or MSN Live Search, find more information by searching for these words or phrases: biotechnology, agroeconomic, agroecosystems, biocontrol, bioinformatics, biopharmaceuticals, genetic code, genetic engineering, genomics, DNA, RNA, micropropagation, proteomics, and transgenetic.
Table 13-1 Brief History of Genetic Engineering Year Event 1944 DNA identified as genetic material 1953 Double strand DNA structure identified 1973 First transgenic bacteria prepared 1976 First genetic engineering company (Genentech) established 1980 First patent for genetically engineered microbe 1982 Approval of first genetically engineered drug 1986 First field test of genetically engineered plant 1987 Genetic engineering patent extended to higher life forms Table 13-2 Genetically Modified Plants Crops Vegetables Flowers Trees Alfalfa Asparagus Arabidopsis Apple Canola Cabbage Petunia Pear Corn Carrot Poplar Cotton Cauliflower Walnut Flax Celery Potato Horseradish Rice Lettuce Rye Peas Soybean Tomato Sugar beet Sunflower Tobacco Table 13-3 Long-Term Goals of Plant Biotechnology Agronomic traits Quality traits Specialty chemicals Herbicide tolerance Oil composition Plastics Insect control Solids content Detergents Virus resistance Nutritional value Pharmaceuticals Fungal resistance Consumer appeal Food additives
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|Title Annotation:||PART 4: Evolution and Diversity|
|Publication:||Fundamentals of Plant Science|
|Date:||Jan 1, 2009|
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