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OCR for page 109
Barbara A. Schaal
Genomits and
Biote~hl1o/ogy ill
Agri~u/ture
Agriculture, like medicine, is rapidly changing be-
cause of advances being made in molecular biology,
particularly in the fields of genomics and biotech-
nology. However, although the application of
genomics and biotechnology to agriculture has
much potential benefit for the human population, these technologi-
cal advances have raised widespread debate about a number of scien-
tific, ethical, and social issues. In fact, the current public debate
about the application of biotechnology to agriculture is extremely
active and visible because the agricultural varieties produced by di-
rect genetic modification are now widely planted and products from
these genetically modified organisms (GMOs) are widespread in the
marketplace. The debate is also international in scope, and it is of-
ten exceedingly bitter, with episodes of test plants being uprooted in
fields and arson occurring in laboratories.
109
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1 10 THE GENOMIt REWLUTION
But just as genomics provides the basis for future advances in
medicine, the application of genomics holds great promise for agri-
culture. Genomics will provide improved varieties of crops for the
U.S. market as well as entirely new products for our economy, with
potentially reduced environmental consequences, such as reductions
in agrochemical use, including pesticides, herbicides, and fertilizers.
One of the most important uses of biotechnology is the application
of genomics to agricultural issues in the developing world, particu-
larly in tropical regions where most of the world's poor reside and
where continual challenges are presented by food shortages. Thus,
biotechnology can contribute to the food security and nutrition of
the world's poorest people, and, in fact, because good health is predi-
cated on adequate nutrition, if the poor are to benefit from modern
medicine and if medicine is to be ultimately successful in the devel-
oping world, the human population must be well fed and nourished.
I would like to outline some of the work currently in progress
regarding plant genomics and discuss how this work contributes to
international efforts in agriculture; I will then briefly compare and
contrast traditional plant breeding with the production of new plant
varieties by genetic engineering; and finally, I will outline the
controversy surrounding GMOs, using examples related to cassava,
an important tropical subsistence crop.
What is biotechnology? The term itself can cause confusion.
Some define the new biotechnology as "the use of biological materi-
als, cells and molecules, to solve problems or to make useful prod-
ucts."i Many aspects of biotechnology are included in this broad
definition, such as genomics, genetic engineering, and plant tissue
culture. It is also important to point out that not all aspects of bio-
technology are controversial the use of genomic markers to pro-
duce a new variety of tomato by traditional breeding or the use of
tissue culture to grow orchids does not create concern. In addition,
the use of tissue culture to replicate, or clone, an apple variety is
generally not considered controversial. However, when we cross
kingdom lines to clone sheep and pigs, public concern becomes evi-
dent. Even so, the greatest area of concern at this time remains
direct genetic modification the insertion of a gene from one species
OCR for page 111
Genomics anal Biotechnology in Agriculture 111
into the genome of another that is, genetic engineering, or the
production of GMOs (see Box 1~.
Plant Genomics
Parallel to the Human Genome Project, projects have been com-
pleted to directly sequence the entire genome of several plant species,
including rice the most important crop worldwide and the model
plant Arabidopsis thaliarta, a member of the mustard family. Other
plant species have extensive physical maps of their genome under
construction using a variety of polymorphic markers, such as micro-
satellites, the highly variable markers used in DNA fingerprinting.
Genomic mapping studies can be used to identify genes of agricul-
tural importance, just as we have seen for cancer-related genes in the
human genome. Plant scientists are specifically interested in the
number and location of genes that confer resistance to pathogens-
that is, genes that are involved in disease resistance and in genes
that convey tolerance to drought, temperature, or other environ-
mental stresses that cause an estimated $500 million of lost crop
production per year. This would include genes that confer tolerance
for heavy metals or other pollutants and, of course, genes that
increase both the yield and nutritional composition of plants. One
area in which agricultural genomics directly differs from human
genomics is its application to direct breeding. Although the thought
of breeding humans is repugnant, we breed plants and animals all
the time. Genomic information the association of mapped markers
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1 12 THE GENOMIt REWLUTION
with a desirable trait can be used to increase the efficiency of tradi-
tional plant and animal breeding in a process known as marker-based
selection.
A major issue in traditional plant breeding is identifying suitable
traits for crop improvement. Where do we turn to find the genes
that add value, such as disease resistance or nutrition, to crop or
animal varieties? One application of genomics involves characteriz-
ing the degree of similarities and differences among collections of
plant varieties that are used as the basis of breeding programs for
crop improvement. Genomics can help explore whether a collection
of varieties represents all the variation within a crop or whether crop
improvement efforts are inevitably doomed to failure because the
necessary traits are not available (see Box 2~. Yet another use of
genomics, only recently widely appreciated for its importance in pro-
viding new crop traits, is understanding the origin of a crop. Wild
ancestors usually contain 75 percent more variation than the de-
rived domesticated crop, and included in this natural variation may
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Genomics and Biotechnology in Agriculture 113
be traits that can dramatically improve crop varieties. Finally,
genomics can provide genetic markers to identify specific varieties of
crops or a specific animal, while a genetic fingerprint can be used to
identify a variety and thus protect the work of breeders from unlaw-
ful use. Fingerprints have also been used in plant forensics and in
tracing the origin of particular varieties or breeds and, in a sad com-
mentary, in efforts to ensure that the animals judged in 4-H compe-
titions are the same ones that a child began raising.
Use of Genomics to Study Cassava
Examining some of the uses of genomics in the study of cassava
(`Mar~ihot esculer~ta) is instructive. Cassava is also known as yuca, and
in the United States it is known as tapioca. Cassava is the primary
source of carbohydrates for more than 600 million people in tropical
regions, mainly in Africa and South America, although its use in Asia
is rapidly increasing. Cassava is grown for its starchy tubers, which
are most often used to prepare farina or flour, and it is the primary
source of carbohydrates in sub-Saharan Africa. It ranks sixth in over-
all world production. Yet despite its clear importance in feeding the
developing world, cassava has been considered an orphan crop or
one that is not commercially viable. Until recently it was grown
primarily by the poorest of subsistence farmers, with minimal local
or international trade. Because there has been little economic incen-
tive for development, the crop has received much less attention from
plant scientists than mainstream crops such as corn, soybeans, rice,
or wheat. However, this picture has changed because of the efforts of
such organizations as the Rockefeller Foundation, and cassava is now
generally acknowledged as an important crop that holds a central
role in the enhancement of food security in the tropics.
Efforts to improve cassava make use of genomic research. In fact,
an international effort is under way to map the genome of cassava in
order to identify genes of importance in enhancing food security
and nutrition and to expedite traditional breeding. Other studies
have examined the genetic basis for future crop improvement by
cataloging the diversity of germ plasm or variety collections. Finally,
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1 14 THE GENOMIt REWLUTION
genomic studies of the origin and domestication of cassava have
yielded important new traits for breeding efforts.
As part of the international effort to improve cassava, collec-
tions of varieties at international agriculture stations were surveyed
to provide new traits for breeding. It became clear that most collec-
tions of varieties were assembled for flour production and that there
was little variation in other agronomic traits. In order to advance
cassava development, new traits were needed. A two-pronged ap-
proach to provide more variation for the cassava breeder is being
used. One part of the approach is to find additional natural varia-
tion in the plant species itself, while the second is to genetically
engineer new traits into the crop.
As recently as 1990, the wild species that gave rise to cassava-
the wild progenitor of cassava was unknown. Dramatically differ-
ent hypotheses were set forth about cassava's origin, one localized to
Mexico, the other a single wild progenitor in Brazil. But because
traditional methods of morphological analysis were unable to re-
solve the origin of the crop, an arsenal of genomic information was
employed. One such genomic study used a combination of DNA se-
quences from two different genes in the cassava genome.
Genomics can be used to further refine the hunt for suitable
traits and genes. Where in the range of this wild species was the
plant domesticated? The wild progenitor, M. flabellifolia, occurs in
the transition zone between the Amazon forest and the cerrado, a dry
savanna region of Brazil along the southern border of the Amazon
region. Ken Olsen, a former graduate student at Washington Univer-
sity, conducted this work using variations in microsatellites (DNA
fingerprint loci) as well as DNA sequences of various genes, in this
case an intron of a metabolic enzyme, glyceradehyde-3-phosphate
dehydrogenase. The intron is a noncoding sequence that accumu-
lates mutations rapidly and provides fine-scale resolution. Using
these data, we can see that the populations of flabellifolia only in one
part of its range contain variants found in cassava, providing strong
evidence that domestication occurred in this region of the Amazon
basin. In fact, cassava is part of an agricultural complex. Jack beans,
chili peppers, and peanuts were all domesticated in the same region.
OCR for page 115
Genomics and Biotechnology in Agriculture 115
This information on the precise geographical location of domestica-
tion can be used to guide the search for new traits and to target
geographical regions for conservation efforts and provides a good
example of genomics informing conservation.
In the case of cassava, we can also look at the efforts of the tradi-
tional people of the Amazon as they selected natural variations in
the crop for their own use. For many crop species, such as corn or
wheat, varieties involved in the early stages of domestication are
lost. This is not the case with cassava, which provides a unique
opportunity to look at early varieties of the crop and to obtain infor-
mation on the process of plant domestication.
Throughout the southern part of Brazil, large fields of cassava
are grown for flour and starch in a manner similar to the way we
grow crops in the United States. In the Amazon, however, where
cassava was first domesticated and where there has been a long his-
tory of association between the crop and humans, we find a very
different situation. The crop is grown in small intercropped fields
with many other crops. There is a diversity of uses, with some
varieties used for flour, some for boiling the roots, some for their
green leaves, and some for a fermented drink. We can see the
astounding diversity of the crop in the Amazon in the shape of the
root, in the deposition of starch, and in the color of the root. One of
the color variants, yellow, has high concentrations of beta-carotene,
a significant finding because a major health problem in the tropics is
lack of vitamin A, resulting from a deficiency of beta-carotene in the
diet. Lack of vitamin A causes night blindness, with hundreds of
thousands of children, particularly in Southeast Asia, affected. These
types of variants, already in the crop, are extremely important, and
because they are integrated into the plant genome, it will be easier to
incorporate them into other varieties of cassava, either by traditional
breeding efforts or genetic engineering.
Introducing New Traits into Crop Varieties
So how do we transfer genetic traits into crop varieties and how do
crop breeders develop new varieties? Modification of plants for
OCR for page 116
1 16 THE GENOMIt REWLUTION
human use is hardly new. Humans from the earliest times have
sought to use plants and animals for their own benefit. The earliest
farmers in the Middle East, China, Mexico, and Africa began to grow
plants they had collected for food or fiber first in the wild. They
chose plants with traits that they favored, the individual with bigger
seeds or with longer and tougher fibers, and they used the seeds of
these plants to begin the next generation. Thus, slowly, over many
generations, differences accumulated between the domesticated crop
and its wild relative.
In some cases, such as corn, the process so changed the crop that
the wild parent species of the crop is no longer obvious. Think about
cauliflower there is nothing that looks like it in nature. Thousands
of years ago early farmers intercrossed plant species growing in their
local region to produce new varieties of crops, and when the new
varieties were useful, they traded seeds and animals over vast geo-
graphical scales. In fact, in the development of some crops such as
wheat or kale, different species have been crossed in order to
incorporate genes from one species into the genome of another (see
Figure 1~. Thus, the concept of using genes from different species as
a basis for crop improvement is hardly new, while interestingly one
of the major concerns about biotechnology has been the introduc-
tion of foreign genes into a species.
Crop breeders follow the same principles today as did those early
farmers, although they use genomic information the association of
a trait with a marker to raise the efficiency of breeding. In the
example of traditional breeding shown in Figure 1, two lineages are
crossed, and the progeny are examined for desirable and undesirable
traits. The best-suited plants or animals are then used to start the
next generation, and the process continues for what can be many
generations.
What are some of the characteristics of traditional crop breed-
ing? First, a source of new genes or traits is obtained. The source in
traditional breeding comes either from other varieties of the same
crop or from wild relatives or closely related species. Traditional
crop breeding is an inexact science, and many genes beyond those
for the selected trait, such as disease resistance, are introduced,
OCR for page 117
Genomics and Biotechnology in Agriculture 117
Variety A
Hybrid
1
Hybrid or back cross line
Variety B
Artificial selection
~ (many generations)
New varieties
FIGURE 1 Traditional agriculture.
sometimes even whole sections of chromosomes that often may
contain some genes that produce an undesirable trait (such as early
dropping of seeds) or that impair crop development (genes of oppo-
site effect that are linked). After the initial cross, the progeny and
their progeny are crossed repeatedly over several generations in order
to eliminate undesirable genes and to concentrate desirable traits.
The process may be very slow, particularly in the case of perennial
crops such as bananas or cassava for which the generation span the
time to first flowering may be several years. Even in annual crops
the process is slow. This is not, of course, to suggest that traditional
breeding is unsuccessful. All of our crops are based on traditional
plant breeding, including those used in the United States as well as
those of the green revolution, and this has increased the yield of
important crops such as rice in Asia. Regardless of future technologi-
cal advances, traditional plant breeding will be an important source
of new varieties or will provide the background stock for new crops
produced by genetic engineering. In fact, traditionally bred varieties
of crops are extremely important in this age of GMOs. The choices
OCR for page 118
1 1 8 THE GENOMIt REWLUTION
of which background and which variety to use for genetic transfor-
mation are critical. Some of the earliest efforts at producing GMO
crops were far from successful because a relatively poor variety was
chosen as the stock for transformation. This occurred in tomatoes,
making the GMO lineage commercially nonuseful.
Genetic engineering presents an alternative to traditional plant
breeding. Using the techniques of molecular biology, a single gene
that codes for a desired trait, such as insect resistance, increased pro-
tein content, or tolerance to drought, is isolated and then combined
with a promoter sequence that will allow the gene to be expressed.
This combination of genes is then introduced directly into the plant
genome. The concept is simple, although the techniques are tech-
nologically complex. Introduction into the plant genome can be
accomplished by physical means through particle bombardment or
can be done biologically. The bacterium Agrobacterium tumefacierls,
which causes crown gall disease in plants, is used to introduce foreign
DNA. Leaf disks are made of the target species the plant species
that will be altered, genetically modified, or transformed. The leaf
disks are incubated with the bacteria, which infect the cells of the
leaf disk the plant cells. The bacterium contains a plasmid, a circu-
lar piece of DNA that holds the gene and promoter sequence. When
the bacteria infect the plant cells of the leaf disk, in some cases the
plasmid DNA with its genes is carried along and is inserted into the
genetic material of the plant. These genetically transformed cells are
then grown by tissue culture into whole adult plants that now con-
tain the foreign gene and can produce seeds by standard crossing or
the pollination of one plant by another. Thus, the plants can
replicate, and the seed companies can build up stocks of seed that
will produce new plants that will also have the new inserted gene.
How do plants produced by genetic engineering differ from those
produced by traditional breeding? First, the process is highly specific.
Only targeted DNA is introduced into the plant that is, specific
genes are added to the target species, as opposed to many genes
introduced by traditional breeding. Second, genes can be introduced
from a wide variety of organisms. Traditional breeding is limited to
closely related species, within the same plant genus for the most
OCR for page 119
Genomics and Biotechnology in Agriculture 1 19
part. Genetic engineering can use genes from across kingdoms, and
plants can be engineered to contain genes from bacteria, fungi, and
animals, which in turn can dramatically increase the range of traits
that a plant can express. Plants are currently being engineered to
serve as factories to produce useful compounds that are unlikely to
occur in nature, such as pharmaceuticals, plastics, and human vac-
cines. A final difference between traditional breeding and genetic
transformation to produce new varieties is the time involved. Breed-
ing studies take years, while genetic transformation can be accom-
plished relatively quickly and more efficiently. In a perennial crop
such as cassava or bananas, it takes a long time to conduct breeding
studies, and because of generation time it also requires vast amounts
of space and labor to grow large the numbers of individuals needed
to be able to screen for selected traits. Genetic transformation oc-
curs in the laboratory and only after it is successful are plants trans-
ferred to the greenhouse and ultimately the field.
Potential Benefits of Genetically Modified Crops
Advocates of biotechnology emphasize several advantages. By intro-
ducing insecticides that are directly produced in the plant, their re-
peated application can be reduced. Likewise, the nutritional content
of food can be increased, novel compounds such as pharmaceuticals
and vaccines can be developed, and crop yields can be stabilized by
increasing resistance to drought, temperature, salinity levels, and
pests. There are, of course, several famous examples of genetically
modified plants. Bt corn is a well-known and controversial example
that gets its name from Bacillus thurir~ger~sis, a common soil bacte-
rium that produces an insecticide in the form of cry proteins. There
are several different varieties of Bt corn, and they differ in the specific
cry protein used and where in the plant it is expressed. The bacterial
gene for the cry protein is engineered into corn to protect the plant
from the European corn borer, a severe corn pest in the United States.
Bt is considered a natural insecticide and is used as such by the
organic farming industry. The controversy that surrounds Bt corn
occurs in two main areas. One is the killing of nontarget organisms,
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120 THE GENOMIt REWLUTION
such as monarch butterfly larvae. Some studies have shown that
monarch larva die when fed Bt pollen, although other studies of
swallowtail butterflies show little effect. The other area of concern
regarding Bt corn is the development of resistance to Bt by insects.
The organic farming industry is concerned about this resistance be-
cause Bt use is an important component of its farming practices.
A less controversial example of genetic engineering is the devel-
opment of rice to express high levels of beta-carotene, the precursor
to vitamin A. This is an encouraging use of biotechnology with
great potential for improving the health and nutrition of the poor,
particularly in Asia, where many children are fed only rice and de-
velop symptoms of vitamin A deficiency, including blindness and
retardation. Rice grains that are engineered to express beta-carotene
have a clear yellow color, with the beta-carotene genes coming from
narcissus plants. Intellectual property rights issues surround the de-
velopment of golden rice, with more than 70 different disputes in-
volved, as various companies, countries, and individuals make claims
to biological materials or the genetic processes used in the rice's de-
velopment, from the choice of plant variety to the techniques of
genetic modification. Usually such claims are resolved by the pay-
ment of royalties. In the case of golden rice, many of the intellectual
property rights claims are being waived as a gesture of goodwill. But
these issues will be a major factor in the development of new
varieties, particularly those intended for the developing world, where
financial resources are slim. Finally, plants can be engineered to
absorb pollutants, which can be an important component of envi-
ronmental remediation. For example, tobacco plants can absorb
heavy metals, mercury, copper, and lead. Under development are
plants that absorb pollutants. These plants are then harvested and
properly disposed of, reducing the level of pollutants in the soil.
Concerns About Genetic Engineering of Crops
Although these developments clearly have their beneficial aspects,
genetic engineering has come under close scrutiny and criticism, as
illustrated by the Bt corn example. The issues surrounding
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Genomics and Biotechnology in Agriculture 121
biotechnology are extremely complex, and many of the criticisms,
concerns, and fears are scientific in nature. Proponents of biotech-
nology argue that crop varieties produced by biotechnology are
carefully regulated by the U.S. Department of Agriculture, the Envi-
ronmental Protection Agency, and the Food and Drug Administra-
tion and have undergone detailed testing far in excess of traditional
crops. Critics of biotechnology point out that long-term effects have
not been monitored and that the effect on the food supply is
unknown because foods produced by GMOs are not labeled. But
many concerns about biotechnology also are founded on much
broader social issues, such as the ethics of inducing genes into vastly
different species, the control of agriculture by large multinational
companies, and our right as consumers to know what is in our food.
What are some of the specific scientific concerns? One concern
involves the safety of food, in particular the possibility of the intro-
duction into food of a foreign protein that may be allergenic to some
members of the public and that is an unsuspected food component,
based on consumers' experience. The example often cited is the
well-intentioned effort to introduce a brazil nut protein into soy-
beans to enhance protein quality, even though some people are
highly allergic to this protein and would not expect to encounter it
in their food. This product was never developed. Another concern
involves the escape of genetically modified organisms into natural
environments. This is an issue particularly in marine organisms such
as fish or shellfish. What would the consequences be if salmon twice
as large as normal began to reproduce in a natural ecosystem? We
simply do not know. Also of concern is possible contamination by
GMOs the mixing of seeds in the food supply or in seed lots sold to
farmers for planting. A good case in point is a recent story about
GMO corn that was approved only for animal consumption being
found in taco shells.
Another concern is hybridization of GMOs that affect the biol-
ogy of native species and have negative effects on nontarget organ-
isms for example, the killing of monarch butterfly larvae by pollen
from Bt corn. Other issues include the development of disease resis-
tance and the use of antibiotic markers in developing GMOs. These
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122 THE GENOMIt REWLUTION
issues must be addressed through scientific study and the determina-
tion of relative risks. This is a complex mix of questions that involve
many different species and for which there will be no single set of
answers. Instead, answers will be specific not only to the issue but
also to the species and the location. For example, in the case of Bt
corn, contamination by genetically engineered corn of wild progeni-
tors of maize is an issue in Mexico where the progenitor grows, but it
not an issue in the U.S. Midwest, which has no close relatives of
corn. The effect of Bt corn on butterfly populations depends on
which butterfly species is being considered and which genetic con-
struct of corn is planted as well as on whether or not the larvae are
eating at the same time that pollen is being shed, which will vary
across the country.
Conclusion
How do we deal with these issues of biotechnology as a society?
Doing nothing means that we forego employing a powerful technol-
ogy, one that holds great promise for improving human health and
nutrition, developing sustainable agriculture with reduced environ-
mental consequences, and developing new products and compounds
that provide economic growth. On the other hand, it is clear there
are a number of scientific issues that must be addressed. In order for
agricultural biotechnology to reach its full potential, those directly
involved in biotechnology must listen to the public debate and con-
cerns, and careful scientific studies that are open to scrutiny and
discussion must be conducted. Finally, the public must be an in-
formed participant in the process.
Acknowledgments
The author acknowledges grant support from the National Science
Foundation.
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Genomics and Biotechnology in Agriculture 123
Note
1. H. Kreuzer and A. Massey, 1996, Recombinant DNA and Biotechnology,
American Society for Microbiology, Washington, D.C.
OCR for page 124
Representative terms from entire chapter:
traditional breeding
