Research Update: what do all these genes do?

From a molecular geneticist’s perspective, there are just too many genes in rice. Forty one thousand by my last count. Many seem to carrying out identical functions. If we knock out one, another one compensates. This makes it very confusing to elucidate the role of each gene.

Why bother with this work then? Well if we can figure out what each rice gene does this information can be used to develop new rice varieties with useful properties such as tolerance to flooding or resistance to disease.

In our new paper, we report a method to efficiently overcome the obstacle of gene redundancy by combining information on gene expression data with mutant phenotypes. We first developed a 45K oligo-microarray (PLoS One in press) and used it to examine genes expressed in the light vs. the dark. We then screened for rice lines with mutations in the strongly light-induced genes. This analysis effectively provided candidate functions for genes of previously unknown function.

We also examined the expression of a set of genes in specific biochemical pathways. This analysis allowed us to predict genes likely involved in these pathways. We validated this model by analyzing rice lines carrying mutations in ten of these genes.

We are now using this strategy to identify all the genes that control disease resistance in rice.



ronald, .Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice.

"I highly recommend the book" says Sean Feder

Check out the latest review of Tomorrow's Table published in Capital Press, the most comprehensive online source of daily farm and ranch news

By WES SANDER
For the Capital Press

Pamela Ronald and Raoul Adamchak say they're not proposing a seismic change in mainstream farming practices - just the next step in a long evolution.

Ronald and Adamchak are the husband-and-wife authors of the book "Tomorrow's Table: Organic Farming, Genetics and the Future of Food," published in April. Ronald is a professor of plant pathology and chair of the Plant Genomics Program at the University of California-Davis; Adamchak manages UC-Davis' organic farm.

"It's not so much replacing conventional agriculture as (altering it)," Adamchak said.

The authors advocate combining genetically engineered crops with organic growing practices as a means of feeding the world in a sustainable manner. They say they've heard criticism from both sides.

The organic-farming community tends to show a protectiveness of federal organic-certification standards, they say. Defined by federal rules in the 1990s, organic certification cannot be awarded to any crop created through genetic modification. But these authors don't want to mess with organic standards.

"One of the things we're encountering is that people are posing this false choice - conventional or organic?" Ronald said.

Those categories tend to be defined by current realities. For example, bioengineered crops are often connected with large corporations that control the distribution, pricing and use of seeds.

Observers describe such practices as counterproductive in impoverished regions of the globe. Ronald and Adamchak are not advocating any current market structures - they're describing the value of two growing systems from the perspective of agricultural science.

As organic farming gained popularity in the last 15 years, bioengineering has also ascended the market. Now, bio-engineered crops account for 50 to 90 percent of commercial crops for which they are available, the authors say - notably cotton, corn, canola and papaya.

When a virus nearly wiped out Hawaii's papaya crop in the mid-1990s, scientists responded by engineering a resistant strain. Today, that strain accounts for most of Hawaii's papaya crop, allowing for a reduction of chemical usage.

Engineered crops do have their limits. Chinese cotton growers found success with a bio-engineered crop that is resistant to caterpillars. But when they found it susceptible to other pests, they turned again to chemical pesticides.

Ronald and Adamchak say those growers might still have avoided chemicals by combining the bio-engineered plant with organic growing techniques, such as crop rotation and integrated pest management. It's that sort of combining of practices that is necessary to feed the world's population in a sustainable manner, the authors say.

Because they cannot use chemical crop applications, organic growers rely on the best-performing seeds they can get, Adamchak said. Those seeds were developed through selective breeding, a technique by which new strains have been created for centuries. The end result of that process, Ronald says, is no different from what is created by laboratory methods.

"To me it doesn't matter if it's genetically engineered or conventionally bred," she said.

Ronald has worked for years with several other researchers to modify a rice strain to tolerate consecutive weeks of submergence beneath floodwaters. The findings were published in 2006, and the rice has become popular in Bangladesh, where flooding periodically destroys rice crops.

"We have to put things in perspective, and I think people are fixated on how dangerous (genetic engineering) is, without knowledge to back it up," said Sean Feder, an agricultural professional who oversees organic-crop inspections in California.

Feder works for California Certified Organic Farmers and stressed that his opinions are not his employer's.

"I highly recommend the book," he said. "I think we can use a bit more of an open mind."

Freelance writer Wes Sander is based in Sacramento. E-mail: wes@wessander.com.

Review of Tomorrow's Table: A soothing draught and an easy glide

This review just in from Edible East Bay, a quarterly newsletter that celebrates the abundance of local foods, season by season:

"Our world is facing several converging crises—environmental, social, and political—that are affecting, or will affect, the availability of food to all people. This convergence on the issue of food is making our food policies and production practices more visible than ever. Genetic engineering has become a topic of hot debate in this climate, and it is long overdue for citizens to educate themselves on the matter...

In Tomorrow’s Table: Organic Farming, Genetics, and the Future of Food, we hear from practitioners in the field of genetic engineering: Pamela Ronald, professor of plant pathology and chair of the Plant Genomics Program at UC Davis, and her husband, Raoul Adamchak, a veteran organic farmer who assists in his wife’s research. The two believe that the technology can be (and is being) put to work to the benefit of humanity and global environmental stewardship. In these confusing times, I for one find such creative solutions to the world’s problems to be a soothing draught, and the arguments put forth in this book are compelling enough to make one want to rethink the whole matter. Ronald and Adamchak wrote the book, tag-team. It’s such an easy glide that we are happily led back through lessons we once slept through in high school, like basic biology and what constitutes the scientific method. This book also includes memorable characters, recipes, and a fabulous glossary of terms useful in the debate over genetic engineering."

Cheryl Koehler

Redefining “Natural” in Agriculture: A review of Tomorrow’s Table in PLoS Biology

Check out the latest review of "Tomorrow’s Table" published in PLoS Biology.

Here is a response to one of the points raised in the review as to what is “natural” or appropriate for agriculture.

Because plants are rich in sugars, proteins, vitamins and minerals, they make obvious and tempting treats for various predators. Plants cannot run away, so instead they have evolved a set of defenses to protect themselves. Celery is seemingly benign, yet it produces toxic compounds called psoralens to discourage predators and avoid being a snack too early in its life cycle. Sometimes humans are the accidental victims of psoralen poisoning.

Breeders have selected celery with relatively high amounts of psoralens because farmers prefer to grow insect resistant plants and consumers prefer to buy undamaged produce. Unfortunately, workers who harvest such celery sometimes develop a severe skin rash (NAS 2004), an unintended consequence of this conventional breeding.
Raoul, who is an organic farmer discovered that green potatoes make pretty good rodent poison. One day he went into the certified organic hoophouse to find three dead mice near some freshly eaten green potatoes. Potatoes produce glycoalkaloid solanine, a toxic compound, although most varieties have amounts so small that they are considered nonhazardous to animals. Some potato varieties, however, have higher levels than others and certain conditions such as light can cause hazardous levels of the toxin to be produced.

So far, compounds that are toxic to animals have only cropped up in foods developed through conventional breeding approaches. There have not been any adverse health or environmental effects resulting from commercialized GE crops. This may be because foods produced by GE undergo additional scrutiny, or it may be that there simply are not yet many GE crops on the market. Whatever the reason, this important fact is sometimes lost in the debates on GE food.

Many people view genetic engineering of crops as “unnatural” and see it as an inappropriate tool to use in crop breeding.

What sort of criteria, then, can we use to assess its benefits? An appropriate technology, as asserted by the economist Schumacher in his book Small is Beautiful, should promote values such as health, beauty, and permanence (Schumacher 1973). Low cost and low maintenance requirements are also of prime importance in Schumacher’s definition. Considering both Schumacher’s observations and our goals for ecological farming, it is apparent that GE will sometimes be appropriate for food modification and sometimes not. This is because GE is simply a tool that can be applied to a multitude of uses, depending on the decisions of policy makers, farmers, and consumers.

Still, as we attempt to show in our book, GE comprises many of the properties advocated by Schumacher. It is a relatively simple technology that scientists in most countries, including many developing countries, have perfected. The product of GE technology, a seed, requires no extra maintenance or additional farming skills. Its arrangement of genes can be passed down from generation to generation and improved along the way. It is therefore clear that humans will likely reap many significant and life-saving benefits from GE. This is because even incremental increases in the nutritional content, disease resistance, yield, or stress tolerance of crops can go a long way to enhancing the health and well-being of farmers and their families. There is also potential for applications of GE to reduce the adverse environmental effects of farming and enable farmers to produce and sell more food locally. Indeed, the use of GE has already drastically reduced the amount of pesticides sprayed worldwide, saved the U.S. papaya industry, and provided new tools to save the lives of impoverished children.




Trewavas, T. (2008). Redefining “Natural” in Agriculture. PLoS Biology, 6(8), e199. DOI: 10.1371/journal.pbio.0060199

A society where ideology is a substitute for evidence can go badly awry

Olivia Judson has a lovely piece today on why it is important for evolution to be taught in beginning biology classes. One important point that she makes is this:

"A society where ideology is a substitute for evidence can go badly awry."

She goes on to say:

"In his book, 'The Republican War on Science,' the journalist Chris Mooney argues persuasively that a contempt for scientific evidence — or indeed, evidence of any kind — has permeated the Bush administration’s policies, from climate change to sex education, from drilling for oil to the war in Iraq. A dismissal of evolution is an integral part of this general attitude".

I would argue (as does she) that we see this substitute for ideology over science on the left end of the political spectrum as well. In the case of genetically engineered crops, for example, there is a pervasive ideology that GE crops are harmful to human health and to the environment, even though there has not been a single case of harm in over 10 years of cultivation.

Basic concepts in science: Crop genetic engineering

Some scientists and policy decision-makers have proposed that genetic engineering (GE), a modern form of crop modification, will help create a new generation of plants that will dramatically reduce our dependence on pesticides, enhance the health of our agricultural systems, and increase the nutritional content of food. They believe GE will be a dramatic step forward that will topple decades of criticism about the dangerous overuse of pesticides and toxic herbicides, leading us to a more ecological way of farming.

Or will it? While the public has generally accepted the application of GE for the production of new medicines, some consumers indicate grave unease over the consumption and production of GE food, viewing it as unnatural, potentially unsafe to eat and environmentally disruptive. Of these skeptics, the organic farming community has been particularly vocal in its criticism. Some consumers believe that because organic farmers have learned how to produce healthy nutritious food, GE plants are not needed.

Definition:

GE is not a farming method. It is a modern form of crop modification that
differs from plant breeding in two basic ways:

1. Plant breeding allows gene transfer only between closely related species. With genetic engineering, genes from the same species or from any other species, even those from animals, can be introduced into a plant. Therefore genetic engineering creates a vast potential for crop alteration.

2. Plant breeding mixes large sets of genes of unknown function, whereas
genetic engineering generally introduces only one to a few well-characterized genes at a time.


History:
For thousands of years, farmers have deliberately selected and improved plants with desired characteristics from wild and cultivated plants. For example, 10,000 years ago farmers in ancient Mesopotamia developed a hybrid between wild species of wheat and cultivated wheat that became the ancestor of our modern bread wheat. Today breeders manipulate plant species to create desired combinations of traits for specific purposes. In rice and corn, this artificial selection process is generally carried out using pollination. In this process the breeder transfers the male pollen grains to the female part of the flower.

Using these techniques, breeders have been highly successful in developing new varieties; so successful in fact that corn varieties only faintly resemble their predecessors and survive only in human-made environments.

Today, all of our principal food crops come from domesticated varieties. As with breeding, the goal of genetic engineering is to alter the genetic makeup of the crop.

The Process of plant genetic engineering
There are a couple of ways to genetically engineer a plant. One method is to use particle bombardment, or biolistics. In this process, millions of DNA-coated metal particles are shot at target cells or tissues using a biolistic device or gene gun. The DNA elutes off the particles that lodge inside the cells, and a portion may be stably incorporated in the host chromosomes.

Another method is called “Agrobacterium-mediated” transformation. For rice, the starting material is an immature and still doughy seed, which carries the precious embryo and the genetic material within. If left to mature, the embryo would become edible grain.

A quick dip in ethanol, followed by a soak in bleach and a spray of sterile water will protect the rice embryo from contaminants in the air—bacteria and fungi that are harmless to humans but can kill the delicate rice cells. The hulled grains are placed onto a freshly prepared plate carrying nutrients that will nourish the embryo and moved to a growth chamber that will supply adequate light and heat.

In about two weeks, the grain will grow into a glistening mass called a “callus,” a sort of stem cell open to direction, not yet having decided whether to develop into a particular organ, such as a leaf or root. The new callus is separated from the grain with tweezers. The next step is to introduce a new gene into the cells of the rice callus; to do this scientists rely on a soil bacterium called Agrobacterium. This bacterium can do something that virtually no other organism can do; it can form a bridge to the plant cell and then transfer some of its own genes across the plant cell wall, then across the membrane and into the nucleus.

This ancient process, known to biologists for a century, was only understood in detail over the last thirty years. It is now known that this gene transfer “transforms” the plants into food production units for the bacteria. You can tell if a plant is infected by the appearance of large tumors at the base of the plant. Sometimes the results are dramatic—one of the oak trees on the UC Davis campus has a crown gall tumor the size of a small car.

Biologists, faithful to their long tradition of manipulation and exploitation, have cleverly removed the bacterial genes that cause the tumor so that the bacteria can infect without disrupting plant growth. They have also figured out that it is possible to replace some of the bacterial genes with genes from other species. The bacteria, unaware that the genes have been swapped, will deliver the new genes into the plant. To carry out this subterfuge, biologists employ other tools of our trade: restriction enzymes that act like tiny scissors to cut out the bacterial genes and ligases that act like glue to insert the new genes into the genome of Agrobacterium.

This cutting and pasting method is used to introduce genes-of-interest, say a resistance gene or stress tolerance gene into Agrobacterium. The callus can then be dipped into a broth containing the engineered bacteria. At this point, the bacterium acts like a courier delivering the gene-of-interest into the genome of the cultivated rice species. The bacteria must first identify its target, then infect the cell, transfer its DNA across the rice cell membrane into the nucleus, and finally into DNA that is bundled into chromosomes in each nucleus. In nature and in the lab, the bacteria do the work of gene delivery.

Scientists cannot predict where the new gene will land beforehand, although it is straightforward to determine the location of the new gene after it is integrated into the crop DNA. Sometimes the gene will land in a spot that disrupts a critical function of the rice cell, in which case that cell will no longer grow. In most cases, however, the transformed cell will thrive and reproduce carrying a new bit of genetic material along with it.

How unnatural is this? If we insert genes into random sites in a genome, won’t we destabilize a structure that has evolved over millions of years? It turns out that plant genomes are used to this kind of abuse. It is now well documented that rice and other organisms contain pieces of DNA that move around (called transposable elements) in a seemingly erratic fashion. Not only do they insert themselves into new places, but sometimes they pick up pieces of other genes and take those fragments along for the ride as well. For example, a recent study showed that in the rice genome there are over 3000 of these pieces of DNA-containing fragments, called pack mules, from more than 1000 genes (Jiang et al. 2004). Sometimes several fragments are picked up from different genes, rearranged, fused, and then expressed as new proteins. By looking at the genome sequences, we also now know that plants have acquired genes from many different organisms. It seems then that the genetic engineering process we carry out in the lab has certain similarities to that which occurs in nature.

Not all of the bacteria will be successful in transferring their DNA to the cell; only a very few of the rice cells will receive the new gene and be “transformed.” How then does the biologist distinguish the genetically engineered cell from the thousands of rice cells lacking the genes? In fact, this would not be possible without another tool, called the marker gene. In early experiments of plant transformation, the commonly used marker was a gene that encoded resistance to an antibiotic. In this process, not only is the new gene transferred to the cell, but the marker gene is as well. Today, other markers are available, such as those that allow the transformed plant to grow on high levels of particular sugars; in essence this marker is a sugar enablement gene that allows it to grow on sugars it cannot otherwise use. By placing the infected rice cells on the “selection” (sugar or antibiotic) media only the transformed cells will survive, inhibiting growth of the rest of the plant cells. In other words, the marker genes bestow properties of survival only to those cells that are genetically engineered, allowing biologists to pluck the newly transformed cells from a lawn of dying, untransformed cells.

In two more weeks the newly transformed cells will give rise to new cells carrying the marker gene and the gene-of-interest. These new cells appear as tiny clumps of whitish, nearly translucent globs about the size of small beads. These cells are genetically identical to the starting material (the rice seed), except that they also possess the desired gene-of-interest and the marker gene. Once transferred to nutrient plates containing plant hormones, the cells will produce roots and shoots. The GE seedlings can be transplanted into soil-filled pots. They will reproduce and produce seed like any other rice plant.

Today, one billion acres of GE crops have been grown; hundreds of millions of people have eaten GE food for more than a decade without a single verifiable case of adverse side effects to the environment or to human health. Still, GE provokes controversy, and, sometimes, violent protests.


Potential for using GE to boost crop yields

One way to boost yields is to develop crops that can survive harsh conditions such as drought, cold, heat, salt, and flooding. Many of the world's poorest people farm in areas that are far from ideal, and freshwater sources are decreasing in quantity and quality throughout the world. New crop varieties designed to survive in difficult environments will have a significant human and ecological impact. In the future this is where genetic engineering will likely play an important role. Crops with enhanced tolerance to drought, for instance, would allow farmers to produce more food using less water. Already there are varieties of genetically engineered wheat that can tolerate drought, as well as rice that can tolerate flooding and tomato plants that can tolerate salt.
Another important challenge is to fight pests and disease, which take an estimated 20 to 40 percent bite out of agricultural productivity worldwide. Reducing this loss would be equivalent to creating more land and more water. But current pesticide use is a health and environmental hazard, and organic and genetic engineering offer complementary solutions. Genetic engineering can be used to develop seeds with enhanced resistance to pests and pathogens; organic farming can manage the overall spectrum of pests more effectively. Genetically engineered crops have already enjoyed major success against pests. For example, on farm field trials carried out in central and southern India, where small-scale farmers typically suffer large losses because of pests, average yields of genetically engineered crops exceeded those of conventional crops by 80 percent. In Hawaii, the 1998 introduction of an engineered papaya plant that could resist the papaya ringspot virus virtually saved the industry. There was no organic approach available then to protect the papaya from this devastating disease, nor is there now.

Genetic engineering can also help achieve other goals of the ecological farming movement. By reducing the use of pesticides and by reducing pests and disease, it can make farming more affordable and thus keep family farmers in business and assure local food security. It can also make food more nutritious: In 2011, plant breeders expect to release "golden rice," a genetically engineered variety that will help fight Vitamin A deficiency in the developing world, a disease that contributes to the deaths of hundreds of thousands of young children each year.

Opposition to GE crops
To many people, genetically altering crops feels fundamentally wrong or unnatural. They believe that farmers already have enough tools for a productive and healthy farming system.

On an environmental level, many worry that genetically engineered crops will cross-pollinate nearby species to create a new kind of weed that could invade pristine ecosystems and destroy native plant populations. On a personal level, many consumers worry that genetically engineered foods are unsafe or unhealthy to eat.
So far, however, it appears those concerns are driven more by technological anxiety than by science. Virtually all scientific panels that have studied this matter have concluded that pollen drift from genetically engineered varieties currently grown in the United States does not pose a risk of invasiveness. (Although this does not mean that future crop varieties will also be harmless: each new crop variety must be considered on a case-by-case basis.) And in terms of food safety, a report by the National Academy of Sciences concluded that the process of adding genes to our food by genetic engineering is no riskier than mixing genes by conventional plant breeding.

Today 70 percent of all processed foods in the United States have at least one ingredient from genetically engineered corn, cotton, canola, or soybean. Unlike the well-documented adverse effects of some pesticides, there has not been a single case of illness associated with these crops.

Intellectual property
Many opponents of genetic engineering fear that a blizzard of patents on genetically engineered plants and seeds will put control of agriculture in the hands of a few giant companies that produce the seeds.
Yet there are many new and imaginative methods that businesses and universities are now using to ensure that breakthroughs and useful technologies benefit less developed countries and small-acreage farmers. For example, the nonprofit initiative Public Intellectual Property Resource for Agriculture brings together intellectual property from more than 40 universities, public agencies, and nonprofit institutes and makes these technologies available to developing countries around the world for humanitarian purposes.

Tomorrow's Table in the classroom

"I really enjoyed the book. It did a great job of keeping everything in perspective. Use again !"

"Use again! A great resource and easy to understand"

"The textbook was great. It had a story line to it. It was easy to remember."

These are some of the comments from Oregon State University students who read the book, "Tomorrow's Table: Organic Farming, Genetics and the Future of Food".

Steven Strauss, Distinguished Professor of Forest Biotechnology at Oregon State University, who directs the OSU Program for Outreach in Resource Biotechnology, chose the book for his course, which give students and the public scientifically reliable information about the use of genes and chemicals in agriculture and natural resources.

Thanks Steve, for being the first to use it in the classroom!