Genetic map of all plants, animals is goal of genomics
WEST LAFAYETTE, Ind. The state-of-the-art in life science biology, medicine, and agriculture resembles the situation geographers found themselves in centuries ago.
Early cartographers had a small bit of information and tried, with obvious errors, to produce a view of what the world looked like. The maps of that era were equally off target, with misshapen or missing continents and dire warnings about the dangers that existed in the unknown waters.
A teacher in the third century A.D., Lactantius Firmianus, said: "Can there be a place on earth where things are upside down, where the trees grow downwards, and the rain, hail, and snow fall upward? The mad idea that the earth is round is the cause of this imbecile legend."
Although early concepts of the world are comical now, those ideas of how the world worked were then quite reasonable, given the information they had.
Just as explorers such as Columbus, Magellan and Cortez brought rapid change to the understanding of the earth, a new field of biology promises to bring great and fast strides into the understanding of living organisms.
The new area of study focuses on understanding the genes of living organisms: first by mapping out the structure of all of the individual genes of the organisms, and then by figuring out what all of those thousands of genes actually do.
This new map of life is called genomics.
This new focus on genomics promises to change the way life science research is done at universities such as Purdue.
"This is not a fad. It's the best way to do biology," says Jeffrey Bennetzen, Purdue's H. Edwin Umbarger Distinguished Professor of Genetics. "When molecular cloning came on the scene there were people in biology who said, 'Its a fad.' Now everybody does molecular biology; nobody is called a molecular biologist anymore because it has become a part of every biologist's tool kit. In five years genomics will be the same way. We expect to see everyone in life science move into the field to a degree."
The first step
"It's quite a change to think that any of this is possible," Bennetzen says. "Six or seven years ago, we wouldn't have even thought about doing these genomics experiments."
Over the past several years, however, new laboratory techniques have been developed that allow scientists to make discoveries that just a decade ago seemed impossible.
The genomics revolution has been spurred in part by new automated machines that can quickly determine the structure of genes. "Before, it might have taken us two years to determine the structure of one particular genome," Bennetzen says. "Now we expect to do the same region in a couple of weeks."
Before genomics techniques were developed, if a scientist was interested in finding the genes that caused a certain trait, it was not unheard of for him to spend his entire career identifying those genes. That process required painstakingly comparing the genes of the plant or animal that had the trait with the genes of those in which the trait was lacking.
With genomics, however, scientists take a different approach. They use automated equipment to rapidly map out the sequence of all the genes in an organism. Then, in a step that is still somewhat painstaking, they go back and figure out what each of those genes does.
Although the gene sequencing of important organisms is obviously a finite activity, Randy Woodson, director of Purdue Universitys Office of Agricultural Research Programs, says genomics is a field of science that will be around for decades.
"The science of genomics isn't going to be over tomorrow," he says. "There will be a five- to 10-year period of intense activity, especially in the sequencing of genes. At that point, we will have come full circle and come back to a point where physiology and biochemistry and other sciences will be needed to understand the functions of the genes and how these processes work."
Bennetzen says that when scientists understand all of an organism's genes and what each of them does, they will have a near complete understanding of how the organism works.
"That's it. That's biology," he says. "That's why genomics is such a big, blossoming field. Now we can understand an organism comprehensively.
"Of course there are a lot of organisms out there. In the end, what genomics has as its goal is to understand all of the genes in all of the organisms on the entire planet."
The idea we may know all of the genes of all of the organisms on the planet may seem absurd. But to a 15th century mapmaker, the idea that someday there would be topographical maps for every continent, island and speck of land seemed equally absurd.
Biologists have an easier task before them in making maps of all living organisms than faced those early cartographers, because, as surprising as it sounds to a non-scientist, the genes of nearly all living organisms are almost identical.
Viva la difference
Although the external differences are not subtle, most creatures are very much alike in their genetic codes. Humans and chimpanzees differ by less than 1 percent in their genes.
"For example, on the surface it would appear that cows and humans are very different," Woodson says. "Yet, when one examines the genes that make up a cow, generally the same gene or a version of the same gene is present in humans. The differences are very slight.
"Take corn and a tomato as another example. They're very different plants, but they have a lot in common genetically."
The reason for this similarity, Bennetzen says, is that nature doesnt like reinventing the wheel. "Creation of new genes is very rare, maybe happening only a few times in tens of millions of years," he says.
Scientists call this similarity "genetic conservation." Once nature finds something that works, it sticks with it, even if the organisms are strikingly different. Twenty or 30 percent of the genes in a human may be the same as those in a single-celled organism such as E. Coli or an amoebae because these genes are necessary for any living organism. Likewise, the same gene might be found in both humans and mice but not in corn, which would indicate that particular gene is necessary for mammals but not for plants.
Nature takes this genetic conservation to some unexpected extremes. The eyes of the octopus and humans are created from different tissues when the body is an embryo, yet scientists have discovered the eyes in both creatures are coded by the same genes.
"Twenty years ago, if you had told a biologist that the eyes of a human and an octopus arise from the action of the same gene, he would have thought you were being ridiculous," Bennetzen says.
Woodson says these slight differences in gene structure and gene function determine the amazing diversity in organisms. "The science of genomics will begin to unravel this mystery, opening up untold opportunities for the application of genetic technology to crop and livestock production, as well as to human health."
Making maps of plants
Genetic conservation goes beyond just having certain genes in common. Plant scientists have discovered in the past few years that if they determine the location of a gene for a specific trait in one plant, another plant in the same family is likely to have the gene in the same place.
This is a boon to plant breeders. Today, the fastest way to improve corn might be to study the genetics of sorghum. Corn's genome is three times larger than sorghum. By identifying genes for a desired trait, such as drought tolerance, in sorghum, researchers know where to look for it in corn.
For example, Purdue horticulture professors Ray Bressan and Michael Hasegawa will use the techniques of genomics to locate genes that help plants withstand stresses such as drought, heat, cold and poor nutrition.
"They're using an approach called EST, or Expressed Sequence Tags," Woodson says. "They take a plant that's resistant to a certain stress and one that's susceptible to that stress, and they compare the genes of the two plants to see what the resistant plant has done to overcome this stress. They can then take the genes and put them into the sensitive plant to see if they are able to transfer this resistance trait to other plants."
Sources: William R. "Randy" Woodson, (765) 494-8362; firstname.lastname@example.org
Jeffrey Bennetzen, (765) 494-4763; email@example.com
Writer: Steve Tally, (765) 494-9809; firstname.lastname@example.org
Purdue News Service: (765) 494-2096; email@example.com