ALTERNATIVES  TO  GENETIC  MODIFICATION - New York Times

ngin comment:   Although there’s lots of pro-GE spin in this article, it makes clear:

1.    many important traits - bigger fruit, higher yield, disease and pest resistance
       - can often be found within the crop species itself

and contrary to the spin of the article:

2.    “Maybe in five to eight years we’ll look back on this argument over transgenics and
        say, ‘How arcane,’ Not because it became unpopular but simply because it got by-
        passed by the advances made by breeding powered by genomics.”

- Dr. Goodman, who once headed research at Calgene, the company that marketed the first genetically modified crop

March 7, 2001

Gene Research Finds New Use in Agricultural Breeding
By Andrew Pollack - New York Times, 7 March 2001

As the controversy surrounding genetically modified foods intensifies, scientists are trying to use the rapidly growing knowledge about genes to enhance conventional breeding of crops and livestock rather than implant genes from one species into another.

Many say such an approach is less likely to arouse the public objections that have been raised by the development of genetically altered plants and animals.

The enhanced breeding approach involves testing which genes are in a plant or animal, allowing researchers to select more easily which ones to cross. That can shave years off the breeding of a new variety.

“Before we knew where the genes were, we were  still breeding in the dark,” said Dr. Steven Briggs, head of genomics for Syngenta, a Swiss seed and  agrichemical company.  Compared with genetic engineering, this enhanced  breeding has technical advantages and disadvantages. But its biggest advantage is political. Many  opponents of bioengineered foods do not object to the
technique because it avoids artificially transferring genes between organisms.

It is that transfer that opponents say is unnatural and poses risks to human health and the  environment.  Indeed, some opponents of genetically altered  plants and animals even champion the approach as a way for society and companies to reap some of the  benefits of genetic science and avoid the risks.

“I think that’s where the future is, to upgrade classical breeding,” said Jeremy Rifkin, a prominent critic of the biotechnology industry. “Classical breeders  and geneticists can use the genome but not do gene splicing.” Mr. Rifkin calls this approach the soft path, and says better understanding of genes could evenbe used to improve organic farming.

But agricultural biotechnology companies like Monsanto and Pioneer Hi-Bred International, say that the two technologies are good for different tasks but cannot be substituted for each other. So, while they are using the new breeding techniques, they remain  committed to genetic engineering as well.

“We don’t see it as an alternative to genetic engineering,” said Tony Cavalieri, vice president for trait and technology development at Pioneer, a unit of DuPont.

And some executives say that even with improvements, crossbreeding is inefficient compared with
genetic engineering. With genetic engineering, scientists can transfer just the gene they want, whereas with crossbreeding, the genes of two parents are thoroughly mixed.

“It’s sort of a blunt instrument,” said David W. Summa, chief executive of Mendel Biotechnology, a plant genetics company in Hayward, Calif. “You’re  moving around lots and lots of genes when you breed.”

Still, a number of companies are turning to the  approach because it avoids the regulatory reviews
required of genetically modified foods and is not expected to stir resistance from consumers. The
approach is called marker-assisted breeding  because it uses genetic markers to guide the process.

“Marker-assisted selection is the first choice if  we can solve the problem,” said Wally Beversdorf, head of plant science and agribusiness for Syngenta,  which was formed by the merger of the agricultural businesses of Novartis and AstraZeneca. While Syngenta is still committed to genetic engineering, Dr.Beversdorf said, it is applying that technique “where we have to, where there is no opportunity for marker-assisted breeding.”

Some newly formed companies are deliberately steering clear of genetic engineering. AniGenics, a
start- up in Concord, Mass., aims to identify genes associated with higher milk production, more tender meat and other desirable traits of cattle and other livestock. But that knowledge would be used to guide conventional breeding, not to create genetically altered herds.

“It may or may not be faster biologically,” said Steven M. Niemi, the president. “It’s certainly faster politically.”

The marker-based approach is being made easier by an explosion of knowledge about genes. In January, Syngenta announced it had determined the complete genetic code of rice, the first crop to have its genome sequenced. A month earlier, scientists had completed the DNA sequence of arabidopsis, a weed that is the plant world’s equivalent of the laboratory rat. And there are less detailed genetic maps available or being developed for virtually every other important crop or farm animal.

The biggest drawback of the breeding approach is that it is limited to traits that are already contained in a species. Scientists would [not] be able to use it, say, to breed a blue tomato if they could not find a tomato containing blue-pigment genes to start the process.

Syngenta, for instance, tried for 12 years to use conventional breeding to develop corn that was resistant to the European corn borer but ended up with a variety that reduced the pest damage only about 10 percent, Dr. Beversdorf said.

But some bacteria make a toxin that kills the borer. It took the company only five years to splice the bacterial gene into corn and develop a crop - known as BT corn - that can almost completely eliminate damage from the borer.

Dr. Cavalieri of Pioneer said it would probably be impossible to develop plants with healthier oils
without genetic engineering. And scientists say it would also probably be impossible to use breeding alone to develop “golden rice,” which could help combat vitamin A deficiency in developing countries. The genes to provide the vitamin A were transferred to the rice from daffodils and bacteria.

Still, scientists say that many important traits - bigger fruit, higher yield, disease and pest resistance - can often be found within the crop species itself.

At the Agriculture Department, Anna McClung recently used the technique to develop rice that would be soft on the outside and firm on the inside after processing. The work was done with a company hoping to sell the rice in Europe, where opposition to genetically modified crops is high. So genetic engineering was out of the question.

Both Pioneer and scientists at Purdue University used the technique to develop soybeans that are
resistant to the cyst nematode.

Classical breeding can be a long and tedious affair. Breeders might take a plant with a desirable
characteristic, like disease resistance, and cross it with another plant with other desirable traits, like high yield. They then examine the offspring, hoping to find plants that have both disease resistance and high yield. Those desirable plants might be then crossed to make a new generation. The whole process can require 10 or more generations, thousands of crosses and 5 to 15 years.

To see which offspring have the desired traits, the new generation usually must be allowed to grow up, and even then detection is often not easy. To test which of her rice plants had the right cooking characteristics, Dr. McClung would have had to analyze them chemically.

If scientists can test the genes, however, they can tell if the plant has the desired trait when it is still a seedling. “By having a genetic tag, you’re able to see the presence or absence of the trait every time,” Dr. McClung said. With the marker, she developed the rice in 5 years, instead of the 7 to 10 it would have otherwise taken.

Usually, scientists do not test for the genes themselves, since many of the genes are still not known. Instead, they look for markers along the chromosome that are near the gene and therefore tend to travel with the gene from one generation to the next. The advantage of this technique is that the markers can be used even if the breeders have not identified the gene. Genetic engineering can be done only if the gene is known and isolated.

It is also possible to use markers to follow numerous traits through the breeding process. Genetic
engineering is at present limited to transferring only one or a few genes. Yet many traits, like the yield of a crop, are governed by multiple genes.

But marker-assisted selection can be extremely difficult and has not lived up to the expectations scientists had when the technique was first developed in the late 1980’s, said Nevin D. Young, professor of plant pathology and biology at the University of Minnesota. “Traditional breeding is like a dice-rolling experiment,” he said. “Markers are like loaded dice, but they’re hardly precise surgical instruments.”

It can take years to find the associations between markers and traits, and sometimes links cannot be found at all, he said. It also now costs about $1 to test one marker in one plant, which makes it very expensive to test numerous genes in thousands of plants. Still the costs of such genetic analysis are expected to drop rapidly with the advancement of new DNA testing methods that are also being developed for medical diagnosis.

One of the biggest opportunities presented by marker-assisted selection is to improve the harnessing of wild relatives of crops. Human beings domesticated plants by selecting for obvious traits, like bigger fruit. But over time, the genetic variation in commercial crops has become limited, so when breeders cross these crops, the possible outcomes are also limited.

“We’ve left behind in this process a huge reservoir of natural variation,” said Steven D. Tanksley,
professor of plant breeding and plant biology at Cornell. All the commercially grown tomatoes in the world, from the tiniest cherry tomato to the beefiest beefsteak, have less genetic variation than the wild tomatoes in a single valley in Peru, he said.

Breeders have tried to cross wild relatives with commercial crops but with limited success. One problem, Dr. Tanksley said, is knowing which wild plants to pick. Wild tomatoes often are small and green and taste bad. Someone just looking at them would not think of using them in breeding.

But even small, green tomatoes can contain some genes for redness and large fruit. The marker studies allow these genes to be found. “The markers allow you to scan through the whole genome,” he said. “You can pick out the flavor genes away from the yucky gene.”

Indeed, Dr. Tanksley has crossed wild green tomatoes with commercial red ones and produced even redder ones. And he crossed small wild tomatoes with big commercial ones and got even bigger ones.

Robert Goodman, a professor of plant pathology at the University of Wisconsin, said there was still a risk that marker-assisted breeding could run into the same opposition as transgenic crops because people might fail to make any distinction. But if that does not happen, he said, the breeding approach could provide a way out of the contentious debate.

“Maybe in five to eight years we’ll look back on this argument over transgenics and say, ‘How arcane,’ “ said Dr. Goodman, who once headed research at Calgene, the company that marketed the first genetically modified crop, a tomato. “Not because it became unpopular but simply because it got bypassed by the advances made by breeding powered by genomics.”