Cotton research: Mapping RGAs could unlock traits

The discovery and genetic mapping of resistant gene analogues (RGAs) could help plant breeders unlock a plant's hidden traits — using conventional breeding techniques. The first use of this technology in southern agriculture occurred in 2005 with the mapping of an RGA for resistance to root-knot nematode in cotton.

According to Roy Cantrell, vice president, agriculture research, Cotton Incorporated, RGAs are like genetic synonyms, similar gene sequences in different plants that do the same thing.

The discovery of the RGA that confers resistance to root-knot nematode is part of a Cotton Incorporated research effort to “to get closer to identifying genes and cotton germplasm that have resistance to root-knot nematode,” according to Cantrell.

Cantrell noted that every cotton plant has variants of genes for root-knot nematode resistance. “The particular DNA sequence determines whether the trait is expressed or not.”

For example, “We all have genes that determine hair color. It's the exact same gene, but there is a variant in mine that makes mine blond and someone else's black. But the gene is there.”

Doug Hinchcliffe, a Cotton Incorporated Fellow and molecular biologist at New Mexico State University, and Jinfa Zhang, a cotton breeder, initiated the RGA project in July 2003. First, they found gene sequences for root-knot nematode resistance from extensive plant DNA databases, and then they launched a search for similar sequences in cotton.

According to Hinchcliffe, RGAs make finding specific traits in plants a lot less difficult — it's like going from finding a needle in a thousand haystacks to finding a needle in a single haystack.

“In tomatoes, we know the gene that confers resistance to nematodes and that gene has the same motifs (patterns) that we're using to look for RGAs in cotton. It narrows the search.”

“Doug not only found those genes in cotton,” noted Cantrell, “but he went one step further and placed them on a genetic map.”

This will be of immense help to cotton breeders, according to Cantrell. If they can spot the RGA in the lab, they can shorten the time needed to breed a specific trait into a plant. “If you're selecting for root-knot resistance using traditional breeding techniques, you might get one gene and not the other, or different combinations. That's been the history of breeding. It's very complex at that point in the process. You're not looking at the genes themselves, you're looking at the trait.”

With RGAs “you focus on screening germplasm with genetic potential for resistance in your breeding nursery instead of a costly field evaluation. The latter is still necessary, but you kind of stack the deck in your favor. It's quite remarkable. You can fish them out of all the DNA in cotton and you don't have to start from scratch.

“The research will add to our understanding of the genes involved in resistance to root-knot nematode and the location of these genes, which will allow their experimental use in breeding,” Cantrell said. “This helps us dissect resistance. We're going in with a little sharper knife.”

Because the genes already exist in cotton, and all scientists are looking for is the right sequence, a non-GMO approach can be used to bring the traits to the cotton producer.

“Not that we're trying to avoid genetic engineering, and these may be targets for genetic engineering, but genetic engineering is not really essential in this situation because these genes already exist. We haven't had the tools to work with them in a way that's really precise.”

Cantrell added that the approach is considered a greener form of biotechnology, “although I'm a strong proponent of genetic engineering and its safety. But there is a lot of research going on to improve what's there rather than taking a gene from something else and putting it in. We need both.”

The research has been published and deposited in the national DNA database. It is now in the hands of breeding companies, technology providers and public breeders to use in their selection programs. “This will shorten the time by a couple of years in terms of developing new varieties. But just as important, it will add certainty and precision to the discovery of those varieties.”

The research provides a framework for mapping future genes, according to Cantrell. “There are quite a few of these RGAs in most plants. And as they're discovered, they may be involved in resistance to diseases like verticillium wilt and fusarium wilt. We are a little further behind on finding RGAs for reniform resistance. We do not have resistant germplasm in any cottons or other cultivated crops.

“Cotton has a huge amount of complicated DNA that we're just now starting to unravel. This is one of the most modern tools we have today. It will let us sort through all the DNA and the genes.”

The Cotton Belt's average annual yield loss to nematodes for the last 50 years is estimated at 2.13 percent by the Beltwide Nematode Survey and Education Program. The highest cotton yield loss to nematode damage was 4.39 percent, or about 750,000 bales, in 2000.

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