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Big things brewing for cotton, Tech with research grant

By Elliott Blackburn / Avalanche-Journal / Dec. 14, 2007 / Page 1
Texas Tech researcher will spend the next year beginning to unlock the secrets of the region’s king cash crop. Tech cotton genome researcher Thea Wilkins will work to map the genomes of two breeds of cotton plant in 2008, ancestor plants to the ubiquitous modern version that blankets the Lubbock region from May to December. 

A Tech-sponsored research grant of just under $1 million will allow Wilkins’ team to process the two plants, ship them to a cutting-edge New Mexico lab to be rendered into raw data and then take the reams of data to pore over for years, Wilkins said.

Wilkins isn’t looking to build a super plant, a freak breed that can belch a T-shirt from its bolls and spit enough seeds to feed a cow. But her work could significantly improve breeding techniques that produce the region’s multibillion-dollar cash crop and spark new degrees, research and funding at the university.

To move this forward, we would be decades ahead,” Wilkins said in October after seeking the grant. “The impact on it, making progress, I just get shivers.”

Fun, But Inefficient.  Most all the methods growers use to coax their fluffy crop from the West Texas plains have changed since John Gannaway helped out around his parents’ cotton farm in Haskell as a boy.

Big, green strippers that can pluck eight rows at a time replaced the two-row contraption his family towed behind a tractor, battering him with rocks, bolls and grit as he forked the fiber into a trailer. Cotton buyers who once thrust their arms into a bale and rubbed the fluff between their hands to gauge quality now turn cotton over to machinery that judges the fiber with puffs of air.

The technology in the little seeds spread across his family’s acreage improved, too – insect resistant, herbicide proof, higher yielding, braced against wind. But the process feeding that evolution hasn’t changed much at all.

Gannaway, a cotton geneticist with the Texas Cooperative Extension Service, showed visitors around a greenhouse north of Lubbock where researchers probe the insect- and salt-resisting powers of a huge catalog of wild cotton culled from across the world.

Bolls as big as limes or small as blueberries hang from tree-like cotton plants. A species from East Africa carpets a greenhouse corner like morning glory vine, sprouting bolls the size of wild strawberries. Rich red, cream and yellow flowers, looking more like an ornamental plant than a cash crop, peek out of the thick green rows.

Each have traits that might work well with commercial cotton, if the breeders can unlock them. One species produces a short, incredibly strong fiber that could make cloth more durable. Another breed helpfully discards its own leaves around the fluffy lint, which would mean less trash to gin out of a stripped field.

“The mills would absolutely love this,” Gannaway said as the fallen leaves crumbled in his hands.

Breeders raise hundreds of plants and groom the few that extol the trait they seek. They play the numbers, planting crops of 300 or even 400 plants to hunt for the traits they need. The more plants, the better the odds a breeder will spot the traits he or she needs.

As the study crop progresses into field tests, breeders must hope that traits they’re cultivating show up as planned. If the environment or the crop doesn’t cooperate, scientists wasted a bunch of plants. Under the current methods, it can take a decade for a promising strain to make it to a farmer’s field.

“Obviously, it’s not a very efficient method,” said Jane Dever, Bayer CropScience’s cotton breeding manager. “It’s fun, but it’s not very efficient.”

Drawing A Map. Labs can confirm the presence of certain genetic traits, as long as they’ve already been found – like a lost traveler without a map, a breeder must hope someone’s already visited that spot of the genetic code. Wilkins’ work could expand the cotton map from a few roads to an atlas.

Scientists today have the same rough idea of where cotton qualities are hidden as an out-of-state tourist might have of Texas, said Brian Scheffler, a computational molecular biologist with the Agricultural Research Service in Mississippi.

“I may know where Dallas is, where Houston is,” Scheffler said. But once they get to the border, there’s no sense of which highway takes the traveler where, or through what.

“If you have the complete sequence, then you have a complete road map,” Scheffler said. “It doesn’t tell me what’s in Houston or what’s in Dallas. But now at least I know that I’m looking in that area.”

Wilkins proposes spending less than $1 million to map two cotton varieties.

The first, an ancient plant called Kirkii, produces a silky, hard-to-spin fiber that would make a crummy cloth. Mapping Kirkii gives researchers a baseline to compare with more recent plants.

The second plant, called “A,” is a plant still grown in Asia. A map of key parts of the plant’s genetic code, compared with Kirkii, could provide clues to how genomes collaborate to produce good cotton fiber.

Maps of their genetic sequences will be valuable for studying all breeds, Wilkins said – from the much more genetically sophisticated commercial crops in the field to the bizarre collection at the experiment station.

“We’re building on that to something that’s a little more complex,” Wilkins said. “Every step we have is a part of the puzzle and we’re going to be contributing enormous parts of that puzzle.”

Tech will use its relationship with the National Center for Genome Resources in Sante Fe, N.M., to crunch the genomes down into raw data. Then researchers at the university will work to assemble their genome.

Wilkins hopes the project will spark interest in mathematics and computer sciences departments to help crunch down and translate the reams of data the project will produce.

The $999,000 grant was awarded through an internal competition started two years ago by university Vice President of Research Dean Smith. Wilkins leads a group of seven co-principal investigators, most of them from within the university.

Smith said the effort should reinforce Tech as leader in cotton research and could lead to related research in the future.

“The holy grail for cotton breeders is to get the genetic code,” Smith said. “It puts a star on the university.”

New research grant awarded
Winners of the second year of a $1 million grant competition out of the vice president of research’s office will work on sequencing the cotton genome.
• Award: $999,000
• Projects submitted: 40
• Total requests: $21.3 million
• Winning team: Thea Wilkins, Bayer CropScience Regents Professor in Genomics, lead; Eric Hequiet, research associate professor; Noureddine Abidi, research assistant professor; Robert Wright, assistant professor; Dick Auld, Rockwell Professor of Plant and Soil Science; Randy Allen, professor; Craig Bednarz, associate professor; Gregory May, National Center for Genome Resources

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