Cotton Fields of the HudsonAlpha Institute for Biotechnology

That Old South anthem “Dixie, ” maundering for the “land of cotton, ” may well have been picturing Alabama, but certainly not the Alabama cotton fields of the HudsonAlpha Institute for Biotechnology.

It’s not “look away” but way ahead that the gene scientists of HudsonAlpha have in mind when they think about cotton.

“The cotton research community wants to be able to do things faster, such as import a trait for pest resistance or disease resistance. Instead of multi-year trials, it can happen much more quickly with all the genetic information in hand, ” says HudsonAlpha faculty investigator Jeremy Schmutz. A leading genomics researcher out of Stanford University, Schmutz relocated to Alabama in part to be closer to the current focus of his attention as head of the plant program at the U.S. Department of Energy’s Joint Genome Institute — Gossypium raimondii.

That’s Lineaus Latin for the most basic cotton genome there is.

By starting with basics, Schmutz hopes to open a wide array of applications for improved cotton — from drought-resistant fluff for blue jeans to hardy fiber for biofuel.

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Schmutz’ team has isolated the genome for the simplest cotton genome and mapped it in comparison to other cotton species — research that was recently published in the journal Nature. The findings are now available for use by cotton researchers and breeders everywhere to help develop cotton with the traits they desire.

“We’re trying to understand more about the biochemistry of the cotton, how the plants actually function, and how to adjust the plant’s interaction with the environment, ” Schmutz says. “By accumulating genetic markers from a variety of species for a variety of qualities, we can facilitate better and targeted cotton strains.”

Cotton may not be one of the top plants produced in the United States, but it still carries an important economic impact. More than 200, 000 U.S. jobs are related to cotton production and processing, with an aggregate influence of $35 billion on the annual U.S. gross domestic product. The value of cotton fiber grown in the United States is more than $6 billion per year, and including cottonseed oil and meal by-products, the value is more than $7 billion per year.

While much of the cotton grown in the United States is used in textiles, the cotton data uncovered by the HudsonAlpha-led study will accelerate the study of gene function in cellulose biosynthesis, which is a fundamental process in biofuels production.

“The Department of Energy funded this study because they are interested in cotton as a fuel source, and having this genetic information available to researchers makes it easier to develop cotton strains that will be more viable for fuel production, ” Schmutz says.

In addition to textiles and biofuels production, the field of environmental remediation also can benefit from isolating the specific traits of the cotton genome.

“Cotton can absorb many times its weight in oil and can be useful for cleanup efforts [such as for the Deepwater Horizon spill], ” Schmutz says. As a metal concentrator, the cotton plant draws metals up into its leaves and removes heavy metals from soil, he says.

Unlocking the secrets of the cotton genome doesn’t just make it easier for researchers to breed the plant for new uses, such as environmental remediation and biofuels production. It also allows cotton breeders to more quickly develop plant varieties that will resist pests, improve disease resistance and promote more efficient water usage.

“The way you normally would breed a plant for a desirable trait — to take the plants that have the traits you want and keep replanting them, discarding those with undesirable traits — is done blind to the plant’s genetics and DNA, ” Schmutz says. “With genetic mapping, you can figure out what your traits are and use markers associated with a trait of interest, and the whole process can happen much faster and more accurately. It’s what we call genomics-enabled breeding.”

Before coming to Alabama and HudsonAlpha in 2008, Schmutz and several of his fellow researchers worked at Stanford University in California on the Department of Energy-funded Human Genome Project, heralded as a major feat in both basic science and technology. Through the landmark project, scientists mapped and sequenced the haploid human genome’s 22 autosomes and two sex chromosomes. The project fueled discoveries and speeded the research process.

“After the Human Genome Project was over, the DOE wanted to apply the same process to biologic fuels, or crops, ” Schmutz says.

Before studying cotton, Schmutz and his group studied the genomes of soybeans, peaches, poplar trees and other crops that offer cellulose that could be targeted for fuel production. The cotton genetics project came about when members of the cotton industry submitted a proposal. “The Department of Energy reviewed their proposal and decided it was important enough to fund the research, ” Schmutz says.

As researchers in human health and disease have benefited from the Human Genome Project, cotton researchers now have the information they need to more quickly develop the strong plants with the traits they desire — whether those traits are for better textiles, new fuel sources or environmental remediation.

Studying Cotton in the Cotton State
For Schmutz, Alabama has been an ideal place to conduct research of the cotton genome. “By coming to Alabama, we got a lot closer to almost everybody we work with, because we study plants that grow mainly in the Midwest and the South, ” he says.

HudsonAlpha’s cutting edge facilities and a town that supports research are encouraging for the team.

“I run into people who have all sorts of questions and want to hear about what we’re doing, ” Schmutz says, adding that many of them know somebody who raises cotton.

According to the Alabama Cotton Producers, the state ranks ninth in the nation in cotton production, and Madison County, which includes Huntsville, is among the top cotton-producing counties in the state, along with Baldwin, Cherokee, Colbert, Escambia, Geneva, Limestone, Lauderdale, Lawrence and Monroe. Studying the science of cotton with cotton fields in view outside the office windows just keeps the work authentic.

Nancy Mann Jackson is a freelance writer for Business Alabama. She lives in Huntsville.

Text by Nancy Mann Jackson

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