New Methods for Cotton Research

New Methods for Cotton Research

UNT Diving Eagle
October 25, 2021

By Brittney Dear

A team of three researchers in UNT’s BioDiscovery Institute are working to reduce damage to cotton plants from aphids and Fusarium fungal infections after having received a National Institute of Food and Agriculture grant from the U.S. Department of Agriculture. The research has the potential to considerably reduce the need for insecticides and fungicides, and also has significant economic impacts since one-third of the total U.S. cotton production is from Texas. The grant will support three years of research.

Aphids are insects that feed on the nutrient-rich sap flowing from the photosynthetic leaves to the developing cotton bolls. Aphids rob the plant of the food needed for robust growth while also creating an array of other challenges. Additionally, aphids take more sugar from the plant than they can use, and the excess is excreted as ‘honeydew’ that can make the fiber sticky and reduce quality.

Fusarium is a devastating pathogen that is present in the soil and can affect a variety of important crops, including cotton. When Fusarium fungus infects, it chokes off nutrient flow, causing the plants to die. 

“Fusarium in the Southern U.S. is particularly insidious because it lingers in the soil for years,” Roisin McGarry, research assistant professor, says. “Even though you’ve lost one crop, it doesn’t mean your next crop is going to be any better — it’s probably going to be worse because Fusarium is very difficult to get rid of.”

Their research will test the functions of several potential resistance genes using virus-induced gene silencing and CRISPR-based-technology for genetic mutation. CRISPR stands for "clusters of regularly interspaced short palindromic repeats” and has revolutionized research in all avenues of biology. 

“The advantage of CRISPR is that we can make an engineered change within the plant, but without leaving behind any foreign DNA. Our research material would not be genetically modified organisms,” says Brian Ayre, professor of biochemistry and molecular biology. “At both the regulatory level, and also at the level of consumer acceptance, cotton varieties emerging from our work would be more attractive for agricultural production.” 

Ayre serves as the project director and is responsible for overseeing the research as well as reporting progress back to the USDA. Ayre has worked in plant genetics for over 30 years.

“We wanted to look at new technologies, specifically CRISPR, to benefit pest resistance in cotton plants,” Ayre says. “The call from the USDA fit this team’s interests perfectly.”

McGarry, who has worked with plants since her undergraduate days, previously collaborated with Ayre to develop "virus induced flowering” to benefit cotton breeding. They are now continuing that collaboration to develop CRISPR-based technologies for cotton research. In the lab, McGarry will be working alongside two graduate students to change gene expression in response to aphid infestations and Fusarium infections by silencing the genes with viruses. After the cotton plants grow, the lab will analyze them to determine whether they have the expected changes in gene expression in relation to the control group. 

“This is going to be a great body of research using the virus approach to really gauge how well the genes are targeting and responding to these insect and pathogen challenges,” McGarry says. 

The next step will be to move toward CRISPR approaches to target those genes for permanent, heritable mutations. This step, although long-lasting, is more time-consuming, whereas virus-induced gene silencing generates fast results. 

“Using CRISPR usually requires long periods of tissue culture — growing the plant tissues in sterile cultures — because we have to generate a whole plant from a single cell,” Ayre says. “We’re trying to avoid that with this technology. We’re combining our virus-based techniques with the new technology of CRISPRs in intact plants, so we can avoid laborious tissue culture from a single cell.”

Using both methods together, the investigators hope to speed up research, not just for this problem of aphids and Fusarium in cotton, but also in a range of other applications. Their method is intended to bypass the amount of tissue culture required to test important genes in the plant.

“If it works for this particular problem, then it also will work for other problems,” Ayre says. “And that could really change the way we do cotton biotechnology.”

“It could go beyond cotton,” says Jyoti Shah, professor of biochemistry and molecular biology, and chair of the Department of Biological Sciences. “It could set the stage for people to look at other crops. It could be used for other things besides insects and fungus. The technology has broad application.”

While McGarry and Ayre work with cotton, Shah has worked with aphid populations and has experience in plant-pest/pathogen interactions. He will offer valuable insight regarding the pests and pathogens used in this research. 

“The timing was right for this grant, the expertise we had was right, the technology is still developing and both sides just came together,” Shah says. “As a scientist, before you retire, you would like to see what you’ve done come out as a product that will benefit society, and I think that’s what becomes most appealing and satisfying in the end.”