By Lara Ivanitch

Spoorti Gandhadmath carefully placed 3.5-inch pots on a shelf in a growth chamber. Within seven days of sowing, newly sprouted leaves had fully emerged from each of the carefully selected seeds, representing diverse cotton genotypes.

Gandhadmath, a doctoral student in crop science at NC State University, then inoculated the seedlings with race 18 of the cotton bacterial blight pathogen as part of her work in the Kuraparthy Lab. Seven days after that, she checked the tiny leaves for water-soaked spots that indicated infection, or dry, dead patches that revealed the plant had resistance to this particularly virulent strain of blight.

Known as phenotyping, Gandhadmath tracked the plants’ observable responses to the bacterium as the first step in a study recently published in The Plant Genome. This study explored the genetic makeup of cotton plants in search of the source of their resistance to bacterial leaf blight, which has reemerged as a threat to cotton production in the United States.

“Our team was surprised by what we found,” Gandhadmath says. “The cotton lines we studied showed strong resistance to the aggressive race 18 of the disease.”

A Growing Concern

Cotton bacterial blight, also known as angular leaf spot, begins as small, dark green, water-soaked spots on the undersides of cotton leaves. As the spots grow, leaf veins restrict their spread, giving them an angular shape. Larger lesions appear on both sides of leaves, develop reddish-brown borders and can spread along major veins.

The disease thrives in warm, humid, rainy conditions and can affect cotton throughout its life cycle, from germination to harvest. It attacks all parts of the plant, including seeds, stems and bolls, causing premature defoliation, lint discoloration and seed rot.

No treatment exists to stop the blight once it spreads within a field, leaving farmers with prevention as their only defense. Growers reduce risk by planting blight resistant cotton varieties, using acid-delinted seed, spacing plants to lower humidity and destroying crop debris after harvest.

“Since this disease is actually transmitted through seed, acid de-linting, a chemical process to remove seed fuzz, significantly reduces seed surface-borne bacterial populations and has, to some extent, contributed to controlling the spread of this disease,” says Vasu Kuraparthy, a professor and cotton breeder in the Department of Crop and Soil Sciences and Gandhadmath’s advisor.

However, since 2011, increasing numbers of bacterial blight outbreaks have originated from weeds, stubble and alternative host plants harboring the bacterium. When favorable conditions such as warm nights and high humidity occur, the disease spreads into cotton fields.

Kuraparthy explains that in the United States, the deployment of genetic resistance to cotton bacterial blight drastically declined in varieties released between the late 1990s and 2009. As a result, by 2009, over 75% of planted cotton acreage was highly susceptible to this disease, leading to a resurgence across the Cotton Belt by 2011.

“An outbreak of this disease, mainly caused by race 18, damaged the cotton crop in the midsouth, including Texas, Mississippi and Oklahoma, causing major losses in cotton productivity in those regions,” he says. “In absence of proper control measures, the losses can be up to 60 percent.”

At this point, cotton bacterial blight has only appeared in pockets of North Carolina and hasn’t become a major concern in the state. “However, changing weather conditions, such as higher temperatures and increased humidity, combined with the use of susceptible cotton varieties, raise the risk of future outbreaks,” Kuraparthy says. “If the disease spreads, it could result in significant economic losses for cotton producers.”

Genetic Findings

After screening cotton plants for their response to bacterial blight, Kuraparthy’s team examined their DNA to understand the mechanisms underlying resistance to the disease. The goal was to find which parts of the genome are responsible for protecting plants from infection.

To do this, they performed a genome-wide DNA scan of cotton plants using about 63,000 genetic markers to help pinpoint regions linked to important traits. This analysis, called GWAS (genome-wide association study), revealed one major region in the cotton genome strongly associated with resistance to race 18 of bacterial leaf blight. Follow-up studies using different genetic mapping populations confirmed the finding and showed that this resistance is largely controlled by a single dominant gene.

“We initially expected that this resistance would be controlled by several different genes, especially because the cotton accessions used in the study came from diverse backgrounds developed over many years in the U.S.,” Gandhadmath explains. “However, our research revealed something unexpected: despite this diversity, resistance was largely linked to a single key region in the cotton genome.”

Practical Applications

The study has led to several practical tools for cotton breeding programs. The research identified cotton lines with strong resistance to bacterial blight, produced reliable screening methods to identify resistant plants and developed DNA markers that allow breeders to accurately track and introduce this resistance into new varieties.

While the project aimed to identify the gene responsible for bacterial blight resistance, Kuraparthy notes that resistance based on a single major gene can be fragile. Over time, the bacterium can evolve and potentially overcome those defenses.

Under Kuraparthy’s direction, Gandhadmath has continued the research to pinpoint the gene’s exact location and better understand how it works at the molecular level. By studying how the resistance gene interacts with the bacterium, the team hopes to design more durable, long-lasting protection for cotton crops.

“We have to stay one step ahead in this host-pathogen battle to make the resistance durable in cotton,” says Kuraparthy. “Understanding the basic molecular and genetic mechanisms behind resistance is the first step toward that goal.”

This post was originally published in College of Agriculture and Life Sciences News.