LSU AgCenter molecular biologist Niranjan Baisakh is studying DNA markers in sugarcane associated with resistance to the brown rust fungus. (Photo by Olivia McClure)

News Release Distributed 02/20/14

BATON ROUGE, La. – Brown rust fungus poses a serious threat to Louisiana's nearly $1 billion sugarcane industry. Thanks to funding from the American Sugar Cane League, LSU AgCenter molecular biologist Niranjan Baisakh is studying DNA markers in sugarcane associated with resistance to the fungus. He hopes to help sugarcane breeders develop varieties that block the fungus at the molecular level.

The fungus, which creates orange to reddish brown lesions on sugarcane leaves, is spread by spores that blow through the wind. The lesions’ damage prevents leaves from collecting enough light to effectively perform photosynthesis. Thus, the plant cannot produce sufficient energy to grow and be healthy.

Baisakh said the yield of nonresistant cane varieties can be reduced by 20 percent to 50 percent.

Scientists have been studying sugarcane resistance to brown rust fungus for more than 20 years, Baisakh said, but a gene called Bru1 is the only indicator of resistance located so far in sugarcane. The frequency of Bru1 in Louisiana sugarcane varieties is low, meaning it has not been used effectively as a means of breeding resistant varieties, he said.

However, there are some varieties that are resistant to the fungus that do not contain Bru1.

Baisakh's goal is to track DNA characteristics of fungus-resistant varieties to determine genetic components of resistance. Once resistance genes besides Bru1 are discovered, varieties containing them can be crossed with those with Bru1 to form "gene pyramids" that force the fungus to overcome multiple genes instead of one.

It is important to identify these alternate resistance genes because brown rust fungus often adapts to sugarcane varieties as acreages increase.

"If you have just one variety planted and it is resistant, then the fungus has the ability to adapt and overcome resistance because the fungus has no known alternative host," Baisakh said. "You can't depend on just one resistance gene."

Baisakh works closely in this effort with other AgCenter researchers – Jeff Hoy, Collins Kimbeng, Michael Pontif and Kenneth Gravois – and Anna Hale, a researcher with the U.S. Department of Agriculture-Agricultural Research Service Sugarcane Research Unit in Houma.

Gravois said brown rust fungus arrived in Louisiana in 1979. Today, it is "probably one of top two diseases we deal with."

In 1993, the AgCenter released the high-yielding sugarcane variety known as LCP 85-384, a variety that became so popular that it made up 91 percent of Louisiana sugarcane acreage by 2004. It was highly resistant to brown rust fungus when it was released, Gravois said, but the disease eventually made its way in and hurt the industry.

Today, LCP 85-384 is grown on less than 1 percent of acreage in the state. Gravois said the replacement was HoCP 96-540, which came out in 2003. Over the years, it too became susceptible to the disease.

"The good thing about that situation is the percentage of 540 in the Louisiana sugar industry never got above 45 percent," he said. "When you get a variety on a large percent of acreage, it puts more pressure on the disease organism to change and adapt."

Until about three years ago, the only way to deal with the fungus was to develop varieties that resist it, Gravois said. Growers now have a couple of fungicide options that help extend the life of some sugarcane varieties, but they are expensive. They also do not take away 100 percent of the damage, so Gravois said varietal resistance remains the best option.

Sugarcane breeding, however, takes 12 to 14 years, and molecular studies are slow because sugarcane is a genetically complex plant that does not have a fixed chromosome number. Baisakh said sugarcane is much more difficult to manipulate than crops such as rice.

Epidemics of brown rust usually happen early in the growing season, Baisakh said. Fortunately, young plants can be tested for resistance, which saves time and money. DNA of thousands of plants can be tested in a laboratory inside small tubes, which is easier than planting an entire field just to see if a variety is resistant, he said.

Baisakh said this season has been colder than usual, so farmers may assume their cane is safe from the fungus when, in fact, they may be growing susceptible varieties. If they plant the same varieties next year and the weather is warmer, they may be surprised with a severe outbreak of rust.

Olivia McClure