Huanglongbing, or citrus greening, has devastated global fruit production, and continues to spread. Caused by the insect-vectored, phloem-limited Candidatus Liberibacter asiaticus, Huanglongbing is thought to have originated in China during the early 1900s. Citrus greening was recognized as widespread in Brazil in 2004, and made its first appearance in the US in 2005, affecting citrus farms across Florida, where 75 percent of the country's citrus is produced.
"If you talk to anyone in the world of citrus, they'll tell you that Huanglongbing is the greatest threat to the survival of the industry," said the University of Florida's Fred Gmitter at the seventh annual US Department of Energy Joint Genome Institute User Meeting, held in Walnut Creek, Calif., in mid-March. While certain varieties display some degree of disease tolerance, "there is no known genetic resistance within the citrus germplasm pool," he added.
Later that month, the US Department of Agriculture confirmed cases of citrus greening in Los Angeles County, marking the first appearance of the disease on the American West Coast.
To stop the spread of Huanglongbing, the fix is simple — but costly. The early identification and removal of infected plants is ideal, "but if you're a citrus grower and find a tree with one branch that has some symptoms on it and the rest of the tree is full of money — fruit — it's awfully hard to justify removing those trees," Gmitter said.
However, he added, the global spread of citrus greening has had a silver lining of sorts. "This motivated many of the industries in the world to generate funds for research. One of the first things they were convinced was a worthwhile investment was to move forward with some citrus genome sequencing projects," Gmitter said. Funding agencies and industry groups agreed that having citrus genomes at the ready was the first step toward understanding the mechanisms of the disease and developing breeding schemes to promote resistance.
"In 2003, we established the International Citrus Genomics Consortium. At that point in time we were looking at an estimated cost of $10 million to sequence a genome," Gmitter said. "It's amazing how things have changed."
That group reported the first citrus genomes — for the sweet orange and Clementine mandarin varieties — in January 2011. Now, with more than five citrus genomes complete and several more in the pipeline, researchers have begun to apply their findings.
"One of the more interesting things is to use this resource to develop good marker-assisted breeding technology," Gmitter said. "From a more fundamental point of view, understanding host-pathogen interaction is critical."
Comparing healthy and infected rough lemons and sweet oranges to detect molecular differences between tolerant and susceptible plants, Gmitter and his colleagues have taken a holistic approach, using transcriptomic, proteomic, and metabolomic techniques. In one array-based study, Gmitter's team found that several genes involved in cell wall biosynthesis are upregulated in tolerant, infected lemons, while those same genes are downregulated in susceptible, infected oranges, pointing to a potential disease mechanism.
Understanding disease susceptibility "is important for the citrus breeders' dream of recreating the sweet orange, but modifying certain critical characteristics, perhaps identifying genes for disease tolerance that could be incorporated," Gmitter said.
There are several potential applications for citrus genomics beyond disease resistance. "Ultimately, as a breeder, I want to get to the underlying genetics of these characteristics and the specific points within them to be able to make selection a more efficient process," Gmitter added.