Retracing Citrus’ Earliest Roots to Find Clues for Healthier Future

University of Florida scientists led an international research team that analyzed the genome sequences of 10 diverse citrus varieties for the first time.

Their findings, published online Sunday by the journal Nature Biotechnology, could help the citrus industry find and deploy genes for resistance to citrus greening, a bacterial infection devastating crops in North America.

Fred Gmitter, a UF Institute of Food and Agricultural Sciences faculty member, led the team of researchers from the United States, France, Italy, Spain and Brazil as part of a decade-long project to sequence and understand citrus genomes.

They analyzed and compared the genome sequences of sweet and sour oranges, along with several important mandarin and pummelo varieties. By understanding the relationships between the various cultivated species they describe as having “very narrow genetic diversity,” the researchers hope to enable genetic modifications and traditional breeding, which could lead to crops more resistant to disease and environmental stress, as well as better flavor and health-promoting benefits.

“Citrus has incestuous genes – nothing is pure,” said Gmitter, who is based at UF’s Citrus Research and Education Center in Lake Alfred. “Now that we understand the genetic structure of sweet orange, for example, we can imagine reproducing early citrus domestication using modern breeding techniques that could draw from a broader pool of natural variation and resistance.”

New citrus trees are almost always produced by grafting, a method of propagation that binds the fruit bearing part of one tree to the root system of another. That produces trees that more quickly bear genetically identical, uniform, high quality fruit. But because of that uniformity, if one tree is susceptible to disease, they all are.

Citrus is the world’s most widely cultivated fruit crop. In Florida, it is a $9 billion industry, employing 75,000. But it is under attack from a tiny bug, the Asian citrus psyllid, which sucks on leaf sap and leaves behind the citrus greening bacteria.

The disease, which renders fruit unsuitable for sale and eventually kills trees, could wipe out the industry in the next decade if a viable treatment is not found.

UF/IFAS researchers have attempted everything from trying to eradicate the psyllid to breeding citrus rootstocks that show better greening resistance. Current control methods include removing and destroying infected trees, controlling the psyllid, and providing additional nutrition in an attempt to keep infected trees productive.

Citrus was first domesticated in Southeast Asia thousands of years ago before spreading throughout Asia, Europe, and the Americas via trade.

One of the two wild species, Citrus maxima, gave rise to today’s cultivated pummelo, the largest citrus fruit, which can often weigh 2 to 4 pounds or more. The small, easily peeled mandarins were, in contrast, found to be genetic mixes of a second species (Citrus reticulata, the ancestral mandarin species) and pummelo. Sweet orange, the world’s most widely grown citrus variety, was found to be a complex hybrid, with mixed bits and pieces of the mandarin and pummelo genomes. Seville, or sour orange, commonly used in marmalade, is a simple hybrid between the two ancestral species.

The U.S. Department of Energy’s Joint Genome Institute, Genoscope in France, the Institute for Genomic Applications in Italy, and 454 Life Sciences, a Roche company, contributed to the citrus genome project.