University of Florida scientists have achieved a major milestone in their quest to develop a citrus greening-resistant tree by sequencing the genome of a fruit plant that’s a close cousin to citrus trees.

You’d need to print 54,000 pages of copy paper to see the complete genome sequence. But within it, scientists believe they’ve found genes to lay the groundwork to make citrus more tolerant and even resistant to certain diseases, including citrus greening.

Researchers sequenced the genome from trifoliate orange. The new genome will help those who breed new citrus trees that will survive under today’s challenging conditions, including invasive pests, viruses and changing climates. Their research provides a powerful new tool to control the deadly consequences of the greening disease, which has severely damaged the state’s multibillion dollar-a-year citrus industry.

“Very importantly, trifoliate orange and its hybrids have genes that can confer high tolerance to citrus greening and resistance to the Asian citrus psyllid, the insect that transmits greening to citrus,” said Zhanao Deng, a professor environmental horticulture and a senior author on the new UF/IFAS-led study. “This genome can be used as a reference template to sequence widely used trifoliate orange hybrid rootstock varieties.”

“Most people – even citrus growers – rarely see trifoliate orange. This is because they usually are the rootstock part of the tree, mostly underground,” said Fred Gmitter, a UF/IFAS professor of citrus breeding genetics and a co-author on the study.

Trifoliate oranges or their hybrids are grown at nurseries, and farmers use them as rootstock to grow the citrus that’s above ground. Trifoliate orange and its hybrids were used as the rootstock for more than three million citrus trees in Florida alone in 2018-2019, UF/IFAS researchers say.

Trifoliate orange and its hybrid rootstocks accounted for 82% of the top 20 rootstocks used in the 2018-2019 citrus propagation cycle in Florida.

“Our trifoliate orange genome will allow scientists to develop new tools that can more speedily transfer beneficial genes into sweet oranges, grapefruit and breeding of new scion cultivars, which grow above the ground,” Mr Deng said.

“Releasing the first trifoliate orange genome can be valuable for our citrus gene-editing efforts,” Mr Gmitter said. Scientists are using gene editing to produce canker-resistant and greening-tolerant citrus.

“Because of our high-quality genome, re-sequencing of trifoliate orange hybrid rootstock varieties will be much easier, much quicker and much more cost-efficient,” said Mr Deng. “Re-sequencing will enable development of new breeding tools, such as DNA marker-based selection, genomic selection of new rootstock varieties with resistance and tolerance to citrus greening, citrus tristeza virus and citrus nematodes. The new varieties might give higher yield and fruit quality.”

Citrus breeders want to introduce desirable genes from trifoliate orange into sweet orange, grapefruit and other varieties. It took decades to produce the first citrus scion variety (‘Sun Dragon’) from crossing trifoliate orange and transferring some of its genes across multiple generations into sweet orange. With this new information from genome sequencing, that timeline can be dramatically reduced.