Trifoliate orange and its hybrids have been widely utilized as rootstocks in citrus production. They accounted for 82% of the top 20 rootstocks used in the 2018-2019 citrus propagation cycle, according to Dr. Zhanao Deng, professor of Environmental Horticulture at UF. He also led and coordinated the trifoliate genome sequencing, analyses, and mining efforts, and oversaw the production of the final paper.
“The most popular rootstock at present time, US-942, is a trifoliate orange hybrid,” says Deng.
Trifoliate orange and its hybrids benefit scion citrus cultivars in multiple ways including resistance to citrus tristeza virus, citrus nematodes, tolerance to citrus seedling damping-off, root and foot rot, and gummosis.
Very importantly, trifoliate orange and its hybrids possess genes that can provide a high level of tolerance to citrus greening and resistance to Asian citrus psyllids. Deng says trifoliate orange has been a very important breeding parent for citrus breeding and a major source of valuable genes for improving citrus. It can provide valuable genes and gene sequences for using the latest biotechnologies and precision breeding to improve varieties, for resistance to citrus greening and other major diseases.
The high-quality trifoliate orange genome assembly is freely available online to citrus researchers and other researchers at their fingertips. Dr. Deng mentions this genome has become a genomic resource of enormous value to them. It can facilitate their effort to clone genes or edit genes for citrus greening disease resistance, save their time, reduce costs, or speed up the development of new resistant cultivars.
“We identified strong candidate genes that may control trifoliate orange’s tolerance to citrus greening, strong candidate genes for citrus nematodes, candidate genes for cold hardiness, and others,” Deng says. “These candidate genes seem to be good targets for engineering or editing for citrus greening resistance.”
This genome sequence will make it much easier to develop new citrus breeding tools that can be used to speed up the development of citrus cultivars. New DNA markers can be used to select desirable, promising citrus plants years before they flower and bear fruit. DNA markers can help citrus breeders eliminate hundreds or thousands of unwanted citrus plants when the plants are only several months old. In finding rare plants with better citrus greening resistance. The sequencing, analysis, and releasing of the trifoliate orange genome are direct results of close collaborations among Deng laboratory at the UF Gulf Coast Research and Education Center, Gmitter laboratory at the UF Citrus Research and Education Center, Rokhsar laboratory at the UC Berkeley, and Albert Wu and Shengqiang Shu at the U.S. Department of Energy’s Joint Genome Institute (JGI). With the status our citrus industry is I hope this is sooner rather than later in developing better tolerant citrus to HLB.