UF scientists make big stride toward greening-resistant citrus trees

by Brad Buck 

University of Florida scientists 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.

UF/IFAS researchers sequenced the genome from trifoliate orange, in collaboration with scientists from the University of California at Berkeley, the U.S. Department of Energy's Joint Genome Institute and UF's Interdisciplinary Center for Biotechnology Research. 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,” Deng said.

“Releasing the first trifoliate orange genome can be valuable for our citrus gene-editing efforts,” 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 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.

This project was funded by two grants from the Citrus Research and Development Foundation (CRDF) and a grant from the USDA/NIFA Citrus Disease Research and Extension (CDRE) program.

To see a video about the research and its implications, click here.

FredGmitter at it.  Photo credit: Brad Buck, UF/IFAS.

Ben Faber and Brad Hanson

This is not good. You find an avocado tree with sun blotch or it is time to thin the orchard and you remove the offending tree. You know that if you don't remove the sucker, you'll end up with some rootstock growth that just gets in the way of the other trees. Avocado suckers can look like a valued tree until it's time for harvest several years later, and then you are likely to find that it's not the variety that you thought it was. Homeowners often find this problem several years after a freeze and the lemon tree that regrew from the freeze damage turns out to be the rootstock variety and produces some gnarly, seedy, juiceless fruit. Even without a frost, sometimes rootstocks which are selected for their vigor, can be more vigorous than the scion variety and will overgrow it. You then end up with whatever the rootstock fruit turns out to be.

In some situations, it is legal and common to use a “cut stump” treatment to kill stumps and prevent resprouting. In these cases, glyphosate or triclopyr is sprayed, drizzled, or painted onto a freshly cut stump. Relatively high concentrations of the herbicide are applied to the cambium, which is the living tissue just under the bark.   Cut stump treatments work well in many situations, including citrus orchards. This type of cut and spray treatment is commonly done to remove undesirable plants, like arundo and weedy tree species. However, in some trees, like avocado and many forest species, there can be root grafting, which are tree-to-tree root connections.

Due to root grafting in a mature avocado orchard, it really can be one giant root system, one tree connected to all the other trees. And if a systemic herbicide is injected in one tree, the surrounding trees can be affected – they might get enough herbicide through the root graft to be injured or even killed along with the target tree. This technique has been used in Florida to remove Laurel Wilt Disease infected avocado trees which can rapidly infect surrounding trees with the killer fungus. This is a helpful technique, because it removes any doubt that all infected trees have been killed to prevent the spread to healthy trees in the orchard.

In a healthy orchard in California, this is not a really good way to remove avocado stump sprouts. Every year reports come in of glyphosate killing good trees that surround a removed tree. The photo below is a recent case where the stump (circled in blue) was scored and painted with glyphosate. Within two weeks the surrounding tree were also killed. The systemic material was translocated from the cut surface by way of root grafts to the neighboring trees. And those trees are now dead, too.

So what to do? One thing done by those with a front-end loader or a backhoe, is to pull the stump and have an end to the sucker problem. It also reduces the possibility of chronic armillaria fungus persisting to infect trees. The problem is that it leaves a big hole to deal with which can open up a slope to erosion. If on a slope, it requires a decent sized tractor that can safely be operated on the slope without tearing up everything, including the irrigation system. And in the end, it's expensive.

The other approach is to just cut the tree down as low as possible without damaging the chain saw. Then as the irrigator makes inspections, just physically knock off the suckers as they come up. If walking the irrigation lines, it's not a problem. Covering the stump and immediate area with a physical barrier such as thick, black plastic sheet (greater than 5 ml), can reduce the number of suckers. To speed degradation of the stump, the top of the cut can be scored and a salt such as urea or magnesium sulfate (both at 10 pounds per stump) can be applied. At this rate, rather than fertilize the stump, under moist conditions, this treatment facilitates the activity of wood-decaying microorganisms; it can also damage or reduce the regrowth of the suckers.

There are also a range of registered contact herbicides that can be used to burn out the suckers. Materials, such as Scythe, Axxe and Suppress are all registered for avocado sucker control. There are others. These contact herbicide work best on small tender suckers so don't let the suckers grow more than a foot or so. For best control of suckers, apply them at the highest allowable rate with an approved adjuvant at a spray-to-wet rate. Because these products are not systemic, you'll likely need repeat applications, as new fresh buds break and new suckers erupt.

Using a contact spray means the grower would still need to be out in the orchard controlling the suckers. The grower still needs to be out in the orchard checking the irrigation lines. Why spray the suckers when they can just be broken off?

Although systemic herbicide can be used effectively to control suckers or stump sprouts in some tree crops or situations where root grafting does not occur, this is not a recommended practice for avocado because of the risk of damage to nearby trees.

The false chinch bug (FCB), Nysius raphanus (Hemiptera: Lygaeidae), is a pest of many plants. FCB is a generalist and has been found to be a problem in many cropping systems such as soybeans, quinoa, tobacco, cotton, broccoli and other Brassicaceae plants. FCB adults (above) is mostly light to dark gray, elongate, and about 0.12 inch (3 mm) long. Females lay eggs on host plants or in cracks in soil. The mostly pale gray nymphs have inconspicuous reddish to brown abdominal markings. FCB has 4-7 generations per year with all stages being potentially present throughout the year. All stages can be present throughout the year. They also can be found invading homes in the southwest. Their populations generally start in unmanaged fields with lots of weeds and are an issue for crops when they build up large numbers and move into the crops from the unmanaged, weedy fields.

Photos: Surrendra Dara

This year it's host of choice is young avocado plantings in Ventura County. False chinch bug occasionally causes severe injury on young trees by sucking sap from shoots and young stems. Infested shoots wither and die suddenly after attack, which typically occurs in May and June. Economic damage normally occurs in groves away from the coast only on young trees in border rows adjacent to uncultivated areas or grasslands. Otherwise healthy mature trees tolerate bug feeding.

Here are photos of damage to young avocado provided by Tom Roberts, Integrated Consulting Entomology.

To best manage FCB, a grower will need to catch it before it establishes and the populations explode. This is difficult because the pest will not reoccur every year on regular basis. From what has been seen in the field this year, FCB appears to prefer young avocado plantings and thus, a targeted approach is to monitor only in new plantings right as summer temperatures are rising. In paper in the journal, Phytoparasitica from 2006, the authors investigated what color sticky trap was best for monitoring and found that yellow worked best. Thus, passive monitoring with yellow sticky cards that are placed throughout the field and monitored weekly is a potential option. However, this approach can be expensive with the labor hours needed to properly process the sticky cards. A more practical approach is to sweep net weedy areas on the outside of avocado groves and adjacent unmanaged areas nearby weekly in search for the first signs of FCB.

In conventional avocado production, there is only one insecticide recommended for use against FCB. Malathion 8 at 16 oz/acre.

Not everything you see on a tree's bark is disease, although that's usually the first thought of a plant pathologist. Below are bacterial canker and black streak which are both significant problems in some California avocado orchards. Their cause is normally an issue of water/salt management.

But sometimes these patches are innocuous. In a recent farm call, and the “thing” on the bark was a hybrid organism called a lichen. This is a classic odd ball of nature. It consists of a blue-green algae called a cyanobacteria – photosynthetic single cells making sugar – and a fungus that serves to protect the algae from the elements.  The fungus is farming the algae, in a way.  Neither, though, does well on its own.  In fact, it's been difficult to recreate the lichen relationship in the lab, starting with the separate,  independent partners.

These are tough “beasts” surviving on most continents, in some very harsh environments. When the going gets rough, they just close up on themselves and survive until the right moisture conditions occur.  And, within an hour they can spring forth full of color. The rest of the time, they might just hang on a rock.

Some of the algae also fix nitrogen from the air, so lichen really are self-sustaining. They just need somewhere to grow, a tree, a rock, a roof. They take amazing shapes and colors and they are also known for producing some interesting toxins that could be used as medicines.

These life forms have been studied for over 150 years and have been recognized as kind of the standard for a "mutualism", a symbiosis where the two participants benefit from each other. Only in the last few years has it been recognized that there is often a third component to this symbiosis - various yeasts that are the likely producers of the toxins.   Toxic for some life forms like other bacteria, algae or animals, but  not others. For some animals, lichens can be an important food source, such as for caribou, reindeer and musk ox. Animals and lichen that are all growing in a harsh climate.

The California state lichen is Spanish Moss or Lace Lichen, neither moss nor lace nor Spanish, but Ramalina menziesii. It is not to be confused with that other Spanish Moss found around the world, in the genus Usnea. It's all worth reading about, because it can get so confusing