In a major breakthrough in avocado breeding, researchers at UC Riverside and UC Davis have identified the gene that controls whether an avocado tree has an A- or B-type flowering pattern. These flowering patterns determine how neighboring trees exchange pollen, making them an important factor in avocado production.
While growers historically had to wait 5 to 10 years for trees to mature and flower to identify their type, this discovery enables scientists to predict these vital traits directly from seedling DNA, unlocking unprecedented efficiency and precision in avocado breeding programs.
The study, published in the Proceedings of the National Academy of Sciences, identified the gene referred to as SDMYB — a transcription factor controlling flowering behavior.
The primary impact of genetic screening is resource savings rather than a faster timeline to commercial production, says Eric Focht, staff research associate in UCR’s Department of Botany and Plant Sciences and study co-author.
While classical avocado breeding remains a lengthy 15- to 20-year process due to tree maturity rates, early screening acts as a strict initial filter, he says. Instead of relying on an unscreened 50-50 mix of A and B flowering types, Focht says researchers can now determine precise ratios before planting and avoid planting seedlings that don’t make the cut. Ultimately, this informs breeding decisions that could provide substantial savings in field space, labor, water and management costs.
“This is why it is so important to start out with the best selection criteria for the seeds you are planting; screening for A or B flower type is a big deal for this reason,” says Focht. “If we had other genetic markers for other desirable traits, we could do the same with them. Our success rate in the first planting phase is around 1-2% of the seedlings make it out of this phase, so everything we can do to narrow the field to begin with just ensures that the 1-2% already have at least one or more of the traits we are looking for.”
Avocado breeding programs require tremendous patience, agrees Mary Lu Arpaia, professor of cooperative extension at UCR.
“Typically, if you’re lucky, you can get some fruit in the third or fourth year, but it’s very little fruit,” she says. “It’s easy to identify the seedlings that have junk fruit so that you can get rid of those seedlings. But you still need to collect two or three years of data, even on the stuff that ends up not being any good.”
Arpaia says researchers spend five to seven years identifying seedlings that have traits of interest, before they are planted.
“You have to replicate those trees so that you can look at them more to look at yield, and as you get more fruit, the post-harvest quality of the fruit,” she says. “This knowledge about the flower type is going to help us be more selective in what we go into that phase 2 with.”
Solving a Century-Old Pollination Mystery
Avocado pollination is complex, with all avocado flowers opening first as female before reopening later as male. The exact timing of these phases determines the classification as Type-A or Type-B, preventing self-fertilization and encouraging cross-pollination.
The UCR team says it provided hundreds of genetically diverse avocado trees to the study, representing numerous varieties and related species.
And because temperature swings can alter flower timing, the UCR team logged night-and-day field observations to determine an optimal sampling schedule.
“Previous studies have shown that environmental conditions, particularly temperature, can delay or advance the timing of floral phases without changing the underlying A/B flowering type,” says Marllon Soares dos Santos, a postdoctoral researcher in UCR’s Department of Botany and Plant Sciences and a co-author of the study.
Soares dos Santos worked with Jeffrey Groh, who led the project as a doctoral student at UC Davis, to first characterize the local flowering behavior before establishing the sampling windows.
“Our PNAS study demonstrated that the SDMYB marker is a robust predictor of the genetic A/B flowering type,” Soares dos Santos says. “While extreme temperatures may alter the timing of flower opening, the underlying genetic identity remains stable. We are currently conducting additional studies to better understand the environmental plasticity of these groups.”
Through the UC Davis and UCR study, researchers compared avocado genomes with those of related tree species and found that the same two versions of the gene are shared by at least 26 relatives, suggesting this flowering strategy has persisted for roughly 42 million years.
“I just think it’s amazing that we found the gene. It’s sort of a holy grail for breeding,” says Arpaia. “Because if your goal is to find a high-value B flower type, then it really is going to make breeding because you could germinate thousands of seeds and then only plant out the ones that show the marker to be a B flower type. So, it can make breeding very much more efficient.”
Immediate Commercial Impact
UCR says California avocado growers currently dedicate about 10% of an orchard to B-type pollinizer trees that help nearby A-type trees like hass to produce more fruit. But those pollinizers often produce fruit with little commercial value.
When it comes to the financial impact on grove revenue once breeders can reliably pair top-tier fruit quality with B-type pollination performance, the practical benefits of the SDMYB discovery for avocado breeders, nursery managers and commercial operations are potentially great.
“Theoretically you get a higher return on everything you grow, but I can’t give you an exact number,” says Arpaia. “But the idea here would be that nothing’s going to be identical to hass. It’s going to be something unique. It’s like comparing apples — gala to fuji or one of the other apple varieties. They’re all good eating, but they’re different from themselves.”
Focht says it depends on the value for the pollenizer fruit.
“If it is equal to the primary — likely hass — crop, then instead of your field being 90% maximized in crop value, it is 100% maximized in crop value.”
Focht says while farmers will ultimately need to determine how they want to manage their fields, having a marketable B flower type to increase the set in their main A flower type commodity is “a big step forward.”
“You could even see a farmer trying a more equal mix of A and B flower types if the price somehow made sense,” he says. “However, in the current model, with the very poor price for bacon, zutano, and other low-quality B flower type pollenizer fruit, any price beginning to approach a hass or other quality commodity fruit is a big improvement over the status quo.”
Through its breeding program, UCR has already developed the Luna, a commercially desirable B-type avocado. Researchers say discoveries like this one could help them develop more varieties with the same combination of high-quality fruit and pollination benefits.
Building the Next Generation of Avocados
While gene editing is still years away, this new genetic discovery in avocados offers breeders an immediate tool for selecting seedlings with the most desirable traits before committing years of time and valuable orchard space.
“The more genetically distinct but commercially successful varieties we have, the better,” says Focht. “In the long run, we will need to continue to generate new promising selections at the same time that we are optimizing the ones that we already have, whether through CRISPR or other means.
“Basically, if science is extending the boundaries of what is known, then this discovery is a significant expansion and there are likely many more to be made,” continues Focht. “The genetic information for avocado has now been around for a couple years and continues to expand, but it’s also the increased power of our computing/bioinformatics that is making it easier to mine the existing data for information.”
