Breeding apple rootstocks

Prof. Gennaro Fazio leads the Cornell-Geneva rootstock-breeding programme. He spoke to Fresh Quarterly about the science of apple-rootstock development. By Anna Mouton.

The Cornell-Geneva rootstock-breeding programme is a joint venture between the United States Department of Agriculture and Cornell University that has given growers worldwide the well-known Geneva apple rootstocks.

Prof. Gennaro Fazio is a plant breeder and research geneticist with the USDA-ARS Plant Genetic Resources Unit in Geneva and an adjunct professor at Cornell University. He believes that rootstock development has transformed apple-tree productivity and efficiency.

“In the process of breeding new rootstocks, we have discovered new traits that affect fruit quality and productivity, nutrient management, and water-use efficiency,” says Fazio, “but there’s still a lot to do.”

The long game of rootstock development

Rootstock development begins with crossing parents likely to contribute desirable characteristics to their offspring. “The most recent patent that we submitted was for a cross made in the 1970s,” says Fazio. “The scientific papers that we produce all have a common set of words: long-term.”

Although the Cornell-Geneva programme focuses on specific traits, it does have an exploratory component. “We try to have a percentage of crosses that go outside the norm so that we can discover new phenotypes,” says Fazio.

Up to 10 000 seeds are harvested from each crossing. After germination, the seedling trees are exposed to diseases such as fire blight and Phytophthora to eliminate susceptible individuals.

The survivors are screened using molecular markers to identify those with desirable genotypes. For example, when selecting dwarfing rootstocks, vigorous plants can be disqualified early by testing young trees for the two main genetic factors involved in dwarfing.

Promising trees are planted in fields to assess their rooting characteristics and to provide rootstocks for further trials. Of the original 10 000 seeds, fewer than ten trees will make it to this stage.

The first trial orchards are generally established 5–6 years after the rootstocks were bred, and the trees are evaluated for 8–12 years. Propagation and further testing — including exposure to woolly apple aphids and a combination of waterlogging and Phytophthora inoculation — of the best performers already starts during this time.

Trees that make it through qualify for elite orchard trials replicated in multiple locations. The next step is commercial propagation trials, which generate the tree numbers required for large grower trials.

“If you add up the trial years after evaluating these new rootstocks in multiple locations and environments in 10-year increments, you end up with 300–400 years of trials for some rootstocks,” says Fazio. “Even then, you will not have accounted for all the observable interactions that will appear once you produce millions of that rootstock.”

New insights into rootstock-scion interactions

Genetics-based technologies help to streamline apple breeding. But Fazio stresses that the most important part of a breeding programme is accurately measuring phenotype — finding objective methods to quantify observable characteristics under diverse environmental conditions. Rootstock phenotyping is complicated by the interaction between rootstock and scion genetics.

“We’re improving our ability to measure phenotype by applying many different technologies,” says Fazio. “We use X-rays in our laboratory to look at graft unions. And we use a technology called XRF [X-ray fluorescence] to measure the nutrient content of leaves and fruit in real time.”

His laboratory also studies water uptake and utilisation in aeroponic systems in which tree roots are continually exposed to oxygen and nutrients in a misting chamber. This has led to a firmer grasp of the rootstock-scion interaction and the potential of the rootstock to modify scion behaviours such as transpiration.

“As we improve our phenotyping methods, we are beginning to better understand root architecture and how it affects the whole tree,” says Fazio. “We’re looking at how it affects things like water-use efficiency, hormones and drought tolerance.”

He explains that basic research into the genetics and physiology of apple trees is essential to rootstock development. “The physiological traits are intertwined with breeding because we’re trying to influence tree physiology by changing the genetics of the rootstock. And we are still progressing — we haven’t achieved our maximum understanding of rootstock-scion interactions.”

One of the biggest shifts has been the discovery that nutrient uptake differs for different rootstocks under different soil pH. These differences impact everything from the productivity of the tree to fruit quality and storability. For example, rootstock genetics affects the potassium-to-calcium ratio linked to bitter pit development.

Collaboration contributes to success

According to Fazio, working with other countries has contributed to the success of the Cornell-Geneva rootstock-breeding programme. “We have strong collaborations in Brazil and some places in Europe. There’s a long history of collaboration and cooperation with South Africa — field trials and materials have gone over to South Africa for almost three decades.”

White root rot — Rosellinia — is one example Fazio thinks could be a productive area for future collaboration with South African researchers. “We have material that we crossed many years ago that has field resistance to Rosellinia, but it hasn’t been further developed into a rootstock,” he says.

Clonal apple rootstocks are a relatively new technology. The deliberate breeding of apple rootstocks only began about a hundred years ago with the first trials at East Malling in England. The Cornell-Geneva programme started as the Cornell University rootstock-breeding programme in 1968. So far, the results have transformed apple production, and growers can look forward to many years of further improvements.

“If we don’t breed new apple rootstocks, we’ll be stuck as an industry,” comments Fazio. “And we won’t be able to face new challenges like climate change and new diseases. There are a lot of things on the list of not-quite-yet-done goals for apple rootstocks that will require decades of continued improvement.”

Bonus: genotype and phenotype

All organisms — whether humans or apple trees — have a genotype and a phenotype. Genotype refers to genetic makeup, whereas phenotype refers to observable characteristics resulting from gene expression. Environmental and other factors determine gene expression — this is one reason why the same scion-rootstock combination can behave differently at different sites.