New technologies could help breed more disease-resistant, high quality apples

Apple tree with spring flowers on a natural background.Plant scientists at Washington State University are exploring how advanced technologies could help breed delicious apple cultivars that can also resist many devastating diseases, such as blue mold and fire blight, which cost millions in damaged fruit and dead trees every year.

In two recent papers in the journal Tree Genetics and Genomes, Fei Xiong Luo, former doctoral student in the tree fruit genetics program of WSU Horticulture Professor Cameron Peace, shared results of promising experiments on improved development of resistant varieties.

Head shot of Luo
Fei Xiong Luo

In every species, apples included, some individuals carry gene variants that help protect them from disease. Most current disease-resistant apple varieties have only single gene variants for resistance, which leaves them vulnerable when diseases mutate.

Apple breeders cross varieties to add new genetic sources of resistance, often tapping into closely related crab apple species. But the resulting hybrids that show desirable resistance are often commercially unacceptable because their wild parents pass on poor genetics for fruit quality—think small, astringent, bitter, and squishy fruit.

To improve quality, plant breeders turn to a method called pseudo-backcrossing—crossing hybrids back to commercial cultivars to reduce unwanted attributes. This process is time-consuming, both because of the years it takes to grow trees to the point of flowering, and because it takes many generations to dilute out most of the wild genetics and recover high-quality fruit.

To speed up the breeding process and reveal promising cultivars, scientists track the DNA tags linked to important traits coming from each parent species.

“We are looking for genetic factors associated with disease resistance and fruit quality,” said Luo. In a process called background selection, “we’re looking for genes that cause poor fruit quality inherited from disease-resistant parents.

DNA markers from an SNP array—a DNA profiling method that looks at genetic variation across the entire genome at once—can show where these genetic factors are, and where they were inherited from.

Luo, under the supervision of Peace, USDA plant pathologist Jay Norelli, WSU apple breeder Kate Evans, and WSU statistical geneticist Zhiwu Zhang, experimented with the SNP array profiling data to develop tools to assist with breeding blue-mold resistant apple cultivars.

They developed a diagnostic tool that can identify resistant parent plants, and tell the difference between plants with smaller and bigger symptoms from the disease. In each offspring’s chromosomes, it can also discern where, and how many, DNA segments carried over from wild species or elite cultivar ancestors.

With these tools, fruit breeders are encouraged to take advantage of the wider gene pools available in wild relatives, said Peace. While their demonstration was only for blue mold resistance, resistances to other diseases from other species can be more precisely and efficiently combined into individual cultivars. The strategy also enables more effective development of durable resistance to single diseases.

Head shot of Peace.
Cameron Peace, WSU Department of Horticulture

“Genetic factors for resistance from multiple species can be funneled into single cultivars of the future,” Peace said.  “Multiple resistance factors provide a defense that is very difficult for pathogens to overcome. In both cases, old-fashioned crossing is done, and the genetics ‘magnifying glass’ is then used to find the right offspring to use as parents for the next generation.”

Biotechnological innovations for rapidly cycling through generations—going from seed to flower in less than a year—were also part of the team’s strategy. Recently retired West Virginia USDA researcher Jay Norelli provided expertise and grew the hybrid apple trees used in the experiment for proof of concept.

“We learned that we can precisely track the inheritance of genetic factors from resistant parent plants, and from parents with elite fruit quality, and quickly achieve desired genetic combinations, by the combined use of the latest biotechnologies,” said Luo. “The implication for growers is that new elite apple cultivars that are durably resistant to multiple diseases are possible.

“New technologies will enable breeders to overcome the limitations of cultivar development,” he added.

Find the team’s paper, “Introgressing blue mold resistance into elite apple germplasm by rapid cycle breeding and foreground and background DNA-informed selection,” here.

Read the paper, “Prospects for achieving durable disease resistance with elite fruit quality in apple breeding,” online.