Genetic markers are speeding up the process of fruit breeding and making breeding programs more efficient, says Washington State University’s apple breeder Dr. Bruce Barritt.

"There hasn’t been a revolution in tree fruit breeding for a long time, and finally, it’s come with genomics."

Typically, it has taken 15 years or more to develop a new variety. For example, Honeycrisp, which originated from a cross made in 1960, wasn’t released until 1991.

Since WSU’s breeding program began in Wenatchee in 1994, Barritt has typically grown between 5,000 and 8,000 seedlings from crosses he’s made each year. The seeds are grown in a greenhouse, and the seedlings are transferred to a nursery. After another year in the nursery, a bud from the seedling is chip-budded onto a Malling 9 rootstock. In the fifth year after the cross was made, the seedling trees are ready to be evaluated in an orchard setting at the Tree Fruit Research and Extension Center in Wenatchee. In the second through fourth years in the orchard (six to eight years from the time of the cross), they produce enough fruit for evaluation. The very best (fewer than 1 percent) are selected and propagated for second-test trials at three locations in Washington.

Now, thanks to genetic markers, some seedlings can be eliminated without the need to grow them until they fruit. Researchers in Japan and Italy have identified two genes in apple trees that are correlated with high ethylene levels in the fruit. Apples with high ethylene tend to soften quickly and have poor storability.

Using that information, molecular biologist Dr. Yanmin Zhu at the U.S. Department of Agriculture’s research lab in Wenatchee, is able to determine, simply by testing a leaf from a young seedling, whether that selection has DNA that relates to the high-ethylene genes or not. This is known as genotyping.


Zhu said the process is fairly quick, and high-throughput machines at WSU in Pullman can deal with 500 plants a day. The most difficult part is isolating the DNA from the leaf tissue, he said. Checking if the genes of interest are there is relatively easy.

This means that Barritt can now have 10,000 seedlings in the greenhouse tested and eliminate all those that don’t have low ethylene production, which will probably leave him with about 1,250 for further evaluation. Only one out of eight seedlings will have the gene forms (alleles) for low ethylene production.

"The savings is huge in dollars," he said. "Instead of spending $60,000 in the nursery to grow those trees we don’t want, we can grow just those seedlings that have the genes we want."

Zhu said a molecular marker has been used elsewhere for scab resistance, but since the disease is not a serious problem in the Pacific Northwest, he thinks selecting for fruit quality traits is a priority.

Skin color

Scientists in Australia recently announced that they have identified the gene that controls the skin color of apples. They used molecular technology to measure how much particular genes were activated in the skin as the fruit ripened and colored. By identifying master genes that were activated by light, they were able to pinpoint the gene that controls the formation of anthocyanins in the skin, and found that the gene is not expressed as much in green apples as in red apples, according to a report from Biology News Net. Working with apple breeders at the Department of Agriculture and Food in Western Australia, the scientists showed that skin color could be predicted in seedlings by measuring the form of that gene.

Zhu said he’s going to check that out and see how reliable it is.

Meanwhile, he is working to identify the genes responsible for juiciness, crispness, aroma, and postharvest diseases and disorders, such as storage scald.