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Dr. Kate Evans, Washington State University’s apple breeder, checks the growth of young seedlings in the greenhouse. A leaf sample from each plant is tested with genetic markers to predict fruit quality traits. Those likely to produce poor quality fruit are eliminated and never grown into trees. (Geraldine Warner/Good Fruit Grower)

Dr. Kate Evans, Washington State University’s apple breeder, checks the growth of young seedlings in the greenhouse. A leaf sample from each plant is tested with genetic markers to predict fruit quality traits. Those likely to produce poor quality fruit are eliminated and never grown into trees. (Geraldine Warner/Good Fruit Grower)

New technology is speeding up the process of developing new apple varieties and helping breeders improve their chances of developing high-quality new apples.

Scientists can test young plants with genetic markers to gain insights into the quality of the fruit they will produce without needing to see or test the fruit. This increases the efficiency of the breeding program and reduces costs.

Washington State University’s apple breeding program is using genetic markers relating to fruit texture, crispness, juiciness, acidity, firmness, bitter pit susceptibility, and skin color, and will soon have markers for fructose (sugar content) and fire blight susceptibility. Some markers can be used to screen a wide range of progeny, while others are specific to certain families (the offspring of two specific parent varieties).

Here’s how the program works each year:

Year 1:

During bloom, trees of about 10 to 15 selected varieties are pollinated with pollen from a second variety. Between 10,000 and 20,000 seeds are collected from the fruit of the mother trees in the fall.

Years 2-4:

Seeds are germinated and grown into seedlings in the greenhouse. Soon after they begin growing, Dr. Kate Evans and her staff cut off a fragment of a leaf from each seedling and send it to the lab of WSU geneticist Dr. Cameron Peace for testing with genetic markers.

Seedlings predicted to have poor fruit quality traits are eliminated, and, in May, the remaining seedlings are taken to Willow Drive Nursery in Ephrata, Washington, to be budded onto Malling 9 rootstocks, and grown into trees—a process that takes two years. Historically, about 8,000 trees have been produced in this phase, but with the use of genetic markers, the number has been reduced to 4,000 in 2014.

Years 5-8:

(Click to enlarge) Graphic shows the timeline of breeding process.

(Click to enlarge) Graphic shows the timeline of breeding process.

The nursery trees are planted in a WSU research orchard to be evaluated when they bear fruit. This is Phase 1 of the evaluation program. By having eliminated the less promising seedlings early in the process, the breeding program can save money on ground, irrigation, trellis, and maintenance, as well as the time needed to walk the plots to evaluate the fruit.

However, Evans said using the markers also gives her the option of making more crosses in the first place and planting the traditional number of trees.

Wood is collected from promising Phase 1 selections to make trees for evaluation in Phase 2. The rest of the trees are removed to make room for subsequent Phase 1 seedlings.

Years 9-13:

Advanced selections go into Phase 2 plantings with five trees at three locations in different parts of the state. There are currently 42 selections in this phase. Evans said she would like to increase that number by not planting all of the advanced selections at all three sites, but extrapolating the data.

Years 14-18:

In Phase 3 of the breeding program, a small number of elite selections goes into on-farm trials with 10 to 100 trees at about four sites. There are currently two selections in this phase.  The next step is release and commercialization.

Evans hopes to streamline the process even further. Rather than having all the promising seedlings made into single trees, she hopes using marker screening will reduce the family size sufficiently from some crosses to justify growing them in the greenhouse to the point where there’s enough budwood to make several trees so they can go straight into Phase 2 of the program. This would speed up the process by four years, as well as reduce costs.

Phase 1 seedlings at WSU's Columbia View Orchard north of Wenatchee, Washington are ready for fruit quality evaluation. (Courtesy Washington State University)

Phase 1 seedlings at WSU’s Columbia View Orchard north of Wenatchee, Washington are ready for fruit quality evaluation. (Courtesy Washington State University)

Parents

To improve the chances of finding superior apples, Evans and Peace are also using genetic markers to identify parents that have desirable traits and a high likelihood of passing them on to their offspring.

When Dr. Bruce Barritt began the breeding program 20 years ago, he used a limited number of commercial varieties as ­parents. WSU’s first release, WA 2, is a cross of Splendour and Gala; WA 38, WSU’s latest release, is a cross of ­Enterprise and ­Honeycrisp.

Evans wants to bring more diversity into the program in terms of flavor and mildew resistance, and is using material from the core apple germplasm collection at Geneva, New York.

She’s also making crosses using some of WSU’s elite selections, which have been identified as having superior quality and are adapted to Washington conditions.

“Most of the crossing we’re doing will incorporate at least one of those advanced lines,” she said. “We know a lot about them because we’ve included them in this marker screening.”

Storability

Genetic markers are becoming available for more traits, and Evans is still awaiting one that she thinks is particularly important for the industry—something that would enable her to select for long storability.

Although technology is greatly improving the efficiency of the program and providing insights into the quality of the selections, the fruit still needs to be evaluated by human beings.

“We still haven’t managed to achieve any way of doing this without eating an apple to taste it,” Evans said. “No matter what we do in terms of instrumental analysis or molecular analysis, all it’s doing really is showing us the ones we would be less likely to like—but that’s good. Ultimately, we haven’t yet developed ­anything to replace the human ­palate.” •