Ancestry tests aren’t just for people or pets as University of Minnesota scientists prove.
Thanks to DNA-based tracking, U-M researchers have traced the family tree of the Honeycrisp apple — one of the top 10 varieties produced in the United States.
Recently published in HortScience, the findings are the result of sifting through thousands of DNA markers to unwind the pedigrees of many of U-M’s best apple cultivars. Researchers were able to follow the roots back to European ancestral varieties and the first days of the U-M apple breeding program, which began in 1908 at the Horticultural Research Center. Since then, the program has introduced 28 cultivars, including Honeycrisp, and those sold under the Zestar, SweeTango, First Kiss and Rave trademarks.
In the program’s early years, researchers collected seeds from orchards around the state in hopes of finding new cultivars that could survive and thrive in Minnesota’s harsh winters. Even though controlled breeding began in 1916, non-standardized practices and fragmentary documentation left many ancestries up for interpretation. Now, with readily available DNA markers from around the world, the chance to solve the Honeycrisp ancestry mystery was within reach.
Former U-M graduate student and postdoctoral researcher Nicholas Howard, now an apple breeder in the Netherlands, first developed ancestry tracking techniques using DNA markers to determine the true parents of Honeycrisp as part of his dissertation research. Through an exhaustive, collaborative effort with U-M apple breeders Jack Tillman, David Bedford and Professor Jim Luby, Howard attempted a Herculean task — documenting the pedigree of all 28 U-M apple cultivars.
Howard enlisted numerous national and international collaborators to assemble a database of DNA fingerprints for more than 6,000 apple cultivars based on over 10,000 single nucleotide polymorphism markers. Additionally, he tapped Ana Poets and Kevin Silverstein of the Minnesota Supercomputing Institute to develop custom software that could help uncover genetic relationships between cultivars by tracking pieces of DNA shared by relatives through multiple ancestral generations.
“A large, collaborative database effort, combined with new genetic techniques, allowed us to identify the specific parents, grandparents and even more distant ancestors of U-M cultivars,” Howard says. “Based on these analyses, we could confirm, correct or complete the parentage of 16 of the 22 cultivars introduced between 1920 and 1991.”
The researchers found there were two pervasive founding ancestors in Honeycrisp’s family tree. One was “Duchess of Oldenburg,” a Russian cultivar introduced to Minnesota in the late 19th century, appearing in the pedigrees of 27 out of 28 U-M cultivars. The second was “Reinette Franche,” a French cultivar that appears in Honeycrisp’s family tree, several other university cultivars and in historically important and commercially relevant cultivars — such as Gala and Golden Delicious.
The next step for the researchers is to explore the family tree even further, connecting thousands of cultivars across the globe, as well as identifying genomic contributions from “Duchess of Oldenburg” and “Reinette Franche” to highlight regions to target for future selection.
“Extended pedigrees will be very useful to breeders in determining future crosses,” Luby says. “The more we know about their ancestry, the better we can predict the inheritance of desirable traits based on that DNA-confirmed ancestry — which provides a useful feature for nurseries and apple growers when promoting their products.”
Their research was partially supported by the Minnesota Agricultural Experiment Station with funding from the USDA National Institute of Food and Agriculture.
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