A bad apple doesn’t always ruin the bunch. In fact, it might make the bunch a little bit stronger. A new study published in Horticulture Research from Ben Mansfeld, an assistant professor of biology in Arts & Sciences at Washington University in St. Louis, is providing apple breeders with a genomic resource that helps harness the power of humble crabapples.
The study examines the genetics of Malus angustifolia. This apple, also known as the Southern crabapple, is one of four native crabapple species in North America, and it’s filled with untapped genetic information. “These species are really not included in the history of the breeding and domestication of apples at all,” Mansfeld said. “They’re what we call a genetic treasure trove.”
Mansfeld is familiar with the potential waiting inside of these crabapples. Together with Christopher Gottschalk at the U.S. Department of Agriculture (USDA), Mansfeld already has assembled the genome of another North American native, the Pacific crabapple, and investigated its resistance to fire blight, a common and deadly bacterial disease.
But the Southern crabapple sits at a unique intersection. It is both remarkably resistant to fire blight and abiotic stressors. That means that it has evolved to thrive in conditions that commercial apple varieties struggle with, including high temperatures, drought and severe weather.
As climate change continues to increase the frequency of these less-than-ideal conditions, identifying genetic traits that can help crops adapt is becoming more important. This is especially true for perennial crops such as apples, which grow year after year from the same plant. “You’re not planting for next year,” Mansfeld explained. “You’re planning for the next 25 years.”
Historically, researchers have lacked the tools to fully understand the genetics associated with the Southern crabapple’s stress response. While a small collection of trees is housed at the USDA Apple Collection in Geneva, N.Y., there are not enough of them for proper genetic studies.
But Mansfeld’s colleague Gottshalk found a collection of crabapple seeds that had been stored for decades but previously overlooked. “It’s a valuable collection that’s never been sequenced before,” Mansfeld said. His new study — with collaborators including Gottschalk at the USDA and Zoë Migicovsky at the University of Acadia — changes that.
Together, the researchers generated a high-quality, haplotype-resolved reference genome for M. angustifolia, and then they sequenced the genomes of more than 150 additional wild apple samples from across the species’ native range using that discovered seed collection. The scientists then combined this genomic information with climate data from the locations where each sample originated.
This approach allowed Mansfeld and his team to search for genetic variants associated with environmental conditions like seasonal precipitation and temperature. In the end, they identified 242 DNA regions associated with these types of climatic factors.
Importantly, researchers looked for larger structural variants in the DNA in addition to single-nucleotide changes, also called SNPs. “We’re coming to understand that it’s not just single ‘letter’ mutations, but large changes in genomes that can contribute to traits,” Mansfeld said. “I was surprised by how amazingly diverse these apples are in their structural variation.”
This work ultimately could help apple breeders identify parts of the crabapple genome carrying useful traits that they can incorporate into their own apple varieties, either through gene editing or through development of rootstock varieties, where one species of apple is grafted onto the roots of a different variety.
The team also found out that there were diverse genetics in this new collection of trees that are not currently in the live USDA orchard collection. This includes important trees that originate from Missouri — a state that isn’t currently represented in that orchard collection.
In the future, the Mansfeld lab will continue its work on native North American crabapples and their unique resistance to fire blight, looking toward Malus coronaria and Malus ioensis. But future applications don’t just have to be about stress response or disease. Now that this genome has been assembled and all these new trees are sequenced, the data will be available for any researcher to use, no matter which traits they seek. Furthermore, the trees that represent missing diversity will be donated to the USDA collection to ensure better representation of these wild natives.
For Mansfeld, unlocking the secrets of apples starts with recognizing the value of these wild and native species. “They’re beautiful and amazing, but also incredible for our environment,” Mansfeld emphasized. “We want to maintain them, but they might have hidden secrets that will hopefully help us make the world a better place.”
Mansfeld BN, et al. New genomic resources and local adaptation GWAS in wild Malus angustifolia reveal genetic regions for enhancing abiotic resiliency in apple. Horticulture Research, 2026; uhag336, DOI: https://doi.org/10.1093/hr/uhag336
Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S and Gottschalk C. (2023). A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. Plant J, 116: 989-1002. DOI: https://doi.org/10.1111/tpj.16433