A recent study has taken a closer look at the apple family, not in terms of flavor or popularity, but through the lens of genetics. The research, published in the journal Nature Genetics on April 16, offers a comprehensive examination of the genus Malus, which includes the familiar domesticated apple along with its many wild relatives. Conducted by an international team of scientists including biologists from Penn State, the work dives deep into how apple species are related and how their genomes have shifted and evolved over nearly 60 million years.
Dr. Hong Ma, Huck Chair in Plant Reproductive Development and Evolution and professor of biology in the Eberly College of Science at Penn State and an author of the paper, explained that although apples are among the most widely consumed fruits globally, their evolutionary genetics haven’t been explored in much detail until now. “There are roughly 35 species in the genus Malus, but despite the importance of apple as a fruit crop, there hasn’t been extensive study of how this group’s genomes have evolved,” Ma said.
Genetic: Sequencing 30 Apple Genomes, One by One
To unravel these questions, the research team sequenced and assembled the genomes of 30 Malus species, including the well-known Golden Delicious variety. Of these 30 species, 20 were diploid, meaning they had two sets of chromosomes, like humans do. The remaining 10 were polyploid, with three or four copies of each chromosome. This variation is believed to have resulted from hybridizations that occurred over the course of evolution.
By comparing around 1,000 genes in each species, the researchers built a genetic family tree of the Malus genus. This analysis traced the roots of the genus back to Asia, around 56 million years ago. The findings painted a picture of a complex evolutionary path marked by events such as whole-genome duplications and frequent cross-breeding between species.
According to Dr. Ma, these hybridization events and duplications added layers of complexity that made earlier genetic comparisons between species quite difficult. However, by having high-quality genome sequences for such a wide range of species, the researchers were finally able to map out the relationships more clearly.
A Broader Lens: The Power of Pan-Genomics
To take the analysis further, the team employed a method known as pan-genomics. This approach looks at the entire set of genes from a group of closely related species to see what is shared, what is unique, and how these sequences are organized or rearranged across different species.
One of the key insights from this analysis came from looking at structural variations — differences in large segments of DNA that can affect how genes are expressed. For instance, using the pan-genome framework, the team identified a specific region in the genome linked to resistance against apple scab, a fungal disease that causes dark blotches on the leaves and fruit and is a significant issue for apple growers worldwide.
Dr. Ma noted that having the pan-genome graph — a tool developed during the research — was essential in finding this variant. The graph allowed the researchers to visualize and track gene duplications, deletions, and movements across the 30 species, offering a more nuanced view than would have been possible with traditional methods.
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The Hidden Trade-offs of Selective Breeding
Beyond disease resistance, the study also explored the genetic underpinnings of traits like cold tolerance and flavor. One particularly interesting discovery was a genomic region that contributes to both disease and cold resistance — but may also result in apples with a less pleasant taste.
This finding highlights a common challenge in agricultural breeding: improving one trait may come at the cost of another. In the case of apples, it appears that breeding for better taste over time may have inadvertently reduced the fruit’s natural resilience to harsh conditions and diseases.
“It’s possible that in the efforts to produce the best tasting fruit, there was an inadvertent reduction of the hardiness of domesticated apples,” Ma said. “Understanding the structural variations in the Malus genomes, the relationships among the species and their history of hybridization using pan-genome analysis could help guide future breeding efforts so that the beneficial traits for good taste and disease-resistant can both be retained in apples.”
Guiding the Future of Apple Breeding
While this study focuses on long-term genetic trends, it also has practical implications for the future. By mapping out which parts of the genome are linked to beneficial traits, breeders can make more informed decisions when developing new apple varieties. This could lead to apples that are not only more resistant to disease and extreme weather but also maintain the taste and texture that consumers enjoy.
The team behind the research includes postdoctoral researcher Taikui Zhang from Penn State, and their contributions were supported by the Eberly College of Science and the Huck Institutes of the Life Sciences. A full list of international collaborators and supporting institutions is detailed in the published paper.
What this work ultimately shows is that the apple, a fruit with a long and complex history, still has much to teach us. With the tools of modern genomics, scientists are uncovering layers of information that were previously hidden, offering not just a deeper understanding of nature but also a clearer path toward cultivating better crops.
