New genomic analysis findings could help inform breeding efforts for apples that are tastier and more resilient.
A comprehensive new study comparing the genomes of species within the Malus genus, including the domesticated apple and its wild relatives, has uncovered how these species are related and how their genomes have evolved over nearly 60 million years. By analyzing structural variations across the genomes, the researchers developed techniques to pinpoint genes linked to valuable traits such as flavor, disease resistance, and cold tolerance. These insights could play a critical role in shaping future apple breeding efforts.
The findings, from an international team that includes biologists from Penn State, were published in Nature Genetics.
“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,” said 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. “In this study, we were able to do a deep dive into the genomes of Malus, establish an apple family tree, document events like whole-genome duplications and hybridizations between species, and find regions of the genome associated with specific traits, like resistance to apple scab disease.”
The team newly sequenced and assembled the genomes of 30 members of the genus, including the domesticated golden delicious apple variety. Of the 30 species, 20 are diploid, meaning that they have two copies of each chromosome, like humans, and 10 are polyploid, having three or four copies of each chromosome, likely due to a relatively recent hybridizations of diploid and other relatives in Malus. By comparing the sequence of nearly 1,000 genes from each species, the researchers built a family tree of the genus and then used biogeographical analysis to trace its origin to about 56 million years ago in Asia.
Unraveling Complex Evolutionary Histories
“The evolutionary history of the genus is quite complex, with numerous examples of hybridization between species and a shared whole-genome duplication event that make comparisons difficult,” Ma said. “Having high-quality genomes for such a large number of the species in the genus and understanding the relationships among them allowed us to dig deeper into how the genus has evolved.”
To further analyze the history and evolution of the Malus genomes, the team examined the 30 sequenced genomes in an analytical approach called pan-genomics. This approach involved comprehensive comparison for both shared, or conserved, genes and other sequences, such as transposons — sometimes called jumping genes for their ability to move in the genome — across the 30 genomes, as well as genes that are only present in subsets of the genomes. Pan-genomic analyses combine the genomic information from a closely related group to understand evolutionary conservation and divergences, and were greatly facilitated by the pan-genome graph tool.
“The use of the pan-genome of 30 species was powerful for detecting structural variation, as well as gene duplications and rearrangements, among the species that might be missed by comparisons of only a few genomes,” Ma said. “In this case, one of the uncovered structural variants allowed us to pinpoint the genome segment associated with resistance to apple scab, a fungal disease that impacts apples worldwide.”
The team also developed a pan-genome analysis tool to help find evidence of selective sweeps, a process where a beneficial trait rapidly increases in frequency in a population. Using this method, they identified a genome region responsible for cold and disease resistance in wild Malus species that also may be related to unpleasant taste in fruit.
“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.”
Reference: “Pan-genome analysis reveals the evolution and diversity of Malus” by Wei Li, Chong Chu, Taikui Zhang, Haochen Sun, Shiyao Wang, Zeyuan Liu, Zijun Wang, Hui Li, Yuqi Li, Xingtan Zhang, Zhiqiang Geng, Youqing Wang, Yi Li, Hengtao Zhang, Weishu Fan, Yi Wang, Xuefeng Xu, Lailiang Cheng, Dehui Zhang, Yao Xiong, Huixia Li, Bowen Zhou, Qingmei Guan, Cecilia H. Deng, Yongming Han, Hong Ma and Zhenhai Han, 16 April 2025, Nature Genetics.
DOI: 10.1038/s41588-025-02166-6
In addition to Ma, the research team also included postdoctoral researcher Taikui Zhang at Penn State. Ma and Zhang’s contributions to this research were supported by the Eberly College of Science and the Huck Institutes of the Life Sciences at Penn State.
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