New Genome Study Unveils the Evolution and Diversity of the Apple Genus

Malus is a genus comprising over 35 species that thrive in the temperate Northern Hemisphere, spanning regions from East Asia to Europe and North America. This genus includes the cultivated apple, Malus domestica, along with its wild relatives. Recent research has unveiled the evolutionary connections among Malus species and traced their genetic development over the past 60 million years.

“There are around 35 species within the Malus genus; however, despite the significance of apples as a fruit crop, comprehensive research on the evolution of this group’s genome has been lacking.”

“This study provided insights into the Malus genome, established the apple family tree, documented genomic events including whole-genome overlap and hybridization among species, and identified genomic regions linked to specific traits, such as resistance to apple scab disease.”

Professor Ma and his team compiled the genomes of 30 species by sequencing their DNA, focusing on the Malus genus known for its delicious golden apple varieties.

Among the 30 species, 20 are diploid, meaning they possess two chromosome copies per set, similar to humans, while 10 are polyploid, indicating they have three or four chromosome copies, likely resulting from recent hybridization with diploid relatives of Malus.

By scrutinizing nearly 1,000 gene sequences across these species, researchers constructed a phylogenetic tree for the genus and employed biogeographical analysis to trace its origins back to Asia approximately 56 million years ago.

“The evolutionary narrative of the genus is intricate, showcasing numerous instances of hybridization among species and shared whole-genome events that complicate comparisons,” stated Professor Ma.

“Access to high-quality genomes for a large number of species within the genus has enabled us to explore how Malus evolved and the interrelationships among these species.”

Further research into the evolutionary history of Malus genomes utilized analytical techniques called pan-genomics.

This methodology encompasses a thorough comparison of conserved genes and so-called ‘jumping genes’ that can move within the genome across the 30 species, along with genes found only in a subset of the genomes.

The analysis of pan-gene dynamics benefited greatly from the use of a pangenome graph tool, which amalgamates genomic data from closely related groups to elucidate evolutionary conservation and divergence.

“Utilizing 30 pangenomes significantly aided in identifying structural variations, gene duplications, and rearrangements among species that could have been missed with fewer genome comparisons,” remarked Professor Ma.

“Notably, one structural variant uncovered allowed us to pinpoint genomic segments related to apple scab resistance, a fungal disease impacting apples globally.”

The researchers also developed a pangenome analysis tool designed to detect evidence of selective sweeps, a process whereby advantageous traits rapidly increase in frequency within a population.

With this approach, they pinpointed genomic regions linked to cold and disease resistance in wild Malus species, which might also correlate with undesirable fruit taste.

“Attempts to cultivate the best flavor in fruit may have inadvertently diminished the hardiness of cultivated apple varieties,” noted Professor Ma.

Understanding structural variations in Malus, including hybridization histories, interspecies relationships, and pangenomic insights can inform future breeding strategies aimed at retaining both flavor and disease-resistant traits in apples.

Research findings published in the journal Nature Genetics.

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W. Li et al. Pangenome analysis reveals evolution and diversity in Malus. Nat Genet. Published online on April 16th, 2025. doi:10.1038/s41588-025-02166-6