Clues from apple genes could sweeten the future of fruit

The bounty of apple varieties – from Honeycrisp to Granny Smith – obscures a deeper truth: nearly all of them share a lineage that stretches back tens of millions of years. Until recently, however, scientists had only a sketchy understanding of how those ancestral species diversified, swapped genes, or survived ice ages and shifting continents.

A sweeping new study changes that, unveiling a detailed genetic atlas for 30 species in the genus Malus – and providing breeders with a treasure map for tastier, tougher fruit.

“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, an expert in plant development and evolution at the Pennsylvania State University and one of the paper’s senior authors.

“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.”

Complex evolution of apples

To reconstruct the family tree, Ma and an international consortium of researchers sequenced and assembled high-quality genomes from 30 Malus species, including the iconic “Golden Delicious.”

Twenty of those species are diploid – possessing two copies of every chromosome, as humans do – while the remaining ten are polyploid, carrying three or four copies thanks to relatively recent hybridization events.

By comparing nearly 1,000 genes shared across the roster, the team traced the genus’s roots to Asia approximately 56 million years ago. From that ancestral stock, lineages radiated outward, sometimes merging back together in hybrid bursts that left behind telltale patterns of duplicated DNA.

Those duplications, known as whole-genome duplication events, complicate efforts to align chromosomes species by species – much like comparing two scrapbooks whose photographs have been rearranged multiple times.

“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 explained.

“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.”

Exploring the genes of apples

Standard genome comparisons can miss critical differences when researchers look at only a few individuals. To widen the lens, the team built what geneticists call a pan-genome – a composite reference that catalogs which genes are shared across all 30 species and which appear in only a subset.

They also logged transposons, the so-called “jumping genes” that can copy or paste themselves into new chromosomal locations, reshuffling genetic instructions along the way.

“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.”

Selective genes in wild apples

Beyond structural quirks, the researchers were keen to identify regions of DNA that have raced through populations because they confer a survival edge – so-called selective sweeps. To do that, they built a computational tool tailored to pan-genomes.

One of their discoveries: a sweep encompassing genes tied to cold tolerance and pathogen resistance that is widespread in hardy wild apples but usually missing from juicier commercial cultivars.

“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 noted.

The sweep appears to carry genetic baggage that affects fruit chemistry – and, by extension, flavor. That raises a tantalizing breeding challenge: can scientists break the genetic link so future cultivars keep robust disease resistance without compromising sweetness or aroma?

A bigger apple family tree matters

Modern apple breeding is a decades-long endeavor. Finding candidate parents with the right blend of sweetness, crunch, shelf life, and disease resistance normally involves screening thousands of seedlings in orchards before a single promising cross emerges.

A detailed genetic map could change that paradigm, enabling breeders to predict desirable traits inside a lab years before trees bear fruit. Knowing the full evolutionary backdrop also helps safeguard the wild relatives that could rescue the crop from tomorrow’s climate extremes.

Traits such as drought tolerance, pest resistance, or cold hardiness often linger in remote species not yet tapped by commercial breeding – but if habitat loss or disease erases those wild gene banks, rescuing the domesticated apple becomes harder.

Apple genes: Next-generation orchards

For now, Ma and colleagues plan to refine their pan-genome, adding the handful of Malus species not yet sequenced and teasing apart how each duplication or rearrangement has influenced everything from tree architecture to sugar content.

They also hope to share their analytic pipeline so other crop researchers – from wheat to citrus – can identify hidden genetic assets in their own plant families.

“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 resistance can both be retained in apples,” Ma said.

The humble apple has traveled a winding genetic road over 56 million years. With this new map in hand, breeders – and perhaps consumers – stand to reap a richer, more resilient harvest from that ancient journey.

The study is published in the journal Nature Genetics.

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