Study Finds Genetic Mechanisms Behind High-Yield Apple Trees

Apples rank among the world's most valuable fruit crops, with production spanning more than 100 countries. Some apple trees naturally develop into what farmers call "spur-type" varieties—compact trees that are more productive and easier to maintain. But the genetic mechanisms underlying this coveted trait have remained elusive—until now.

An international team of researchers began by creating the first "fully phased" genome of the popular Fuji apple—essentially a complete genetic blueprint that clearly distinguishes between genes inherited from each of the two parents.

With this new blueprint in hand, the team studied 74 Fuji clonal varieties and identified significant somatic variations—mutations that occur during the plant's lifetime rather than being inherited. Somatic variations can lead to new traits, and in apples, it's the reason we see trees with unique characteristics like early maturation or the spur-type growth habit.

"Farmers prize spur-type apple trees," explained Zhangjun Fei, professor at the Boyce Thompson Institute and one of the study's lead authors. "They exhibit more concentrated flower bud formation and increased fruit yield while requiring less pruning. This makes them ideal for modern orchards, especially in challenging growing conditions."

The Fuji apple, which originated in 1939 as a cross between the Red Delicious and Ralls Janet varieties, is known for its sweet flavor and crisp texture. In countries like China, where over 70% of apple cultivars are based on Fuji clones, spur-type varieties have boosted productivity and adapted well to areas with poor soil and frequent drought.

The study’s key discovery centers around a gene called MdTCP11, which acts like a growth control switch. The researchers found that compact apple trees have a small but significant deletion in the DNA near this gene, which causes it to become more active and results in shorter branches and a more compact tree structure.

But the story doesn't end there. The researchers also discovered that the DNA methylation levels—a process that can turn genes on or off—were lower in spur-type varieties compared to standard types. This lower methylation level allows MdTCP11 to be more active, further enhancing the spur-type characteristics.

This research could have significant implications for apple breeding. Understanding these genetic traits could help breeders develop apple varieties that combine compact growth with other valuable characteristics, such as disease resistance.

It could also lead to more sustainable apple production, as compact trees require fewer resources to maintain and can produce more fruit in a smaller space. It's a perfect example of how understanding the genetic code of our food crops can lead to more efficient and sustainable farming practices.

The study was recently published in the journal Nature Communications.