Apples are among the most significant fruit crops globally, cultivated in over 100 nations. Some apple trees spontaneously grow into what are known as “spur-type” varieties—these are smaller trees, which offer higher yield and are simpler to manage. However, the genetic factors that contribute to this desirable characteristic have been unclear—until now.
A worldwide group of scientists has established the first “fully phased” genome of the renowned Fuji apple. This essentially creates a complete genetic map that distinguishes between genes received from each parent.
With this comprehensive map, the team examined 74 clonal varieties of Fuji and uncovered notable somatic variations—mutations that occur during the apple plant’s life rather than being passed down from the parents. These somatic variations can introduce new characteristics, such as early ripening and spur-type growth, that set certain apple trees apart.
“Spur-type apple trees are highly valued by farmers,” stated Zhangjun Fei, a professor at the Boyce Thompson Institute and one of the study’s primary authors. “They produce more concentrated flower buds and yield greater fruit while needing less pruning, making them perfect for contemporary orchards, especially in tough growing environments.”
The Fuji apple, first developed in 1939 through the crossing of Red Delicious and Ralls Janet varieties, is popular for its sweet taste and crunchy texture. In countries like China, where over 70% of apple varieties come from Fuji clones, spur-type types have significantly improved productivity and have adapted well to poor soil and conditions with limitedwater supply.
The critical finding of this research revolves around a gene referred to as MdTCP11, which functions as a switch for growth control. The scientists discovered that compact apple trees possess a minor but significant deletion in the DNA near this gene, resulting in its increased activity and, consequently, shorter branches and a denser tree structure.
However, the research goes further. The scientists also found that DNA methylation levels—the mechanism that can activate or deactivate genes—were lower in spur-type trees compared to standard types. This reduction in methylation allows MdTCP11 to be more active, further promoting spur-type traits.
This research could greatly influence the breeding of apples. By understanding these genetic features, breeders could create apple varieties that marry compact growth with other essential traits, such as resistance to diseases.
Additionally, this could lead to more sustainable apple cultivation, as compact trees demand fewer resources and can yield more fruit within a smaller area. It’s a excellent example of how grasping the genetic foundations of our agricultural crops can pave the way for more efficient and eco-friendly farming methods.
