The Apple’s Code of Life (2024)

An apple’s genome has twice as many genes as a human’s. Its sequencing has improved understanding and allowed more targeted fruit breeding.

Part of an apple genome sequence © Nicola Busatto

In 2010 the genetic sequence of an apple – Golden Delicious – was published. This was the result of three years’ of detailed analysis led by what is now Fondazione Edmund Mach in the Trentino Alto Adige apple growing region of northern Italy.

Professor Fabrizio Costa © Nicola Busatto

“In simple terms, a sequenced genome is usually compared to a book or to a puzzle”

Professor Fabrizio Costa, a scientist involved in the sequencing, explains:

“A book because the DNA of an individual, often called the code of life, is represented by the linear sequence of four simple letters (ATCG). The sequencing is basically the reading of these four letters and the genes in the genome are the words. When you sequence these letters, you read only a certain short stretch, so to complete the book you have to assemble all these myriad pieces in the right order, like doing a puzzle. If you succeed in doing this, then you can finally understand the meaning of the book, the code of life hidden in the genome. The reading of the letters, the assembly of all the puzzle’s pieces, and the interpretation of the words are complicated and time-consuming work, needing several types of expertise.”

The work was therefore shared between 19 institutions around the world, with apple scientists bringing different skills. They found that an apple has 57,386 genes, more than twice the number in the human genome due to the duplicated origin of the apple’s genome which created more ‘junk’ DNA. The sequencing of its genome was a fundamental step in understanding the entire biological life of the apple.

“Having a complete and characterized genome is like having a navigator, now you have a tool indicating to you where to go, and the place you want to visit is a gene controlling a specific trait.”

Over centuries, people have selected and bred apples for different colour, texture, and storage.

Understanding the genome now allows more targeted fruit breeding. Scientists know the areas of the genome regulating the production of the flavonoid anthocyanin that causes red pigment in apple flesh and skin, and the parts controlling the cell wall enzymes that determine crunchy texture. In the laboratory, the important quality of apple crunch can be scientifically tested by resistance of an apple to mechanical force and by acoustic profiling.