Apple PHG

The Apple PHG is a project to "build" a practical haplotype graph (PHG) for the iconic fruit found in basically every grocery store: the domesticated apple, Malus domestica. The genus in which the beloved apple belongs, Malus, is native to the temperate regions of the Northern Hemisphere, with a diverse range of species found in parts of North America, Europe, and Asia.

Apples are cultivated commercially all over the world, with thousands of named cultivars in existence. Its presence is ubiquitous in supermarkets and groceries the world over, and thus its improvement via plant breeding is a perennial focus among amateur and commercial researchers.

Given its global spread and many dozens of species, the apple has accumulated excellent genetic diversity over the course of its evolution, which makes it a perfect candidate for bioinformatics-based investigation.

Our goal is to assemble a practically-useful PHG which can be used to impute genotypes for use in plant breeding programs. This objective is threefold:

• Collect and build a PHG using a diverse range of publicly-available genotypes.
• Open source all code, and methodically document its usage.
• Demonstrate how a PHG may be used in practice, and tailored to the needs of a breeding program.

The source is available on GitHub.