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Genomic consequences of apple improvement.

Zoë Migicovsky1, Kyle M Gardner1,2, Christopher Richards3

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Summary

Modern apples share ancestry with Malus sieversii, with cider varieties also drawing from Malus sylvestris. Genetic analysis reveals a complex, interconnected family tree for most US apple cultivars, highlighting selection for traits like red skin and firmness.

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Area of Science:

  • Agricultural Science
  • Genetics
  • Horticulture

Background:

  • Apples (Malus domestica) are a globally significant perennial crop, with centuries of breeding efforts focused on improvement.
  • Understanding apple genetic diversity is crucial for future crop enhancement and breeding strategies.

Purpose of the Study:

  • To genetically characterize a large collection of apple accessions.
  • To elucidate the ancestry and pedigree relationships among apple cultivars.
  • To identify signatures of selection related to desirable apple traits.

Main Methods:

  • Genomic analysis of over 1000 apple accessions using more than 30,000 single-nucleotide polymorphisms (SNPs).
  • Examination of the United States Department of Agriculture (USDA) apple germplasm collection.
  • Comparative analysis of genetic contributions from progenitor species (Malus sieversii, Malus sylvestris).

Main Results:

  • Confirmed Malus sieversii as the primary progenitor of modern apples.
  • Identified greater Malus sylvestris ancestry in cider apples compared to dessert apples.
  • Revealed a complex, interconnected pedigree within the USDA collection, with many accessions linked to top US cultivars.
  • Detected strong selection signatures for red skin and increased firmness.

Conclusions:

  • Most US apple cultivars originate from a relatively narrow genetic base.
  • Future apple improvement could benefit from greater utilization of diverse genetic resources.
  • Breeding efforts have significantly shaped the genetic makeup of commercially important apple varieties.