Gene Study: 'Elite' Cultivars Impoverish Apple Diversity

The genetic heritage of just a handful of apples dominates commercial production, according to an analysis in the science journal Horticultural Research this month.

The top 8 cultivars (really, top 3) dominate the orchard genome

The authors ( Migicovsky et al.) suggest that the lopsided use of these "elite cultivars" by apple breeders "leaves the apple industry vulnerable to evolving pests and pathogens and a changing climate."

The study applies recent advances in gene-sequencing technology to the USDA apple germplasm collection. These new methods make feasible an analysis of this scope.

The study, "Genomic Consequences of Apple Improvement," describes the results of sequencing the genes of 1,949 apples, and analyzing 1,005 domestic apples in the collection. (A small number of recent varieties were deliberately excluded.)

The authors focus a portion of their analysis on first-degree relationships ("parent-offspring, full sibling, or equivalent"). Among their findings:

• "15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA" (see chart above).
• "The cultivars 'Golden Delicious' and 'Red Delicious' were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders."
• The authors also "detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness."

All in all, "Americans are eating apples largely from a single family tree" compared to the potential benefits of the fruit's "tremendous natural genetic diversity."

Brave New World

Genetic sequencing has corrected the pedigrees of some apple cultivars, though many remain untested. 

For example, Honeycrisp was originally thought to be a Macoun x Honeygold cross. 

Gene sequencing in 2017 showed its parents to be Keepsake and an unnamed (and uncommercialized) offspring of Golden Delicious and Duchess of Oldenberg.

I'd like to know how a major breeding program gets a seed parent wrong. But probably similar revelations await for other varieties as well.

Big Picture

Pedigrees of individual cultivars are interesting, of course, but the real promise of DNA analysis lies in studies like Migicovsky et al. that look at entire populations. A key finding:

The use of a small number of "elite" cultivars in apple fails to exploit the immense genomic and phenomic diversity available and leaves the apple industry vulnerable to evolving pests and pathogens and a changing climate.

The authors also find that the European crabapple "likely had a greater genomic contribution to cider apples than to dessert apples."

Ultimately, germplasm collections such as the USDA apple collection...will serve as an essential source of diverse accessions and wild relatives, which have enormous potential for future plant improvement.

Migicovsky, Zoë, Kyle M. Gardner, Christopher Richards, C. Thomas Chao, Heidi R. Schwaninger, Gennaro Fazio, Gan-Yuan Zhong, and Sean Myles. "Genomic Consequences of Apple Improvement" Hortic Res 8, 9 (2021). https://doi.org/10.1038/s41438-020-00441-7; figure via Creative Commons license.