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Title: Genetic diversity in Malus × domestica (Rosaceae) through time in response to domestication

Author
item GROSS, BRIANA - University Of Minnesota
item Henk, Adam
item Richards, Christopher
item Fazio, Gennaro
item Volk, Gayle

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2014
Publication Date: 10/10/2014
Citation: Gross, B., Henk, A.D., Richards, C.M., Fazio, G., Volk, G.M. 2014. Genetic diversity in Malus × domestica (Rosaceae) through time in response to domestication. American Journal of Botany. 101(10):1770-1779. DOI: 10.3732/ajb.1400297.

Interpretive Summary: There have been recurring questions about how the genetic diversity of commonly grown crops has been lost over the years. This process is generally referred to as genetic erosion. This is reflected in rising consumer interest in heirloom cultivars and their conservation in the face reliance on modern cultivars. The issue has also sparked interest in how well the USDA conserves diversity of these older cultivars in gene banks. We investigate this question in apple by measuring the changes in genetic diversity using a set of variable simple sequence repeat (SSR) DNA markers. Apple cultivars are clonally propagated by grafting, and thus the genotype doesn’t change. SSR diversity in sets of accessions from the collection that were developed or identified centuries ago can be directly compared with more modern varieties. The experiment used 1228 cultivars of apple conserved in the National Plant Germplasm System collection that includes both modern and ancient cultivars. By comparing the age of the cultivars with their measured SSR diversity one can assess the magnitude and direction of genetic erosion over the course of apple breeding in the last few centuries. Results indicate that SSR diversity did not statistically vary among cultivars that dated in the 1200-1600s, 1700s, 1800s, 1900-1950, and 1951-2000. Overall, domesticated apple has retained high genetic diversity throughout the domestication and improvement process. While apple diversity is effectively preserved in germplasm collections, it is not used in apple cultivation. Eleven of the 15 cultivars currently used for 90% of worldwide production show a lower diversity. Careful management of germplasm collections is needed to ensure that collections remain intact and can be accessed for future breeding efforts.

Technical Abstract: Patterns of genetic diversity in domesticated plants are affected by geographic region of origin and cultivation, intentional artificial selection, and unintentional loss of diversity referred to as genetic bottlenecks. While bottlenecks are mainly associated with the initial domestication process, they can also affect diversity available for crop improvement. Here, we investigate the impact of the improvement process on the genetic diversity of domesticated apple and compare it to other perennial and annual fruit crops. Apple cultivars developed ranging from the 13th through the 20th century and 11 of the 15 apple cultivars used for 90% of the apple production in the US were surveyed for genetic diversity based on either 9 or 19 simple sequence repeats (SSRs). Diversity was compared using standard metrics and model-based approaches based on expected heterozygosity at equilibrium. Improvement bottleneck data for fruit crops were also collected from the literature. Domesticated apples showed no significant reduction in genetic diversity through time across the last eight centuries. Diversity was generally high, with an average He > 0.7 for apples from all centuries. However, diversity of the apples currently used for the bulk of commercial production was lower. The genetic bottleneck that occurred during improvement of domesticated apples appears to be mild or nonexistent. This contrasts with improvement bottlenecks in many annual and perennial fruit crops. The low diversity of the subset of cultivars used for commercial production, however, indicates that an improvement bottleneck may be in progress for this perennial crop.