2b-RAD sequencing of Malus florentina populations reveals strong population structure and signals of balancing selection at disease resistance loci

Background: Crop wild relatives of Malus domestica represent exceptional value as breeding resources and ornamental trees, nonetheless their natural populations are under threat due to anthropogenic factors. Malus florentina is an apple species endemic to the Balkans and Italy, and our current knowledge on its population genetics and conservation biological status is strongly limited. Results: In the current study we used a 2b-RAD-seq approach to investigate the population genetic structure and diversity of four M. florentina populations from three different countries. We detected strong genetic differentiation among populations and a substantial risk of inbreeding within them. Furthermore, we identified candidate genes under selection associated with various stress responses including biotic resistance, salt stress and drought stress tolerance, further supporting local adaptation. Our enrichment analyses based on non-synonymous SNP counts at resistance loci revealed a significant 2.4-fold change, indicating that disease resistance genes are under selection. Conclusions: According to this study M. florentina populations face considerable risk, and fragmentation of the studied populations cannot be ruled out. Despite this, the assessed populations exhibit considerable diversity at disease resistance loci, likely maintained by balancing selection. These findings highlight the importance of conserving the genetic diversity of wild apple populations for key agronomic traits such as disease resistance.