Exploring additive and non-additive genetic models to decipher the genetic regulation of almond tolerance to Diaporthe amygdali

Constriction canker (Diaporthe amygdali) is one of the main diseases affecting almond cultivation. To unravel the genetic basis of the tolerance to the disease, a germplasm collection of 123 almond accessions (111 selected in Sicily, Italy, complemented with widely cultivated Italian and International varieties), was employed for a Genome-Wide Association Study (GWAS). Accessions were phenotyped employing a detached-twig inoculation assay, here employed for the first time for a GWAS, ensuring high throughputness and reproducibility. The most susceptible and tolerant accessions were also inoculated in planta and the two phenotyping methods showed a significant correlation of 0.7. Genotyping was performed using the Axiom™ 60K almond array, resulting in the identification of 47,496 robust markers. Both additive and non-additive GWAS models were tested leading to the identification of nine SNPs significantly associated with tolerance to D. amygdali. Candidate genes in linkage-disequilibrium with the significant SNPs were functionally characterized and a subset of 20 were further validated through RT-qPCR in both the most tolerant (the Sicilian ‘Cuti’) and susceptible (‘Ferraduel’) genotypes at 0 and at 2 days after in planta inoculations. The results provide novel insights to understand the genetic regulation of the tolerance to D. amygdali and for the set-up of marker-assisted selection plans in almond.