GWAS analysis of an almond germplasm collection unravels the genetic regulation of aroma in fresh and roasted kernels

Almond (Prunus dulcis Mill. D.A. Webb) cultivation rapidly spread throughout the Mediterranean area from central Asia, reaching Sicily while it was under Greek colonization. The long history of cultivation resulted in the selection and propagation of hundreds of selections characterized by a wide variability in terms of kernel quality, ripening period, and resistance to biotic and abiotic stress. Kernel quality is one of the leading aspects influencing the marketability of the product. Almonds are particularly priced for their sensory, nutritional, and health attributes and kernels are often consumed fresh, toasted and/or as ingredient in food productions. To decipher the genetic mechanism of the aroma, a germplasm collection of 140 almond accessions (including Sicilian accessions and Italian and international varieties) was genotyped using the Axiom™ 60K almond SNP array leading to the selection of 47,946 robust SNPs. The SNP-genotyped individuals of the almond collection were also phenotyped for the production of volatile organic compounds (VOCs) using a proton-transfer time-of-flight mass spectrometer (PTR-TOF-MS). This analysis was carried out both on fresh and roasted (15 min at 150°C) kernels, resulting in the detection of 165 mass peaks. Some peaks, such as those related with sulfur compounds, furan containing compounds, and aldehydes formed by Strecker degradation, significantly increased during roasting, while VOCs belonging mostly to alcohols and terpenes, significantly decreased. The GWAS analysis enabled the identification of 85 and 130 mass peaks characterized by an association with one or more SNPs for raw and toasted almond kernel aroma, respectively. The detection of molecular markers linked to different VOCs will help both the understanding of their regulation and the selection of novel varieties with enhanced aromatic profile through marker-assisted selection