Direct-injection spectrometry and whole-genome genotyping unravel the genetic regulation of fresh and roasted kernels of almond

Almond (Prunus dulcis Mill.) is particularly appreciated for its nutraceutical value and aromatic profile of the kernels. To decipher the genetic mechanism of aroma production, genotyping of 106 almond genotypes (including Sicilian accessions and Italian and foreign cultivars) was performed using both the Illumina Infinium®18K Peach SNP array and the Axiom™70K almond SNP array. The same individuals were phenotyped for two consecutive years for volatile organic compounds (VOCs) using a proton-transfer time-of-flight mass spectrometer (PTR-TOF-MS). The profiling of the almond aroma was carried out on fresh and roasted kernels, enabling the detection of 150 mass peaks. Some, such as those related to sulphur compounds, furan-containing compounds significantly increased during roasting, while VOCs belonging mostly to alcohols and terpenes, significantly decreased. A total of 938 robust SNPs were selected from the Illumina Infinium18K Peach SNP array and employed for population genetic studies. Structure analysis detected significant genetic stratifications for K=2, while the linkage disequilibrium decay across the genome was equal to r2=0.048. The Axiom 70K almond SNP array was employed for genome-wide association analysis (GWAS), which enabled the identification of at least one SNP marker each for 152 VOCs. A precise elucidation of the genetic regions involved in the production of different VOCs is a fundamental step toward the understanding the physiology and regulation of almond aroma. The detection of molecular markers linked to different VOCs will help in understanding their regulation and the selection of novel cultivars with enhanced aromatic profile through marker-assisted selection