Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)

This paper presents the creation of an Affymetrix 60K SNP almond array for SNP genotyping of almond accessions used in Genetic GWAS or mapping studies. As part of an international consortium, we participated in the sequencing of the almond genome in 2019. With this consortium, we resequenced 52 almond varieties in addition to the varieties already available on the NCBI site, and identified the SNPs (Single Nucleotide Polymorphism) variants observed between these varieties. From this initial set of SNPs, we applied selection filters to obtain a set of 60K SNPs well distributed over the genome and with a good 'p_score' index, which was estimated for the Affymetrix technology from the sequence of 70 bases flanking the SNP. To validate this almond array, we genotyped our almond collection and some other accessions of the subgenus amygdalus, including peach and Prunus davidiana clones. We showed that this microarray is well suited to detect intraspecific polymorphism in almond, but also interspecific polymorphism between amygdalus species. It could be used to search for genes of interest in almond trees, but also in peach x almond or peach x davidiana rootstocks. We have integrated two marker SNPs for the RMja nematode resistance gene and the Sk bitterness gene and the results obtained are consistent with the expected results (see figure). This almond array PdSNPV1 is marketed by Thermo Fischer Scientific and the cost price per sample integrating the price of the array and the price of the genotyping will be about 30€ per accession.