Genomic approaches for almond traceability from nursery and along the food chain

Abstract

Almond is widely cultivated in the world thanks to the quality and healthy features of the kernel. Almond kernel is consumed fresh or employed in the food industry. Hundreds of almond cultivars were selected throughout the long history of cultivation; in this context, an efficient method for varietal identification is essential to ensure cultivar traceability along the chain. This study surveyed the widely employed commercial kits and protocols for DNA extraction from several almond matrices including leaves, kernels (fresh and roasted) and several processed products. Commercial kits (though with minor modification) outperformed the other extraction methods for the isolation of DNA suitable for molecular analysis from all the tested matrices. In parallel, a germplasm collection composed of 140 accessions (123 Sicilian genotypes complemented with widely known national and international cultivars) was genotyped with the Axiom™ 60K almond SNP Array enabling the detection of 6 374 unique SNPs that can be readily used for varietal traceability. A subset of unique SNPs was further validated employing a high-resolution melting (HRM) assay on a discovery panel encompassing ten of the most widely cultivated accessions. The DNA extracted from leaves and kernels of five cultivars was genotyped with eight SSRs allowing the identification of the maternal origin of each kernel. The paper integrates the survey of the widely employed protocols for DNA extraction with the high-throughput genotyping of 140 almond accessions. In this context, unique SNPs validated and optimized for an HRM assay and the availability of SSR markers demonstrated their efficacy in traceability analysis along the chain.