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.

中文翻译：

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杏仁从苗圃到整个食物链的可追溯性的基因组方法


杏仁因其仁的品质和健康特性而在世界各地广泛种植。杏仁仁新鲜食用或用于食品工业。在漫长的种植历史中，精选了数百个杏仁品种；在这种情况下，有效的品种识别方法对于确保品种链上的可追溯性至关重要。本研究调查了广泛使用的商业试剂盒和方案，用于从几种杏仁基质中提取 DNA，包括叶、仁（新鲜和烘烤的）和几种加工产品。商业试剂盒（尽管稍作修改）在从所有测试基质中分离适合分子分析的 DNA 方面优于其他提取方法。同时，使用 Axiom™ 60K 杏仁 SNP 阵列对由 140 个种质（123 个西西里基因型，辅以广为人知的国内和国际品种进行补充）组成的种质库进行了基因分型，能够检测 6 374 个独特的 SNP，可轻松用于品种追溯。在包含 10 个最广泛栽培的种质的发现组上采用高分辨率熔解 (HRM) 测定进一步验证了独特 SNP 的子集。从五个品种的叶子和籽粒中提取的 DNA 使用八个 SSR 进行基因分型，从而可以识别每个籽粒的母本起源。该论文将对广泛采用的 DNA 提取方案的调查与 140 种杏仁的高通量基因分型结合起来。在此背景下，针对 HRM 测定进行验证和优化的独特 SNP 以及 SSR 标记的可用性证明了它们在整个链条的可追溯性分析中的功效。