A Whole-Genome Sequencing-Based SNP Protocol for Accurate Plant Variety Identification: Application in Blueberry

Plant variety/genotype identification has many applications in establishing the identity of plants, including the protection of intellectual property rights and the management of ex situ conservation of genetic resources. The variety may be important for operational reasons based on field performance or post-harvest processing. Blueberry (Vaccinium corymbosum L.), an economically important crop, is propagated by cuttings and commercially important accessions require an accurate variety traceability regime for the maintenance of purity, protection and policing ownership. Genome sequencing methods have improved and are feasible for use, making examination of the whole genome for all possible information on the genotype the ultimate way to distinguish plant varieties. We identified 5.3–5.5 million high-confidence homozygous SNPs with over 99% accuracy, enabling the distinction of 41 blueberry varieties. We developed a novel data-noise identification and filtering framework, which correctly determined the identity of ten unknown samples to be the Masena variety with 100% accuracy. The approach of using a data-noise filtration step minimized the impact of sequencing errors and coincident sequencing of only one allele of any heterozygous base. This SNP-based protocol with the establishment of sequence databases for all varieties of important plant species can potentially be adopted in providing reliable variety identification in critical industrial or legal applications.