A Standard Protocol for Plant Variety Identification Based Upon Whole Genome Sequencing

Plant variety/genotype identification has many applications in establishing the identity of plants including protection of intellectual property rights. The variety may be important for operational reasons based on field performance or post-harvest processing. Genome sequencing methods have improved and become more feasible for use, making examination of the whole genome, which provides all possible information on the genotype, the ultimate way to distinguish plant varieties. Here, we present a standard protocol that could be used to identify a genotype of any plant species of interest from whole genome sequence data. The method was tested by application to the distinction of 41 varieties of tetraploid blueberry (Vaccinium Corymbosum L.). Using minimum mapping-coverage threshold, stringent variant filters and accurately identifying and excluding data-noise resulted in the generation of high confidence homozygous SNP uniquely shared between an unknown and a reference for utility in variety identification. The approach used aimed to minimize the impact of sequencing errors and coincident sequencing of only one allele of any heterozygous base. Adoption of a standard protocol and the establishment of sequence databases for all varieties of important plant species will be required to provide reliable variety identification in critical industrial or legal applications.