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Due to large scale, extensive, and unrecorded hybridization in the past 40 years, this vernacular naming convention has become unreliable and inadequate for identifying or selecting strains for clinical research and medicinal production. Additionally, cannabidiol (CBD) dominant strains and balanced strains (or intermediate strains, which have intermediate levels of THC and CBD), are not included in the current classification studies despite the increasing research interest in the therapeutic potential of CBD. This paper is the first in a series of studies proposing that a new classification system be established based on genome-wide variation and supplemented by data on secondary metabolites and morphological characteristics. This study performed a whole-genome sequencing of 23 cannabis strains marketed in Canada, aligned sequences to a reference genome, and, after filtering for minor allele frequency of 10%, identified 137,858 single nucleotide polymorphisms (SNPs). Discriminant analysis of principal components (DAPC) was applied to these SNPs and further identified 344 structural SNPs, which classified individual strains into five chemotype-aligned groups: one CBD dominant, one balanced, and three THC dominant clusters. These structural SNPs were all multiallelic and were predominantly tri-allelic (339\/344). The largest portion of these SNPs (37%) occurred on the same chromosome containing genes for CBD acid synthases (CBDAS) and THC acid synthases (THCAS). The remainder (63%) were located on the other nine chromosomes. These results showed that the genetic differences between modern cannabis strains were at a whole-genome level and not limited to THC or CBD production. These SNPs contained enough genetic variation for classifying individual strains into corresponding chemotypes. In an effort to elucidate the confused genetic backgrounds of commercially available cannabis strains, this classification attempt investigated the utility of DAPC for classifying modern cannabis strains and for identifying structural SNPs.<\/jats:p>","DOI":"10.1371\/journal.pone.0253387","type":"journal-article","created":{"date-parts":[[2021,6,28]],"date-time":"2021-06-28T17:25:34Z","timestamp":1624901134000},"page":"e0253387","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms"],"prefix":"10.1371","volume":"16","author":[{"given":"Dan","family":"Jin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6475-1714","authenticated-orcid":true,"given":"Philippe","family":"Henry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacqueline","family":"Shan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7925-3729","authenticated-orcid":true,"given":"Jie","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,6,28]]},"reference":[{"key":"pone.0253387.ref001","unstructured":"Hillig KW (2005) A systematic investigation of Cannabis, PhD thesis, Indiana University. 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