A single nucleotide polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated north American cannabis

Rojas

et al. 2021

Genes

Hemp (Cannabis sativa L.) has recently become an important crop due to the growing market demands for products containing cannabinoids. Unintended cross-pollination of C. sativa crops is one of the most important threats to cannabinoid production and has been shown to reduce cannabinoid yield. Ploidy manipulation has been used in other crops to improve agronomic traits and reduce fertility; however, little is known about the performance of C. sativa polyploids. In this study, colchicine was applied to two proprietary, inbred diploid C. sativa inbred lines, ‘TS1-3’ and ‘P163’, to produce the tetraploids ‘TS1-3 (4x)’ and ‘P163 (4x)’. The diploid, triploid, and tetraploid F1 hybrids from ‘TS1-3’ × ‘P163’, ‘TS1-3 (4x)’ × ‘P163’, and ‘TS1-3 (4x)’ × ‘P163 (4x)’ were produced to test their fertilities, crossing compatibilities, and yields. The results indicated a reduction in fertility in the triploids and the tetraploids, relative to their diploid counterparts. When triploids were used as females, seed yields were less than 2% compared to when diploids were used as females; thus, triploids were determined to be female infertile. The triploids resulting from the crosses made herein displayed increases in biomass and inflorescence weight compared to the diploids created from the same parents in a field setting. Statistical increases in cannabinoid concentrations were not observed. Lastly, asymmetric crossing compatibility was observed between the diploids and the tetraploids of the genotypes tested. The results demonstrate the potential benefits of triploid C. sativa cultivars in commercial agriculture.

Section: Introductionmentioning

confidence: 99%

Characteristics of the Diploid, Triploid, and Tetraploid Versions of a Cannabigerol-Dominant F1 Hybrid Industrial Hemp Cultivar, Cannabis sativa ‘Stem Cell CBG’

Rojas

et al. 2021

Genes

“…Like the results presented here with nuclear SNPs (Supplementary Figure 2A, 3A, 4A, 5B, 6B, 7B and 8B), Henry et al . (2020) reported k = 5 as the number of groups which best delineated samples [43] though this number is variable [44]. In plastid data, previous work representing a mix of wild and domesticated populations in China revealed three distinct groups [45], however this differs from published work from law enforcement agencies which suggested five to eight groups [46] [47].…”

Section: Discussionmentioning

confidence: 99%

Examining population structure across multiple collections of Cannabis

Halpin-McCormick

Heyduk

Kantar

et al. 2022

Preprint

Cannabis sativa L. (Cannabaceae) is an annual flowering herb of Eurasian origin that has been associated with humans for over 26,000 years. Multiple independent domestications occurred with different events leading to use as food, fiber, and medicine, with human intervention likely accelerating a division in the genus with varietals broadly known today as either hemp-type or drug-type. Using publicly available sequence data, we assessed genome wide diversity and population relationships across seven independently developed datasets. Phylogenetic analysis was conducted, with data sources providing a unique sampling of Cannabis varieties, with landrace and modern cultivars represented. Comparing nucleotide diversity over chromosomal length in landrace and domesticated modern drug-type varieties, genomic regions with decreased diversity where humans may have selected for specific traits were identified. Population structure was evident based on use type. Evidence of hybridization was extensive across the datasets. In a subset of landrace individuals where geographic origin was known, population separation was observed between varieties collected from Northern India in the Hindu Kush Mountains and Myanmar. The use of publicly available data provides an initial impression of the complexity within the Cannabis genus and adds to our understanding of the genetics underlying evolutionary history and population stratification, which will be critical for future crop improvement for any potential human use.

“…). C1 is a THC dominant cluster and includes six THC dominant strains (11,17,18,20,21, and 23-THC) and one balanced strain (1-balanced). C2 is another THC dominant cluster and includes five THC dominant strains (12,14,15,16, and 19-THC).…”

Section: Plos One Plot Of 23 Cannabis Genotypes Is Shown In Fig 1(c) the Grouping Assignment For Individual Strains By Dapc Is Listed In mentioning

confidence: 99%

“…Tri-allelic SNPs are reported to have a higher power of discrimination than bi-allelic SNPs requiring fewer markers and lowering costs [18,20]. However, tri-allelic SNPs have been excluded in cannabis population structural analysis in the current literature [6,21].…”

Section: Introductionmentioning

confidence: 99%

Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms

Jin

Henry²,

Shan

et al. 2021

PLoS ONE

Self Cite

The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strains with high tetrahydrocannabinol (THC) levels. 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.