Constructing a Draft Map of the Cannabis Proteome

Jenkins, Conor; Orsburn, Benjamin C.

doi:10.1101/577635

Cited by 6 publications

(6 citation statements)

References 27 publications

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“…The Cannabis (2n = 2x = 20) draft genome has a haploid genomic sequence of over 876Mb – 1000Mb (Laverty et al, 2019; McKernan et al, 2020) and transcriptome of at least 30,000 genes (van Bakel et al, 2011, Jenkins and Orsburn, 2019a,b,c). The genome displays large amount of polymorphism with a single nucleotide polymorphism (SNP) present every one in a hundred to one in fifty base pairs (McKernan et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Given the recent release of the 10 chromosome map of the cannabis genome (Grassa, 2018; Laverty et al, 2019), metabolomic and proteomic insight (Jenkins and Orsburn, 2019a,b) as well as a fully annotated version of the cannabis genome resulting from the completion of the NCBI Cannabis sativa Annotation Release 100 (Jenkins and Orsburn, 2019c), we set out to characterise the functional basis of the SNPs used in the study. The previously designed targets developed using Cansat 3 (von Bakel et al, 2011) were subjected to a BLASTn search (Altschul et al, 1990) constrained to the taxa Cannabis using the NCBI online interface (https://blast.ncbi.nlm.nih.gov) accessed October 31, 2019.…”

Section: Methodsmentioning

confidence: 99%

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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

Henry¹,

Khatodia²,

Kapoor³

et al. 2020

Preprint

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BackgroundThe taxonomic classification of the Cannabis genus has been delineated through three main types: sativa (long and less branched plant with long and narrow leaves), indica (short but highly branched plant with broader leaves) and ruderalis (wild type with short stature, less branching and small thick leaves). While still under discussion, particularly whether the genus is polytypic or monotypic, this broad classification reflects putative geographical origin of each group and putative chemotypic and pharmacology.MethodsHere we describe a thorough investigation of cannabis accessions using a set of 22 highly informative and polymorphic SNP markers associated with important traits such as cannabinoid and terpenoid expression as well as fibre and resin production. The assay offers insight into cannabis population structure, phylogenetic relationship, population genetics and correlation to secondary metabolite concentrations and demonstrate the utility of this assay for rapid, repeatable and cost-efficient genotyping of commercial and industrial cannabis accessions for use in product traceability, breeding programs, regulatory compliance and consumer education.ResultsThe main outcomes are the identification of 5 clusters in the sample set available, including industrial hemp, resin hemp which likely underwent a bottleneck to stabilize CBDA accumulation (Type II & III). THC resin (type I) make up the other three clusters with terpinolene (colloquial “sativa” or “NLD”), myrcene/pinene and myrcene/limonene (colloquial “indica”, “BLD”), which also putatively harbour an active CBCAS.ConclusionThe functional basis of key traits is also discussed as recently enabled by the NCBI Cannabis sativa Annotation Release 100, allowing for hypothesis testing with regards to secondary metabolite production as well as other key traits of importance for adaptable and compliant large-scale seed production under the new US Domestic Hemp Production Program.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

Henry¹,

Khatodia²,

Kapoor³

et al. 2020

Preprint

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“…It has a diploid genome (2n=20) estimated to be 843 Mb for male plants and 818 Mb for female plants. Additionally, the species is believed to possess almost 30,000 genes (Jenkins and Orsburn, 2019b, 2019a; Henry et al, 2020; Hurgobin et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Population genomics of a naturalCannabis sativaL. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

Dehnavi,

Damerum,

Taheri

et al. 2024

Preprint

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Future breeding and selection of Cannabis sativa L. for drug production and industrial purposes require a source of germplasm with wide genetic variation, such as that found in wild relatives and progenitors of highly cultivated plants. Limited directional selection and breeding have occurred in this crop, especially informed by molecular markers. Here, we investigated the population genomics of a natural cannabis collection of male and female individuals from differing climatic zones in Iran. Using Genotyping-By-Sequencing (GBS), we sequenced 228 genotypes from 35 populations. The results obtained from GBS were used to perform association analysis identifying links between genotype and important phenotypes, including inflorescence characteristics, flowering time, plant morphology, tetrahydrocannabinol (THC) content, cannabidiol (CBD) content and sex. Approximately 23,266 significant SNPs of high quality were detected to establish associations between markers and traits, and population structure showed that Iranian cannabis plants fall into five groups. A comparison of Iranian samples from this study to global data suggests that the Iranian population is distinctive and, in general, is closer to marijuana than to hemp, although some populations in this collection are closer to hemp. The GWAS results showed that novel genetic loci, not previously identified, contribute to sex, yield and chemotype traits in cannabis and are worthy of further study.

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“…It also provides comprehensive genetic information [22], as studies showed that differences between fiber-and drug-type cannabis are at a genome-wide level and not necessarily limited to genes involved in THC production [5]. The recent release of the 10-chromosome map of the cannabis genome [23][24][25][26][27] may improve the understanding of the genetic architecture, identify a superior set of SNPs associated with interesting traits, and reduce future targeted genotyping costs by using fewer but more accurate SNPs [28].…”

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

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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.

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Constructing a Draft Map of the Cannabis Proteome

Cited by 6 publications

References 27 publications

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

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

Population genomics of a naturalCannabis sativaL. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

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

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