[{"id":273,"title":"Applying Genomic tools to Cannabis Breeding ","sha":"46acc95d5b851cf28facc88ff54b30e7","user_id":null,"state":"published","body":"Humans share a long history with Cannabis, perhaps going back even further back than the dawn of agriculture. As such this plant has traveled the world alongside humanity, consequent introductions of novel variants into the pool of genetics available to farmers and breeders has been both diverse and poorly recorded. While a general consensus has been reached in terms of the general classification of Cannabis into four groups: European Hemp and Chinese Hemp (which can be characterized by low psychoactive potential) and \"sativa\" and \"indica\" drug-type plants, the numerous other traits displayed by the genus have been given little attention.  The availability of genomic resources for Cannabis now enables us to implement marker assisted selection programs aimed at identifying the particular genetic variant(s) responsible for traits of interest, such as cannabinoid, terpenoid and anthocyanin profiles responsible for the pharmacological, recreational and coloration properties of common strains. As this information becomes available to breeders, one can only expect that the monopoly enjoyed by some clandestine and licensed operations will be thwarted by brute force produced by the creative and intuitive farmers that have cultivated this plant and introduced and maintained genetic variation into the gene pool of this fascinating domesticated plant. Major benefits include the acceleration of targeted homozygosity.","created_at":"2016-01-08T18:21:49.457Z","updated_at":"2022-04-19T06:00:34.586Z","zenodo_id":92720,"doi":"http://dx.doi.org/10.5281/zenodo.44530","subject":null,"tags":["cannabis","breeding","hemp","mj","genomics","marker assisted selection","agriculture","domestication","single nucleotide polymorphism","quantitative trait loci","homozygosity"],"vote_count":0,"view_count":1,"score":3.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":"AlpineRocket.jpg","attachment_content_type":"image/jpeg","attachment_file_size":218629,"attachment_updated_at":"2016-01-08T18:21:48.730Z"},{"id":279,"title":"On Domestication and Feralization: re-rethinking invasive species from a genetic perspective","sha":"1a766837d477249d9af2f53638baf08a","user_id":null,"state":"published","body":"The new wild is an attractive concept recently synthesized by Fred Pearce, which in essence states that we have vilified invasives and have spent tremendous effort in eradicating them, often with limited success. But we were the ones to bring them there in the first place! Such issues spawn from the static nature of the biological species concept and our lack of understanding of the theories underlying selection, adaptation and the dynamic nature of the environment. In a recent Nature News Feature, Ewen Callaway elegantly describes preliminary data from the feral population of chickens from Kauai that exemplify my point. Feral chickens have adapted to their new environment in part due to introgression of domesticated genes into the feral gene pool. Selection is thus able to draw from disparate gene pools in order to result in a temporally optimal phenotype. This implies that the concept of genetic pollution should be extended to include genetic enhancement, particularly within the framework of our dynamic environment in the anthropocene. The dynamic nature of our climate will alter selective pressure, and the presence of an \"invasive\" gene in the pool of \"natives\" may well be a recipe for survival in the new wild.  ","created_at":"2016-01-21T20:06:05.239Z","updated_at":"2016-01-22T06:01:07.729Z","zenodo_id":94321,"doi":"http://dx.doi.org/10.5281/zenodo.45084","subject":null,"tags":["the new wild","invasive species","domestication","feralization","rethinking","wilderness","humanity","genetic pollution","genetic enhancement","anthropocene"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":"Feralization.pages.pdf","attachment_content_type":"application/pdf","attachment_file_size":2710911,"attachment_updated_at":"2016-01-21T20:06:04.959Z"},{"id":304,"title":"Cannabis and human creativity: hyper-priming, eureka moments and intermittent abstinence  ","sha":"ceebf9ed644a4a7d844cdeaa4594df34","user_id":null,"state":"published","body":"Cannabis has undeniably been used to prime our imagination and creativity for centuries. As critical thinkers of all walks of life explore the use and impact of cannabis on today's society, one cannot omit the clear ability of the plant to bestow eureka moments upon our senses. Some have termed this experience hyper-priming #http://www.ncbi.nlm.nih.gov/pubmed/20122742, or the ability to transcend different areas of knowledge to build connections between seemingly unrelated fields. Scientific insight should be applied to harness the potential benefits of cannabis hyper-priming and to make it into an effect cognitive tool. Recent research suggests that chronic cannabis use reduces the expression of Cannabinoid 1 receptors (CB1R) in several areas of the human brain. It was also observed that upon controlled abstinence #http://www.ncbi.nlm.nih.gov/pubmed/26858993, CB1R expression is restored to full potential after only 48 hours. Conventional wisdom would thus have it that intermittent abstinence at intervals of 24-48hours, by restoring CB1R expression would provide for enhanced hyper-priming leading to more efficient use of cannabis for cognitive insight. Forget that plant with the 1001 molecules, think about the billion possible ways to use it more effectively to achieve originality and productivity through transcendence.","created_at":"2016-05-20T03:07:46.045Z","updated_at":"2016-07-10T19:01:53.125Z","zenodo_id":113729,"doi":"http://dx.doi.org/10.5281/zenodo.51795","subject":null,"tags":["cannabis","hyper-priming","eureka","intermittent abstinence"],"vote_count":1,"view_count":1,"score":1.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":532,"title":"Two Single Nucleotide Polymorphisms Tease Apart Hemp, CBDA and THCA Expressing Cannabis","sha":"199d82d72bf64234b8ace849cc20896c","user_id":null,"state":"published","body":"The classification of Cannabis varieties has been increasingly discussed in the past years, particularly within the scope of intellectual property development and protection [Henry 2016](/ideas/46acc95d5b851cf28facc88ff54b30e7). Several publications have developed molecular markers useful to classify these two groups [e.g. Henry 2015](https://peerj.com/preprints/1553/), and the USPTO has begun assessing patent applications, such as that for 100 or more SNPs shown to tease apart hemp from marijuana based on opportunistically collected data [Sawler \u0026 Myles, 2016](https://patents.google.com/patent/WO2016197258A1/en). \r\n\r\nMore recently, the release of the complete Cannabis chromosome assembly into ten chromosomes (previous public version contained 135'164 scaffolds), brings much needed insight into the inheritance and adaptive introgression of CBDA expression in drug-type cannabis [Grassa et al. 2018](https://www.biorxiv.org/content/early/2018/11/01/458083). \r\n\r\nBased on data from 192 samples, we here propose the use of a set of two Single Nucleotide Polymorphisms (SNPs) found in two disparate regions of the cannabis genome; the mitochondria and the THCA synthase gene (**Table 1**). In conjunction these two molecular markers provide a rapid and cost-effective means to identify **hemp** derived (low) CBDA producing accessions from drug-type (high) **CBDA** and **THCA** expressing varieties.  \r\n\r\n**Table 1.**\r\n\r\n| **Type** | **Mito_318'683** | **THCAS_8'374** |\r\n| :---:    |     :---:      |    :---: |\r\n| Fibre/Hemp   | A/A     | A/A    |\r\n| CBDA/Drug     | C/C       | A/A      |\r\n| THCA/Drug     | C/C       | G/G or G/A      |","created_at":"2018-11-06T01:11:03.163Z","updated_at":"2022-04-19T06:00:35.588Z","zenodo_id":1495246,"doi":"https://doi.org/10.5281/zenodo.1495246","subject":null,"tags":["single nucleotide polymorphism","fibre vs drug-type","cannabis","snp","cbda vs thcas expressing cannabis"],"vote_count":0,"view_count":1,"score":1.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":795,"title":"A set of SNPs and Indels in the psilocybin biosynthetic pathway cluster: candidates markers for chemotypic expression in two species of Psilocybe mushrooms","sha":"b27121d63442d928ef654dc499ae3ef1","user_id":null,"state":"published","body":"Renewed interested in the application of psychotropic compounds to mental health and societal issues has let to the revival of [psychedelic research](https://pubmed.ncbi.nlm.nih.gov/28763571/). While groups are racing to patent composition or processes, having proper traceability tools and an understanding of chemotypic expression will be paramount to regulated supply of psychedelics. Two species of psychotropic mushroom from the Psilocybe genus, P. cubensis and P. cyanescens are known to express different ratios of prodrugs psilocybin and baeocystin, making them suitable to different application, where P. cyanescans may be considered more potent and rather suited to recreational use and P. cubensis may be better suited to medical application, in the treatment of clinical depression for example. Here, we use data available from the public domain [public domain](https://genomevolution.org/coge/GenomeInfo.pl?gid=59605) to identify single nucleotide polymorphism (SNP), insertion and deletions in the psilocybin biosynthetic pathway gene cluster. We identify 91 SNPs, 16 insertions and 9 deletions, including 9 SNPs and one major deletion upstream of the methyltransferase PsiM which may be associated with the chemotypic expession in P. cubensis and P. cyanescens, particularly the higher accumulation of baeocystin and psilocybin in P. cyanescens. ","created_at":"2021-01-13T17:10:46.072Z","updated_at":"2021-05-21T06:01:19.642Z","zenodo_id":4775044,"doi":"https://doi.org/10.5281/zenodo.4775044","subject":null,"tags":["psilocybe cubensis","psilocybe cyanescans","single nucleotide polymorphism"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":false,"attachment_file_name":null,"attachment_content_type":null,"attachment_file_size":null,"attachment_updated_at":null},{"id":933,"title":"Tri-allelic SNPs outperform functional candidates for biochemical profile in Cannabis","sha":"de37a87e482cd4204a0d3ada4df6ea9b","user_id":null,"state":"published","body":"Genomic technologies have revolutionized the fields of evolutionary biology and genetics, bringing with it the promise of our understanding of the functional basis and inheritance of key traits of interest. On the other hand, the stupendous amount of data generated by such means have not been matched by computer power and as such, many genomic studies use quality control measures to reduce the number of marker retained in analyses, resulting in most studies retaining bi-allelic *Single Nucleotide Polymorphisms* (SNPs) [Henry 2018](/ideas/199d82d72bf64234b8ace849cc20896c).\r\n\r\nWe set out to compare the utility of a select tri-allelic SNPs panel against three functionally validated bi-allelic SNPs underlying monoterpene, sesquiterpene and cannabinoid expression [Watts et al 2021](https://www.nature.com/articles/s41477-021-01003-y#MOESM3). We leveraged data from [Jin et al 2021](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253387) containing genotypes from [23 cannabis accessions with associated chemotypic profiles](https://www.frontiersin.org/articles/10.3389/fpls.2021.699530/full), which clustered into THC, CBD and intermediate (THC/CBD) categories. Low sesquiterpene content was noted in the CBD and intermediate groups.  An independent compilation of data from the public domain available from the [International Cannabis Research Consortium](https://www.icgrc.info/) was used to demonstrate the power of the tri-allelic panel.\r\n\r\nWe show near perfect assignment to the predefined chemotype groups, and demonstrate that the three tri-allelic markers can be used in combination as predictors of biochemical makeup in *Cannabis*, providing a simple means to categorize cannabis into groups based on their monoterpene, sesquiterpene and cannabinoid content.\r\n\r\n\r\n","created_at":"2022-04-18T23:39:27.720Z","updated_at":"2022-06-15T06:00:38.172Z","zenodo_id":6643865,"doi":"https://doi.org/10.5281/zenodo.6643865","subject":null,"tags":["single nucleotide polymorphism","tri-allelic","tri-allelic snps","cannabis","chemotype"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":"Henry2022JBriefIdeas.pdf","attachment_content_type":"application/pdf","attachment_file_size":3480720,"attachment_updated_at":"2022-04-18T23:39:27.645Z"}]