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CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa

By October 8, 2024October 17th, 2024No Comments

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. 2024 Oct 8;2024:gigabyte135. doi: 10.46471/gigabyte.135

CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa

PMCID: PMC11480739  PMID: 39416656

Abstract

A growing interest in Cannabis sativa uses for food, fiber, and medicine, and recent changes in regulations have spurred numerous genomic studies of this once-prohibited plant. Cannabis research uses Next Generation Sequencing technologies for genomics and transcriptomics. While other crops have genome portals enabling access and analysis of numerous genotyping data from diverse accessions, leading to the discovery of alleles for important traits, this is absent for cannabis. The CannSeek web portal aims to address this gap. Single nucleotide polymorphism datasets were generated by identifying genome variants from public resequencing data and genome assemblies. Results and accompanying trait data are hosted in the CannSeek web application, built using the Rice SNP-Seek infrastructure with improvements to allow multiple reference genomes and provide a web-service Application Programming Interface. The tools built into the portal allow phylogenetic analyses, varietal grouping and identifications, and favorable haplotype discovery for cannabis accessions using public sequencing data.

Availability and implementation

The CannSeek portal is available at https://icgrc.info/cannseekhttps://icgrc.info/genotype_viewer.

Statement of need

Background on Cannabis sativa

Cannabis sativa (cannabis, NCBI:txid3483) is an ancient, versatile and highly plastic crop that has been used for food, fiber and medicine for millennia. The first evidence of cultivation for use as fiber for ropes, textiles, and paper is from China, dating back to 4000 B.C. The use as medicine (for rheumatic pain, constipation, female reproductive disorders and malaria) by the ancient Chinese was reported in the Pen-ts’ao Ching, the first pharmacopeia from 2700 B.C. It was also used as an anesthetic during surgery in 110–207 AD []. Early nomads from Central Asia helped spread cannabis to Europe around 4000 years ago, and Arab traders introduced it to Africa around 2000 years ago []. While it was spread globally and used extensively throughout the 18th and 19th centuries, playing a crucial role in the colonial expansion of European nations, the use of C. sativa became largely prohibited worldwide throughout the second half of the 20th century, classified as a narcotic drug, and enforced through the United Nations Single Convention Treaty on Narcotic Drugs []. Over the last decade, however, there has been a global resurgence in cannabis use, spearheaded by the same nation that enforced its widespread prohibition.

There are clear legislation and market-driven distinctions between low-tetrahydrocannabinol (THC), industrial hemp (for food and fibers), and high-THC medicinal cannabis (for medicinal and recreational purposes). Industrial hemp is now a global multibillion-dollar industry with a diverse product range competing with oil, protein, biomass and fiber crops in diverse markets []. Equally, medicinal cannabis has quickly grown into a multibillion-dollar industry with a multitude of medicinal applications and a relaxation of regulation on its recreational use. However, due to its widespread prohibition in the 20th and early 21st century, C. sativa has missed out on many technological advances that have greatly benefited the improvement of traditional crops [].



CannSeek? Yes we Can!

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