One of the earliest domesticated plant species, Cannabis sativa L. (marijuana, hemp; Cannabaceae) has been used for millennia as a source of fibre, oil- and protein-rich achenes (“seeds”) and for its medicinal and psychoactive properties. From its site of domestication in Central Asia, the cultivation of cannabis spread in ancient times throughout Asia and Europe and is now one of the most widely distributed cultivated plants .
Hemp fibre was used for textile production in China more than 6000 years BP (before present) . Archaeological evidence for the medicinal or shamanistic use of cannabis has been found in a 2700-year old tomb in north-western China and a Judean tomb from 1700 years BP [3, 4].
Currently cannabis and its derivatives such as hashish are the most widely consumed illicit drugs in the world . Its use is also increasingly recognized in the treatment of a range of diseases such as multiple sclerosis and conditions with chronic pain [6, 7]. In addition, hemp forms of cannabis are grown as an agricultural crop in many countries.
Cannabis is an erect annual herb with a dioecious breeding system, although monoecious plants exist. Wild and cultivated forms of cannabis are morphologically variable, resulting in confusion and controversy over the taxonomic organization of the genus (see  for review). Some authors have proposed a monotypic genus, C. sativa, while others have argued that Cannabis is composed of two species, Cannabis sativa and Cannabis indica, and some have included a third species, Cannabis ruderalis, in the genus. In light of the taxonomic uncertainty, we use C. sativa to describe the plants analyzed in this study.
The unique pharmacological properties of cannabis are due to the presence of cannabinoids, a group of more than 100 natural products that mainly accumulate in female flowers (“buds”) [9, 10]. Δ9-Tetrahydrocannabinol (THC) is the principle psychoactive cannabinoid and the compound responsible for the analgesic, antiemetic and appetite-stimulating effects of cannabis [11, 12]. Non-psychoactive cannabinoids such as cannabidiol (CBD), cannabichromene (CBC) and Δ9-tetrahydrocannabivarin (THCV), which possess diverse pharmacological activities, are also present in some varieties or strains [13, 14, 15].
Cannabinoids are synthesized as carboxylic acids and upon heating or smoking decarboxylate to their neutral forms; for example, Δ9-tetrahydrocannabinolic acid (THCA) is converted to THC. Although cannabinoid biosynthesis is not understood at the biochemical or genetic level, several key enzymes have been identified including a candidate polyketide synthase and the two oxidocyclases, THCA synthase (THCAS) and cannabidiolic acid (CBDA) synthase, which form the major cannabinoid acids [16, 17, 18].
Cannabinoid content and composition is highly variable among cannabis plants. Those with a high-THCA/low-CBDA chemotype are termed marijuana, whereas those with a low-THCA/high-CBDA chemotype are termed hemp. There are large differences in the minor cannabinoid constituents within these basic chemotypes. Breeding of cannabis for use as a drug and medicine, as well as improved cultivation practices, has led to increased potency in the past several decades with median levels of THC in dried female flowers of ca. 11% by dry weight; levels in some plants exceed 23% [10, 19]. This breeding effort, largely a covert activity by marijuana growers, has produced hundreds of strains that differ in cannabinoid and terpenoid composition, as well as appearance and growth characteristics. Patients report medical marijuana strains differ in their therapeutic effects, although evidence for this is anecdotal.
Cannabis has a diploid genome (2n = 20) with a karyotype composed of nine autosomes and a pair of sex chromosomes (X and Y). Female plants are homogametic (XX) and males heterogametic (XY) with sex determination controlled by an X-to-autosome balance system . The estimated size of the haploid genome is 818 Mb for female plants and 843 Mb for male plants, owing to the larger size of the Y chromosome . The genomic resources available for cannabis are mainly confined to transcriptome information: NCBI contains 12,907 ESTs and 23 unassembled RNA-Seq datasets of Illumina reads [22, 23]. Neither a physical nor a genetic map of the cannabis genome is yet completely available but different scientists have estimated its transcriptome to more than 30,000 genes.
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