A physical and genetic map of Cannabis sativa identifies extensive rearrangement at the 2 THC/CBD acid synthase locus

CBDAS and THCAS are mutually exclusive alleles (i.e. very different isoforms, as the protein
70 sequences are only 84% identical). Genetic analysis supports this model, with approximately
71 1:2:1 segregation of chemotypes in a cross of drug-type vs hemp (de Meijer et al. 2003)

818 Mb and 843 Mb for female and male, respectively (Sakamoto 1998)). Overall,
123 90.3% of 30,074 previously-described PK transcripts (van Bakel et al. 2011) mapped to the PK
124 assembly (82.3% mapping completely within a single scaffold). Each assembly also contained
125 >95% of eudicotyledon single-copy orthologs from OrthoDB, of which >97% were complete

@Elephant found the most important news of the year this paper is required reading. If you are doing any breeding.

A physical and genetic map of Cannabis sativa identifies extensive rearrangement at the 2 THC/CBD acid synthase locus

Conclusions

  1. we can create an assay of new plants and figure out at seedling stage if we want or don’t want.

  2. Polyploidy will be the fastest way to improve grams per kilo dry wieght.

  3. Polyploidy will give the highest secondary plant compounds per gram.

  4. Pull out all your old work on how to use Colchicine, in your breeding operation.

With a gleefully heart happy new year

From the voices in my head
Ethan.

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More really important data in this paper. This shows the completeness of the map they are working with.

Here we see chromosome 6 and the distribution of the THC and CBD loci within the scaffolding.

This is critical in breeding

Genomic organization of cannabinoid pathway genes. 205

We next examined the positions of genes encoding known cannabinoid biosynthetic enzymes 206

on the chromosomes. With the exception of the functional copies of CBDAS and THCAS, which 207

are considered below, the cannabinoid-related genes are distributed in a mostly random fashion 208

across the genome (indicated in Supplemental Fig. 5). The new map also finds that C. sativa 209

encodes one copy of AAE1 (hexanoyl-CoA synthetase) and two tandem copies of tetraketide 210

synthase (“olivetol synthase”). The genome sequences of both PK and FN also contain the 211

THCAS-like gene described by Kojoma (Kojoma et al. 2006) which led to the two-locus 212

THCAS/CBDAS hypothesis. This THCAS-like gene is 96% identical to THCAS at the nucleotide 213

Cold Spring Harbor Laboratory Press on December 31, 2018 - Published by genome.cshlp.org Downloaded from

And the conclusion offers real hope and and opertunities to improve our selection criteria.

Cannabis and cannabinoids are increasingly employed in medicine, and recently have been 345

legalized for recreational use in many jurisdictions. The new map should facilitate vastly 346

improved genetic analysis, including QTL mapping, which will accelerate crop improvement 347

efforts. Drug prohibition has restricted access to cannabis by plant breeders and researchers, 348

and as a result it has received less attention than other crops. Cannabis suffers from insect 349

pests, widespread fungal diseases and has a number of agronomic issues such as flowering 350

time requirements that make it difficult to grow in some environments. In addition, breeding of 351

cannabis types with specific cannabinoid and terpene profiles is desirable for the development 352

of new varieties for medical and recreational use. The fact that a strong and interpretable result 353
was obtained by re-examining a previously described marker correlating with total cannabinoid 354

content (Weiblen et al. 2015) clearly shows the potential of this approach as it applies to 355

cannabinoid metabolism. Due to the relatively high rate of polymorphism in cannabis, it should 356

be possible to employ resequencing (e.g. low-coverage short-read Illumina protocols) on either 357

crosses or at a population level to associate variants or variation with traits and genes, using the 358

genetic map. 359

The next step is developing a simple method of analyzing F1 candidates by testing for the presence of precursor proteins. A pregnancy test for F1 plants that is non distructive. If we could test root hairs for the proteins. We know which plants are going to be CBD/CBD+THC/THC producers in a1:2:1 ratio. We can leverage this in better selection.

From the voices in my head.
Ethan.

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