cannmed2016 molecular phylotyping of cannabis...14 ak47 recon felina322 uso312 diana2 carmagnola1...
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CannMed2016Molecular Phylotyping of Cannabis
Ryan Lynch PhD
Background
• Bacterial genomics since 2008
• Cannabis genomics since 2013, started in Nolan Kane’s Lab
• Medicinal Genomics scientist since late 2015
Cannabis diversity—phenotypic and genetic
What can we do with Cannabis DNA?
• Past, Present and Future
• Current efforts to unravel plant history– How many species?– ‘indica’ vs ‘sativa’? Hemp? ruderalis?
• Genetics of specific chemoprofiles of cannabinoids and terpenoids?
• Strain name issues– Is my OG Kush the real OG?
• Certifications set now
• Future prediction of traits from DNAseq– Custom strain development
DNA: genomes contain information about nearly all aspects of biology, even if we cannot yet interpret it.
≠Informationisnotknowledge:AlEinstein/FrankZappa
Step 1: Sample Collection
7
Restriction-siteassociatedDNAsequencing(RADseq)
http://www.floragenex.com/rad-seq/
Relatedness among strains--phylogenetics
Rootedv.Unrooted
The network of recent Cannabis breeding
https://www.icmag.com/ic/showthread.php?t=147494
MajorgroupsoftheCannabisFamilyTree(v3.1):
Lynchetal.GenomicandChemicalDiversityofCannabisNewPhytologist(2016)inrevieworpre-printisuponBioRxiv
Narrowleafletdrug typeI
Broadleafletdrug typeI
Narrowleafletdrug typeI
EuropeanHemp
=JackHererorJacksomething
11
Chemical Diversity of Genetic Groups
•Afterremovingtheindividualswithmissingvalues,wehadatotalof351individuals: 94BLDT,229NLDT,and28hemp.
Lynchetal.GenomicandChemicalDiversityofCannabisNewPhytologist (2016)inrevieworpre-printisuponBioRxiv
Scaling up with strainSEEKtm
• CO, CA, MA, ME, WA, Spain samples… so far• On average, our Rad seq protocol yields at least 10x
coverage of 625,000 sites of the current reference genome. These sites contain 25,000 to 30,000 informative single nucleotide polymorphisms (SNPs)
• This April will witness over 100,000 genetically certified METRC tracked products hit the CO market (~60 strains)
Kannapedia– TheDistributedConsensusonCannabisGenetics
• Optionalpublication toKannapedia• Allowspublishing of strainuser
comments/reviews• Allowspublicdistribution ofStrain
QRcode• Enablescommunityverificationof
strainqualities• Enablesratingsystemfordesired
qualities• Customerreviews• http://www.medicinalgenomics.co
m/kannapedia/
13Confidential
14
AK47
Recon
Felina322
USO312
Diana2
Carmagnola1
Monoica1Tygra1
Bialobreski1
Lovrin1
Ivory1
Ferimion1Santhica271
Fedora171Futura751
Dacia1
Tisza1
Mengm
a1Trainwreck
Otto
Ghost_Train_H
aze_X_Snow_Dog_TLE
Pineapple_tsu_EC
2nd_HarletTsu
Harlequin_Tsunam
i
CBD_Mango_H
aze
Critical_M
ass_EC
Cannatonic_E
C
Incredible_Power_E
C
ACDC2nd
Catatonic_ACDC_EC
Cannatonic
Bhutan_EC
CBDIACDC
Guerilla_Meds_EC
Moonshine_Haze124
Luvberry_EC
Pineapple_tsu2nd_EC
In_The_Pines
Landrace_Jamaican1_TLE
Space_Queen_TLE
Sierra_Gold
Arch_Angel_TLE
Green_Crack
Loven_Hope_EC
Blazin_GrapefruitGS
CXAK47Ha
rlequin_EC
Harlequin_TL
E
Green_
Crack_TLE
Critical_
Mass_T
LEDr_W
ho228
Purple_Ca
ndy_Cane
Cannatsu_TL
EDeath_S
tar_TLEKong_TLEBlue_Dream_TLE
Snoops_Dream
Blubonic_TLE
Cactus
Girl_Scout_Platinum
Dream_Beaver
CitriSoul_TLE
Banana_Kush_TLE
Charlie_Murphy_TLE
GrandDaddyPurple_ctrl2
Grand_Daddy_Purple_ctrl4
1988_Hash_Plant_TLE
Old_School_Blueberry_TLE
Unity_EC
Snowcap_TLE
Bubblegummer
Liberty_Haze_ctrl2
Liberty_Haze_ctrl
Lambs_Bread_TLEBreakthrough
Chernobyl
Harlet_Tsu
Northern_Lights
Cherry_Lim
eadeChocolope
Hash_P
lant_Puck_TLEAfghan_K
ush
Durban_TLE
Durban_P
oison_TLE
Super_Lemon_Haze_TLE
African_Haze_TLE
Lucky_Charms
NYC_Diesel
Girl_Scout_Cookies
Vitamin_CBD_EC
MangThai_Doo
Sugar_Cookies_TLE
White_Fire_TLE
Triangle_OG_TLE
Headband_TLE
Chemmy_Jones_TLE
Lemonhead_OG
El_Diablo_TLE
Face_Off_OG_TLE
Jesus_TLE
OG_Kush
Girl_Scout_Cookies_TLE
F-Cancer_EC
Trident_EC
Witches_W
eed_TL
E
Chedda
r_Head
Serious_H
appiness
GFU_x_Mr_
Nice_TLE
Sage-n-Sour
Corleone_Kush_T
LE
Bubba_Kush_TLE
Lemon_Skunk
0.01
strainSEEKTM Aprilupdate:sistersfromthesamemister?
=CBD:THCof2<31
Future Developments…
www.nationalgeographic.com
Summary
• DNA sequence analysis can tell you things about the plant (or plant microbial community) that are not otherwise apparent
• DNA data is an additional layer of information, not a substitute for other types of data like chemical analytics or patient responses.
• We have just scratched the surface of Cannabis potential as it produces at least 113 phytocannabinoids and at least 120 terpenoids, yet what is available on the market or for research today is quite limited!
MGC Acknowledgments
• KevinMcKernan• JeremyRualo• DouglasSmith• PeterDougherty• JessicaSpangler• YvonneHelbert• Wendall Orphe• LeiZhang• ChristinaSutera• AdrianDevitt-Lee• BenAmirault• JohnGeanacopoulos• Vasisht Tadigotla
17Confidential
DigiPath:CindyOrserGlenMarquez
TheListExchange:RobertoLopesino
OrrinDevinskyEricMarshRussel Saneto
UniversityofColorado:NolanKane
Kannapedia– TheDistributedConsensusonCannabisGenetics
19Confidential
MaleFemaleqPCR testing
• Worksona2nd Leaf• ProvidesXYanswer
inhours• $10/Test
20Confidential
Wholegenomeshotgunmethodfor43Cannabissamples
NolanKaneatworkonthefarm...
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