I’m not sure when they started, I know it was a bit ago, but they’ve got reference genomes for Cannabis now. Maybe they arent available for business or they just didn’t know, but they are out there and improving with each version.
I’ve met some of the people who work at Phylos a few times at conventions and conferences, and they are super nice people and have been very generous to me in terms of freebies and sneak peeks so I’d love for them to do well.
I think part of their issue is also that the cannabis genome is a little fucked after years of amateur breeders making noise on the internet and flipping F1 hybrids with no consistency. Folks buy them then immediately cross them to their favorite hybrid then the cycle repeats.
I have a lot of interest in helping breeders achieve their goals bit it’s a long road to something that’s consistent.
I’m not sure why they didn’t start their process by genotyping IBLs and using a set of like 10 of those as their parent references. I assume cost is the answer, sequencing is much cheaper today than it was even 5 years ago.
Anyone have more background on Phylos here? Id be interested in talking with their science team to see where we could improve some of their processes and hear their original SOPs
Thank you all for those insights. This is consistent with my experiences in practice as well. One of my exercises is breeding backwards. I have been able to select backwards 3-5 generations back to the near exact likeness of prior parents skipping over and moving almost all dominant traits of both lines into recessive. Sometimes in one move, parental selection. There have been plants on opposite ends of the phylos galaxy that is positioned in contradiction to what has already been effective.
So to narrow my question further. Would whole genome mapping identified the 2 most extreme outliers in a population as having the exact same parents. I know it works very accurately on many other species, but what about with the plasticity of cannabis?
I could imagine it being very accurate with the population as a whole, but what about the outliers? I have had outliers so extreme that in 500 plants the 2 that would be placed on opposite ends based on all visible and metabolic traits actually share the same parents…Would whole genome mapping positively identify the parents in this most extreme example?
So that depends on what is being used to genotype. If you look at genes vital to life, so photosynthesis and reapiration genes, they tend to be conserved because of how important they are. A mutation here could be deadly. Genotyping those should be more accurate than a random approach.
Even for outliers, if your sequencing is deep enough (# of reads per sample, more means more data means stronger stats) you should be able to relate it back to the parent. The plasticity of Cannabis is mostly an environmental response, it may make phenotyping difficult for some traits, but the genetic part should still match.
I very much admire what they are trying to do. But I think the made some assumptions about the Cannabis genome that ended up not being true.
I am certain that I may have made many assumptions that are not true. But it has resulted in very uncommon results. Most breeding efforts seem to be working from or starting with uniformity rather than selecting outliers deeper into complexity. I do not think my practices would fit into a tradition academic approach. Lol, It might be almost the opposite.
Uniformity in Cannabis is pretty rare, even in hemp lines. Cannabis breeding is different from a lot of other ag and hort crops.
Seedlines these days are more like a snapshot of a population than a homogenous group of phenotypes. Its both a plus and a minus, makes pheno hunting and selection possible but also means you need to sprout many seeds which is costly in space and resources. Its because the community at large takes this year hot hybrid and cross it with last years hot hybrid to find next year’s hot hybrid. When you going hybrid to hybrid to hybrid to hybrid, you lose a lot of power to detect parents based on short reads alone
From my understanding, unless they’ve gone back and fully sequenced the lines they have, their entire database is virtually worthless due to their cheaping out by going with the shotgun approach.
I have no hope’s for their future. It’s all greed to my eyes with more patents soon to follow. Their own GMO work, etc. The future is open to them in numerous ways, none of which I see as good for the community nor the common grower
I understand that much well. It was more to illustrate that the last place an academic control group for research would be sought would be the haze lines I am familiar with.
I am enjoying learning about ploidy, but there is a lot I don’t understand. My experience is based on thorough documentation over generations and know very well that the greater the population that greater the comprehension and familiarity with the line. 100 plants is a threshold, but more is always going to give great insight.
Similarly It seems like 100 documented and developed natural occurrences of poloidy would give greater insights. Do you happen to know how many instances of naturally occuring poloidy in NLD or BLD have been identified and researched at this time?
Thats a very fair viewpoint on them. I did like that they told breeders their sequences represent IP for the breeder so it can’t be patented. Although genetic patents are complex and now more rules govern what you can do.
If you are interested in different ploidy levels, there is a lot of info in blueberries and strawberries and they are crazy ploidy. This will give you an idea of how ploidy effects growth and how it works broadly.
I have only recently gotten into reading about polyploid cannabis but don’t have much of an opinion yet. Im waiting to learn more before I make up my mind. That being said, I think it is more popular in hemp because you can get funding for genetic research pretty easily.
I read one article. Strawberry being an octoploid or something of that sort. I’m still learning. I invited another individual who has compiled a great deal of information on the subject. My impression is that it’s a very incomplete area of study with a relatively solid baseline. (Regarding cannabis)
Like the act of breeding itself. Our understanding is within the limits of 1000 plants. And then one plant changes all that preconception with new answers and new questions.
My friend and I were discussing ploidy and I copy pasted what I found to be a helpful introduction/primer on the subject He included visual aids, but I am not sure they will upload.
Hopefully he’ll find the time to join the discussion at some point *edited. I see the images did not load and will add them in later
Concerning 69 haze pedigrees, chromosome irregularity(aneuploid, polyploid, chimera) documented in landrace populations and the different forces at play when it comes to taking advantage of the extreme phenotypes produced by unbalanced genomes. and most importantly how these observations can be uncovered and put to use in a functional way to elevate diversity and "secondary potency " breeding targets.
first some science definitions to wrap our minds around what “polyploid” is all about
cannabis is a diploid with 20 chromosomes. its n number is 10 meaning each parent donates 10 chromosomes towards fathers pollen and mothers eggs. polyploids are all cannabis plants with a chromosome count other then 20.
most of the time, the count number increases in increments of the haploid number(10), so a tetraploid has 40(20 from each parent), a triploid 30 etc. increased poloidity increases cell size which offers numerous advantages in plant breeding.
however the most extreme phenotypes are produced by plants with abnormal chromsome counts that dont follow the haploid number-aneuploids… so any count outside of 20, 30, 40 50 etc is known as aneuploid. the most common form of aneuploid has 21 chromsomes is called a trisomic . each of the 10 parental chromsomes will create a different trisomic phenotype dependent on the genes located at the specific chromosome. these 10 phenotypes are refered to as karyotypes. here is an example using datura karyotypes it was the first plant trisomics to be discovered. there is also a link below with more in depth genetic information on polyploids if anyone wants more info https://s10.lite.msu.edu/res/msu/botonl/b_online/e12/12.htm
the aneuploids power thrives off of polymorphic strong textdosage sensitive traits this means when theres extra copies of a gene present it increases a pre cursor supply and increases the output of the gene. polymorphic means the strength operates on a scale of severity, rather then being present or absent.
terpenes are an example of a polymorphic trait, they depend on a precursor GPP . trisomics with GPP genes in their duplicated chromosomes have shown massive terpene increases one of the most exciting trisomics for cannabis would include the X chromosome. recently its been discovered that the cbg synthase genes are all located on the X. there are 3 seperate cbg synthases known as pt1, pt4 and pt7. there are significant differences in copy number of pt1 and pt4 when comparing hemp to drug type cannabis. its also likely that feminized/selfed seeds may have increased these copy numbers inadvertently . the cbg synthase genes control cannabinoid production levels and determine varin pre cursors as well.
heres a chart of chromosome numbers and the different synthase enzymes located on each
aneuploids in the wild are caused by unreduced gametes in male pollen. normally male pollen will have the haploid number of 10 chromosomes. however in extreme enviorments meoitic errors can lead to pollen having 20 chromosomes- double the normal amount!
this double pollen creates triploids(tetraploid x diploid=triploid). if we are after unbalanced dosage sensitive traits this is a best case scenario. when triploids breed with each other or with a normal diploid many aneuploids are created. the chromosome pairs cant evenly divide because there are 2 poles but 3 sets to divide. a chain reaction occurs when different ploidity pollen comes into an area. triploids, aneuploids and tetraploids will be created as a result. this is known as an aneuploid swarm.
where are wild cannabis aneuploids found? the cold high altitude deserts, kashmir, lahu, spiti, himchal pradesh down to uttakarhand is a massive center of diversity with several documented polyploid populations.
the official list of polyploid/aneuploid landrace cannabis marked in the map below
tetraploid cold desert darcha india
triploid male uttakarhand
aneuploids/cyto chimeras-
himchal pradesh-shimla, kullu, malana and mardan pakistan
the high altitude cold desert is an anthropogenic press for polyploids. the harsh enviorment of high altitude and no moisture means larger cell size is very advantageous. here in chamba a wild tetraploid population is found. this area is also located right in the intersection of xinjiang wild plants and the beginning of the charas hashplants. xinjiang basal plants have been linked as the founder for the entire northern pakistan/kashmir/afghan pool.
this map shows the xinjiang basal area seperated by ladakh pass(where we find tetraploid) then the marked areas in himchal pradesh are documented aneuploid populations found in shimla , kullu and malana. this is ground zero for the ancestral hashish trade. yarkand/hotan is home to the chinese muslim minority ugyhurs and has been known since ancient times for hashish. more recently in 2019 when the basal cannabis pool xinjiang plants are identified as an important group. but these plants while drug type have low total cannabinoids around 3 percent. and yet across the ladakh pass and into kashmir(polyploid zone) all of sudden theres a wealth of diversity and above all extreme potency in himchal pradesh etc. this area in india has served as a resevoir for the earliest ganja cultivars taken down from the high altitude mountains and domesticated. it appears to be a chain reaction of basal chinese plants from xinijiang being introduced into the cold desert of inda/pakistan and then shaking all the way down to south india and beyond.
marked 3 in uttakarhand is the triploid male found during most recent ploidity research paper. this survey identified areas in the major drug producing regions with significantly larger flow cytology scores.
to help identify possible aneuploids in haze populations, learning the visual characteristics of landrace types has allowed stoneguru to recognize the incredible potential of aneuploids. lets take a look at the identifiers from the research. cold desert tetraploids
the populations with less then 100 percent viable pollen signals aneuploids within the population along with the tetraploids from darcha, kullu khoksar manali and trilokinath populations
aneuploids from shimla and lahu
here are some pictures of various aneuploids found in the above populations
malana valley sterile aneuploid/triploid
mardan pakistan aneuploids
the journey begins and ends with nevils cannabis castle 1 to 1 haze pedigree breeding program. after purchasing entire lot of the oldest haze seeds sam had collected nevil ended up with 7 germinated haze plants of the earliest filial generations late 60s- from which the 2 males A and C would rise and change cannabis breeding forever. and then in 2010 nev was kind enough to return to mr nice and download his entire breeding program, pedigree records with the public which culimated witth the grail thread and subsequent work with kangativa. ultimatly before he died nevil would perfect outback haze. with the intention of adding more of the buddha lowland leathery spicy thai to the best nevils haze females out of 50 from 97.
mutant plants have always been prevalent in haze, but when karma brought a5 back into the community and piffcoast farm pulled back the curtain on nyc piff clones it became clear that haze A especially has significant abnormalities in nearly all of his progeny. and since ace was nice enough to terpene test all of the old holland cuts and after 2 years of piffcon tests the terpenes and cannabinoids responsible for that incense church in the air and relationships between copy number of haze A and C lines and the mutant phenotypes they coorelate with.
the first verified high flow cytology 69 haze progeny grown by markus in the dankness of mr nice was u2 which uses the a/c male from shanti -(a5 x skunk C) . marcus noted fused cotyledons, ecotopic trichomes and a faciated hypocotyl.
double 69 haze f1s produce a high volume of transgressive phenotypes. while the test doesnt tell us which chromosome # is the extra, but the math works out to 21 chromosomes in this aneuploid making it trisomic(1 chromsome has an extra copy)
heres an induced tetraploid from a breeder on BB we see the same type ecotopic trichomes
stones close eye for important observation and believing in the breeding power of these unbalanced genomes has taught me so much. there are other factors which could influence these lovely haze mutants . right now alot of research is being done on the clavata/wus stem cell mutants which could be induced by aneuploidity or an additional meristem mutation. i hope this helped out!
Thanks to B! I’ll insert the images later. My processes and perspectives are more a convergence of art, philosophy with the methodology and discipline of science. Only light research outside of developing tech and applicable tools for my goals. This is all fascinating at a whole new level for me😄.
Here is some more useful material sourced by @CocoaCoir
It’s really exciting indeed. I had found a mutation in '95 seed from TSB. I had called them traits rather than mutation. When I started sharing my work it started to be referred to as mutation.
In ~30 years of growing in numbers and spending way to much time looking online I had never seen another plant remotely like what I had until I started finding the traits/mutations again ~25y later and developing the accessions. The one above is fascinating. My germination rate might be under 15%. I had not looked at the pollen under a scope to find out if it is irregular pollen grain size. This is another one of the potential indicators of ploidy.
Another theory/observation about natural occuring ploidy (if it is). It’s presence can come and go in the life cycles of the plant, but further it can be amplified or completely buried in successive generations(regarding visual indicators) . This would mean the potential could be there in commonly known cultivars and no one would even realize it. The right recombination can also exploit this.
I am currently testing this theory out on a cultivar with no clear signs of visual mutations in the line. However, A trai that I associate with mutation is in the parental lines. When I crossed it to the Alpine genetics it exploded this recessive trait that I associate with mutation many times over.
I am still testing all of these makes out and documenting. Regardless of what is determined it adds to the knowledge base. Art and chaos are the domain of creation, the domain of science is to isolate, put into context and craft the tools of reproducing and bringing order out of chaos and art into science.
Another thing about the 5haze we had back then. 4 of are still alive. All still in the industry in various ways. Traveled the world and none have ever found terpenes or cannabinoid level on par in over 30 yrs since. Turned it all to LaCroix. A hint o real haze there. Or as one friend says. They are all empty. Chasing one target ever since
Assumption based on observation is still a part of the scientific process and then it’s up to you to prove your assumptions that are based off your observations. Wouldn’t your assumptions be the basis of a hypothesis? People that shit on the observation process arent understanding the importance of it. When it comes to things that haven’t been studied long term all we can do is observe, assume and then prove it to be either right or wrong. so either way it’s a process that still yields scientific results. The term watch and learn comes to mind. I for one like your findings and find them very interesting. Cheers
@GreenHighland as a scientist I can confirm the importance of observation. Assumptions are just things we do to make experiments easier or we change as new information is gained. When there isn’t a lot of info available, as long as your assumptions are logical your conclusion can still be valid.
I also think a key factor that is confused when people talk about science (scientists and non-scientists alike) is that science isn’t trying to, now can it, prove anything. At it’s heart, science is a quest for truth, and they way it should be taught, explained, and practiced is that science experiments are performed to falsify, not prove, hypotheses. If we can’t falsify it with experiments, we have to accept that is closer to the truth.
@GreenHighland and the @ThePotanist . Very well said both of you. Some of this progression on the subject of ploidy has certainly been humbling and insightful for me. My projects were referenced quite a bit in the context of mutation and I had incorporated it into my descriptions without having completed due diligence or research into it myself.
My daughter is entering graduate school for plant breeding and molecular biology and started conversing with one of her professor’s who took an interest. I expect the ploidy topic on these particular genetics will be answered at some point this season.
I also want to reiterate that ploidy is not the value or objective for why I incorporated the visual markers/mutations.
When NLD/equatorials are crossed to BLD it can be relatively easy to identify, differentiate and organize documentation of observable visual traits from F2 on. The problem is that BLD metabolics as represented through cannabinoids and terpenes overtake the novel profiles and effects of the equatorials and it becomes mottled. The market has attempted this for decades and it has always fallen short by the standards of equatorial efficiandos.
I do not have a botany background, but most of my life has been spent in the gardens and observing the natural world. What I do have is the experience of many years working with thousands of plants from common background though many fgen and accessions. I have recorded and observed the holistic dynamics and patterns over time to the point that it is almost intuitive. Predictive outcomes or even how to bring parents 3+ gen back to dominance. Profile and all visual markers in a single move. I am just now learning more about how and why.
So. My objective was to accurately document and breed equatorials. It is why I reverse males. To gain and record information about trichomes field density, pistils, profiles that it is actually imparting rather than guess by leaf shape or structure… previously It was extremely difficult and often inaccurate to observe the crossings of haze and equatorials. The Silk S was an extreme NLD/equatorial haze having a mutation like swarm of uncommon traits. Roots would grow right through the hardened trunk 6" above soil, petioles exploding with mutations…what’s fascinating is there is even correlations between which type of petiole mutation and profile (generally/line specific). Nodes that appear half way up the stem with no fan leaf, variegation etc.
To me ploidy is a nominal value relative to adding and compounding the observable traits and interrelationships for breeding purposes. It is really exciting and there are many patterns and correlations that were not previously perceivable. The challenge is that it also compounds complexity.
With greater complexity it becomes more important to consider holistic patterns and dynamics without the resources to quantify 100’s or thousands of cultivars. This is what makes it an art for all of us. All documentation the same. Are you an ENFJ or an INTP? Did you make your final selection at breakfast or dinner? Was it sunny or cloudy?
I listened to a world renowned perfumer recently. She makes custom fragrant for clients. Invariably their favorite changes over time. Even the base essences she uses. Something they would not know or comprehend. They all are different at different stages of our development.
Aside from selection hierarchy and the discipline of documentation my own personal selection criteria has more to do with the practice and philosophy of rope dart than breeding. Playing off the variable, adaptation, anchor points, tension. Being in the flow state and dance of dynamic energy rather than a rigid apparatus of it. Just as sure. Our perspective shapes reality itself once we participate.
This particular work. nigerian haze. has numerous mutation on both the Silk and 5haze side. I have numerous hypothesis of what may occur through selecting an outlier throwback like Alpine 1.0 back into it’s ancestory…we will see
“When tillage of the earth begins, other arts follow”. Daniel Webster
“Though I am but an old man, I am a young gardener”. Thomas Jefferson
Super interesting stuff. My meds are wearing off and I am having a hard time reading through this right now, as much as I want to and find it very interesting my ADHD is having none of it. Ill have to come back later and do a read of this thread…
I am not a long time cannabis grower, less than a decade, and I have seen quite a few of the mutations or traits you have described. Not on one plant but I have encountered trichome stems, stem roots, leafs that have a little bud at the centre. I do feel lucky that I went straight to good sativas quickly in my grow journey from some very knowledgeable people over at IC imparting some of their tastes in cannabis on me.
Sorry if I missed it earlier but what is the ultimate goal of this Alpine Haze work? Are you trying to isolate a specific pheno within the NJ Silk for smell or specific cannabinoids? Or just trying to mix NLDs to find a grail which checks all boxes?
