Population Genetics "Conservation of allele frequencies"

[acespicoli]

A de Finetti diagram. The curved line is the expected Hardy–Weinberg frequency as a function of p.

A de Finetti diagram is a ternary plot used in population genetics. It is named after the Italian statistician Bruno de Finetti (1906–1985) and is used to graph the genotype frequencies of populations, where there are two alleles and the population is diploid. It is based on an equilateral triangle, and Viviani's theorem: the sum of the perpendicular distances from any interior point to the sides of said triangle is a constant equal to the length of the triangle's altitude.

Example: Autosomal dominant trait​

The diagram shows the inheritance of freckles in a family. The allele for freckles (F) is dominant to the allele for no freckles (f).
At the top of the pedigree is a grandmother (individual I-2) who has freckles. Two of her three children have the trait (individuals II-3 and II-5) and three of her grandchildren have the trait (individuals III-3, III-4, and III-5).
[What is the genotype of individual I-2?]

Example: X-linked recessive trait​

The diagram shows the inheritance of colorblindness in a family. Colorblindness is a recessive and X-linked trait (Xb)(X�). The allele for normal vision is dominant and is represented by XBX�.
In generation I, neither parent has the trait, but one of their children (II-3) is colorblind. Because there are unaffected parents that have affected offspring, it can be assumed that the trait is recessive. In addition, the trait appears to affect males more than females (in this case, exclusively males are affected), suggesting that the trait may be X-linked.

6.2: Pedigrees review

bio.libretexts.org

By analyzing a pedigree, we can determine genotypes, identify phenotypes, and predict how a trait will be passed on in the future. The information from a pedigree makes it possible to determine how certain alleles are inherited: whether they are dominant, recessive, autosomal, or sex-linked.

SNP 1	SNP 2	SNP 3	SNP 4	SNP 5	SNP 6	SNP 7	SNP 8
Sample 1	0	1	0	0	0	0	1	0
Sample 2	1	0	1	0	0	0	1	0
Sample 3	0	1	1	0	0	1	0	0
Sample 4	0	0	0	0	1	0	1	1
Sample 5	0	0	1	0	0	0	1	0
Sample 6	0	0	0	1	0	1	1	0
Total	1	2	3	1	1	2	5	1

In population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum,
is the distribution of the allele frequencies of a given set of loci (often SNPs) in a population or sample.

Allele frequency spectrum - Wikipedia

en.wikipedia.org

Table 1 Statistics, population genetic metrics and main chemotypes for inferred clusters K1-K5
Full size table
Fig. 1

Neighbour-joining tree. Showing the relative phylogenetic location of the 420 cannabis accessions typed at 23 single nucleotide polymorphisms (SNP). Discriminant analysis of principal component (DAPC) clusters are shown with K1-K5 represented by different colors. K1-K4 are resin type cannabis and K5 is the fiber type cannabis or hemp. Colored dotted circles highlight individuals assigned differently between the neighbor-joining tree and DAPC clusters. Type-III plants are shown with a dotted black circle and type-II plants are shown with dotted grey circle
Full size image
Fig. 2


Discriminant analysis of principal component (DAPC) scatterplot. Showing the relative location of each individual sample in two dimensional space, overlaid by a minimum spanning tree calculated from the squared distance between individual to represent the phylogenetic relationship between inferred clusters. K5, hemp or “ruderalis” appears ancestral and the most differentiated group, followed by K4, terpinolene dominant resin accessions. The genetic distance between groups (Fst) is indicated on the respective branches of the minimum spanning tree
https://jcannabisresearch.biomedcentral.com/articles/10.1186/s42238-020-00036-y/figures/2
J Cannabis Res
. 2020 Sep 11;2:26. doi: 10.1186/s42238-020-00036-y

A single nucleotide polymorphism assay sheds light on the extent and distribution of genetic diversity,​

population structure and functional basis of key traits in cultivated north American cannabis​

 

[Mate Dave]

Daves kinda Busy.. He's in his 3rd country this year laying the pipe on the 14th Feb after planting on a full moon. All legal.. Spent last night on the beach casting spells on the beach chanting having a fire collecting ashes and drinking Rum.

You need enough males for the allelel distributions. You can't grow cannabis wild without a few runs at acclmatizing it and you probably want some haploids and the mother and the males ..

Basil genovese has to have 217 plants as those are needed for the traits fir it to be such.. All cannabis is outcrossing unless made not to do.. Haploids..

My latest project thread is a carry on from an idea 20 years ago i have with a member in PM but using a education now and I think we need males.. Less females and males. Depending on the goal of the line and the side to be used in a cross. out of 100 females I'd probably select 10 and have 3 favatouts but one can't say without walking the fields what you'll find in any frequency using Algebra. You can only use what's there so if there is 1 male in 10.000.000 if you can get tthat many in Morocco that's all you can use

 

[Mate Dave]

What ever you use to drive evolution, push the frequency in your favour make sure they're good

 

[acespicoli]

In population genetics, the Hardy–Weinberg principle, also known as the Hardy–Weinberg equilibrium, model, theorem, or law, states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences.

These influences include

• genetic drift,
• mate choice,
• assortative mating,
• natural selection,
• sexual selection,
• mutation,
• gene flow,
• meiotic drive,
• genetic hitchhiking,
• population bottleneck,
• founder effect,
• inbreeding
• outbreeding depression.

Minimum viable population size​

Main article: Minimum viable population
In conservation biology, minimum viable population (MVP) size helps to determine the effective population size when a population is at risk for extinction.[5][6] The effects of a population bottleneck often depend on the number of individuals remaining after the bottleneck and how that compares to the minimum viable population size.

Founder effects​

Main article: Founder effect
A slightly different form of bottleneck can occur if a small group becomes reproductively (e.g., geographically) separated from the main population, such as through a founder event, e.g., if a few members of a species successfully colonize a new isolated island, or from small captive breeding programs such as animals at a zoo. Alternatively, invasive species can undergo population bottlenecks through founder events when introduced into their invaded range.[7]

Distribution of fitness effects (DFE)

Fixation index - Wikipedia

en.wikipedia.org

Web PopGen

Note: Inbreeding has been disabled while a program bug is identified.

Chapter 6: Population Genetics – Crop Genetics

iastate.pressbooks.pub

Chapter 8: Inheritance of Quantitative Traits – Crop Genetics

iastate.pressbooks.pub

Ecol Evol
. 2023 Mar 28;13(3):e9926. doi: 10.1002/ece3.9926

A review on Q ST – F ST comparisons of seed plants: Insights for conservation​

 

[acespicoli]

Deviations from Hardy–Weinberg equilibrium​

The seven assumptions underlying Hardy–Weinberg equilibrium are as follows:[3]

• organisms are diploid
• only sexual reproduction occurs
• generations are nonoverlapping
• mating is random
• population size is infinitely large
• allele frequencies are equal in the sexes
• there is no migration, gene flow, admixture, mutation or selection

Violations of the Hardy–Weinberg assumptions can cause deviations from expectation. How this affects the population depends on the assumptions that are violated.

• Random mating. The HWP states the population will have the given genotypic frequencies (called Hardy–Weinberg proportions) after a single generation of random mating within the population. When the random mating assumption is violated, the population will not have Hardy–Weinberg proportions. A common cause of non-random mating is inbreeding, which causes an increase in homozygosity for all genes.

If a population violates one of the following four assumptions, the population may continue to have Hardy–Weinberg proportions each generation, but the allele frequencies will change over time.

• Selection, in general, causes allele frequencies to change, often quite rapidly. While directional selection eventually leads to the loss of all alleles except the favored one (unless one allele is dominant, in which case recessive alleles can survive at low frequencies), some forms of selection, such as balancing selection, lead to equilibrium without loss of alleles.
• Mutation will have a very subtle effect on allele frequencies through the introduction of new allele into a population. Mutation rates are of the order 10−4 to 10−8, and the change in allele frequency will be, at most, the same order. Recurrent mutation will maintain alleles in the population, even if there is strong selection against them.
• Migration genetically links two or more populations together. In general, allele frequencies will become more homogeneous among the populations. Some models for migration inherently include nonrandom mating (Wahlund effect, for example). For those models, the Hardy–Weinberg proportions will normally not be valid.
• Small population size can cause a random change in allele frequencies. This is due to a sampling effect, and is called genetic drift. Sampling effects are most important when the allele is present in a small number of copies.

In real world genotype data, deviations from Hardy–Weinberg Equilibrium may be a sign of genotyping error.[4][5][6]

 

[acespicoli]

Genetics
. 2005 Jan;169(1):1–7. doi: 10.1093/genetics/169.1.1

The Limits of Theoretical Population Genetics​

infinitely large...

 

[nepalnt21]

You say we are not creators only stewards ?

Atomic gardening - Wikipedia

en.wikipedia.org

jhc, that is insane! i love it.

5 acre plots, plants arranged around a radiation source... the ones in the middle were completely toasted to hades, wow what a technique.

sorta like the less specific, cody's lab version of colchicine i guess?

man, i need a bunker and a "retractable radiation source" to make good weed? dang it!

 

[CharlesU Farley]

Genetics
. 2005 Jan;169(1):1–7. doi: 10.1093/genetics/169.1.1

The Limits of Theoretical Population Genetics​

infinitely large...

Keep 'em coming Ace, don't have the time to read 'em now but have them bookmarked.

Is that Mentor thing new? You know me, I'm a dinosaur and can't remember shit but if it is new, congratulations you _certainly_ earned it.

 

[acespicoli]

Keep 'em coming Ace, don't have the time to read 'em now but have them bookmarked.

Is that Mentor thing new? You know me, I'm a dinosaur and can't remember shit but if it is new, congratulations you _certainly_ earned it.

@CharlesU Farley It is faily a new thing im still trying to get used to https://www.icmag.com/threads/news-regarding-mentors-and-new-mentor-starting-today.18133207/
The short story is im just going to keep doing what im already doing, admittedly now I feel more obligated to being an accountable member and to remaining humble
CRS STRONG you and me both.

Owe alot of it to members here and a big thanks to Gypsy and IC staff, Thanks man

 

[acespicoli]

Allele frequencies can be expressed as a decimal or as a percent and always add up to 1, or 100 percent, of the total population. For example, in a sample population of humans, the frequency of the IA allele might be 0.26, which would mean that 26% of the chromosomes in that population carry the IA allele. If we also know that the frequency of the IB allele in this population is 0.14, then the frequency of the i allele is 0.6, which we obtain by subtracting all the known allele frequencies from 1 (thus: 1 – 0.26 – 0.14 = 0.6). A change in any of these allele frequencies over time would constitute evolution in the population.

 

[acespicoli]

Nucleotide diversity and population divergence across the four groups.
Values in parentheses represent measures of nucleotide diversity (π) for the group,
and values between pairs indicate population divergence (FST).

Principal component analysis (PCA) with the first two principal components,
based on genome-wide SNP data. Colors correspond to the phylogenetic tree grouping.

 

[acespicoli]

Below the three plot schemes are the gene models in the genomic regions.
Below each gene model are the SNP allele distributions
along each of the four genes for the two groups (green, heterozygous site; orange, homozygous site of reference allele; blue, homozygous site of alternative allele; gray, missing data).

***
There are gaps in the data ...

 

[PetePrice]

The Punnett square is a visual representation of Mendelian inheritance, a fundamental concept in genetics discovered by Gregor Mendel.[10] For multiple traits, using the "forked-line method" is typically much easier than the Punnett square. Phenotypes may be predicted with at least better-than-chance accuracy using a Punnett square, but the phenotype that may appear in the presence of a given genotype can in some instances be influenced by many other factors, as when polygenic inheritance and/or epigenetics are at work.
View attachment 19150804
For example, using 'A' as the representative character for each allele, a homozygous dominant pair's genotype would be depicted as 'AA', while homozygous recessive is shown as 'aa'.

Punnett square - Wikipedia

en.wikipedia.org

A single trait Punnett Square tracks two alleles for each parent. The square has two rows and two columns. Adding more traits increases the size of the Punnett Square.

The PS is really only useful if narrowing down, ie really useful when going through selfed lots.

"(should I make hybrids? what would happen to my keeper freq?)
Ok first things first, how many plants do I need to maintain the pure THCAS gene that presents at lets say 3% which is 3/100 ?
We want the complete active THCAS and the inactivating CBDAS"

Well we know P and Q = 1

• Frequency of AA (p^2) = 0.97^2 = 0.9409
• Frequency of Aa (2pq) = 2 * 0.97* 0.03 = 0.0582
• Frequency of aa (q^2) = 0.03^2 = 0.0009

This gives us the allele frequency required and you'd put that in the Hardy-Weinburg equilibrium calc to give you the gene freq assuming all things equal etc so of top of my head if you grew out a thousand roughly you'd get about 4 of the plants you're after assuming you captured them at the start.
(id check my maths though)

 

[acespicoli]

four genes influence drug type vs hemp type, THCAS vs CBDAS maybe this is enough ?

Our genome-wide analyses corroborate the existing archaeobotanical, archaeological, and historical record [reviewed in (5, 6, 31–33)] and provide a detailed picture of the domestication of Cannabis and its consequences on the genetic makeup of the species. Our genomic dating suggests that early domesticated ancestors of hemp and drug types diverged from Basal cannabis ~12,000 years B.P. (95% confidence interval: 6458 to 15,728 years B.P.; Fig. 2BOpens in image viewer and table S3), indicating that the species had already been domesticated by early Neolithic times.

Consistent with this history, our model shows a gradual increase in the Ne of hemp and drug types. On the basis of both demographic and phylogenetic analyses, we propose that early domesticated Cannabis was first used as a primarily multipurpose crop until ~4000 years B.P., before undergoing strong divergent selection for increased fiber or drug production.

 

[acespicoli]

The PS is really only useful if narrowing down, ie really useful when going through selfed lots.

"(should I make hybrids? what would happen to my keeper freq?)
Ok first things first, how many plants do I need to maintain the pure THCAS gene that presents at lets say 3% which is 3/100 ?
We want the complete active THCAS and the inactivating CBDAS"

Well we know P and Q = 1

• Frequency of AA (p^2) = 0.97^2 = 0.9409
• Frequency of Aa (2pq) = 2 * 0.97* 0.03 = 0.0582
• Frequency of aa (q^2) = 0.03^2 = 0.0009

This gives us the allele frequency required and you'd put that in the Hardy-Weinburg equilibrium calc to give you the gene freq assuming all things equal etc so of top of my head if you grew out a thousand roughly you'd get about 4 of the plants you're after assuming you captured them at the start.
(id check my maths though)

I had posted before reading your post, nice because it clearly shows were on the almost exact same page
In a drug type cultivar id expect 90% +/- of the population to express the fully functional THCAS gene and also the CBDAS inactive gene

 

[Genghis Kush.]

View attachment 19151184
A de Finetti diagram. The curved line is the expected Hardy–Weinberg frequency as a function of p.

A de Finetti diagram is a ternary plot used in population genetics. It is named after the Italian statistician Bruno de Finetti (1906–1985) and is used to graph the genotype frequencies of populations, where there are two alleles and the population is diploid. It is based on an equilateral triangle, and Viviani's theorem: the sum of the perpendicular distances from any interior point to the sides of said triangle is a constant equal to the length of the triangle's altitude.

Example: Autosomal dominant trait​

The diagram shows the inheritance of freckles in a family. The allele for freckles (F) is dominant to the allele for no freckles (f).
At the top of the pedigree is a grandmother (individual I-2) who has freckles. Two of her three children have the trait (individuals II-3 and II-5) and three of her grandchildren have the trait (individuals III-3, III-4, and III-5).
[What is the genotype of individual I-2?]

Example: X-linked recessive trait​

The diagram shows the inheritance of colorblindness in a family. Colorblindness is a recessive and X-linked trait (Xb)(X�). The allele for normal vision is dominant and is represented by XBX�.
In generation I, neither parent has the trait, but one of their children (II-3) is colorblind. Because there are unaffected parents that have affected offspring, it can be assumed that the trait is recessive. In addition, the trait appears to affect males more than females (in this case, exclusively males are affected), suggesting that the trait may be X-linked.

6.2: Pedigrees review

bio.libretexts.org

By analyzing a pedigree, we can determine genotypes, identify phenotypes, and predict how a trait will be passed on in the future. The information from a pedigree makes it possible to determine how certain alleles are inherited: whether they are dominant, recessive, autosomal, or sex-linked.

SNP 1	SNP 2	SNP 3	SNP 4	SNP 5	SNP 6	SNP 7	SNP 8
Sample 1	0	1	0	0	0	0	1	0
Sample 2	1	0	1	0	0	0	1	0
Sample 3	0	1	1	0	0	1	0	0
Sample 4	0	0	0	0	1	0	1	1
Sample 5	0	0	1	0	0	0	1	0
Sample 6	0	0	0	1	0	1	1	0
Total	1	2	3	1	1	2	5	1

In population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum,
is the distribution of the allele frequencies of a given set of loci (often SNPs) in a population or sample.

Allele frequency spectrum - Wikipedia

en.wikipedia.org

Table 1 Statistics, population genetic metrics and main chemotypes for inferred clusters K1-K5
Full size table
Fig. 1

Neighbour-joining tree. Showing the relative phylogenetic location of the 420 cannabis accessions typed at 23 single nucleotide polymorphisms (SNP). Discriminant analysis of principal component (DAPC) clusters are shown with K1-K5 represented by different colors. K1-K4 are resin type cannabis and K5 is the fiber type cannabis or hemp. Colored dotted circles highlight individuals assigned differently between the neighbor-joining tree and DAPC clusters. Type-III plants are shown with a dotted black circle and type-II plants are shown with dotted grey circle
Full size image
Fig. 2


Discriminant analysis of principal component (DAPC) scatterplot. Showing the relative location of each individual sample in two dimensional space, overlaid by a minimum spanning tree calculated from the squared distance between individual to represent the phylogenetic relationship between inferred clusters. K5, hemp or “ruderalis” appears ancestral and the most differentiated group, followed by K4, terpinolene dominant resin accessions. The genetic distance between groups (Fst) is indicated on the respective branches of the minimum spanning tree
https://jcannabisresearch.biomedcentral.com/articles/10.1186/s42238-020-00036-y/figures/2
J Cannabis Res
. 2020 Sep 11;2:26. doi: 10.1186/s42238-020-00036-y

A single nucleotide polymorphism assay sheds light on the extent and distribution of genetic diversity,​

population structure and functional basis of key traits in cultivated north American cannabis​

The K2 cluster looks like it had been isolated more than the other resin clusters.
do you know anything about those samples? does the paper say where they were collected?

also , what does this mean?
" Type-III plants are shown with a dotted black circle and type-II plants are shown with dotted grey circle"
what are type 2 and 3 plants?

thank you

 

[CharlesU Farley]

also , what does this mean?
" Type-III plants are shown with a dotted black circle and type-II plants are shown with dotted grey circle"
what are type 2 and 3 plants?

I haven't read the complete article as I don't have time, but traditionally Type II plants are generally considered what most people call Indica (I _think_ RC Clark proposed to call them BLD for broad leaf drug) that are characteristically high in both THC and CBD. Type III plants are what most people call hemp, very low THC-variable CBD and I'm not sure how Clark categorizes these.

Type I are what most people consider Sativa, high THC - very little CBD referred to as NLD now I believe, and Type IV are a combination of Type I and Type 2, commonly called hybrids. I'm not sure how Clark describes these, because the leaf pattern can be variable, depending on the dominance of the parental units.

Again, I have not read the article and it may be referring to something else. I can't remember who originally came up with the Type designation but it makes perfect sense to me and I'm surprised it did not catch on.

 

[acespicoli]

Haze | Kannapedia

kannapedia.net

This chart represents the Illumina sequence coverage over the Bt/Bd allele. These are the three regions in the cannabis genome that impact THCA, CBDA, CBGA production. Coverage over the Active CBDAS gene is highly correlated with Type II and Type III plants as described by Etienne de Meijer.

Coverage over the THCA gene is highly correlated with Type I and Type II plants but is anti-correlated with Type III plants.
Type I plants require coverage over the inactive CBDA loci and no coverage over the Active CBDA gene. Lack of coverage over the Active CBDA and Active THCA allele are presumed to be Type IV plants (CBGA dominant).

While deletions of entire THCAS and CBDAS genes are the most common Bt:Bd alleles observed, it is possible to have plants with these genes where functional expression of the enzyme is disrupted by deactivating point mutations (Kojoma et al. 2006).

If you go to the link above and click on one of the "i" buttons it will show you many popular cuttings and their synthase genes, be cautious and keep a eye open for data entry errors
@Dime had previously pointed out a error and they have been contacted to correct it

The K2 cluster looks like it had been isolated more than the other resin clusters.
do you know anything about those samples? does the paper say where they were collected?

also , what does this mean?
" Type-III plants are shown with a dotted black circle and type-II plants are shown with dotted grey circle"
what are type 2 and 3 plants?

thank you

The above link and site data and web graphics explore in depth this topic better than words alone would explain it and Haze is an excellent example

Kojoma M, Seki H, Yoshida S, Muranaka T. DNA polymorphisms in the tetrahydrocannabinolic acid (THCA) synthase gene in "drug-type" and "fiber-type" Cannabis sativa L. Forensic Sci Int. 2006 Jun 2;159(2-3):132-40. doi: 10.1016/j.forsciint.2005.07.005. Epub 2005 Sep 6. PMID: 16143478.

Really get into the details on that site there is alot to take in
The other thing if your inclined to use the information is inheritance of the synthase genes

Schematic diagram of filial generations. Parental breeding lines were screened for cannabinoid composition and eight plants high in either FC3 as well as Ftricyclic or FC5 as well as Fdicyclic values served as parents for two biparental reciprocal crosses, generating four F1 hybrid families. A single male and female plant from the F1 hybrid family which demonstrated the highest level of FC3/FC5 homogeneity served as parents of an F2 population segregating for FC3/FC5 and Fdicyclic/Ftricyclic cannabinoid composition. C5 alkyl cannabinoid fraction (FC5); C3 alkyl cannabinoid fraction (FC3); dicyclic cannabinoid fraction (Fdicyclic); and tricyclic cannabinoid fraction (Ftricyclic).
https://www.nature.com/articles/s41598-019-47812-2/figures/1
Welling, M.T., Liu, L., Raymond, C.A. et al. Complex Patterns of Cannabinoid Alkyl Side-Chain Inheritance in Cannabis. Sci Rep 9, 11421 (2019). https://doi.org/10.1038/s41598-019-47812-2

Bt:Bd thcas
Plants (Basel)
. 2019 Nov 12;8(11):496. doi: 10.3390/plants8110496

 

[acespicoli]

Finally, highly reliable markers were identified, including the CBDAS deletion polymorphism and the 33 identified SNPs (the eight loci in the CBDAS gene and 25 loci in the THCAS gene). We refer to the associated score as (d). The score achieved an AUC of 100%, sensitivity of 100% (95% CI: 100.00–100.00%), and specificity of 100% (95% CI: 83.33–100.00%) at the zero threshold. A boxplot of CBD and THC percentages is shown in Figure 5 (p < 0.001). These markers were not previously described by other authors such as Kojoma [10] and Rotherham-Harbison [15]


As with other crop species, the domestication and diversification of Cannabis involved several complex steps, leading to a geographical radiation and the deliberate breeding of varieties involving selection on traits to maximize yield and quality (38). We applied an integrative approach (π, FST, and XP-CLR; see Materials and Methods) to identify candidate genes involved in divergence of hemp and drug types after their early domestication. The three approaches combined allowed us to identify a total of 510 candidate genes in hemp-type samples and 689 in drug-type samples, when compared to the Basal cannabis group, of which 253 are overlapping (fig. S9), while 134 and 472 genes are specific to hemp- and drug-improved cultivars, respectively, when compared to each other (tables S4 to S9). Several genes bearing signals of positive selection in hemp-type–improved cultivars are involved in inhibiting branch formation (e.g., D14 and KNAT1), associated with flowering time and photoperiodism (e.g., FLK and EHD3) and involved in cellulose and lignin biosynthesis (e.g., SS and SPS1). In drugs, we infer selection on genes promoting branch formation (e.g., NDL2 and DTX48), associated with flowering time (e.g., HUA2 and FPF1) and involved in lignin biosynthesis (e.g., CSE and C4H; Fig. 2, C and DOpens in image viewer, and tables S10 and S11). In addition, we also detected signals of positive selection in drug-type cultivars when compared to hemp-type cultivars on the gene HDR (tables S5 and S10) coding for the last enzyme in the methylerythritol phosphate pathway (producing essential substrates for cannabinoid biosynthesis) and which has been shown to be potentially associated with variance in total cannabinoid content [i.e., potency (18)]. These results are consistent with traits expected to have been affected by selection during domestication of C. sativa, i.e., leading to unbranched, tall hemp plants maximizing cellulose-rich/lignin-poor bast fibers in the stems versus well-branched, short marijuana plants with lignin-rich woody cores, maximizing flower and resin production (3, 39, 40).


There is a wealth of breeding knowledge in these articles

@Genghis Kush. Great idea to post it here
The K2 cluster looks like it had been isolated more than the other resin clusters.
do you know anything about those samples? does the paper say where they were collected?

A: from the supplemental files linked in the article



Table 1,10 have some interesting data

 

[PetePrice]

I had posted before reading your post, nice because it clearly shows were on the almost exact same page
In a drug type cultivar id expect 90% +/- of the population to express the fully functional THCAS gene and also the CBDAS inactive gene

Id expect so with the gene you'd be after being linked to allele Bt so in a pure drug type cannabis pool ie type 1/2 chemotype would be mostly represented with Bt/Bd and Bt/Bt but you'd be best to make sure you have Bt/Bt to make sure you have type 1 as you'll still be getting active CBDAS with type 2.
I've also seen it reported that a pseudogene gives a reading as if it's active that will give some false reports on that site .
I guess you could use the marker B1080/B1192 to find plants with THCSA if that was what someone was after or just isolate Bt.

That haze plant seems nice and Bt/Bt I guess but listed as Bt/Bd the Y ratio thing baffles me, I'll have to read on the site about the info etc