Mind of a Breeder.

This thread is for me to get all my crazy thoughts out of my head and into real life so I can reference them, add resources and utilize them in my attempts at breeding superior strains of cannabis.

Normally im all for free exchange of info, sharing and all that jazz but I kind of want to keep this thread clear of chatter and banter so myself and others can use it as a resource and not a conversation thread so please dont hack it! if you wanna talk about anything in the thread please PM me or start a new thread with that as the topic. anyway, thanks for checking it out, Enjoy!

Relationship Between Gameness in Dogs, Psychoactive Potency of Cannabisand Yield + Outcrossing Brainstorm



Starting a new project in the coming year and I came across this excerpt which is entirely anecdotal and offers mostly speculative conclusions based on observation. even though its not 100% rock solid science it still brings up some very valid points

1) Game dog breeders have noticed when 2 superior game tested animals from distinct lines are bred most of the resulting pups are often curs (high degree)

2)Outcrossing to distantly related lines seems to mitigate this negative consequence

3)Often times the traits we covet are those that are the most extreme and in many instances recessive or made up of a combination of recessive traits that can easily be masked or blocked entirely rather than creating heterosis as is often the goal of an outcross. (cant breed based just off what is observable [phenotype])

4)Initial crosses may not yield the desired outcome, however, this is not to say that the cross was completely unsuccessful or that the traits your after have disappeared. Inbreeding will bring out the recessive traits and from there individuals that carry all your after in regards to recessives. (note: only a very small percentage [maybe less than 25%] of individuals produced from such a full sib F1 to F2 breeding will carry the desired recessive traits, the majority will still be undesirable)

5) Finding a combination of unrelated individuals that will produce superior offspring from an outcross IS possible


interpretation of information and data.
Why?


Heritability of traits- (relationship of gameness and potency)
I often compare gameness, potency and yield because they are all quantitative traits that are highly desirable.



Qualitative Vs. Quantitative Vs. Threshold

very simple explanation of qual vs quant
basically qualitative traits are YES, NO and quantitative have to be measured


Qualitative [cannabis]
(flower color, leaf color, leaf shape, flower shape,

Quantitative [cannabis]
(potency, yield, height,

Threshold

• 
  A threshold trait is a trait, which is inherited quantitatively, but is expressed qualitatively. Normally a lot of genes form the basis of a threshold trait, which is why it should be treated as a quantitative trait.

• 
  A common characteristic of threshold traits and Mendelian traits is that they occur family wise.

• 
  When dealing with diseases with low population frequency it is not possible to differentiate between a Mendelian inherited disease and a threshold disease. In both cases the frequency of the disease will be much higher in close relatives of an affected animal, than the frequency in the population.

• 
  The distinction between the two forms of inheritance can only be based on test mating, in which the exact segregation ratio for Mendelian inherited diseases can be predicted. This is not the case for threshold diseases.

Or in other words (threshold)

Quantitative traits that are discretely expressed in a limited number of phenotypes (usually two), but which are based on an assumed continuous distribution of factors that contribute to the trait (underlying liability).






Heterosis (A.K.A) Hybrid Vigor


Backcrossing (bro science Vs. reality)

Backcrossing (stoner science vs. reality)

I will often refer to maize, triticale/wheat, tomatoes and hemp when discussing genetics because maize has the same number of chromosomes and many other similarities with cannabis, hemp IS cannabis, triticale/wheat because so much research exists on it and tomatoes because I like them



Backcrossing is a crossing of a hybrid with one of its parents or an individual genetically similar to its parent, in order to achieve offspring with a genetic identity which is closer to that of the parent.

BC not BX- Backcrossed hybrids are sometimes described with acronym "BC", for example, an F1 hybrid crossed with one of its parents (or a genetically similar individual) can be termed a BC1 hybrid, and a further cross of the BC1 hybrid to the same parent (or a genetically similar individual) produces a BC2 hybrid.

Continuous Backcrossing to Transfer Prolificacy to a Single-Eared Inbred Line of Maize1

1. D. N. Duvick2

Abstract
The prolificacy of C103, an inbred line of maize (Zea mays L.), was increased by crossing it to a highly prolific popcorn, backcrossing four times to the inbred with selection in each backcross population for signs of the incompletely recessive prolific trait, and then selfing to homozygosity while selecting for prolificacy. When three selections of the converted inbred were compared to the original in hybrid combinations at three rates of planting, they were more prolific but not higher yielding than the original inbred at low rates; and had less silk delay, were much less barren, and were much higher yielding than the original at high rates. These results agree with the hypothesis that prolific germplasm tends to reduce barrenness at high planting rates. They also demonstrate that continuous backcrossing can be used for rapid transfer of a quantitative trait, such as prolificacy, from exotic to adapted strains.


What do we take from this?
note that :
1) the P1 used to backcross to is an IBL and Homozygous for desired traits (most likely)
2) selections in each backcrossed population towards the recessive trait being backcrossed into the IBL
3) 1 trait was selected for IBL integration not a bunch at once
4) selfed to homozygosity
5)backcrossing is an effective tool for rapid transfer of a QUANTITATIVE trait from exotic to adapted strains


Due to the nature of meiosis, in which chromosomes derived from each parent are randomly shuffled and assigned to each nascent gamete, the percentage of genetic material deriving from either cell-line will vary between offspring of a single crossing but will have an expected value. The genotype of each member of offspring may be assessed to choose not only an individual that carries the desired genetic trait, but also the minimum percentage of genetic material from the original stem cell line.


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Introgression, also known as introgressive hybridization, in genetics is the movement of a gene (gene flow) from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species. Purposeful introgression is a long-term process; it may take many hybrid generations before the backcrossing occurs.

Introgression differs from simple hybridization. Introgression results in a complex mixture of parental genes, while simple hybridization results in a more uniform mixture, which in the first generation will be an even mix of two parental species. Natural introgression does not have human direct interference while the exotic introgression is induced intentionally (as for instance genetically modified organisms[clarification needed]) or not (human activities affecting local races of crops or human disturbances such as by introducing weeds).


An introgression line (IL) is a crop species that contains genetic material artificially derived from a wild relative population through repeated backcrossing. An example of a collection of ILs (called an IL-Library) is the use of chromosome segments from Lycopersicon pennellii (a wild variety of tomato) that was introgressed into Lycopersicum esculentu (a variety of cultivated tomato). The lines of an IL-library usually cover the complete genome of the donor. Introgression lines allow the study of quantitative trait loci, but also the creation of new varieties by introducing exotic traits.

What do we take from this?
does this mean that Lowryder #1 is condidered an introgression line?
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Germplasm
Germplasm is living tissue from which new plants can be grown. It can be a seed or another plant part – a leaf, a piece of stem, pollen or even just a few cells that can be turned into a whole plant. Germplasm contains the information for a species’ genetic makeup, a valuable natural resource of plant diversity.

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The development of lettuce backcross inbred lines (BILs) for exploitation of the Lactuca saligna (wild lettuce) germplasm.

https://www.ncbi.nlm.nih.gov/pubmed/15103409


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Inbred Backcross (IBC) Lines and Populations

Author:

Matthew Robbins, The Ohio State University

This module provides visual and written explanations of inbred backcross population development, characteristics of inbred backcross populations, and examples of the method's use from the scientific literature. Inbred backcross populations can be used to identify genetic factors that underlie quantitative traits and are developed in a two-stage process of backcrossing then inbreeding.
Introduction
The inbred backcross (IBC) population was proposed by Wehrhahn and Allard (1965) as a way of identifying genes or quantitative trait loci (QTL) that contribute to a quantitatively inherited trait. This is accomplished by developing a population that collectively contains most of the genome of a donor parent, divided among each individual line in the population. The majority of the genome of each line is from the recurrent parent, with a small portion from the donor parent. IBC breeding has also been employed for the introgression of exotic germplasm to improve quantitative traits in crop plants. This method has been utilized in bean, oilseed rape, rice , cucumber and tomato for classical breeding and QTL studies.

Development of an IBC Population
The first stage of generating an IBC population (Fig. 1, steps 1–3) is similar to generating a backcross breeding population. One distinction is that many individuals are backcrossed to the recurrent parent to generate an IBC population. The second stage (Fig. 1, step 4) is similar to single-seed descent to generate recombinant inbred lines (RILs).

1. An inbred donor parent is crossed to an inbred recurrent parent to produce an F1, which is fully heterozygous.
2. The F1 is backcrossed to the recurrent parent to generate the BC1.
3. A large number of BC1 individuals are backcrossed to the recurrent parent to generate the BC2 generation. Seed is saved from each individual. Each line is backcrossed to the recurrent parent for several generations. The total number of backcross generations, including the BC1 generation, is called k.
4. Individuals in the BCk population are self-pollinated until they reach homozygosity (usually five or more generations) using the single-seed descent method. The IBC population consists of all of the individual backcross-inbred lines.

Figure 1. Schematic illustrating the development of an inbred backcross (IBC) population. Figure credit: Matthew Robbins, The Ohio State University.

An important consideration in creating an IBC population is the number of backcrossing generations. More backcrossing ensures that the IBC lines will be more like the recurrent parent, since the percentage of the genome from donor parent is reduced by half with each generation of backcrossing (see article on backcrossing). However, the probability of recovering the genes from the donor parent is reduced by half each generation due to the backcrossing process. The probability of recovering the gene(s) from the donor parent is (1/2)k+1 for a single gene and (1/2)2k+2 for two unlinked genes.

Advantages of an IBC Population

• An immortal population. Each line in an IBC population is inbred and can be propagated simply by self-pollination.
• The population can be replicated. Since each entry of the population is a line and not an individual, traits can be measured on a plot basis rather than an individual plant basis. This allows the population to be evaluated in multiple environments over years, which increases the precision of trait measurements.
• A breeding friendly population. Since the majority of the genome of each entry in an IBC population is from the recurrent parent, which is typically an elite line, IBC lines can directly be used in crosses with minimal germplasm improvement.
• Mapping quantitative traits. The structure of IBC populations makes them a good population for mapping quantitative traits using single factor analysis.
• Simultaneous discovery and introgression. Quantitative traits can be mapped and introgressed in the same population.

Disadvantages of an IBC Population

• Time. Developing an IBC population requires a minimum of eight generations (Fig. 1).
• Limited ability to study epistatic interactions. Since only a small part of the donor genome is represented in each line, it is difficult to study the interaction of multiple, unlinked genes from the donor parent.
• Not amenable to some QTL mapping methods. Because the structure of an IBC population is not a simple segregating population, the algorithms of the majority of QTL mapping software are not designed to work with this population type. It is not practical to use interval or composite interval mapping methods on an IBC population.

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to summarize
1) backcross to elite homozygous individuals not heteros
2) if you want to capture a hetero elite, self her

related backcrossing info:

Backcrossing wild tomatoes
http://onlinelibrary.wiley.com/doi/10.1111/tpj.13194/full

Mouse strain, line classification etc.
http://www.informatics.jax.org/silver/chapters/3-2.shtml

Fantastic overview of Backcrossing
http://passel.unl.edu/pages/printinformationmodule.php?idinformationmodule=959723462

Strains: A strain is a partially reproductive isolated group of organisms. A strain generally differs from some other strain in the mean response for some trait. A very amorphous term. A new strain of Drosophila, for example, might be established by collected a few flies from the wild and allowing then to interbreed. Might also be called a line, a stock or a variety.

Isofemale line: Common in Drosophila. A single gravid female is collected from the wild. Her progeny are allowed to interbreed. This line will be partially inbred since it will be founded with a the genes from a single female and from as few a one male.

Inbred strain: An Inbred strain is one that is homozygous at every locus and the alleles at each locus are identical by descent.

Inbred strains take 20 generations of brother-sister matings to achieve. Starting with a single ancestral breeding pair, a brother and sister are chosen each generation. Alternatively, inbred lines can be established by mating offspring back to a parent in a regular pattern. Occasionally, other systems of inbreeding might be used but a line cannot be considered inbred until it reaches an inbreeding coefficient equal to 20 generations of brother sister matings (99% or better). Inbred lines generations are often designated as F generations (F3, F10, F20 etc.)

Substrain: Two inbred lines from a common origin may be considered substrains. This implies that the substrains differ at several loci. If two inbred lines are separated before 40 generations of inbreeding, there will still be enough heterozygosity (less than 1% of the genes would vary) at separation that two genetically different substrains could result.

Alternatively, genetic variation between the branches may have occur by mutation and genetic drift. If the variation is at a single locus this would be a coisogenic line (see below). If it is at several loci, it is a substrain. Finally, if variation between isolated branches of an inbred line can be demonstrated (per haps my microsatellite analyses) they the branches can be considered substrains.

Recombinant inbred (RI) strains are formed by crossing two inbred strains to make an F1 generation. Brother and sister pairs from this F1 generation are used to establish many different inbred lines. These RI lines require 20 or more generations of brother-sister matings.

The RI lines are started from a limited genetic pool. The original inbred lines differed at a number of loci. The RI lines differ at an intermediate number of loci when compared to the progenitor strains.

RI strains are designated by an abbreviation of both parental strain names separated by a capital X. For example, CXB, are recombinant inbred strains derived from a cross of BALB/c x C57BL.

Congenic Strains: The idea is to obtain strains that differ by only a few specified genes (ideally by a single gene). Usually, two inbred lines are crossed to make an F1 generation (here, however, it will be called an N(1) - see below). The F1 progeny are backcrossed to one of the parental inbred lines. These N(2) progeny will now have 75% of their material derived from a single parental line. N(2) progeny are again backcrossed to the same parental line to make an N(3) generation, etc. It takes 10 generations of backcrossing for a line to be considered as congenic.

After 10 generations, the congenic line will differ from the parental line by the gene of interest and a short linked chromosomal segment around that gene.

Speed Congenics: It takes a minimum of 10 generations to get a congenic line. In mice, this is approximately 2.5 years. Speed congenics are an attempt to cut that time.

Speed Congenics are merely a variation on regular congenics. At generation N(2) individual mice (generally males) are genotyped for 60 to 100 microsatellite markers and the mice with the that have the greatest share of the inbred background chromosomes you are interested in are selected as parents. (Males are used since a single male can be backcrossed to many different Parental strain females). This processes may eventually be further accelerated by microarray screens.

The savings can be considerable. Speed congenic technology might give you a congenic strain in 12 to 18 months versus 2 to 3 years.

Coisogenic Strains: Two strains that are genetically identical (i.e. isogenic), except for a single locus. This occurs most often by a spontaneous mutations by many generations of backcrossing. Coisogenic strains are also becoming available due to target mutagenesis (knock-outs) in Embryonic Stem cells (ES). For example, a target mutation is induced in an inbred strain (e.g. 129SV) and the mutant mice are backcrossed repeatedly to the same inbred substrain from which the ES cells were derived would be a coisogenic line. but the possibility of mutations elsewhere should be considered. Similarly, chemically or radiation induced mutants in an inbred background can be considered coisogenic (but only if other mutations are not present).

Recombinant Congenic (RC) A combination of congenic and inbred lines. Two inbred lines are crossed to form an F1. The F1 progeny are backcrossed to one of the parent lines for Strains are formed by crossing two inbred strains, followed by a few (usually two) backcrosses to one of the parental strains (the "background" strain), with subsequent inbreeding without selection for specific. Such a strain is developed by crossing male C57BL/6J mice with BALB/c females, followed by repeated backcrossing of female offspring to male C57BL/6J.

As with congenic strains, a minimum of 10 backcross generations is required, counting the F1 generation as generation 1. For full inbred status, however, you need 20 inbred generation equivalents

One generation of backcrossing is equivalent to two generations of brother-sister matings. Thus, a strain with one backcross [N(2)] is equivalent to a strain with 4 generations of inbreeding F4. For full inbred status, it would require an addition 16 generations of brother sister matings.

Segregating inbred strains: are developed by inbreeding with but one or more loci must remain heterozygous. This generally requires progeny screening each generation and selection of heterozygous parents.

As with any inbred strains it takes 20 generations of brother sister mating. These lines are designated as FH lines to distinguish them from homozygous inbred lines.

Consomic strains are produced by repeated backcrossing of a whole chromosome such as the X or Y chromosome onto an inbred strain. As with congenic strains, a minimum of 10 backcross generations is required.

Two strains A and B are crossed. In the cross A x B the F1 male progeny would have their X chromosome from the A strain and the Y chromosome from the B strain. The autosomes are from both strains. With repeated backcrossing to the A you will obtain a line of animals that have all A-strain autosomes, A-strain X-chromosome and B strain Y-chromosome. Similar methods can be used to get X chromosomes into different backgrounds

The strains are designated as host stain - chromosome (X or Y) and the donor stain. In the example above, this strain would be A-YB

http://ko.cwru.edu/info/breeding_strategies_manual.pdf

breeding strategies for lab mice

would like to recreate this side byside when my strain is developed enough.



Heterosis, hybrid vigor, or outbreeding enhancement, is the improved or increased function of any biological quality in a hybrid offspring. The adjective derived from heterosis is heterotic.

An offspring exhibits heterosis if its traits are enhanced as a result of mixing the genetic contributions of its parents. These effects can be due to Mendelian or non-Mendelian inheritance.


In proposing the term heterosis to replace the older term heterozygosis, G.H. Shull aimed to avoid limiting the term to the effects that can be explained by heterozygosity in Mendelian inheritance.[1]

The physiological vigor of an organism as manifested in its rapidity of growth, its height and general robustness, is positively correlated with the degree of dissimilarity in the gametes by whose union the organism was formed … The more numerous the differences between the uniting gametes — at least within certain limits — the greater on the whole is the amount of stimulation … These differences need not be Mendelian in their inheritance … To avoid the implication that all the genotypic differences which stimulate cell-division, growth and other physiological activities of an organism are Mendelian in their inheritance and also to gain brevity of expression I suggest … that the word 'heterosis' be adopted.

Heterosis is often discussed as the opposite of inbreeding depression although differences in these two concepts can be seen in evolutionary considerations such as the role of genetic variation or the effects of genetic drift in small populations on these concepts. Inbreeding depression occurs when related parents have children with traits that negatively influence their fitness largely due to homozygosity. In such instances, outcrossing should result in heterosis.

Not all outcrosses result in heterosis. For example, when a hybrid inherits traits from its parents that are not fully compatible, fitness can be reduced. This is a form of outbreeding depression. An increase in hybrid vigour called heterosis.

When a population is small or inbred, it tends to lose genetic diversity. Inbreeding depression is the loss of fitness due to loss of genetic diversity. Inbred strains tend to be homozygous for recessive alleles that are mildly harmful (or produce a trait that is undesirable from the standpoint of the breeder). Heterosis or hybrid vigor, on the other hand, is the tendency of outbred strains to exceed both inbred parents in fitness.

Selective breeding of plants and animals, including hybridization, began long before there was an understanding of underlying scientific principles. In the early 20th century, after Mendel's laws came to be understood and accepted, geneticists undertook to explain the superior vigor of many plant hybrids. Two competing hypotheses, which are not mutually exclusive, were developed:[3]

• Dominance hypothesis. The dominance hypothesis attributes the superiority of hybrids to the suppression of undesirable recessive alleles from one parent by dominant alleles from the other. It attributes the poor performance of inbred strains to loss of genetic diversity, with the strains becoming purely homozygous at many loci. The dominance hypothesis was first expressed in 1908 by the geneticist Charles Davenport.[4]
• Overdominance hypothesis. Certain combinations of alleles that can be obtained by crossing two inbred strains are advantageous in the heterozygote. The overdominance hypothesis attributes the heterozygote advantage to the survival of many alleles that are recessive and harmful in homozygotes. It attributes the poor performance of inbred strains to a high percentage of these harmful recessives. The overdominance hypothesis was developed independently by Edward M. East (190[5] and George Shull (190.[6]

Dominance and overdominance have different consequences for the gene expression profile of the individuals. If over-dominance is the main cause for the fitness advantages of heterosis, then there should be an over-expression of certain genes in the heterozygous offspring compared to the homozygous parents. On the other hand, if dominance is the cause, fewer genes should be under-expressed in the heterozygous offspring compared to the parents. Furthermore, for any given gene, the expression should be comparable to the one observed in the fitter of the two parents.



The term heterosis often causes confusion and even controversy, particularly in selective breeding of domestic animals, because it is sometimes (incorrectly) claimed that all crossbred plants and animals are "genetically superior" to their parents, due to heterosis

1)not all hybrids exhibit heterosis
2)"genetic superiority" is an ill-defined term and not generally accepted terminology within the scientific field of genetics

add:A related term fitness is well defined, but it can rarely be directly measured. Instead, scientists use objective, measurable quantities, such as the number of seeds a plant produces, the germination rate of a seed, or the percentage of organisms that survive to reproductive age.[9] From this perspective, crossbred plants and animals exhibiting heterosis may have "superior" traits, but this does not necessarily equate to any evidence of outright "genetic superiority". Use of the term "superiority" is commonplace for example in crop breeding, where it is well understood to mean a better-yielding, more robust plant for agriculture. Such a plant may yield better on a farm, but would likely struggle to survive in the wild, making this use open to misinterpretation. In human genetics any question of "genetic superiority" is even more problematic due to the historical and political implications of any such claim. Some may even go as far as to describe it as a questionable value judgement in the realm of politics, not science.[8]
https://en.wikipedia.org/wiki/Heterosis#cite_note-Risch-8
https://en.wikipedia.org/wiki/Heterosis#cite_note-Risch-8
An example of the ambiguous value judgements imposed on hybrids and hybrid vigor is the mule. While mules are almost always infertile, they are valued for a combination of hardiness and temperament that is different from either of their horse or donkey parents. While these qualities may make them "superior" for particular uses by humans, the infertility issue implies that these animals would most likely become extinct without the intervention of humans through animal husbandry, making them "inferior" in terms of natural selection.




related info:
90 Years Ago: The Beginning of Hybrid Maize
http://www.genetics.org/content/148/3/923


Mendelian Genetics

Heritability is a statistic used in breeding and genetics works that estimates how much variation in a phenotypic trait in a population is due to genetic variation among individuals in that population.[1] Other causes of measured variation in a trait are characterized as environmental factors, including measurement error. In human studies of heritability these are often apportioned into factors from "shared environment" and "non-shared environment" based on whether they tend to result in persons brought up in the same household more or less similar to persons who were not.

Heritability is estimated by comparing individual phenotypic variation among related individuals in a population. Heritability is an important concept in quantitative genetics, particularly in selective breeding and behavior genetics


heritability can change without any genetic change occurring, such as when the environment starts contributing to more variation. A case in point, consider that both genes and environment have the potential to influence intelligence. Heritability could increase if genetic variation increases, causing individuals to show more phenotypic variation, like showing different levels of intelligence. On the other hand, heritability might also increase if the environmental variation decreases, causing individuals to show less phenotypic variation, like showing more similar levels of intelligence.

Always remember that heritability is a characteristic of a particular population in a particular environment. When either of these changes, your estimate becomes less reliable.
Heritability in its widest sense is by definition the relation of genetic variance to phenotypic variance. Both are population parameters, depending thus on the variability of the given genotypes and that of the environment. It approaches zero with increasing genetic uniformity and 1 with decreasing environmental variability and is thus valid only for the given entries within the given environment.

The extent of dependence of phenotype on environment can also be a function of the genes involved. Matters of heritability are complicated because genes may canalize a phenotype, making its expression almost inevitable in all occurring environments. Individuals with the same genotype can also exhibit different phenotypes through a mechanism called phenotypic plasticity, which makes heritability difficult to measure in some cases.

Estimating heritability

heritability must be estimated from the similarities observed in subjects varying in their level of genetic or environmental similarity.

Heritability estimates are often misinterpreted if it is not understood that they refer to the proportion of variation among individuals on a trait that is the result of genetic factors. It does not indicate the degree of genetic influence on the development of a trait of an individual. For example, it is incorrect to say that since the heritability of personality traits is about .6, that means that 60% of your personality is inherited from your parents and 40% comes from the environment.

Heritability estimates are often misinterpreted if it is not understood that they refer to the proportion of variation among individuals on a trait that is the result of genetic factors. It does not indicate the degree of genetic influence on the development of a trait of an individual. For example, it is incorrect to say that since the heritability of personality traits is about .6, that means that 60% of your personality is inherited from your parents and 40% comes from the environment.

Even a highly heritable trait (such as eye color) assumes environmental inputs which are required for development: for instance temperatures and an atmosphere supporting life, etc. A more useful distinction than "nature vs. nurture" is "obligate vs. facultative"

(Obligate:
restricted to a particular function or mode of life.
"an obligate intracellular parasite")
(Facultative:
occurring optionally in response to circumstances rather than by nature.
"prison-style, facultative homosexuality")

Heritability of a trait
The most basic question to be asked about a quantitative trait is whether the observed variation in the character is influenced by genes at all. It is important to note that this is not the same as asking whether genes play any role in the character’s development. Gene-mediated developmental processes lie at the base of every character, but variation from individual to individual is not necessarily the result of genetic variation. Thus, the possibility of speaking any language at all depends critically on the structures of the central nervous system as well as of the vocal cords, tongue, mouth, and ears, which depend in turn on the nature of the human genome. There is no environment in which cows will speak. But, although the particular language that is spoken by humans varies from nation to nation, that variation is totally nongenetic.


high value of low heritability

http://web.altagenetics.com/us/DairyBasics/Details/10347_The-high-value-of-low-heritability.html

Heritability of behavioral traits
http://blogs.discovermagazine.com/gnxp/2012/06/heritability-of-behavioral-traits/#.WExeWX2Sxdw

Phenotypic plasticity is the ability of an organism to change its phenotype in response to changes in the environment.
https://en.wikipedia.org/wiki/Phenotypic_plasticity

Canalisation (or canalization) is a measure of the ability of a population to produce the same phenotype regardless of variability of its environment or genotype
https://en.wikipedia.org/wiki/Canalisation_(genetics)

http://psych.colorado.edu/~carey/hgss/hgssapplets/heritability/heritability.intro.html

Estimation methods
(To be continued... )

Sex Determination in Cannabis
http://link.springer.com/article/10.1007/BF00226975

Why is the hermi aka intersex trait(s) so hard to purge from a line? has anyone ever created a 100% intersex free strain aka truly dioeceous.

Identification of DNA markers linked to the male sex in dioecious hemp (Cannabis sativa L.)

ABSTRACT:
A 400-bp RAPD marker generated by a primer of random decamer sequence has been found associated with the male sex phenotype in 14 dioecious cultivars and accessions of hemp (Cannabis sativa L.). The primer OPA8 generates a set of bands, most of which polymorphic among all the individual plants tested, and 1 of which, named OPA8400, present in all male plants and absent in female plants. A screening of 167 plants belonging to different genotypes for the association of the OPA8400 marker with the sex phenotype revealed that only in 3 cases was the 400-bp band was present in plants phenotypically female; on the contrary, in male plants the band was never missing, while in monoecious plants it was never present. Despite this sex-specific association, the sequences corresponding to OPA8400 were present in both staminate and carpellate plants, as revealed by Southern blotting and hybridization with the cloned RAPD band. The RAPD marker was sequenced, and specific primers were constructed. These primers generated, on the same genotypes used for RAPD analysis, a SCAR marker 390 bp in length and male-specific. This SCAR is suitable for a precise, early and rapid identification of male plants during breeding programs of dioecious and monoecious hemp.

http://link.springer.com/article/10.1007/s001220051043


Plant sex determination and sex chromosomes

Sex determination systems in plants have evolved many times from hermaphroditic ancestors (including monoecious plants with separate male and female flowers on the same individual), and sex chromosome systems have arisen several times in flowering plant evolution. Consistent with theoretical models for the evolutionary transition from hermaphroditism to monoecy, multiple sex determining genes are involved, including male-sterility and female-sterility factors. The requirement that recombination should be rare between these different loci is probably the chief reason for the genetic degeneration of Y chromosomes. Theories for Y chromosome degeneration are reviewed in the light of recent results from genes on plant sex chromosomes.

http://www.nature.com/hdy/journal/v88/n2/abs/6800016a.html


Dioecy occurs in approximately 7% of flowering plant species , among which only a small number of species have cytogenetic and/or molecular evidence for sex chromosomes. In contrast to animals, where dioecism is often accompanied by sex chromosome dimorphism, cytogenetically distinguishable sex chromosomes have been reported only in 19 species, in 16 angiosperm families . Sex chromosomes are thought to have evolved independently in plants many times, suggesting a recent origin of sex chromosome dimorphism in many plants

Many male-specific DNA markers have been identified in C. sativa
despite recent progress in C. sativa genome sequencing and genomics , we know little about its sex chromosome structure apart from the basic karyotype information outlined above

(fantastic article!!!!)
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085118

Sex-linked AFLP markers indicate a pseudoautosomal region in hemp (Cannabis sativa L.)
http://link.springer.com/article/10.1007/s00122-003-1212-5

The pseudoautosomal regions get their name because any genes within them (so far at least 29 have been found)[5] are inherited just like any autosomal genes.
https://en.wikipedia.org/wiki/Pseudoautosomal_region

An autosome is a chromosome that is not an allosome (a sex chromosome).[1] Autosomes appear in pairs whose members have the same form but differ from other pairs in a diploid cell, whereas members of an allosome pair may differ from one another and thereby determine sex.
https://en.wikipedia.org/wiki/Autosome

results indicate that the Y chromosome, especially in its long arm, specifically differentiates in Cannabis sativa and might contribute to the sex determination.
https://www.jstage.jst.go.jp/article/cytologia1929/63/4/63_4_459/_article

The Mechanism of Sex Determination in Dioecious Flowering Plants
http://www.sciencedirect.com/science/article/pii/S0065266008601637

(support for a solid male?)
https://www.thieme-connect.com/products/ejournals/html/10.1055/s-2001-17735

(meh)
http://pcp.oxfordjournals.org/content/36/8/1549.short
Mendelian Genetics

SAM SKUNKMAN on eliminating intersex traits from inbred populations of cannabis
Of course you can reduce intersex in any population. Use big plant numbers and only use the least intersex as parents. Intersex is not dominate, early males do not express intersex more then late males. Using STS to self a female will help show if a single clone has intersex traits as they will be expressed in progeny and then you can avoid them and the parent. It will take 4-5 years to come up with an intersex free line or a population that hardly expresses intersex. Most varieties have some individuals with intersex traits, some like Thai are notoriously intersex, but with work you can breed away from them, try and use intersex free, test any females with stress tests or by selfing the plant and growing the progeny, or both. Avoid using anything intersex, as intersex begets intersex. With South African Durban Poison I used the least intersex the first few years, then intersex free for several years, to create the intersex free population, not 100% but almost.... The first year they were all intersexed to some degree.
-SamS
https://www.icmag.com/ic/showthread.php?t=324406&page=3

Canalisation (genetics)

Canalisation (or canalization) is a measure of the ability of a population to produce the same phenotype regardless of variability of its environment or genotype. In other words, it means robustness.

Genetic assimilation
Waddington used the concept of canalisation to explain his experiments on genetic assimilation. In these experiments, he exposed Drosophila pupae to heat shock. This environmental disturbance caused some flies to develop a crossveinless phenotype. He then selected for crossveinless. Eventually, the crossveinless phenotype appeared even without heat shock. Through this process of genetic assimilation, an environmentally induced phenotype had become inherited. Waddington explained this as the formation of a new canal in the epigenetic landscape.

It is, however, possible to explain genetic assimilation using only quantitative genetics and a threshold model, with no reference to the concept of canalisation. However, theoretical models that incorporate a complex genotype-phenotype map have found evidence for the evolution of phenotypic robustness contributing to genetic assimilation, even when selection is only for developmental stability and not for a particular phenotype, and so the quantitative genetics models do not apply. These studies suggest that the canalisation heuristic may still be useful, beyond the more simple concept of robustness.

Neither canalisation nor robustness are simple quantities to quantify


Evolutionary capacitance
The canalisation metaphor suggests that phenotypes are very robust to small perturbations, for which development does not exit the canal, and rapidly returns down, with little effect on the final outcome of development. But perturbations whose magnitude exceeds a certain threshold will break out of the canal, moving the developmental process into uncharted territory. Strong robustness up to a limit, with little robustness beyond, is a pattern that could increase evolvability in a fluctuating environment. Genetic canalisation could allow for evolutionary capacitance, where genetic diversity outside the canal accumulates in a population over time, sheltered from natural selection because it does not normally affect phenotypes. This hidden diversity could then be unleashed by extreme changes in the environment or by molecular switches, releasing previously cryptic genetic variation that can then contribute to a rapid burst of evolution

Evolutionary capacitance(contd)
Evolutionary capacitance is the storage and release of variation, just as electric capacitors store and release charge. Living systems are robust to mutations. This means that living systems accumulate genetic variation without the variation having a phenotypic effect. But when the system is disturbed (perhaps by stress), robustness breaks down, and the variation has phenotypic effects and is subject to the full force of natural selection. An evolutionary capacitor is a molecular switch mechanism that can "toggle" genetic variation between hidden and revealed states. If some subset of newly revealed variation is adaptive, it becomes fixed by genetic assimilation. After that, the rest of variation, most of which is presumably deleterious, can be switched off, leaving the population with a newly evolved advantageous trait, but no long-term handicap. For evolutionary capacitance to increase evolvability in this way, the switching rate should not be faster than the timescale of genetic assimilation.

This mechanism would allow for rapid adaptation to new environmental conditions. Switching rates may be a function of stress, making genetic variation more likely to affect the phenotype at times when it is most likely to be useful for adaptation. In addition, strongly deleterious variation may be purged while in a partially cryptic state, so cryptic variation that remains is more likely to be adaptive than random mutations are. Capacitance can help cross "valleys" in the fitness landscape, where a combination of two mutations would be beneficial, even though each is deleterious on its own.

There is currently no consensus about the extent to which capacitance might contribute to evolution in natural populations.

Switches that turn robustness to phenotypic rather than genetic variation on and off do not fit the capacitance analogy, as their presence does not cause variation to accumulate over time. They have instead been called phenotypic stabilizers

How breeding the best to the best can be worse
10/15/2014




by Carol Beuchat PhD

An interesting study was just published about the genetics of behavior in the Belgian Malinois (Cao et al 2014). This is a working breed used in some of the same service environments as the German Shepherd Dog (e.g., military, security, etc), so behavior is important to the breed's function. Malinois that perform well, with good drive and initiative for work, tend to exhibit a circling behavior when in confined spaces, which is a form of obsessive-compulsive behavior. Dogs that do not display the circling behavior, and those that have very high levels of circling behavior, don't perform as well.
It turns out that a gene (Cadherin 2, CDH2; or genes in the same genomic block), that has been linked to obsessive-compulsive behavior in both Dobermans and humans might also be involved in the manifestation of these degrees of working and circling behavior in Malinois, from non-existant to extreme. Maintaining the most useful, moderate behavior in the Belgian Malinois is an example of something called "balancing selection", in which the heterozygous condition (e.g., Aa) is advantageous over either homozygous condition (AA or aa). (This is also referred to as "overdominance".) This means that breeding two dogs that are great working dogs and heterozygous won't produce better dogs, because some of the offspring will lack the drive and initiative to be good working dogs (AA), while others will have a double-dose of the CDH2 gene and be too high-strung to be useful. Because the best dogs will be heterozygous, selection tends to favor the gene combination that is the best combination of advantageous (good worker) and disadvantageous (moderate circling).

You might be familiar with other examples of overdominance in dogs. For example in the Whippet, dogs with one copy of a mutated allele of the myostatin gene (which is involved in muscle function) are significantly faster than dogs with the normal gene, but dogs with two copies of the gene are over-muscled (Mosher et al 2007). One again, the heteroygous condition is superior to either of the homozygous options.
One more interesting example is the ridge of the Rhodesian Ridgeback, which is caused by a dominant mutation (Hillbertz et al 2007). Dogs without the mutation don't have the ridge, and dogs with one copy of the mutation have the breed-typical dorsal ridge. However, dogs with two copies of the gene are predisposed to a congenital developmental disorder called dermoid sinus. Dogs without ridges are generally excluded from breeding because this is considered to be a fault, as are those with dermoid sinus. So again, the genotype resulting in the preferred phenotype is the heterozygous condition. But breeding two heterozygous dogs will result not in a litter with better ridges, but some offspring with ridges, some without, and probably some that are afflicted with dermoid sinus. (This is a simple Punnett square problem.)

These are three examples where assuming that breeding "best-to-best" will not result in "even better" because of failure to understand the underlying genetics. In fact, it can result in removing a dog from the gene pool for a genetic issue (e.g., a Malinois with extreme circling), when in fact breeding that dog to the appropriate mate (e.g., a homozygous dog with low drive) would result in heterozygous offspring that could have the perfect blend of motivation and self-control. Likewise, using Ridgebacks without ridges will produce some offspring without ridges, but it also will not produce pups with dermoid sinus.

With so many breeds facing a growing list of genetic issues as a result of the continued loss of genetic diversity, it is especially imprudent to remove dogs from the gene pool that could be used to produce offspring with the desired genotype (that is, heterozygous for the gene of interest) without the collateral damage of pups with unacceptable phenotypes.

• Cao X, DM Irwin, Y-H Liu, L-G Cheng, L Wang, G-D Want, & Y-P Zhang. 2014 Balancing selection on CDH2 may be related to the behavioral features of the Belgian Malinois. PLos ONE 9(10): e110075. (pdf)

• Hillbertz NHCS, M Isaksson, EK Karlsson, E Hellmen, et al 2007 Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs. Nature Genetics 39(11): 1318-1320.

• Mosher DS, P Quignon, CD Bustamante, NB Sutter, CS Mellersh, et al. 2007 A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs. PLoS Genetics 3: 779-786. (pdf)