a basic look into genetics

in Breeding Sun Jan 19, 2014 7:09 pm
by sin inc | 101 Posts | 934 Points

hey fam i found this post while doing some research it might help some of the fam enjoy

by Padre Pokes CHB
So first and foremost a disclaimer: I'm not a genetics major, or professor, nor am I actively involved in the breeding of any plant or animal at the moment. Just a guy that has studied up on the subject enough to possibly shed some light on a confusing topic. You are welcome to disregard any information henceforth and assume I am full of it. If you have a piece of valuable, pertinent information feel free to post it. If you are a genetics student or professor and feel the verbage or information presented here is not good enough, . I am speaking in generalities to make the information listed comprehendable by novice growers and breeders, not to provide geneticists an encyclopedic reference on the subject. Textbooks have been written thoroughly covering the subject already.

Now we can get started,

Again this is a generalized explanation to keep things (kinda) simple.
Genetics is, in its basic form, a study of genes and how they interact. Genes are the basic units of heredity, coming in bundles called chromosomes. Genes come in pairs and are arranged in a linear fashon along chromosomes like beads on a string. It is now known that chromosomes are just big dna molecules, containing millions of gene pairs. The location (locus or plural loci) of these paired genes (called allele or plural alleles) along a given chromosome and how chromosomes (and in turn how alleles) are paired, gives rise to all the variation in a given species. Cannabis has 10 pairs of chromosomes, making a total of 1024 possible chromosome combinations (calculated 2^n whereas n= the number of chromosome pairs) compared to humans who have 23 pairs of chromosomes making 8,388,608 possible combinations and domestic dogs who have 39 chromosome pairs bringing rise to 549,755,813,888 possible chromosome combinations! Chromosomal inheritance is universal in life forms and even though there is a proportional decrease in possible combinations compared with the number of chromosome pairs, there is still an abundance of variation in cannabis.

There are some chromosomes that are involved in reproduction, we know them as the X and Y chromosomes, these chromosomes carry sex-linked traits, an example would be color blindness in humans. Cannabis has 9 pairs of "autosomal" or, non sex chromosomes and 1 pair of 2 sex linked chromosomes, either an X combined with an X, making a female or an X combined with a Y for males.

Meiosis is reproductive cell division where a complete (diploid) set of chromosomes is divid ed into half (haploid). The joining of two haploids again creates a complete set of chromosomes and a new organism is born. Each germ (sex) cell starts out with a diploid set of chromosomes, one of each set coming from each parent. There is never any discrimination as to how the chromosomes are divided, as long at its half, and there is no discrimination amongst the haploids and how they reform to diploid, the only priority being that the diploid is divided in half and the haploid receives a complimentary set of chromosomes to once again become diploid. Meiosis randomly separates the parental pairs and fertilization restores them randomly to their diploid state. Their is also the ability for chromosomes during meiosis to "swap"or "mix and match" some information. This reciprocal exchange of segments of genetic material between two chromosomes places genes in the same sequence and location on the chromosome, but in new combinations. Things can get a little confusing here and I don't want to write a novel so suffice it to say the way chromosomes are divided during meiosis creates the random character of inheritance, this allows us a statistical predictably of traits, giving us a bit of control over said traits.

There are four modes of inheritance, autosomal (non sex-linked) dominant, autosomal recessive, sex-linked recessive, and polygenic (meaning more than one gene is responsible for it's inheritance or expressivity). The modes of inheritance that I will focus on are autosomal recessive or dominant. These are simple to understand and will give you a foundation on the basics. I gave a basic definition of allele earlier, let me elaborate.

The term allele is used to define two genes situated at the same position (locus) on homologous (matched or paired) chromosomes. Alleles are both sides of the same coin, alternate forms of the same gene. The same allele that control how tall somethig may be, paradoxically controls how short it will be. It is again the possible paired combinations of the two forms of a given gene that control what trait will be expressed. There are two forms of alleles at a given locus, one is dominant (denoted with an upper case letter like A) and one is recessive (signified by a lower case letter, a). Thus you have three combinations for the alleles, AA, Aa, aa. In this example I will use height as the trait for simplicity, if the dominant form for the allele controlling height is short stature, written "A", then the recessive form of that allele producing more height is written "a". AA is an example of double dominance and because they are a matched pair they are called homozygous, this double dominance means that the organism will be short, and breed true for the short trait, never producing direct offspring (daughters and sons) that are tall. Aa is a combination that means the organism will be short, but be a carrier for the genes that would produce a taller stature, being an unmatched pair they are called heterozygous. The combination aa would also be considered homozygous because they are a matched pair, but are double recessive, this doubling up of the recessive allele will produce an organism with a higher stature than the majority of the population. The only way a recessive allele can be expressed is if it is matched (homozygous) with another recessive counterpart. An easy way to illustrate the probability of inheritance for a certain trait is a diagram called a punnett square, a simple tool to help visualize the probability of progeny that will express a certain trait. A quick Google search will show how to properly use a punnett square for anyone interested.

So now we see that there is a level of predictably for the inheritance of traits. If a double dominant parent is taken to a double recessive parent,(AA x aa) none of the offspring will express the recessive trait, they all however will carry the recessive trait and have the ability to produce progeny expressing the recessive trait (100% of the offspring will be Aa from a [AA x aa] cross). If a double dominant parent breeds with a heterozygous parent that has both the dominant and recessive version of a given allele, (AA x Aa) then all the offspring will express the dominant trait and only 50% of the progeny will be carriers for the recessive trait, the other 50% will be homozygous and true breeding for the dominant trait (50% AA, 50% Aa). If two heterozygous parents (Aa x Aa) are bred, you will finally find offspring expressing the recessive trait, (25% will be double dominant AA and true breeding for the dominant trait, 50% will express the dominant trait but be heterozygous and carry the recessive trait Aa, the final 25% will be double recessive aa and express the recessive trait without being a carrier for the dominant trait. Remember if a dominant allele is present the trait that allele is "coded" for will be expressed, you cannot express a recessive trait and also carry the dominant, if the dominant allele is present it will be expressed and mask the recessive trait.

This brings us to the most abused genetics jargon in the cannabis community, genotype and phenotype. Phenotype is what is physically observable in a specimen, and in genetics, includes nurture and nature. That is to say if a specimen does not reach its genetically predisposed height due to malnutrition, its height or lack thereof is still part of its phenotype. Genotype is all the genetic information contained in a specimen, dominant or recessive, observable or not. A given specimen in their genotype may contain the information to produce multiple, distinct, phenotypes, but because of the relationship between its inherited alleles, and the fact it can only display one physical manifestation of the genome, can only express one pheno.

Now that we have a better understanding of some of the modes of inheritance, and how genes interact with eachother to produce a certain trait, we can now examine the methods that breeders use to produce strains with set, defined, traits, and are true-breeding for those selected traits. There are only a few terms that have been coined by the breeding community to reflect some sructure or template for their breeding. There is simply inbreeding and out-crossing, that's it. You may have heard of backcrossing, line breeding, in line breeding, inbreeding, cubing (a big one used often by cannabis breeders) or any other format on which to structure your breedings. All of the previously listed terms are a way of saying inbreeding, and if its not inbreeding its an outcross, no exceptions. All breeds of dogs and furthermore all "strains", "bloodlines", "sub species", however you would like to refer to them, are inbred and their uniformity and true breeding nature are a direct result of inbreeding.

Now I know your thinking, "inbreeding is bad right?" "I thought inbreeding made diseases and deformities." Sorry but your wrong, inbreeding has a stigma in our society due to religious and moral views. I'm not suggesting you should start bumpin uglies at the family reunion, but it happens in nature all the time, humans are even inbred. Don't believe me? Do some quick math, take your family tree and trace it back far enough, you will find that at some point there are more ancestral places in your family tree then there were people on the planet at that time.

Since we have discussed how traits are inherited the idea of using closely related specimens for breeding kinda makes sense. When working with specimens that share a common ancestry, you are more likely to double up on certain alleles. The closer related the greater the chance that some of the progeny will inherit matching alleles from their parents that they themselves inherited from a common ancestor. Working within a family you can be more sure that traits will be inherited from one generation to the next, and choosing a closely related mate for a planned breeding assures you that you have a greater chance at setting a selected trait in your line by creating homozygousness at the chromosome. Inbreeding also allows you to perform test breedings, helping you better understand the genotype of the strain you are working with and more importantly, the genotype of your breeding stock, selecting mates not just on their observable traits but their potential genetic contribution to the cross. This is where the use of a punnett square and some deductive reasoning will really aid you in learning about your brood stock. Like we said earlier, inheritance is predictable, and knowing what genes interact with eachother and the probability of a trait being expressed, you can deduce much about the population you are working with.

One thing to always remember is that inbreeding neither adds nor subtracts from the line. It simply doubles up on what is genetically there, creating new possibilities. Inbreeding is not bad, nature is imperfect! Inbreeding does not create problems, deformities, or disease, but it does rapidly bring masked recessive traits to the surface where they can be selected for or against, recessive doesn't always mean bad, it means its recessive. Inbreeding can make an abundance of problems or it can rapidly set desirable traits on the line, making homozygousy, and a true breeding offspring. If an insestual breeding occurs between two specimens and a masked genetic deformity or trait rears its ugly head, do not fear! As we learned earlier the same breeding that will produce offspring affected by a recessive genetic trait will also produce a predictable ammount of offspring completely unaffected by the recessive trait and they will not be carriers for the trait either. A double edged sword that must be respected and used wisely.

Inbreeding depression is a term used when inbreeding is abused and a general lack of vigor, fecundity, and health is lost throug h successive generations. When this occurs breeders usually look for an outcross to bring the inbreeding coefficient down and promote vigor and fertility. Inbreeding depression can happen to any organism but inbreeding is not to blame. Again nature is imperfect, you doubled up on a piece of genetic information already in your line, and now you have a problem, inbreeding didn't cause the problem, it just made it visible. Now that a negative trait has been expressed, its not necessarily time to find an outcross, just select against that trait for future breedings. There are strains of lab mice that are a result of 100s of generations of brother - sister breedings to keep the line uniform and genetically, nearly identical for testing purposes of pharmaceuticals. These lab bloodlines have exhibited no apparent loss of health, vigor, or fertility, with an inbreeding coefficient (a measure of to what extent a specimen is inbreed written in percent) of 95% and in some cases higher. How is this? The original breeding stock was of superior quality, and the breeders culling process was thorough and rigorous, only selecting the best specimens for future breedings.

There is also something called hybrid vigor. It is a term used to describe the phenomena of increased vigor, fertility, health, and disease resistance in breedings where the parents of the vigorous offspring are genetically dissimilar. It is the opposite of inbreeding depression and is widely misunderstood.

Well that's all for now, any questions feel free to ask, if I missed anything I apologise. Hopefully this taught a few people a thing or two, I would encourage people who are interested to do some research on their own and become informed before slinging pollen everywhere. Remember you are in control, good note taking, patience, and rigorously only selecting for the best is the hallmark of a good breeder.
Edited by Padre Pokes CHB, 09 July 2012 - 07:26 AM.

Last edited Sun Jan 19, 2014 7:21 pm | Scroll up

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