I have noticed a few people that seem to be curious about the ins and outs of breeding so I thought I would pass on some basics. I relied heavily on a few sources and a few books lying around for ease of reference/concise explanation. Intention: First what are you trying to do? Create a new strain? continue a genetic line to save a strain? Or cross 2 plants to create a simple hybrid? Your intention will dictate the direction your breeding program takes. Continuing a strain: So you want to continue a strain you have some seed stock of. This is easy. Just mate males and females from the same seed batch from the SAME breeder. The reason for this is that many seed breeders create their own version of popular strains and a mixture would create a great deal of variation. The different versions may exhibit different characteristics from those of other breeders despite being the "same" strain. Remember that even with a male and female from the same seed batch, that in a small gene pool (A.K.A Low population of plants) you may lose some features of the original parents unless the strain your using is an IBL or from VERY stable inbred pure line's. Making a simple hybrid: Again, very easy.Take a male from 1 strain and a female from another. So Jack Herer and Blackberry Kush turns into "JH x BK", but there will be differences in the offspring. Some offspring with exhibit more traits from one parent or the other. Genes not expressed by either parents may turn up. If you want to breed for specific traits by eliminating variations, ultimately creating uniform plants or even IBL, then you need to know the basics of plant genetics. Basic Terminology Of Plant genetics: Genes: Genes are hereditary information transmitted from parent to offspring. Genes are usually responsible for the inherited features of your plant. Such as potency, leaf color, smell, stem structure, yield, etc etc. Gene Pairs: Think of a DNA strand. Now picture it as the zipper on your coat. One half comes from your father and one comes from your mother combined to make a chain of information which dictate the characteristics of the individual. Typically Gene Pairs are denoted by a pair of letters, such as AA, BB, Bb, Pp, pp, etc etc. Capital letters refer to dominant genes while lower case letters refer to recessive genes. For example, B can represent Big bud while b can represent small bud. Any letter can be assigned to any trait or gene pair when you are working out your breeding program. Chromosome: A threadlike structure of acids and proteins in the cell nuclei of higher organisms that carries a set of linked genes, usually pairs. Locus: A position on a chromosome where a particular gene pair is located. Allele: Alleles are any of a number of alternative forms of the gene. For example the gene for purple bud color may have two forms, or alleles, one for purple and one for dark red. Homozygous: Having identical alleles at one or more genetic loci, which is not heterozygous and breeds true. Your plant is said to be homozygous for one feature when it carries the same gene twice in the responsible gene pair, which means both genes of the gene pair are identical. Heterozygous: Having different alleles at one or more genetic loci. Your plant is said to be heterozygous for one feature when the genes of the responsible gene pair are unequal,or dissimilar. Phenotype: A phenotype is all the detectable features of your plant. Taste, smell, color, size, etc etc. Genotype: The Genotype is the genetic features of the plant. It represents the genetic makeup that is past on to offspring. Things like how the plant grows, potency, resistance to mold or disease, frequency of traits, etc, etc. Dominant: Dominant is a gene or allele that is expressed in offspring even when inherited from only one parent. It is also used to describe a hereditary trait controlled by a gene and appearing in an individual to the exclusion of its counterpart, when alleles for both are present. Only one dominant allele in the gene pair must be present to become the expressed genotype and eventually the expressed phenotype of your plant. Recessive: This describes a gene, allele or hereditary trait perceptibly expressed only in homo-zygotes, being masked in hetero-zygotes by a dominant allele or trait. A gene is called recessive when its effect cannot be seen in the phenotype of your plant when only one allele is present. The same allele must be present twice in the gene pair in order for you to see it expressed in the phenotype of your plant. Dominant/Recessive and Genetic Notation: So...Lets say the dominant "B" allele carries the hereditary trait for big bud, while the recessive "b" allele carries the hereditary trait for small bud. Since B is dominant, a plant with a Bb genotype will always produce big bud. The B is dominant over the b. In order for a recessive gene to be displayed in the phenotype, both genes in the gene pair must be recessive. So a plant with the BB or Bb gene will always produce big bud. Only a plant with bb gene will produce small bud. The Hardy-Weinberg Model Of Genetic Equilibrium: For this we must picture a theoretical gene pool in which there is no change or variation at all. At equilibrium there can be no change or evolution. Picture a population whose genes contain the alleles B and b. Assign the letter "p" to the dominant allele B and the letter "q" to the recessive allele b. We know that the sum of all alleles must equal 100%, so: p + q = 100% This can also be expressed as : p + q = 1 All of the random possible combinations of the population would equal: p<sup>2</sup> + 2pq + q<sup>2</sup> Where: p = frequency of the dominant allele in a population q = frequency of the recessive allele in a population p<sup>2</sup> = percentage of homozygous dominant individuals q<sup>2</sup> = percentage of homozygous recessive individuals 2pq = percentage of heterozygous individuals Imagine you have 100 'blackberry diesel' plants from seed purchased from a reputable breeder. Out of those 100 plants 36 have a skunky smell and the other 64 have a fruity smell. After some research you determine which trait is dominant. ( contacting the breeder is a good way). So hypothetically you find out the breeder selected for the fruity smell and the skunky smell is recessive. So call this recessive genotype v v' and use the formula above to answer the following. According to Hardy-Weinberg, what is the frequency of the 'v v' genotype? Answer: Since 36 out of 100 plants have the 'v v' genotype, then it would be 36% of this population of 'blackberry diesel'. What is the frequency of the 'v' allele? Answer: The frequency of the 'v v' allele is 36%. Since q<sup>2</sup> is the percentage of homozygous recessive individuals, and q is the frequency of the recessive allele in a population, the following must also be true: q<sup>2</sup> = 0.36 (q +q) = 0.36 q<sup>2</sup> = 0.6 Thus, the frequency of the 'v' allele is 60% What is the frequency of the 'V' allele? Answer: Since q = 0.6, we can solve for p. p + q = 1 p + 0.6 = 1 p = 1 - 0.6 p = 0.4 The frequency of the 'V' allele is 40%. What is the frequency of the genotypes 'VV and 'Vv'? Answer: Given what we know, the following must be true: VV = p<sup>2</sup> V = 0.4 = p<sup>2</sup> (p x p) = p<sup>2</sup> (0.4 x 0.40 = p<sup>2</sup> 0.16 =p<sup>2</sup> VV = 0.16 The frequency of the genotype 'VV' is 16% VV = 0.16 vv = 0.36 VV + Vv + vv = 1 0.16 + Vv + 0.36 +1 0.52 + Vv = 1 Vv = 1 - 0.52 Vv = 0.48 or 48% Or alternatively, 'Vv' is 2pq, therefore: 'Vv' = 2pq 2pq = 2 x p x q 2pq = 2 x 0.4 x 0.6 2pq = 0.48 or 48% The frequency of 'V' and 'v' (p and q) will remain unchanged, generation after generation , as long as the following remain true: 1. The population is large enough. 2. There are no mutations. 3. There are no preferences, for example a VV male does not prefer a vv female by its nature. 4. No other outside population exchanges genes with this population. 5. Natural selection does not favor any specific gene. The equation p<sup>2</sup> + 2pq + q<sup>2</sup> can be used to calculate the different frequencies. The Test Cross: So how do you know if a trait is homozygous dominant (BB), heterozygous (Bb) or homozygous recessive (bb)? Determining a phenotype is easy. You look at the plant, you smell it, feel or taste it. Determining the genotype however cannot be done through simple observation. Generally speaking, there are three possible genotypes for each plant trait. For example, if golden buds are dominant and purple buds are recessive, the possible genotypes are: Homozygous Dominant: BB = golden buds Heterozygous: Bb = golden buds Homozygous Recessive: bb = purple buds The golden or purple buds are the phenotypes. BB, Bb and bb denote the genotypes. Because B is the dominant allele, Bb would appear purple-ish and not golden. Most phenotypes are visual characteristics but some, like taste, are phenotypes that cant be observed by the naked eye and are experienced instead through other senses (duh right?). For example, when you come upon a population of plants with golden buds and a few display minor purpling to their buds, it suggests that this strains bud color is not "true breeding". Meaning that the bud trait must be heterozygous because homozygous dominant and homozygous recessive traits are true breeding. Some of the strains golden bud traits will probably be homozygous dominant in this population. So how do we know the golden bud trait isn't the homozygous recessive trait and the purple buds the heterozygous trait? Since a completely homozygous recessive population (bb) would not contain the allele ( B ) for heterozygous expression (Bb) or for homozygous dominant expression (BB), it is impossible for the traits for heterozygous (Bb) or homozygous dominant (BB) to exist in a population that is completely homozygous recessive (bb) for that trait. If a population is completely homozygous for that trait (bb or BB), then that specific trait can be considered stable, true breeding or 'will breed true'. If a population is heterozygous for that trait (Bb) then that specific trait can be said to be unstable, not true breeding or 'will not breed true'. If the trait for Bb or BB cannot exist in a bb population for that trait, then bb is the only trait that you will discover in that population. Hence, bb is true breeding. If there is variation in the trait and the Hardy-Weinberg law of equilibrium has not been broken, the trait must be heterozygous. In our example there were only a few purple buds. This means that the purple buds are homozygous recessive and the golden buds are heterozygous and may possibly be homozygous dominant too. You may also notice that the bud is golden on most of the plants. This also suggests that the golden bud color is a dominant trait. If buds on only a few of the plants are purple, this suggests that the purple trait is recessive. You know the only genotype that produces the recessive trait is homozygous recessive (bb). So if a plant displays a recessive trait in its phenotype, its genotype must be homozygous recessive. A plant that displays a recessive trait in its phenotype always has a homozygous recessive genotype. But are the golden bud color traits homozygous dominant (BB) or heterozygous (Bb)? You need to complete a test cross to know. A test cross is performed by breeding a plant with an unknown dominant genotype (BB or Bb) with a plant that is homozygous recessive (bb) for the same trait. For this test you will need another cannabis plant of the opposite sex that is homozygous recessive (bb) for the same trait. An important rule: If any offspring from a cross test display the recessive trait, the genotype of the parent with the dominant trait must be heterozygous and not homozygous. In our example, our unknown genotype is either BB or Bb. The purple bud genotype is bb. We'll put this information into a mathematical series known as Punnet squares. http://en.wikipedia.org/wiki/Punnett_square I b I b ---------I-----------------I------------- B I I ---------I-----------------I------------- ? I I We start by entering the known genotypes. We do these calculations for two parents that will breed. We know that our recessive trait is bb and the other is either BB or Bb, so we'll use B? for the time being. Our next step is to fill the box in With what we can calculate. I b I b ---------I-----------------I------------- B I Bb I bb ---------I-----------------I------------- ? I ?b I ?b The first row of offspring Bb and Bb will have the dominant trait of golden bud. The second row either contain Bb or bb offspring. This will either lead to offspring that will produce more golden bud (Bb) or purple (bb). The first possible outcome (where ? = B ) would give us golden bud (Bb) offspring. The second possible out some (where ? = b ) would give us purple (bb) offspring. We can also predict what the frequency will be. Outcome 1, where ? = B: Bb + Bb + Bb + Bb = 4Bb 100% golden bud Outcome 2, where ? = b: Bb + Bb + bb + bb = 2Bb + 2bb 50% golden bud and 50% purple bud Recall: Homozygous Dominant: BB = golden bud Heterozygous: Bb = golden bud Homozygous Recessive: bb = purple bud To determine the identity of B?, we used another cannabis plant of the opposite sex that was homozygous recessive (bb) for the same trait. Outcome 2 tells us that: -Both parents must have at least one b trait each to exhibit purple bud in the phenotype of the offspring. -If any purple bud is produced in the offspring then the mystery parent (B?) must be heterozygous (Bb). It cannot be homozygous dominant (BB). So, if a golden bud parent is crossed with a purple bud parent and produces only golden bud, then the golden bud parent must be homozygous dominant for that trait. If any purple bud offspring is produced, then the golden bud parent must be heterozygous for that trait. To summarize, the guidelines for performing a test cross to determine the genotype of a plant exhibiting a dominant trait are: 1. The plant with the dominant trait should always be crossed with a plant with the recessive trait. 2. If any offspring display the recessive trait, the unknown genotype is heterozygous. 3. If all the offspring display the dominant trait,the unknown genotype is homozygous dominant. The main reason behind performing a cross test are: 1. When you breed plants you want to continue a trait,like height, taste, smell, etc. 2. When you want to continue that trait you must know if it is homozygous dominant, heterozygous or homozygous recessive. 3. You can only determine this with certainty by performing a test cross. For breeding its always best to deal With the LARGEST population possible in order to get the most accurate results. The more plants you work with, the more reliable the results. Hardy-Weinberg Law, part 2 So how do we breed for several traits, like taste, smell vigor and color? If yoiu breed two plants that are heterozygous (Bb) for a trait, what will the offspring look like? The punett squares can help us determine the phenotypes, genotypes and gene frequencies of the offspring. I B I b ---------I-----------------I------------- B I BB I Bb ---------I-----------------I------------- b I Bb I bb* *Take note of this offspring and compare it with the parents. In this group,the resulting offspring will be: 1 BB - 25% of the offspring will be homozygous for the dominant allele (BB) 2 Bb - 50% will be heterozygous, like their parents (Bb) 1 bb -25% will be homozygous for the recessive allele (bb) Unlike the parents (Bb and Bb), 25% of offspring will express the recessive phenotype bb. so two parents that display golden bud but are both heterozygous (Bb) for that trait will produce offspring that exhibit the recessive purple bud trait, despite the fact that neither of the parents displays the phenotype for purple bud. Understanding how recessive and dominant traits are passed down through the phenotype and genotype so that you can predict the outcome of a cross and lock down traits in the future generations is really what breeding is all about. So how do you know that the traits you want to keep will actually be retained in the breeding process? The test cross. If you create seeds from a strain that you bought from a seed bank, how can you be sure that the offspring will exhibit the characteristics that you like? If the trait you wish to continue is homozygous dominant (BB) in both parent plants then there's no way that you can produce a recessive genotype for that trait in the offspring,as illustrated in the Punnett square below. I B I B ---------I-----------------I------------- B I BB I BB ---------I-----------------I------------- B I BB I BB It is impossible for the recessive trait to appear. And if both parents contain the recessive trait then they cannot produce the dominant trait. I b I b ---------I-----------------I------------- b I bb I bb ---------I-----------------I------------- b I bb I bb In order to breed a trait properly you must know if it is homozygous, heterozygous, or homozygous recessive so you can Predict the results before they happen. Mendel and the pea experiments: Gregor Mendel (1822-1884) discovered the basic rules of inheritance by analyzing the results of a breeding program with two types of pea plants. He noticed that when bred in their own gene pool each variety gave very uniform results. The traits he noticed were. Pea plant #1 Pea Plant #2 Solid Seed Shells Wrinkled Seed Shells Green Seeds Yellow seeds white flowers purple flowers tall plants short plants The offspring all carried the same traits when bred with the same population or gene pool. Because the peas were the same species, Mendel guessed that either solid or wrinkled seed shells were recessive. Using the genotype SS for solid shells and ss for wrinkled, he knew that they couldn't be Ss because one lot didn't exhibit any of the other strains phenotypes when bred within its own gene pool. SS pea plant #1 with solid shell trait results: I S I S ---------I-----------------I------------- S I SS I SS ---------I-----------------I------------- S I SS I SS All the offspring will be SS. Pea plant #2 with wrinkled seed shell results: I s I s ---------I-----------------I------------- s I ss I ss ---------I-----------------I------------- s I ss I ss All the offspring will be ss. The First Hybrid Cross (the F1 Generation) Mendel made his first hybrid cross brtween the two strains and the results were all solid seeds as seen in the chart below. I s I s ---------I-----------------I------------- S I Ss I Ss ---------I-----------------I------------- S I Ss I Ss Up until this point, he didn't know which trait was recessive and which was dominant. Since all the seeds shells were solid, he know knows with certainty that pea plant #1 contained the dominant genotype foe wrinkled seed shells. This meant future test crosses with other pea strains, he could determine if a particular seed shell trait was homozygous or heterozygous because he had identified the recessive trait (ss). -------------------------------------------------------------------------------------------- Most of this is pretty basic and can be found in 1 form or another in any commercial horticulture textbook. Its probably covered better somewhere on this site and I just haven't stumbled across it yet. Let me know if you all have any question, comments or even advice. I'm new-er to forum posting and I'm sure I could use whatever pointers anyone cares to give me. If enough folks have an interest ill add more. Enjoy your plants everybody
Brings me back to dreaded genetics learned in biology. Gotta love it when applied though. Thanks FauxRoux.