This is the simplest explanation I could find online about how the original genetic scientist established terminology for looking at breeding any organism in a scientific way:
Mendel and the gene idea
- the basic rules of inheritance were first demonstrated by Mendel
- at the time of Mendel’s work, most thought that parental traits were fluids that “blend” in offspring
- Mendel recognized that this model did not explain what he observed
- Mendel chose a model system and carefully established testing conditions
- he used pea plants that he could outcross or allow to self-fertilize
- he chose traits that had two clear possible outcomes (yellow or green seeds, etc.)
- he established true-breeding or “pure” lines to use for genetic crosses
- terminology for genetic crosses
- P generation (or P1) = parental generation
- F1 generation = first generation offspring (from filial)
- F2 generation = second generation offspring
- phenotype – appearance or characteristic of an organism
- genotype – genetic makeup of an organism, determines phenotype
- gene – unit of heredity; controls a trait that determines a phenotype
- locus – the location of a particular gene on a chromosome
- alleles – alternative versions of a gene
- dominant – allele that dominates over others in determining phenotype
- recessive – allele whose phenotypic expression is “hidden” when a dominant allele is present
- hybrid – offspring from a cross between two “pure” lines of different, competing phenotypes
- rules and terminology for examination of genetic inheritance
- Mendel’s law of segregation
- when Mendel crossed pure lines of different, competing phenotypes, he found that the F1 generation was uniform and matched one of the parents’ phenotypes
- Mendel’s law of segregation
- example: P1 yellow seed X green seed à all F1 yellow seed
- when F1 plants were crossed or selfed, the F2 plants had both P1 phenotypes in a ratio of roughly 3:1
- using offspring from above F1 X F1 à F2 3 yellow seed: 1 green seed
- thus, contrary to the popular belief of the time, recessive traits are not lost in a mixing of parental phenotypes – they are merely hidden in some “carrier” individuals
- Mendel explained these ratios with what we now call his law of segregation; stated in modern terms: individuals normally carry two alleles for each gene, these alleles must segregate in production of sex cells
- later investigations of cell division revealed the mechanism for segregation: the pairing and subsequent separation of homologous chromosomes during meiosis
- genotype vs. phenotype
- phenotype is the actual appearance or characteristic, and is determined by genotype; knowing the phenotype will not always directly reveal the genotype (recessive traits can be masked)
- genotype is the listing of the actual alleles present; if you know the genotype, you should be able to predict the phenotype
- genotypes are either homozygous or heterozygous
- homozygous – the homologous chromosomes have the same allele at the locus in question
- heterozygous – the homologous chromosomes have different alleles at the locus; if there is a dominant allele the trait of the dominant allele will be expressed
- the same letter is used to indicate all alleles (superscripts or subscripts are sometimes needed, if there are more than 2 alleles known)
- DOMINANT ALLELES ARE CAPITALIZED; recessive alleles are lowercase
So back to filial relationships as it applies to my plans for breeding the American Minigypsy:
The filial number denotes the number of generations the animal is removed from its origins. To determine the filial number for offspring with parents having different numbers, use the parent that is closest to its origins, in other words, the parent with the lowest filial number. P = Purebred parent so P x (mini) = F1 or half, 50% gypsy cob blood
F1 x F1 = F2 OR in my case I am going back to the gypsy cob stock most often, so mine is usually F1 x P = F2 again, and that is 75% or 3/4 gypsy cob breeding. To clarify, according to Mendel’s assorting explained above, we can see the risk for F1 bred to F1 there is the 25% chance you will not get the traits you seek (feather)….3:1 outcome was for the traits that the parents exhibited, that you might have expected to see produced, but there is a hidden throwback kind of effect that comes out in one of four specimens produced. So F2 by itself still has a fair chance of perpetuating traits you might not want in the long run, but if you are trying to “breed up” the F2 generation is necessary in order to carry the traits you DO want.
Then: F2 x P = F3 or 7/8 gypsy cob breeding, or 87.5% gypsy cob breeding. When I have this generation of crosses in my herd, I have used every time crossing back to superior feathered horses and I expect the traits to be quite strong and of similar quality to what I would be able to find and import from UK and Ireland. However, the size will have been inching up as well as the feather factor…so for instance this cross compares to my future plans to breed 12.2 hand purebred registered gypsy mare, to my ten hand 3/4 stud colt. So in that case, I am hoping for something that is heavily feathered and will not mature more than about 11 hands. Which is a great specimen to go back and capture some small size again from an F1 product….and F1 x F3 would bring the strength of the genetic factors that make a pony look like a gypsy horse, back down to F2 level…in reality, the genetic strengths will vary at this point…to where I would expect a 25% chance of getting a baby that did not have desirable feather factor. If all other traits present are desired, this product could still be used for a breeding program; but eventually as numbers increase and the program develops thru the years, this product is better fated to become a pet quality only as it will not contribute to a quality breeding program after a certain point where there are good numbers of breeding stock available.
F2 xF2 = F3 ; looking at this mathematically, this combination offers still, a 25% chance that you will get the throwback effect. But if the individuals are very small, and with good feather, it may well be desired to use this kind of cross; even tho in reality, that F3 generation (distance from the original cross out) will not be as strong for traits in about 50% of the progeny, as using the F2 back to a purebred gypsy cob. However, the decision has to be determined according to the quality of the F2 generation and what traits you feel are most important to perpetuate at that point.
Alternately, F3 might be crossed again back to an excellent small purebred cob and this generation of F4 would be now 15/16 or 93.75% gypsy cob blood. This status is commonly accepted as being pure enough to be considered pure for traits that you desire (especially as to feather factor this generation should have abundant feather to merit being called purebred). This level of genetic purity for traits, will still allow a slight chance for matching up with another specimen who has poor traits hiding in his genetic makeup, and thus giving your program a “throwback”. So, the governing body of the organization offering registration may want to make rules at some point that determine when or how animals are monitored for quality control within the breeding pool. But usually those decisions do not come about until numbers merit the need.
F4 x P = F5 or 31/32 and about 97% purebred traits, so very little chance that throwback progeny will appear. Considering this essentially is filling up a five generation pedigree, that is a lot of information that is valuable to have to refer to.
F3 x F3 = F4
In general when you breed a certain generation back to a lower step generation you will have to consider it rather a step backwards in filial relationship towards the beginning, so
F1 x F3 = F2 and (mini) x F4 = F1; but that is rather loose reference because in reality you are not wanting to focus on the filial relationship but the phenotype that you see produced.
Here is one description paragraph from a college reference book on animal breeding about PUREBRED: …is one which is of a particular breed. The animal has the characteristics of the breed to which it belongs. Both parents must have been purebred. A purebred animal is eligible for registry in the purebred association of that breed and has no disqualifications…..those are set up rules according to the breed association and vary. The ancestors of a purebred animal can be traced back to the original animals accepted for registry in the herd book..
And in a cattle genetics book where it talks about “breeding up”: After the 3rd or 4th cross (back to the breed base–F3/F4) the offspring compare very favorably with purebred stock, and only exceptionally good sires can bring about further improvement….High grade animals that are the offspring of several generations of outstanding purebred sires can be and often are SUPERIOR TO AVERAGE OR INFERIOR PUREBREDS (emphasis mine). So what I get out of that last sentence is that the benefit of genetic variability from that one infusion at the beginning of a breeding up program, helps create a better animal. The thing about PUREBRED animals is that the gene pool is continually being decreased, (this is a byproduct of popular sire design of registered animals) so that genetic variability decreases…the genetic material which makes a healthy animal that responds better to stresses and changes in environment. This has been the basis of breeding recommendations in agriculture throughout the last century. The majority of productive animals have not really been PUREBRED, they have been improved, with breeding up programs. This has applied to farm animals in real production.
When horses of a new breed are “visibly similar in most characteristics” and have reliable documented descent from a “known and designated foundation stock” they can then be considered members of a breed, and, if an individual horse is documented and registered, it can be called purebred. Only documentation of the ancestry from a breed’s foundation stock determines whether or not a horse is a purebred member of a breed, along with its appearance which represents the breed standard.