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Tuesday, August 1, 2017

A Cross by Any Other Name

From [link].
I've been involved in a few discussions online lately about different types of crosses that can be used in plant breeding. There has been some mild confusion about basic terms, as well as about the implications of different types of crosses. A few years ago I wrote about backcrossing. Though that post is somewhat hard for me to read, as I imagine early writings are for most authors, it has some useful information. Here I'm going to try and do a more general overview. Lets see how this little ride goes.

Some of that basic terminology and common abbreviations:
  • P : Parental. An initial variety used in a cross. Multiple parents can be numbered, like in "p1 x p2".
  • F : Filial, relating to progeny generations after an initial cross. F1 is the initial hybrid. F2 is the result of crossing two F1s. F3 is the result of crossing two F2s, etc.
  • Self Cross : Crossing the male and female parts of the same plant.
  • BC : Back cross. Crossing a filial generation back to one of the parents.
  • CC : Complex cross. A cross involving more than two parents.

P : To simplify things, we usually use highly stable varieties as initial parents in a hybridization project. This means that several generations of each parent variety have been grown out without any visible variation appearing. At the basic genomic level, this means the varieties are highly homozygous. In theoretical cases we consider the parents to be absolutely homozygous, though reality is never quite so clear-cut.

F1 : Our initial hybrid between two parents can be written out in a bit longer form like "p1 x p2", or just referred to as an F1 between the two parents. In our idealized scenario, every F1 produced by crossing the same two parents will be identical. F1 stands for "first filial generation".

If a group of F1s aren't identical, this says one or both of the parents wasn't entirely homozygous. (Or new mutations were introduced, or epigenetic effects are at play, or etc. It can get complicated). Because they're (more or less) identical, selection usually isn't very important at this stage.

From [link].
F2 : Our second filial generation is produced by crossing two F1s together. For those plants that can self cross (like peppers and tomatoes), the F2s would generally be produced by crossing one F1 to itself. For those that can't (like tomatillos), the F2s would be produced by crossing two separate F1 siblings.

The F2 generation is where the different alleles from each parent are recombined. Almost any combination of traits from each parent can turn up in an individual among the F2s. This is where the magic happens in a plant breeding project really happens. This generation is where selection is most important.

F3...Fn : Subsequent filial generations would be produced in a similar way to the F2s. If you produced F3s by selfing an F2, each F3 will have about 50% of the heterozygosity of the F2. Selfing another generation will result in another 50% loss of heterozygosity. Continue this process for enough generations and you will have a new stable variety, with an essentially homozygous genome.

If you produced F3s by crossing random F2s, you'll keep mixing up the genetics instead of automatically losing 50% of the heterozygosity each generation. If you do this with relatively few plants, you will still be losing heterozygosity each generation, though calculating exactly how much becomes a bit complicated.

If you produced F3s by crossing specific F2s that had a trait you liked, you'll keep mixing up all the other genetics while selecting for that specific trait. You would be losing heterozygosity near the genes responsible for the trait of interest, but the rest of the genome would still be maintaining heterozygosity through generations.

BC : In basic back crossing, each subsequent generation past F1 is crossed back to one of the parents. BC1 would be diagrammed something like, "[p1 x p2] x p1" (or "F1 x p1"). For one hypothetical mutation found in the first parent, a BC1 individual would have a 50% chance of having two copies (and a 0% chance of having no copies) since it is assured of inheriting one copy from the parental strain used in the backcross.

Through each generation of back-crossing the resulting plants will lose 50% of their heterozygosity, but it will be replaced with whatever mutations are found in the parental strain. The result will end up more and more like the recurrent parent strain over the generations. If you do this randomly, you will end up with essentially a genetic clone of the recurrent parent. To get anything different, you have to persistently select for a trait that was originally only in the second parental variety. Doing this will eventually produce something almost exactly like the recurrent parent, but with the one trait that was originally in the other parent variety. (That's all detailed in the link I mentioned in the intro.)

CC : A complex cross involves three or more parental varieties. A simple case would be taking an F1 and crossing it to an independent F1, "[p1 x p2] x [p3 x p4]". In these scenarios you would get a very diverse population, just like with F2s, but the mutations contributed to the population can come from all four parent varieties.

A mutation that was found in only one of the parental strains would only be found in one copy in 25% of this mixed up population. If one of these plants was selfed, the chance of a plant being homozygous in the next generation is 6.25%.
If the plants were allowed to cross randomly, the chance of a plant being homozygous in the next generation drops to only 1.5625%. You would need to be working with very large numbers of plants to routinely recover double-recessives using this strategy. I strongly advise you not use this strategy.




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