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Old May 3, 2015   #1
Minnesota Mato
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Default Backcrossing

I do a lot of crosses with wild tomatoes and it takes me a long time and a lot plants to recover size. I have been reading about back crosses and how it is best to due two back crosses minimum to recover size. Is it best to start the back cross from the f1 or select a f2 with the most recessive genes to start your back cross?
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Old May 3, 2015   #2
Darren Abbey
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Backcrossing an F1 to the domestic parent is an effective way to transfer over dominant traits from the wildling into the domesticated line.

P1 x P2 => F1 x P1 => BC1 x P1 => BC2 x P1 => BC3 ... etc.

After several generations, you will end up with a line that is essentially the same as the chosen backcross parent, but with the selected dominant traits from the the other parent.

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The case for transferring a recessive trait is move involved.

P1 x P2 => F1 x F1 => F2 x P1 => BC1 x BC1 => BC1:F2 x P1 => BC2 x BC2 => BC2:F2 x P1 => BC3 ... etc.

In each F2 generation, you'd need to grow out enough plants to recover the double-recessive case for the traits of interest. If you don't, then you can easily lose the recessive trait at any stage in the backcross series.

The recessive case takes roughly twice the number of generations as the dominant case, because of the need to check all the time that you haven't lost the recessive traits. If you're lucky, you can identify the "recessive" trait by some subtle effect in the heterozygous condition and then the process will be like the dominant case.
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Old May 3, 2015   #3
Darren Abbey
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So, in short, I would advise going from the F2 with the most recessive traits of interest... and then doing the same thing every two generations.
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Old May 4, 2015   #4
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Selecting in the F2, then doing the cross with the best F2 plant(s) is usually the best choice. There is a factor of how much chromosome fragmentation occurs from cross-over. Doing a backcross using an F2 allows for more effective selection as the fragments become smaller.

With modern DNA tools to assist selection, it is possible to dramatically reduce the number of generations to stabilize a given set of genes. As the cost of a dna profile goes down, we should see tools available that backyard breeders have not previously had access to. I'm still waiting for that $35 tomato DNA test. We may not see it for a few more years, but we will eventually see it.
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Old May 4, 2015   #5
Darren Abbey
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Selecting in the F2, then doing the cross with the best F2 plant(s) is usually the best choice. There is a factor of how much chromosome fragmentation occurs from cross-over. Doing a backcross using an F2 allows for more effective selection as the fragments become smaller.
If you select from the F2s before doing the backcross, you'll be at risk of losing one of the recessive traits being looked for.

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Originally Posted by Fusion_power View Post
With modern DNA tools to assist selection, it is possible to dramatically reduce the number of generations to stabilize a given set of genes. As the cost of a dna profile goes down, we should see tools available that backyard breeders have not previously had access to. I'm still waiting for that $35 tomato DNA test. We may not see it for a few more years, but we will eventually see it.
Once we know which gene is associated with which trait, we can definitely speed things up dramatically. Yes, eventually we'll have a simple test that will tell you which important alleles are found in any given plant... but it may never be all that cheap, because there are relatively few people who will be interested in buying the product.
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Old May 6, 2015   #6
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Selecting in the F2, then doing the cross with the best F2 plant(s) is usually the best choice. There is a factor of how much chromosome fragmentation occurs from cross-over. Doing a backcross using an F2 allows for more effective selection as the fragments become smaller.
.
These concepts are very interesting to me, but haven't been able to do an effective search to learn more about fragment size in different filial generations and how that impacts breeding.
Minn Mato, I have a really small space to work in, so it's hard to grow enough plants at once to find a stack of recessive genes in one plant - my plan is to look for one recessive at a time, and if I can find two of the desired traits in two F2 plants, I'll cross them... That may not work for a six gene trait like fruit size though, if you can't tell which traits are present.

As regards fruit size, I think the smallest fruited can be identified at the bud stage - flower buds very small at maturity. That's what I'm seeing here as I try to select before planting out. Also the 'beefsteak' type buds (example Indian Stripe, Black Early) are fat and round, a different shape from the typical pointed bud of a cherry or a heart or small fruit, in the group of seedlings I'm working with...
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Old May 6, 2015   #7
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Minn Mato, I have a really small space to work in, so it's hard to grow enough plants at once to find a stack of recessive genes in one plant - my plan is to look for one recessive at a time, and if I can find two of the desired traits in two F2 plants, I'll cross them... That may not work for a six gene trait like fruit size though, if you can't tell which traits are present.
The problem with this strategy is that when you cross the two F2s with different homozygous recessives... you end up with a new F1 that is heterozygous for those alleles and you have to then look for the multiple-homozygous progeny again.
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Old May 7, 2015   #8
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The problem with this strategy is that when you cross the two F2s with different homozygous recessives... you end up with a new F1 that is heterozygous for those alleles and you have to then look for the multiple-homozygous progeny again.
Yes, this could happen, but the odds of seedling A being heterozygous for the recessive trait found in seedling B and vice versa are better than none. If recessives are one from each parent, you go back to square one for one trait when backcross to the parent. Backcrossing to the F1 is an even better strategy that gives a 1/2 chance of finding the recessive in the subsequent generation.

Not that I think this is a best way to proceed, but humbly submit in my circumstance I can only take my chances, stir the pot and enjoy the journey for as long as it lasts.
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Old May 4, 2015   #9
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My primary project is crossing a large green tomato with a bright red pimpinellifolium to get a large black tomato. So I have to pick thru red, yellow, green and black. I hope I can cut down the number of plants because with my other crosses I have 200 plants already and things are getting out of hand. Lucky for me my wife likes salsa, ketchup, marinara ect. so I'm not in too much trouble yet.
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Old May 4, 2015   #10
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green-fleshded (gf), yellow-flesh (r), and fasciated (fas) are all recessive.

P1 (gf/gf; r/r; fas/fas) x P2 (Gf/Gf; R/R; Fas/Fas) => F1 (Gf/gf; R/r; Fas/fas)

----
Examining the the F2s... F1 x F1 => 25% gf/gf; 25% R/R; 25% fas/fas

You'd need to grow at least 64 to expect to find the combination you're looking for.

----
Backcrossing to either parent...

BC1:: F1 (Gf/gf; R/r; Fas/fas) x gf/gf; r/r; fas/fas [beefsteak] => [50% Gf/gf, 50% gf/gf]; [50% R/r, 50% r/r]; [50% Fas/fas, 50% fas/fas]

BC2:: F1 (Gf/gf; R/r; Fas/fas) x Gf/Gf; R/R; Fas/Fas [pimpinellifolium] => [50% Gf/Gf, 50% Gf/gf]; [50% R/R, 50% R/r]; [50% Fas/Fas, 50% Fas/fas]

Will fail to get you the combination you're looking for.

----
But, backcross one (BC1) will get you closer. 1/8 of the first backcross will be brown (green-flesh with red) and have large fruit. ([50% gf/gf]; [50% R/r]; [50% fas/fas])

Self such a plant and 3/4 of the next generation will be brown (green-flesh with red) and have large fruit. A third of these will have the combination of alleles (gf/gf; R/R; fas/fas) you're looking for.

I suspect there may be another recessive trait resulting in the large fruit compared to the pimpinellifolium parent, so it may be a bit more complicated. (1/16 of the backcross would have the intermediate state).
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Last edited by Darren Abbey; May 4, 2015 at 02:30 AM.
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Old May 4, 2015   #11
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In short, yes, you can seriously reduce the numbers you'll have to deal with... with a cost of an additional generation. (Actually, two, as you'll need at least one to identify a fully homozygous line.)
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Old May 4, 2015   #12
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I will be trying this plan shortly, my F1 is starting to blush, I am hoping to find what I'm looking for with 40 plants, that's the most room I have. Just for fun how many plants would I need to grow out in the F2 without any backcrosses to get (gf/gf,R/R,fas,fas)
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Old May 5, 2015   #13
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Originally Posted by Minnesota Mato View Post
I will be trying this plan shortly, my F1 is starting to blush, I am hoping to find what I'm looking for with 40 plants, that's the most room I have. Just for fun how many plants would I need to grow out in the F2 without any backcrosses to get (gf/gf,R/R,fas,fas)
Depends on the concentration of those genes in the parents of the cross.

For the worst case scenario, let's assume that one parent provides all of the desired genes, and the other parent doesn't provide any. So with two recessive genes and one dominant the odds of finding the phenotype you are looking for in the F2 are: 1/4 * 1/2 * 1/4 = 1 in 32... However half of plants that match the desired phenotype will only have one copy of the R gene, so the odds are 1:64 that an F2 plant will be homozygous for all the genes of interest. But because the assortment of the genes, and the selection of seeds is random, I figure that you'd need about 320 plants to feel really secure about winning the genetic lottery.
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Old May 6, 2015   #14
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For the worst case scenario, let's assume that one parent provides all of the desired genes, and the other parent doesn't provide any. So with two recessive genes and one dominant the odds of finding the phenotype you are looking for in the F2 are: 1/4 * 1/2 * 1/4 = 1 in 32... However half of plants that match the desired phenotype will only have one copy of the R gene, so the odds are 1:64 that an F2 plant will be homozygous for all the genes of interest. But because the assortment of the genes, and the selection of seeds is random, I figure that you'd need about 320 plants to feel really secure about winning the genetic lottery.
Would you not have to grow out subsequent generations to verify that the variety is homozyqous for the dominant R gene?

I would also refer you to Carol Deppe's book (unless someone knows an online version of her chart), where for a given odd she gives how many plants to plant out for a 95% certainty and a 99% certainty of getting what you're looking for.
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Old May 6, 2015   #15
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Would you not have to grow out subsequent generations to verify that the variety is homozyqous for the dominant R gene?

I would also refer you to Carol Deppe's book (unless someone knows an online version of her chart), where for a given odd she gives how many plants to plant out for a 95% certainty and a 99% certainty of getting what you're looking for.
I think that same information is also given at Keith Mueller's website in a very different way where he explains and gives numbers as to how many gens need to be grown out to give different percentages of purity.

http://www.kdcomm.net/~tomato/

Go to Culture, there go to tomato gene basics, read that and then click on the segregation link at bottom of that.

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