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?
Craig

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.

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.

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.

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.

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)

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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.

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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.

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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).

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.)

[QUOTE=Fusion_power;469958]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.[/QUOTE]

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.

[QUOTE=Fusion_power;469958] 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.[/QUOTE]

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.

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)

[QUOTE=Minnesota Mato;470161]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)[/QUOTE]

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.

[QUOTE=joseph;470167]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.[/QUOTE]

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.

[QUOTE=crmauch;470434]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.[/QUOTE]

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.

[url]http://www.kdcomm.net/~tomato/[/url]

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

Carolyn

[QUOTE=Minnesota Mato;469946]I do a lot of crosses with wild tomatoes and it takes me a long time and a lot plants to recover size.[/QUOTE]

[URL="http://www.genetics.org/content/158/1/413.full.pdf"]Dissecting the Genetic Pathway to Extreme Fruit Size in Tomato Using a Cross Between the Small-Fruited Wild Species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom[/URL]

Minnesota Mato, I don't know if you have seen the above study, but it uses a cross between a [I]pimpinellifolium[/I] and a giant fruited domestic tomato to identify the QTL's that contribute to fruit size. Six loci were identified that made a significant contribution to fruit weight, two of the most significant mapping to the classical genes [I]fasciated (f)[/I] and [I]locule number (lc)[/I]. Not all six of these may be in the large fruited variety in your cross but it is likely there are at least three or four including f and lc so it is going to take some serious selection to recover the size you desire.

If it was me, I would select for size first and color second. For example, if I found a type that was huge fruited but red, I would grow that out in preference to one that was medium sized and black, in the hope that it segregated for gf in the next generation. Actually, a very good backcross would be the largest fruited red (or black) F2 and the green parent, I think that would give you a very big push in the right direction.

[QUOTE=Minnesota Mato;470161]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)[/QUOTE]
Another thought, you could start 200 seeds and plant them out five times as crowded as you normally do, then when the first fruits start to form it will be very easy to identify the majority of small fruited selections and yank them all out leaving your best 20%.

[QUOTE=maf;470480][URL="http://www.genetics.org/content/158/1/413.full.pdf"]Dissecting the Genetic Pathway to Extreme Fruit Size in Tomato Using a Cross Between the Small-Fruited Wild Species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom[/URL]

Minnesota Mato, I don't know if you have seen the above study, but it uses a cross between a [I]pimpinellifolium[/I] and a giant fruited domestic tomato to identify the QTL's that contribute to fruit size. Six loci were identified that made a significant contribution to fruit weight, two of the most significant mapping to the classical genes [I]fasciated (f)[/I] and [I]locule number (lc)[/I]. Not all six of these may be in the large fruited variety in your cross but it is likely there are at least three or four including f and lc so it is going to take some serious selection to recover the size you desire.

If it was me, I would select for size first and color second. For example, if I found a type that was huge fruited but red, I would grow that out in preference to one that was medium sized and black, in the hope that it segregated for gf in the next generation. Actually, a very good backcross would be the largest fruited red (or black) F2 and the green parent, I think that would give you a very big push in the right direction.[/QUOTE]

I knew that the [I][B]f[/B][/I] and [I][B]lc[/B][/I] traits were important in fruit size, as well as an unnamed gene that results in larger cells (and therefor larger seeds and fruit), but I didn't realize there were likely to be three others as well.

The more genes contribute to the large size you're looking for, the more plants (or years) you'll have to work on it... no matter if you can use backcrossing to reduce the numbers you'll need.

I'll set about checking the numbers for six traits, assuming all are recessive(?), and we shall see what sort of task you're engaging in.

Yes, that's pretty much the 'chart' I was looking for. In this case on this page: [URL]http://kdcomm.net/~tomato/gene/genes3.html[/URL] it has a way to enter the number of recessive genes and it gives you the number of plants.

However - can you not speed the selection for dominant genes by following a line of a plant? For each plant that has the set of genes you want, plant out a large number of plants (keeping each set of seeds segregated by parent). If over a very few generations that "line" is not having the recessive gene being expressed, won't you have bred out the recessive in a speedier fashion? This of course assumes other factors like taste, productivity, etc aren't being affected. If none of our lines are 'pure breeding' for the dominant gene, you have to start selecting the best out of your still segregating lines.

[QUOTE=carolyn137;470461]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.

[URL]http://www.kdcomm.net/~tomato/[/URL]

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

Carolyn[/QUOTE]

[QUOTE=Fusion_power;469958]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.
.[/QUOTE]

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...

[QUOTE=bower;470552]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.[/QUOTE]

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.

It is very interesting to see how many different ideas and different ways there are to achieve the same goal. I realize the art isn't in the crossing but in the care and the selecting of the following generations. Anyone can make a cross but knowing what to look for and finding it in the following generation is what makes a plant breeder.

I agree with you, but crossing is an art too. I remember my first year (when I was still trying to vibrate blossoms to get them to expel pollen (I found a *much* better method next year). and with breakage of styles when trying to strip the blossom for pollination. I got only one success take that year.

Last year I got many takes, and would have had even more crosses than I had if late blight hadn't devastated me mid-August.

[QUOTE=Minnesota Mato;470612]It is very interesting to see how many different ideas and different ways there are to achieve the same goal. I realize the art isn't in the crossing but in the care and the selecting of the following generations. Anyone can make a cross but knowing what to look for and finding it in the following generation is what makes a plant breeder.[/QUOTE]

[QUOTE=Darren Abbey;470591]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.[/QUOTE]

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. ;)8-)

[QUOTE=bower;470635]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. ;)8-)[/QUOTE]
Agreed. Fortunately all the plants that don't reach the ideal you're going for will still produce perfectly edible fruit. ;-)

[QUOTE]Fortunately all the plants that don't reach the ideal you're going for will still produce perfectly edible fruit. ;-) [/QUOTE]

Does this mean we get to eat our mistakes? I saw a bumper sticker a few months ago that said "in case of _______, eat the kids first!". Substitute your favorite disaster in the blank.

I have 46 plants of a Sunlucky line growing in the garden in hopes this particular group will be the ephemeral much desired stable cross that produces super sweet bicolor fruit the size and shape of an egg. It takes a LOT of space to do significant selection for fruit traits.

[QUOTE=Fusion_power;470724]Does this mean we get to eat our mistakes? I saw a bumper sticker a few months ago that said "in case of _______, eat the kids first!". Substitute your favorite disaster in the blank.

I have 46 plants of a Sunlucky line growing in the garden in hopes this particular group will be the ephemeral much desired stable cross that produces super sweet bicolor fruit the size and shape of an egg. It takes a LOT of space to do significant selection for fruit traits.[/QUOTE]

I was thinking about that, that you'd need to grow out a lot to verify a stable OP for release, after the seven year selfing, and the selection of the fruit traits which also takes more space.

I hope you got it, but if not... you're going to need some help to eat all those mistakes. ;)
I'd love to know more about the process of taste testing 46 similar or identical fruit... you should make a video. 8-)

interesting discussion. I'm looking into trying my hand at growing and perhaps even attempting crosses with wild tomato species this next summer.

I just learned that Purple Smudge has some S. peruvianum heritage so since S. peruvianum is one of the harder crosses to do i'm wondering if attempting a backcross with Purple Smudge x S. peruvianum would have a higher rate of success since some wild genes may still be floating around (though perhaps very little at this point).

It seems the orange version of Purple Smudge is the only one now commercially available, so i'm not sure if that further dilutes the wild genetics even more. But regardless i think i'll give it a go if i can. I've ordered some seed for the orange fleshed Purple Smudge anyway. Worth a try in my opinion. In my experience sometimes tinkering with things will occasionally pay off. And if not, i'll have fun trying anyway.

I gather from the other species that are more easily crossed they are still essentially one-way crosses by using the more domesticated parent as the pollen receptor since there are fewer genes that will reject it. This seems to hold true with other species like teosinte -> corn crosses and others. So thinking of that it would be best to try using Purple Smudge as the receptive parent and S. peruvianum as the pollen donor.