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Old June 17, 2015   #31
BigVanVader
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When doing these kinds of studies selection of the population is important, you can't have too much minor allele frequency or you have no statistical power to identify association. I found the paper to be quite interesting for what it was and for what their stated objective was.

I found this interesting:

However, the genome-wide genetic basis underlying the divergence between tomatoes for fresh consumption and processing tomatoes was not previously studied.
To search for SNPs underlying this divergence, we computed the population differentiation statistic (FST) of each SNP site for 22 modern processing accessions and the remaining 144 BIG accessions. We observed a non-random distribution of highly divergent sites (the top 1% had FST ≥ 0.4464; the genome average was 0.07). Intriguingly, 90.53% (63,009 of 69,603) of these sites resided on chromosome 5 (Fig. 3a),
spanning the majority of the chromosome (from 3.5 to 62.8 Mb).
We note that a previous study identified three SSC QTLs (ssc5.1, ssc5.2 and ssc5.3) located on the short arm, in the centromeric region and on the long arm of chromosome 5, respectively29. A major fruit firmness QTL, fir5.1, also resides in the centromeric region of chromosome 5 (ref. 30). In addition, the chromosome has a large centromere with a length of ~50 Mb, extending from 10 to 60 Mb on the assembled chromosome14. Therefore, selection of the QTLs for higher SSC and better fruit firmness likely resulted in the hitchhiking of almost the entire chromosome 5, representing a genomic signature of modern processing tomatoes.
Chris could you try and put that in laymen terms for me? Is it saying that by selecting for fruit firmness they inadvertently reduced the diversity?
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Old June 17, 2015   #32
rubbe87
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Which wild tomato species are you currently growing?

I'm growing:

pimpinellifolium
peruvianum, glandulosum

Seeds are arriving soon for:

habrochaites

I'm growing 14 plants that are known or suspected of being inter-species hybrids.
i got no wild ones i might get a few next year.

now im growing sun gold, black from tula, kumato , indigo rose, cornabel, plumtomato, and some other ones i don't know what they are.
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Old June 17, 2015   #33
joseph
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Chris could you try and put that in laymen terms for me? Is it saying that by selecting for fruit firmness they inadvertently reduced the diversity?
Basically one gene/chromosome was isolated from the wild species, and incorporated into the domestic species. The domestic species already had tremendously limited diversity because of the manner in which they were domesticated and commercialized.

Last edited by joseph; June 17, 2015 at 05:39 PM.
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Old June 17, 2015   #34
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I am growing out 2 groups of F2 seedlings from a cross of S. Lycopersicum X S. Pimpinellifolium with 16 plants per in my garden. I have plants lined up to make more crosses this year using S. Habrochaites as the pollen parent.

Crossing all the known tomato species into one plant would of necessity severely decrease genetic diversity in the tomato clade. The way to increase diversity is to domesticate more of the wild species by bringing desirable genes in through crosses. S. Habrochaites and S. Peruvianum have the most potential for stress tolerance genes and for disease tolerance. S. Pimpinellifolium and S. Galapagense have the most potential in very close relatives to the domestic tomato.
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Old June 18, 2015   #35
Darren Abbey
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I am growing out 2 groups of F2 seedlings from a cross of S. Lycopersicum X S. Pimpinellifolium with 16 plants per in my garden. I have plants lined up to make more crosses this year using S. Habrochaites as the pollen parent.

Crossing all the known tomato species into one plant would of necessity severely decrease genetic diversity in the tomato clade. The way to increase diversity is to domesticate more of the wild species by bringing desirable genes in through crosses. S. Habrochaites and S. Peruvianum have the most potential for stress tolerance genes and for disease tolerance. S. Pimpinellifolium and S. Galapagense have the most potential in very close relatives to the domestic tomato.
Different people mean different things by the word "diversity" in a biology context. Some people use the word to refer to increased heterozygosity within a single genome, rather than differences between individuals. Some people use the word to refer to the level of genetic variations available in the most common strains, rather than all available. I had several eye-opening discussions with other biologists at recent seminar series at my university, because of their varied and mutually incompatible uses of this term.

If you crossed all the wild species into the domesticated plant, the resulting plant would likely have more heterozygous loci in its genome... but the vast majority of the genetic diversity in the parent species would have been discarded by the time you got to the final plant. As well, every time you selfed the plant, it would on average lose half of the heterozygous loci it had.

What you really need to maintain diversity (total genetic variation) over a long term is many independent lineages, each composed of a mix of interbreeding individuals. ...exactly the opposite of how people [generally] breed plants.
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Last edited by Darren Abbey; June 18, 2015 at 03:42 AM.
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Old June 18, 2015   #36
rubbe87
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I am growing out 2 groups of F2 seedlings from a cross of S. Lycopersicum X S. Pimpinellifolium with 16 plants per in my garden. I have plants lined up to make more crosses this year using S. Habrochaites as the pollen parent.

Crossing all the known tomato species into one plant would of necessity severely decrease genetic diversity in the tomato clade. The way to increase diversity is to domesticate more of the wild species by bringing desirable genes in through crosses. S. Habrochaites and S. Peruvianum have the most potential for stress tolerance genes and for disease tolerance. S. Pimpinellifolium and S. Galapagense have the most potential in very close relatives to the domestic tomato.
why would crossing all wild tomato species into one plant decrease genetic diversity in that plant should it not become much higher then a normal wild tomato plant?
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Old June 18, 2015   #37
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There are 13 wild tomato relatives that can be crossed with domestic tomato. Embryo rescue is necessary with about half of them. That means you are starting with 14 separate genomes, some of which have more diversity than all of the others combined. (S. Peruvianum) When you combine all of them into a single plant, you have of necessity limited yourself to 2 specific genomes. Selfing that plant will cut you back down to 1 genome. So from 14 highly diverse genomes the result is a single genome with most of the diversity lost along the way.

As Darren Abbey said above, the way to increase diversity is to include as many breeding groups as possible. The more plants in the interbreeding population, the more diversity retained.

There are lots of genes that should be eliminated. For example, S. Habrochaites has a huge cold tolerance gene on chromosome 12. Domestic tomato has very little cold tolerance. It makes sense to eliminate the chromosome section from domestic tomato and keep the one from S. Habrochaites.
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Old June 20, 2015   #38
Darren Abbey
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why would crossing all wild tomato species into one plant decrease genetic diversity in that plant should it not become much higher then a normal wild tomato plant?
One plant produced from inbreeding over several generations (the conventional way of breeding tomatoes) will have no genetic diversity at all, by any definition of biological diversity. You need heterozygosity, multiple plants, or both.
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Old June 20, 2015   #39
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why would crossing all wild tomato species into one plant decrease genetic diversity in that plant should it not become much higher then a normal wild tomato plant?
rubbe87, check out this page that explains some basics of genetics in tomato:

http://kdcomm.net/~tomato/gene/genes.html

In the visual example that's given, the two different alleles are reperesented as green or blue 'half-eggs' representing the genetic content for one trait in a given tomato plant.

In the case of wild tomato relatives, there may be different alleles for the same trait, which aren't found in domestic tomatoes. So for the leaf shape example, suppose there are several, or a dozen different leaf shape alleles other than RL and PL, which could be represented as different colour 'half eggs' as shown in that page. Lets say yellow and red and orange 'half eggs' are also needed to represent all of the leaf shape alleles that exist amongst tomato and relatives, and the diversity of possibilities in any given plant.

But in any given plant, there can only be two alleles at one time (represented as the two half eggs of any colour combination you like). If you have yellow and blue, there's no place left on the "locus" for alleles represented by green and red. If it is a hybrid with two alleles carried, you can cross it with anything else but the offspring can still only have two different alleles max in the single plant. And after it self pollinates for a couple of generations, it will eventually gravitate towards homozygous state ie the same allele is represented twice while the other is lost, and you have conserved only one of many possibilities that existed for that trait.

This is why we need seed banks and breeding programs with as many different varieties (and relatives) as possible to conserve all the alleles and genetic diversity in the tomato.
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