New Genetic Research Shows Low Diversity in Tomatoes

[Fred Hempel]

Frankly, I think Tanksley is underestimating the number of genes responsible for hierloom diversity.

Why? Well, for one thing, a simple story is a fundable story, and I would guess his statement about the small number of genes involved in heirloom diversity is right at the front of all his grant proposals.

[Fusion_power]

Feldon, while I agree that there is significant diversity is shape, color, size, and flavor, that still equates to relatively few genes affecting a fairly broad range of characteristics. Human selection has increased diversity in these traits by accumulating genetic variants. The underlying genome of the domestic tomato is still the narrowest of any commercial crop. Part of this is because the tomato is a natural inbreeder. Part traces back to the limited number of plants that went through early domestication.

The only way to significantly increase variation in domestic tomato is through crosses to wild species.

[Darren Abbey]

Originally Posted by Fusion_power

The only way to significantly increase variation in domestic tomato is through crosses to wild species.

This is being done, both by private and commercial breeders. Solanum cheesmanii, S. chilense, S. hirsutum, S. peruvianum, and S. pimpinellifolium have all contributed genetic material to some varieties.

Unfortunately, most of the crosses bring with them non-ideal flavor attributes and the practice of using back-crosses to isolate only the wild trait of interest (disease resistance, anthocyanins, etc.) returns the breeding lines back to being very similar to the highly inbred types that are most domesticated tomatoes.

[Fred Hempel]

Originally Posted by Fusion_power

Feldon, while I agree that there is significant diversity is shape, color, size, and flavor, that still equates to relatively few genes affecting a fairly broad range of characteristics. Human selection has increased diversity in these traits by accumulating genetic variants. The underlying genome of the domestic tomato is still the narrowest of any commercial crop. Part of this is because the tomato is a natural inbreeder. Part traces back to the limited number of plants that went through early domestication.

The only way to significantly increase variation in domestic tomato is through crosses to wild species.

Sure, domestic tomatoes probably went through a genetic bottleneck while being domesticated, and that is why many traits must come from related species.

But, Tanksley's statement that 10 genes account for most of heirloom diversity does not make any sense to me. There are many more genes discussed here affecting various traits. And then it is common for someone looking into particular shapes or colors or striping, etc. commonly state something like "well it's a little bit more complicated than Gene X and Gene Y...."

[Fusion_power]

I would not agree with 10 genes. I would suggest something less than 100 but more than 10. I can describe at least 20 traits that affect tomato shape, size, color, or vine attributes.

The one interesting bit of information in this thread is the clear skin trait which appears to be from disabling part of one particular gene. Almost all pink tomatoes share the same variant, but a few were found that have different mutations affecting the same gene and yielding the same phenotype, i.e. "pink" tomatoes.

This is a close parallel to the mutation that causes black tomatoes where 5 separate mutations affecting one gene all give nearly identical phenotypes.

[ChrisK]

What I think would be pretty fun would be to genotype an "heirloom" population to assess diversity and phylogeny then GWAS on that population to identify the genetic architecture underlying flavor. I think Klee said one time he thinks he can restore flavor to commercial tomatoes with maybe 5 genes.

GBS is cheap now. I think you can generate a couple hundred K markers for 38 bucks a sample in Buckler's lab. Kickstarter anyone?

[feldon30]

Originally Posted by Fusion_power

Feldon, while I agree that there is significant diversity is shape, color, size, and flavor, that still equates to relatively few genes affecting a fairly broad range of characteristics.

I wish the study had tested that, instead of saying "Look at these 100 canning and similar varieties. They're almost all identical!" In other news, water is wet!

[ChrisK]

Have you read the paper?

Originally Posted by feldon30

I wish the study had tested that, instead of saying "Look at these 100 canning and similar varieties. They're almost all identical!" In other news, water is wet!

[Fusion_power]

I had a field day reading through the varieties list and comparing with TGRC lines I have grown. LA0417 is correctly identified as Cerasiforme! I knew this from growing and enjoying the fruit, but it is still shown as Pimpinellifolium at TGRC.

Correct placement of varieties in species is a very interesting side effect of the genetic analysis. There are 16 varieties placed in different branches in this study. Most were moved from Pimpinellifolium to Cerasiforme or the reverse.

I wish they had tested LA2175 which is the S. Habrochaites line that shows excellent disease tolerance in my garden.

Edit: after studying the varieties in some detail, it is obvious someone had a goal. They tested Richters wild and 2 NC EBR lines. This sheds light on the early blight/late blight breeding work Randy Gardner did while developing the Mountain lines. There are also signs that they hand picked some wild lines because of reported disease tolerance. LA0722, LA0417, and Richters fit this group. There is another group of heritage processing varieties like King Humbert, San Marzano, and Principe Borghese. All in all, the reported conclusions are unremarkable, but the varieties tested can be used to map introgressions from wild species and to pinpoint trait hotspots in the genome.

If you look closely, there are a few duplicates. LA0417 and LA0722 are listed twice. LA0417 is a segregating population as shown by highly variable disease tolerance in my garden last year. They probably tested more than one plant in order to pinpoint the differences.

[bower]

I think the significant conclusion from this work is the importance of conserving wild species diversity by protecting their habitat. Pathogens are diverse and always mutating as well, and the resistance we see from one allele today may require another allele tomorrow.

Meanwhile, kudos to everyone who brings new alleles into the tomato genome, with all the time and space and other resources that requires...

[ChrisK]

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.

[nicollas]

Originally Posted by joseph

It linked to a site where the original paper could be purchased: http://www.nature.com/ng/journal/vao...l/ng.3117.html

I'll be saving up my money to get that one...

It is available here : http://plantbiol.genetics.ac.cn/the_...%20et%20al.pdf

[snugglekitten]

They will go back to self-pollination and genetic endogamy if they keep the trait that controls for the stigma remaining enclosed within the anthers as do most rl lycopersicum, otherwise the genetic diversity could mushroom outwards, and mix more between the wild strains such as pimpillifolium (or however its spelled) and cheesmanii.

[rubbe87]

i would like to see all the wild tomato species crossed into one plant. And use that plant for crossing whit the low diversity tomatoes.

[joseph]

Originally Posted by rubbe87

i would like to see all the wild tomato species crossed into one plant. And use that plant for crossing whit the low diversity tomatoes.

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.