New Genetic Research Shows Low Diversity in Tomatoes
 

Reported over at phys.org:
[url]http://phys.org/news/2014-10-uncover-tomato-genetic-history.html[/url]

That didn't say very much did it?

Linda

It linked to a site where the original paper could be purchased: [url]http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3117.html[/url]

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

Don't bother. This is such old and blase' news that it is not worth reading.

The domestic tomato has less genetic diversity than any other domesticated crop. This is because it descended from just a few plants domesticated somewhere in central America. Charles Rick wrote and spoke quite a bit about this lack of diversity.

What is the significance of this "lack of diversity"? It means that all the variation in colors and shapes are from minor variations in about 50 genes, 12 or so affect shape, about 9 affect color, and the rest affect leaf structure, locules, and other traits. The result is that we can breed tomatoes until we are blue in the face, but we will NOT find good disease tolerance anywhere in domestic tomato. This is why so much effort has been put into crosses with wild tomato species which still have the natural diversity they started with. This is why I grew plants from a cross of Piennolo X LA0417 and another of Piennolo X LA2175. I want some of that diversity in my tomatoes because it means healthier plants and a chance to improve the genome.

Remind me to send you some of the Piennolo X LA0417 seed Joseph. It should have potential in your climate.

Excellent post, Fusion. Thanks.

Here's a little more.

[URL]http://www.the-scientist.com/?articles.view/articleNo/41194/title/360-Degree-View-of-the-Tomato/[/URL]


Sequencing hundreds of lines opens the potential for Genome-Wide Association Studies among other things. So far there has been only one such study that I know of. They used relatively few markers to find genes underlying fruit traits. It'll be open access next June.

[quote]They sequenced the genomes of 333 varieties of red tomato, 10 varieties of wild tomato and 17 modern commercial hybrids.

Despite the wide variation in tomato phenotypes that exist today, Huang and his colleagues found that there is, in fact, very little genetic variation among the modern tomato varieties.[/quote]
Here let me rewrite that to be accurate:
[quote]They sequenced the genomes of 333 varieties of red tomato, 10 varieties of wild tomato and 17 modern commercial hybrids. Huang and his colleagues found that there is [B]little genetic variation among red, round, modern hybrid tomatoes[/B].[/quote]
If they had included tomatoes of all colors, shapes, sizes, and vintages, they would have found plenty of variation.

Stupid is as stupid does.

Some context. "The Scientist" is a free magazine along the lines of "People" x "TIME" x "Popular Science". The writing and accuracy of information is variable, as it is in all secondary sources of information.

I was able to get the full paper today. Attached is the list of varieties/accessions they used.

Here is a GWAS example in the paper:

"Red-fruited tomatoes are widely consumed, but pink-fruited tomatoes are especially popular in China and Japan (31). Two independent studies (31,32) demonstrated that the pink gene y on chromosome 1 corresponds to SlMYB12, which controls the accumulation of yellow-colored flavonoid (naringenin chalcone) in the tomato fruit epidermis (peels from pink fruit are colorless owing to the absence of flavonoid); however, the causative variant remains unknown. To identify the allelic variation underlying this phenotype, we performed a genome-wide association study (GWAS) using 231 tomato accessions with known phenotypes. The strongest association signal (SNP y, P < 1 × 10−32) resided 8,616 bp upstream of the start codon of SlMYB12 (Fig. 3b). We further analyzed the upstream and downstream sequences of the target gene for structural variants and discovered a 603-bp deletion in the upstream region of SlMYB12 (−4,865 bp relative to the start codon) that was present in most pink-fruited accessions (Fig. 3c). Among 205 red-fruited accessions and 122 pink-fruited ones (96 additional pink-fruited accessions were added for this analysis), the 603-bp deletion coincided with the phenotype in all but 4 accessions. We sequenced the genic regions of SlMYB12 in these four accessions and identified two nonsense mutations (a nucleotide substitution (C>T) and a 1-bp insertion (TG>TAG)), both resulting in the introduction of premature stop codons. It is noteworthy that the 603-bp deletion was more diagnostic than SNP y, as two recombinants were found (genotype II and IV in Fig. 3c). We hypothesize that the deletion might impair the transcription of SlMYB12, whose expression is silenced in pink fruits (32)"

ChrisK,

Thanks for posting that. I read through the list of varieties and only recognized a few. The vast majority seemed to be processing/canning varieties.

I stand by the idea that, even if just for control purposes, they should have tested a few varieties known for exceptional taste like Cherokee Purple, Wes, Pink Berkeley Tie Dye, etc.

Some context. "The Scientist" is a free magazine along the lines of "People" x "TIME" x "Popular Science". The writing and accuracy of information is variable, as it is in all secondary sources of information.

I was able to get the full paper today. Attached is the list of varieties/accessions they used plus and GWAS figure.

Here is a GWAS example in the paper:

"Red-fruited tomatoes are widely consumed, but pink-fruited tomatoes are especially popular in China and Japan (31). Two independent studies (31,32) demonstrated that the pink gene y on chromosome 1 corresponds to SlMYB12, which controls the accumulation of yellow-colored flavonoid (naringenin chalcone) in the tomato fruit epidermis (peels from pink fruit are colorless owing to the absence of flavonoid); however, the causative variant remains unknown. To identify the allelic variation underlying this phenotype, we performed a genome-wide association study (GWAS) using 231 tomato accessions with known phenotypes. The strongest association signal (SNP y, P < 1 × 10−32) resided 8,616 bp upstream of the start codon of SlMYB12 (Fig. 3b). We further analyzed the upstream and downstream sequences of the target gene for structural variants and discovered a 603-bp deletion in the upstream region of SlMYB12 (−4,865 bp relative to the start codon) that was present in most pink-fruited accessions (Fig. 3c). Among 205 red-fruited accessions and 122 pink-fruited ones (96 additional pink-fruited accessions were added for this analysis), the 603-bp deletion coincided with the phenotype in all but 4 accessions. We sequenced the genic regions of SlMYB12 in these four accessions and identified two nonsense mutations (a nucleotide substitution (C>T) and a 1-bp insertion (TG>TAG)), both resulting in the introduction of premature stop codons. It is noteworthy that the 603-bp deletion was more diagnostic than SNP y, as two recombinants were found (genotype II and IV in Fig. 3c). We hypothesize that the deletion might impair the transcription of SlMYB12, whose expression is silenced in pink fruits (32)"

I think that's what they were interested in, not capturing all diversity that's out there.

"Genomic analyses provide insights into the history of tomato breeding"

[QUOTE=feldon30;434669]ChrisK,

Thanks for posting that. I read through the list of varieties and only recognized a few. The vast majority seemed to be processing/canning varieties.

I stand by the idea that, even if just for control purposes, they should have tested a few varieties known for exceptional taste like Cherokee Purple, Wes, Pink Berkeley Tie Dye, etc.[/QUOTE]


Edit: T'ville is acting strange when editing posts. Not sure why it's a double post above!

GWAS
 

In case anybody is wondering what Genome-Wide Association Mapping (GWAM also GWAS (Studies)) is, here are some slides I made a while ago to explain it. The slides don't go into the mathematics behind it and are simply a high level conceptual explanation.

Thanks ChrisK for explaining this in such an understandable format.

Very nice presentation Chris. A wee child could understand the GWAS process... and see it as fun. :D

Still confused about the 'low diversity' of tomatoes, though, other than disease/stress resistance traits which seem to have been left behind in the wild. Phenotypic diversity of tomatoes seems pretty impressive, compared with other crops.:surprised:

[url]http://cdn.intechopen.com/pdfs-wm/31476.pdf[/url] [QUOTE]The irony of all this, says Steve Tanksley (geneticist at Cornell University, and precursor of all these studies) "is all that diversity of heirlooms can be accounted for by a handful of genes. There are probably no more than 10 mutant genes that create the diversity of heirlooms you see” (Borrell 2009)[/QUOTE]