Author Topic: Known tomato gene reference  (Read 289 times)

Greenie DeS

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Known tomato gene reference
« on: 2021-07-22, 07:59:12 PM »
Does anyone have a handy reference for what genes are known; whether they're dominant, codominant, recessive, etc; what traits are definitely not confined to a single gene, etc? I've picked up pieces here and there but I've never found one good single reference to seek out when I have a question.

Garrett Schantz

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Re: Known tomato gene reference
« Reply #1 on: 2021-07-22, 10:33:45 PM »
A single reference type of information document is probably hidden in private scientist / breeder-only type of thing.

Some things like orange fruits can vary with what gene causes their coloration. Some orange tomato genes also cause fruit that tastes different.


Things like leaf type, flower color / size - some other things may not be documented very well either. Sometimes these things are mentioned on papers, but not really a main focus. Trichome types / chemicals are starting to get more research.

There appears to be different types of exsertion as well.

Some S. pimpinellifolium types can have slightly exserted flowers, slightly increases the outcrossing rate.

Some S. habrochaites types can be slightly exserted like S. pimpinellifolium or be highly exserted, which increases the outcrossing rate quite a bit.

Some S. peruvianum - arcanum etc - can be VERY exserted. I haven't found these types in Joseph's population. There are some other exserted variants as well.

Most papers won't do much research into the exserted traits. So far from what I can tell, habrochaites / pimpinellifolium exsertedness is usually recessive - I don't know if the different levels of exsertion will give anything different than a non-exserted x highly exserted.


Anthocyanin is an interesting one. Seems to be caused by multiple genes. Some genes cause purpleness in the calyx, others in the stems, root nodules, fruit. And then there are varying degrees of how much anthocyanin are in the stems / fruit etc. When these genes are combined into one plant, they can cause codominance in some areas. The genes for anthocyanin all seem to be somewhat related.

I may attempt to make an "Open Source" type of tomato gene reference document. I would give permissions to some people here, probably make some backups every time it is updated - so that it doesn't get abused.

A lot of papers are also behind paywalls - even if I bought these, added them in as a source - then made a document using the information, I could still get into trouble. A lot of the research papers have license agreements.

I will do my best with public sources - different things will be split into different topics. No idea when I will make / finish something like this though.


Edit: https://tgrc.ucdavis.edu/ has some genes mentioned / part of a database.
« Last Edit: 2021-07-22, 11:03:02 PM by Garrett Schantz »

Nicollas

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Re: Known tomato gene reference
« Reply #2 on: 2021-07-23, 02:14:42 AM »
There are some good list here :

https://tgrc.ucdavis.edu/Data/Acc/dataframe.aspx?start=GenSearch.aspx&navstart=nav.html

http://www.kdcomm.net/~tomato/Tomato/mutant.html

Its handy for single genes, for quantitative traits its usually in scientific publications and would be not be easy to translate to an easy to read form.

Most of the list have genes as an index, it would be cool to make it the other way ("i want orange fruits, what strategies can i take")

William S.

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Re: Known tomato gene reference
« Reply #3 on: 2021-07-23, 10:58:21 AM »
I know the genes I work with most at least in functional ways. Knowing that genes can be dominant, recessive, codominant, and that some traits can be more of a QTL type situation is functionally pretty useful. So I guess my recommendation is to make a cross and see what the F1 is like and then grow a big F2.
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Steph S

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Re: Known tomato gene reference
« Reply #4 on: 2021-07-24, 05:52:34 AM »
The TGRC database is really useful if you know what you're looking for and need to see a pic or find out about dominance.
I usually just google for 'tomato genetics' + pheno and read what comes up.
Anything interesting gets pasted into a txt file...  but it's been a while since I referred to that material.
Starting a thread to discuss some aspect of genetics may be useful, as people can add to it whenever they find something relevant.