I came upon this recent article, which gives a nice overview of the basic genes governing fruit color, shape, size etc. and it reminded me to start a thread for our favorite resources. Will find my old file and add some faves when I get a minute.
Meanwhile please post here any links to articles or videos you found most useful.

Here's the recent article:
https://www.mdpi.com/2073-4425/11/11/1278/htm

And for all the genes not covered there, the ultimate resource is TGRC's searchable database:
https://tgrc.ucdavis.edu/Data/Acc/dataf ... t=nav.html

I think my favorite sources are you, TGRC, TomatoJunction, science news/articles, search engines, experimentation, and patience.

Understanding some principles of the carotenoid biosynthesis pathway definitely helps in making sense the tomato fruit color inheritance. Mendelian inheritance focus on recessive and dominant genes and phenotypes but it does not explain anything on what happens inside the cells. I don’t have any favourite articles one the carotenoid pathway but below is the latest one I have been reading.

https://onlinelibrary.wiley.com/doi/fu ... 03.00018.x

It took me long time to realize that there are often two main types of ”loss of function” genes related to the same phenotype or gene: defect in the gene itself or in the regulation system. The first means that the encoded protein or enzyme is dysfunctional and the second that the encoding does not activate (or there is some other mistake in the regulation). For example, the phenotype of rrtt can be yellow (probably when the yellow flesh phenotype is because a faulty PSY enzyme) but it can be orange too (probably when the yellow flesh phenotype is because the PSY enzyme encoding is not activated correctly but the enzyme is functional). Genes like Beta (high beta carotene) and old gold (high lycopene) are other similar examples. Beta is a ”loss of” in the down regulation of CYC-B enzyme (which happens naturally in red ”wild type” tomato with some beta carotene) and old gold is probably a non-functional CYC-B.

Finding a good information resource that has been written for plant breeders on these topics is surprisingly difficult: they are either oversimplified or too deep on very tiny fragment of knowledge (and often off the breeding topic). No need to say that the classic Frogsleapfarm blogspost is always a good place to start.

http://frogsleapfarm.blogspot.com/2014 ... or-in.html

Working on some wayback machine links for Keith Mueller's old site since it seems to have disappeared and it was the gold-standard for hobbyists.

Home page - https://web.archive.org/web/20231120063 ... t/~tomato/

How to Cross - https://web.archive.org/web/20230829045 ... ngtom.html

Genetics 101 - https://web.archive.org/web/20230829043 ... genes.html

Genetics 102 - https://web.archive.org/web/20230905084 ... enes2.html

Genetics 103 - https://web.archive.org/web/20230930091 ... enes3.html

Basic Gene List (working images) - https://web.archive.org/web/20210125125 ... utant.html

Tomato Genetics Cooperative (University of Florida)

https://tgc.ifas.ufl.edu/

Here's an updated version of the TGRC link:
This might be helpful to search certain genes or traits. It's not a comprehensive database, but there's quite a lot of traits here.
https://tgrc-mvc.plantsciences.ucdavis.edu/Genes/search

The gene links in this page still do not work:
https://web.archive.org/web/20230414210 ... utant.html

Doffer wrote: ↑Wed Feb 19, 2025 11:43 am The gene links in this page still do not work:
https://web.archive.org/web/20230414210 ... utant.html

Looks like the gene links went down sometime in 2021 which would be prior to the date of the archive link I used for Keith's site so that makes sense.

Here's a link to this page from 2021 where the links are working for me. Good catch - I'll update my first post.

https://web.archive.org/web/20210125125 ... utant.html