It is not the same gene, there are mutations in the regulatory element, that permit the anthocyanin development specifically in fruits, but not in spring shoots.
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Very interesting article, thanks a lot! So my understanding was off. This Tcs1 portion of Ruby in blood oranges leads to Ruby expression in fruit tissues under specific conditions (light and cold).
If you had a Valentine pomelo, it would be the best bloody seed parent, as it has about 90% zygous seeds.
It's probably more complicated with these gene variants. I have a yuzu with shoots without anthocyanin, and among its zygous descendants (of which about 10%) there are seedlings with antacyan shoots (a minority, probably, when a homozygote is obtained for this trait). That is, the broken gene is dominant here.
I do have one, but I didn't know it was a good seed parent. It doesn't get a colored rind like Moro or Amoa8, unfortunately, but the flesh is quite nicely colored anyway. I'm hoping it's going to bloom next year then!
Interesting comments about your yuzus, I didn't know there were such variations, as all of my yuzus have had this trait so far.
Citrus Medica has pigmentation in the buds (that's where the lemon inherited it), and yet it was crossed with a blood orange and a red lemon came out (Limone Rosso). But now that I have it, I see that its buds are not anthocyanin-containing.
I'm not familiar with this variety, but I have seen it described as a citron x lemon cross. Also, does the flesh get colored in this one? I've only seen red rind on pictures online, the flesh was still yellow. It seems like it's anthocyanins though, according to what I've read (pigmentation is linked to light and cold, like in blood oranges).
That's interesting—then the F1 should potentially produce 50% blood-colored fruits. That seems straightforward; the real challenge is incorporating the remaining Yuzu characteristics.
I doubt it's so easy, personally. Ruby in blood orange is dominant to Ruby in a regular orange. It seems dominant to pomelo Ruby as well (as seen in Valentine). However, it might not be dominant to Yuzu's version of Ruby. It is seemingly recessive to Poncirus' version, since no blood citranges have been obtained despite such a cross being made. But yeah, keeping all of the yuzu traits can be hard... It'll probably require backcrossing, I don't really see any other possibility for that.
Here is an interesting article on this theme.
Thanks a lot, this was a very interesting read! This image is a good breakdown of which genes do what for pigmentation. Now, it remains to be seen which versions are dominant when crossing with yuzu, or any other hardy citrus...

Do you guys have suggestions that could be viable from the flesh colour point of view?
Based on what Ilya wrote, Marumi x Moro should be good, as long as they produce hybrids. And Amoa8 inherited the red flesh part from Moro, so I guess Amoa8 can also work. Now that I think of it, there can be fairly hardy solutions, too at least on paper, like Marumi/Nameiwa x Sanguine de la Montagne Corse. But this is just a made up idea, I don't know the genetics of that specific blood orange or how its flesh colour is inherited. But sadly, hybrids of that cross would never have ripe fruit before November in my area. Maybe it's a rubbish idea, I don't know.
I believe it can be done, depending on the dominance of the regulatory genes in kumquat compared to blood orange. Kumquats have a shorter juvenility than most citrus, so it can be one to experiment with! Ichangquats can ripen earlier than pure kumquats, and are hardier, so maybe it would be worth it to try using them instead?
I have a question about the dominance of the Ruby gene. There are several hybrids of Ruby orange and PT: Benton, Cunningham, Morton, Sanford, Wallace, Phelps, Savage, Rusk, C-35, C-32. And that's not all. I haven't heard of any of them having bloody flesh. And I have not heard at all that citranges or any other PT hybrids with bloody flesh exist. Therefore, it seems to me that the Ruby allele, which causes staining, is dominant only in relation to the orange non-blood allele. But it is recessive against the non-blood variant of the PT gene. Or, in PT some other genes disrupt the biosynthesis of anthocyanins. What do you think about this?
Yes, this is what I think too! Ruby in blood orange is recessive to PT's Ruby. And it might be the same with ichang papeda, or yuzu, or kumquats... We'll need to try. And as you've said, maybe something else prevents the expression of Ruby in fruits. But I'd expect at least some F2 plants to have red flesh... Yet no reports of that. Curious.