Pea information Pu Pur

[Galina]

I need some help please understanding the following statements from the John Innes website on pea genes.

It says for: Pu
http://data.jic.ac.uk/cgi-bin/pgene/default.asp?ID=552

Description

Together with Pur purple pods, expression requires A. Pu Pur A Am B Gp purple pod; Pu Pur A and am or b or gp red pods.

I only understand that together with Pur it makes solid purple. Expression requires ?. Can't find Am or am


It says for Pur:
http://data.jic.ac.uk/cgi-bin/pgene/default.asp?ID=553

Description

Purple pods when together with Pu. Four alleles reported: Pur, uniform purple; pur<a, major part purple; pur<b, less colour on pod, may limit colour to funiculus. Character can be variable in expression and unstable. Studies have show that a pigmented funiculus differentiates the presence of Pur from Pu (non-pigmented).

What does pur<a mean? pur<b
What are the 4 alleles?

How neat to be able to differentiate Pur from Pu. Will look at the tiny bits that connect the peas to the pod and see whether they are purple (Pur) or not (Pu) in partially purple pod. Next time - too late for this year.

I have a feeling this somehow explains why on the Elisabeth x Sugar Magnolia F2s we saw greener partially purple and more purple partially purple pods, and of course I did not look at the funiculi, because I did not know about them With dried and shelled pods it is a bit too late to see.
Unstable - would that explain why some pods on some plants were much more purple earlier in the year and much greener later on?

Also please, what is a linkage group and why should we know about it? Pu is III and Pur is I.

[Silverleaf]

Any purple expression requires A, because A "switches on" anthocyanin production. Without it, you won't see any purple at all anywhere.

Try looking for am1 or am-1, and am2 or am-2. Both make the flowers almost white in A plants, and apparently restrict the antho in the pod too, or modify it somehow.

The four alleles are:
Pur full purple
pur>a major part purple
pur>b less colour on pod, may limit colour to funiculus
pur no purple on pod (i.e. green or yellow depending on what other genes are at work)

...to be continued...

[Silverleaf]

Linkage groups: well, this involves some biology, but very basically it tells you where the locus is in the genome, physically speaking.

If two loci are close together on the same chromosome, they tend to be inherited together because of the way that whole chromosomes are "shared out" to create the gametes (pollen and ova). Loci are physically connected so they stay together, and instead of the F! producing four types of gamete (e.g. A B, A b, a B, and a b*) you'll only get two (A B and a b). Hopefully my diagram helps!

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But it's not that simple, because the pairs of chromosomes can swap equivalent sections before they split up, like exchanging the heads of two LEGO figures. Unlike with LEGO figures though, the break can occur anywhere, but the break occurs in the same place on both chromosomes so the swap is "fair", if you like. This means that those linked genes that were stuck together can end up separated.


I know, I spelled "separated" wrong... I have a block about that word!

Essentially though, what it means is that if the two genes you're looking at are in the same linkage group, the F2s won't show the 9:3:3:1 ratio as you'd expect. The closer the linkage, the larger the proportion of parental phenotypes you'll see. If you're getting weird numbers, it's always worth checking if they are linked because that might explain things**. Pur and D are linked, so you'll tend to see purple pods and axil pigmentation inherited together.

Hopefully this helps!

* These are examples and not pea genes - A and B are not linked in peas).
** Other things can explain weird numbers, but I'll go into those some other time if you're interested.

[Galina]

Any purple expression requires A, because A "switches on" anthocyanin production. Without it, you won't see any purple at all anywhere.

Try looking for am1 or am-1, and am2 or am-2. Both make the flowers almost white in A plants, and apparently restrict the antho in the pod too, or modify it somehow.

The four alleles are:
Pur full purple
pur>a major part purple
pur>b less colour on pod, may limit colour to funiculus
pur no purple on pod (i.e. green or yellow depending on what other genes are at work)

...to be continued...

Thank you very much, Silverleaf. Still cannot find am-1 or -2, or I don't use their search facility correctly, Leaving that aside, there are still questions.

Pu and Pur are dominant and make full purple pods with A. They are dominant because they have capital letters.

You also need dominant Pu and Pur for red pods (not just one of them) and additionally am or b or gp. Why all the 'or' and not 'and'. What are the options (spelled out for us slow ones) that can make red pods?

What is said about Pur is even more difficult to understand. Dominant Pur and Pu (with A) make purple pods.
Next allele is when pur is recessive (do all peas have either Pur or pur, but it is only because of A that we know about these, as they are suppressed in white flowering 'a' peas?) In this second allele is Pu dominant and pur recessive?

Suppressed because of 'a' is different from pur being recessive? 'a' would still suppress a dominant Pur and a dominant Pu>

pur>a? I don't understand the shorthand - it cannot mean pur greater than a? What does it stand for? It can't mean something like pur together with a, because pur is only effective because of 'A in the first place' . Pur>b is similarly confusing.

What am I not seeing here?
I can't even ask the right questions clearly it seems. Help- brain fog!

[Galina]

Thank you for your very helpful diagram about linkages. I understand that although it is a difficult concept. Basically if we look at the genes we are interested in and they are not in the same linkage group, the ratios work out as expected. Genes in different linkage groups ultimately lead to more phenotypes in plants we breed than if they were in the same linkage group. In the same linkage group they tend not to recombine. Linkage groups do matter a lot.

Thank you very much Silverleaf.

[Silverleaf]

No problem! I'll answer your other questions in the morning. Am1 http://data.jic.bbsrc.ac.uk/cgi-bin/...ault.asp?ID=38 Am2 http://data.jic.bbsrc.ac.uk/cgi-bin/...ault.asp?ID=39

[Silverleaf]

Pu and Pur are dominant and make full purple pods with A. They are dominant because they have capital letters.

You also need dominant Pu and Pur for red pods (not just one of them) and additionally am or b or gp. Why all the 'or' and not 'and'. What are the options (spelled out for us slow ones) that can make red pods?

Just remember that the site is for geneticists (and even I struggle with it a bit), so don't feel stupid if you don't get it right away! You have to think about pod colour being due to two factors mixing - antho (red/purple/pink pigment) and chlorophyll (green/yellow pigment). The antho is only on the very surface of the pod and it lets the base colour show through a little, and in a normal "wild type" pea you're looking at a green pod with reddish-purple over the top which looks like a dull darkish purple.

Okay, so A Pu Pur am (presumably either am1 or am2 will work since they basically do the same thing) makes red pods because the am does something weird to the antho in the pod - I don't know, but I'd guess it either puts less antho in the pod or changes the structure (and therefore colour) of the pod antho. Not a combination I've seen yet.

A Pu Pur b looks like the cross that jayb posted a little while back (an Elisabeth cross I think, but I can't remember exactly), but with fully wine red pods. This happens because b modifies all the antho in the plant so it's a lighter pinky-red colour. You can see the effects anywhere that antho is present, like in the flowers, axils, pods, and even in the testa spots if it has any.

And finally A Pu Pur gp. The antho is the normal red-purple, but the base colour of the pod is yellow instead of green. Red-purple on top of yellow looks red.

I suppose you could combine these and get different shades of red. I'd guess that A Pu Pur b gp would create a lighter red pod, perhaps more of a scarlet red, because it would have light antho over a yellow pod.

What is said about Pur is even more difficult to understand. Dominant Pur and Pu (with A) make purple pods.
Next allele is when pur is recessive (do all peas have either Pur or pur, but it is only because of A that we know about these, as they are suppressed in white flowering 'a' peas?) In this second allele is Pu dominant and pur recessive?

Think of it like some kind of filing cabinet, with a folder for every single locus. In the folder labelled "PUR" there can be two files only, and both have to be a type of Pur (an allele). Every pea has two files in there, each will either be Pur or pur>a or pur>b or pur (all alleles of the Pur locus). And yes, every pea has them unless something extremely weird's going on, but as you say, a can mask it.

This is what I was talking about before with epistasis - if a plant has a then you have no idea what genes it has for flower colour, or pod antho, or axil pigmentation, or testa spots, or whatever, because a means that the plant just doesn't know how to make any antho at all. a is epistatic to all those other antho genes.

In another folder, marked "PU", you have two files which will be Pu (dominant) or pu (recessive). And that folder is actually in a completely different drawer of the filing cabinet than Pur (i.e. that locus is on a different chromosome).

Suppressed because of 'a' is different from pur being recessive? 'a' would still suppress a dominant Pur and a dominant Pu>

Yep, a suppresses all anthocyanin. The folder marked "A" is where the start of the "recipe" for anthocyanin is supposed to be. A is the correct copy. a is basically nonsense. So an aa plant has no functional copies so it can't even get its ingredients together. No antho at all for the aa plant!

The recipe for antho is a complicated one, with many steps and ingredients. At the B stage of the recipe, if the plant has the incorrect instructions (bb), the antho is messed up somehow and turns out pinkish-red instead of purplish-red, for example.

The "PUR" folder is where the instructions are for how to transport antho to the pods and plane it there. Pur is a perfect copy of those instructions, while pur>a and pur>b only tell the plant how to do a partial job and pur is complete gibberish which doesn't make any sense at all and results in no purple going to the pods. You also need the instructions from "PU", of course, for fully purple pods.

So in the aa plant there isn't any antho and so it really doesn't matter whether the plant knows how to deposit it in the pods or not. No point in even looking in the "PUR" folder, or the "PU" folder, or the "B" folder, or any other folder relating to antho in any way. Those files could go in the bin ans far as the plant is concerned!

pur>a? I don't understand the shorthand - it cannot mean pur greater than a? What does it stand for? It can't mean something like pur together with a, because pur is only effective because of 'A in the first place' . Pur>b is similarly confusing.

Yeah, that's confusing. But it's just names, it doesn't mean anything other than "this is another allele of the PUR locus that isn't Pur or pur". It's just pur-type-a, and pur-type-b. Could certainly be clearer.

[Silverleaf]

Sorry it was later than advertised...

[Galina]

Thank you so much! Too much on yesterday anyway and I am only just getting around to reading the above.

[jayb]

Very interesting I'm just re-reading this again, I'll probably need to again a few times!
I picked some peas for seed yesterday, I'll see if any give up some information. Pretty sure Shiraz has purple funiculus.

[Galina]

Looking for something else, I happened to find these two pictures. Both are from the F2 plants of Sugar Beth (Elisabeth x Sugar Magnolia) that Jayb shared with me. The first one is far more purple (but I did not know about funiculi at the time or I would have checked out their colour). It is the kind of purple that is nearly fully covering the mangetout pods. The second type (on a snap pod as it happens) is not very purple at all, and as the season progressed the purple practically disappeared. The first type of purple also got much greener as the season progressed and I am glad that I marked up the pods with coloured string. Is this a representation of either Pur or Pu or different alleles of Pur? Both pods look very differently coloured.

[Silverleaf]

I guess it's Pur (or pur>a or pur>b) being variable in expression and unstable. But I'm only guessing.

[jayb]

F1 cross Boggie x Violet Sugar, mix of pod colours. I'm really not sure why?

[Silverleaf]

On the same plant?

[jayb]

Different F1 plants, all dwarf though, so not a mix up with tall pea pollen.