Blue-1 and Blue-2 in IRN

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Recio
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Blue-1 and Blue-2 in IRN

Post by Recio »

Hi everybody,

I will try to develop a model of two blue loci located in the same chromossome trying to explain the different Blue, Parblue and Emerald combinations producing different phenotypes.

Let's calculate the possible genetic combinations of two possible blue loci in the same chromossome.

Alleles of each locus:
Blue-1: Wild-1, Parblue, Blue .... so that Wild-1 behaves dominant over Parblue, and Parblue behaves incomplete dominant over Blue
Blue-2: Wild-2, Emerald .... so that Emerald behaves incomplete dominant over Wild-2

Blue-2: Wild-2Wild-2
Wild-1Wild1 ..... Wild type
Wild-1Parblue .... Wild type split Parblue
Wild-1Blue ........ Wild type split Blue
ParblueBlue ...... Heterozygous Parblue
ParblueParblue .... Homozygous Parblue
BlueBlue .......... Blue

Blue-2: Wild-2Emerald
Wild-1Wild1 ..... Green SF Emerald
Wild-1Parblue .... 2 possibilities: Emerald linked to Wild-1 or Emerald linked to Parblue .... Green Emerald/Parblue (Mike's female with Emerald linked to Wild-1)
Wild-1Blue ........ 2 possibilities: Emerald linked to Wild-1 or Emerald linked to Blue .... Green Emerald/Blue
ParblueBlue ...... 2 possibilities: Emerald linked to Parblue or Emerald linked to Blue .... Willy's anormal patched Emerald?

ParblueParblue .... Homozygous Parblue SF Emerald .... Patched Emerald?
BlueBlue .......... Blue SF Emerald .... Non fluorescent Emerald ?

Blue-2: EmeraldEmerald
Wild-1Wild1 ..... Green series DF Emerald
Wild-1Parblue .... Green series DF Emerald split Parblue
Wild-1Blue ........ Green series DF Emerald split Blue
ParblueBlue ...... Blue series DF Emerald Heterozygous Parblue
ParblueParblue .... Blue series DF Emerald Homozygous Parblue
BlueBlue .......... Blue series DF Emerald

The first part with the Blue-2 gene showing two wild genes does not show any difficulty since it correlates with our classical inheritance mode of Blue and Parblue.

The last part with the homozygous Emerald can not be correlated to known phenotypes since, at present, only a bunch (3-4 as far as I know) of homozygous birds have been bred and we do not know for sure if they are blue or green series birds.

The most important part is the combinations of heterozygous Emerald (Wild-2Emerald) with the Blue-1 gene. Some questions to think about:
1. Why should we consider that those genes are not completelly independent but that they are tween genes and could share some regulators?
2. Why should we consider that the expression of each gene can be dependent on the expression of the other gene?
3. Is the expression of the same genes combination different depending on the type of linkage present (type 1 or type 2)? See combinations typed in red.

This is just a theoretical model but it allows to better understand our present knowledge about the different phenotypes found in the combinations of Emerald and Blue, Parblue and Wild alleles. It also fits to inheritance patterns and explains that a phenotypic Emerald (genotypic Green Emerald) paired to a Blue bird can produce both phenotypic Emeralds (genotypic Green Emerald) and Blue birds, mimicking parblue inheritance ... but being different. The only hick (which could also be explained but I will not do it for simplicity) is Aaron's bird which still remains to be characterized by uv studies and a pic side by side to a normal green bird.

Waiting for questions ... and for answers.

Recio
Indian Ringneck Vic
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Re: Blue-1 and Blue-2 in IRN

Post by Indian Ringneck Vic »

Recio definately no answers however a question some time ago Terry Martin dismissed the notion of a second blue locas in irn's as being improbable he later on reflection amended his opion as possible then went further to explain (theorise ) this second blue locas could have came about due to the blue 1 locas being disturbed or damaged during it's evolutionary journy causing it to duplicate or fork hence creating the second blue locas that may well exist today. Do I have this bit correct ? Remenber I'm not a scientist so please be gentle.
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Hi Paul,

This is what I also think and you have perfectly explained it.

Recio
madas
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Re: Blue-1 and Blue-2 in IRN

Post by madas »

Recio wrote: Blue-2: Wild-2, Emerald .... so that Emerald behaves incomplete dominant over Wild-2
Hm, hard to follow your argumentation.

So why do you call it a second blue mutation if there isn't any allele on this second locus which is causing a blue phenotype for homozyguos expression?
So for a true second blue locus you need such an allele. But the blue mutation by definition is recessive regarding the wildtype allele (wild-2) so all other
alleles on this locus have to be recessive regarding the wildtype allele too.

So something is wrong with your theory. :(

Sorry.

madas
Last edited by madas on Fri Dec 06, 2013 7:14 am, edited 1 time in total.
Johan S
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Re: Blue-1 and Blue-2 in IRN

Post by Johan S »

madas wrote:
Recio wrote: Blue-2: Wild-2, Emerald .... so that Emerald behaves incomplete dominant over Wild-2
Hm, hard to follow your argumentation.

So why do you call it a second blue mutation if there isn't any allele on this second locus which is causing a blue phenotype for homozyguos expression?
So for a true second blue locus you need such an allele. But the blue mutation by definition is recessive regarding the wildtype allele (wild-2) so all other
alleles on this locus have to be recessive regarding the wildtype allele too.


So far the second blue locus of the budgie is fitting all the needs. :) For you second blue locus of the IRN nothing fits. :(

So something is wrong with your theory. :( Sorry.

madas
Madas, 2 comments regarding the underlined.

1. It is our old definitions that could fail us. What would we call a new incomplete dominant mutation that partially removes psittacin in heterozygous form and completely in DF? Do we give it a new name, or do we focus on psittacin removal making it a blue type?

2. How sure are you about the second blue locus in the budgie? I thought it is a second blue allele at the same blue locus.

No disrespect meant to Recio, but I think 2 above is more plausible than a second blue locus. Considering we already have alleles in the form of blue, indigo, turquoise and possibly sapphire and emerald, to me it seems a rather unstable gene. And further to this, it seems an old gene to occur over so many different parrot species over many continents, and in many of them the same alleles also occur.
madas
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Re: Blue-1 and Blue-2 in IRN

Post by madas »

Johan S wrote: 2. How sure are you about the second blue locus in the budgie? I thought it is a second blue allele at the same blue locus.
Sorry my fault. Your completely right here. So i have edited it on my first post.
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Re: Blue-1 and Blue-2 in IRN

Post by madas »

Johan S wrote: 1. It is our old definitions that could fail us. What would we call a new incomplete dominant mutation that partially removes psittacin in heterozygous form and completely in DF? Do we give it a new name, or do we focus on psittacin removal making it a blue type?
Yeah but emerlad isn't removing the psittacine completely in the DF form. So it is out of question. :D

cheers.
Johan S
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Re: Blue-1 and Blue-2 in IRN

Post by Johan S »

madas wrote:
Johan S wrote: 1. It is our old definitions that could fail us. What would we call a new incomplete dominant mutation that partially removes psittacin in heterozygous form and completely in DF? Do we give it a new name, or do we focus on psittacin removal making it a blue type?
Yeah but emerlad isn't removing the psittacine completely in the DF form. So it is out of question. :D

cheers.
How can you be so sure? It sure looks like some psittacin is left, I agree. But is that proof that it is psittacin?

Let's do a little experiment, just because I love experiments.

So I present to you a green feather with obvious psittacin present.
Image

So we conclude that this isn't a blue feather and can not come from a blue bird, because our definition clearly states that with psittacin present, it can not be blue.

...


...


...


...


Then I apologise for misleading you and the rest of the forum and reveal the truth.
Image

An blue feather from a blue bird with absolutely no psittacin, yet appearing green in a spot because of the use of an alternate yellow source. Sneaky, sneaky... :twisted:

Conclusion: Just because it looks like psittacin, doesn't make it psittacin.

So my two questions to the forum is this:

1) How do we 100% conclusively know for sure that emerald contains psittacin when not a single feather study has been done. :?: To my knowledge, an emerald feather has not even been placed under a microscope.

2) What do you think the above trickery will look like under a UV lamp? Why this question, because from UV observations we know emerald appears different. Does that make emerald a normal psittacin, a modified psittacin with different fluorescent properties (difference in wavelength is clear), a different type of pigment replacing psittacin or something completely different (most likely on the cortex in the form of a structural mutation)?. :?:

Unfortunately, I won't be able to oblige by answering the second question, as Molossus is still in possession of my UV lamp and the 1000km round trip seems a bit excessive to silence my curiosity. :lol:

PS: I just want to clarify, I'm not trying to belittle anyone with this post, especially not Madas who is a good friend of mine. My goal is to get everybody thinking over the weekend. Can we always trust our eyes? For those wondering, I think that emerald has a 95% chance of being a parblue. And for many that is good enough to be 100%. I'm just a curious bugger who can not accept that other 5% until it is proven conclusively. That doesn't mean I'm not 95% onboard, just that I'm 5% short of being convinced.

PPS: I have developed the worlds first 'regressive parblue'. It starts out with a lot of green regions and then completely moults it out in it's first moult, becoming a completely blue bird. :lol:
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

madas wrote:
Recio wrote: Blue-2: Wild-2, Emerald .... so that Emerald behaves incomplete dominant over Wild-2
Hm, hard to follow your argumentation.

So why do you call it a second blue mutation if there isn't any allele on this second locus which is causing a blue phenotype for homozyguos expression?
So for a true second blue locus you need such an allele. But the blue mutation by definition is recessive regarding the wildtype allele (wild-2) so all other alleles on this locus have to be recessive regarding the wildtype allele too.
madas
Hi Madas,

Thank you for your words. Let me answer you with another question: if I remember correctly in lovebirds there is not any blue mutation but there is a parblue mutation, which does not produce any blue bird even in the homozygous form. Does this means that this parblue is not a partial mutation of the blue locus?
Something else: as I wrote we do not own enough homozygous birds in both series to conclude whether it does remove every psittacin or not. I think that the homozygous birds so far produced belong to the green series bird (Chris wrotte me that they produce a number of Emerald offspring anormaly high and his "TurquoiseEmeralds" are not really patched). I guess Willy will be once more the first breeder to obtain the very first DF Emerald in blue series.

You wrote: "But the blue mutation by definition is recessive regarding the wildtype allele (wild-2) so all other alleles on this locus have to be recessive regarding the wildtype allele too". In fact the blue mutation is recessive regarding the wild-1 allele (not the wild-2). The way Emerald and wild-2 behaves is not necessarily the same since it is a different gene.

Regards

Recio
Indian Ringneck Vic
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Re: Blue-1 and Blue-2 in IRN

Post by Indian Ringneck Vic »

Hi all this is from a birdo's view which has been based on observation and although not scientific I believe has merit as myself and some other fanciers have been pondering over the possibility of a second blue at a time when this senerio was out of the question .First some history the blue irn in Aus was a mostly uniform mutation with a light powdery look which we (in this country ) refer to as the old style blue .On the emergence of the of the erroneous named pastelaqua now known as indigo par blue ( even more erroneous name in my opinion ) observations were starting to be evident that there is another blue morph that is deeper less powdery and sharper in it's expression this observation was also commented by Babu who correctly pointed out that both types need to be side by side in an aviary to enable most observers to see the difference we agree with comment however when thie comparison is done and the two types are viewed this way the difference is not that subtle these indigo's also have striking effects when used in American violets and european cobalts and is what attracted me to them in the first place. So now when we talk amoungst ourselves ( my inner circle of fanciers ) we refer to blues as being the old style and the new style I will leave it to the more scientific minded to determine what has driven this second phenotype of blue and I will be watching this thread with bated breath so please don't get to technical.
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Johan S wrote: 1) How do we 100% conclusively know for sure that emerald contains psittacin when not a single feather study has been done. :?: To my knowledge, an emerald feather has not even been placed under a microscope.

2) What do you think the above trickery will look like under a UV lamp? Why this question, because from UV observations we know emerald appears different. Does that make emerald a normal psittacin, a modified psittacin with different fluorescent properties (difference in wavelength is clear), a different type of pigment replacing psittacin or something completely different (most likely on the cortex in the form of a structural mutation)?. :?:
Hi Johan. This is a key question I have been thinking about and for which I do not have the rigth answer but only some feelings. Let's see what we know for "sure":
1. "Normal" psittacin is fluorescent (yellowish fluorescence).
2. The distribution and intensity of the Emerald fluorescence matches the distribution and intensity of the yellowness we can see, thus pointing to Emerald as a type of psittacin.
3. The type of Emerald fluorescence is different than the fluorescence emitted by the "normal" psittacin allowing to think that the molecule of psittacin has changed and/or that a change in feather structure has changed the wavelength going out the feather to our eyes (can the wavelength change when there is a change in the refraction index between the feather and the air, whenever a change in feather structure appears?). The last question is specifically for Johan.
4. According to Willy's report there are fluorescent and non-fluorescent phenotypic Emeralds. Thus the change in fluorescence could be a "colateral" effect of the Emerald mutation when acting on green series birds and making appear the normal psittacin with a different distribution (even distribution) and different hue under uv. Could this special yellow psittacin be the precursor of the "normal" psittacin, which would not be produced because the precursor was not transported to the rigth place?
5. Emeralds show an iridescence pointing to an action on the outer part of the cortex, and thus to a strcutural muttaion. This iridescence seems to disappear in DF birds, further pointing to Emerald as a structural mutation.

All those ideas together make me think that Emerald could initially be a structural mutation, inducing a secondary change in the expresion of psittacins (whenever they are present: green series birds) either by changing the type of psittacin produced or, more likely, by changing its distribution and apparent fluorescence through a change in the physical properties of the feather structure through which ligth is refracted. In Blue series birds (non fluorescents, without psittacins) the yellow colour we see could be structural. In Green series birds the yellow colour would be compounded of the structural yellow and the pigmentary yellow.

Finally let me point to the fact that we know nothing about the metabolism of yellow psittacins or about its chemical structure. We are assuming that Blue and Parblue mutations are affecting psittacin synthesis but it is just a guess. They could just act by afecting the system transporting the pigment to the cortex (most likely a microtubule system) and so to avoid pigment deposition. This would be a structural like mutation, similar to which I have just recall previously.

Regards

Recio
Johan S
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Re: Blue-1 and Blue-2 in IRN

Post by Johan S »

Recio wrote:2. The distribution and intensity of the Emerald fluorescence matches the distribution and intensity of the yellowness we can see, thus pointing to Emerald as a type of psittacin.
This reminds me very much of your model last year, where things were still very simple. You had the even and the patched psittacin, distinguishable by the fact that the even psittacin is non-fluorescent and the patched psittacin becomes fluorescent at adolescence. And emerald was a mutation that mutated the even psittacin. I still like this model, since we see the emerald yellow in the same areas on the bird where the normal wildtype fledgeling appears green. In this case there is probably just a slight modification, with profound effects: i) a much less effective yellow pigment and ii) a fluorescent property is introduced. The transport model can be considered not affected.
Recio wrote:3. The type of Emerald fluorescence is different than the fluorescence emitted by the "normal" psittacin allowing to think that the molecule of psittacin has changed and/or that a change in feather structure has changed the wavelength going out the feather to our eyes (can the wavelength change when there is a change in the refraction index between the feather and the air, whenever a change in feather structure appears?). The last question is specifically for Johan.
The refraction index will not affect the wavelength/frequency, only the velocity of the wave propagation. Notice along the grey line in the image that the spacing (wavelength) between the blue wavefronts are the same in both mediums.

Image
Recio wrote:Finally let me point to the fact that we know nothing about the metabolism of yellow psittacins or about its chemical structure. We are assuming that Blue and Parblue mutations are affecting psittacin synthesis but it is just a guess. They could just act by afecting the system transporting the pigment to the cortex (most likely a microtubule system) and so to avoid pigment deposition. This would be a structural like mutation, similar to which I have just recall previously.
Really? I thought somebody would have done it by now, considering the progress on the analyis and study of feather structure with fancy new techniques. :D
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Indian Ringneck Vic wrote:Hi all this is from a birdo's view which has been based on observation and although not scientific I believe has merit as myself and some other fanciers have been pondering over the possibility of a second blue at a time when this senerio was out of the question .First some history the blue irn in Aus was a mostly uniform mutation with a light powdery look which we (in this country ) refer to as the old style blue .On the emergence of the of the erroneous named pastelaqua now known as indigo par blue ( even more erroneous name in my opinion ) observations were starting to be evident that there is another blue morph that is deeper less powdery and sharper in it's expression this observation was also commented by Babu who correctly pointed out that both types need to be side by side in an aviary to enable most observers to see the difference we agree with comment however when thie comparison is done and the two types are viewed this way the difference is not that subtle these indigo's also have striking effects when used in American violets and european cobalts and is what attracted me to them in the first place. So now when we talk amoungst ourselves ( my inner circle of fanciers ) we refer to blues as being the old style and the new style I will leave it to the more scientific minded to determine what has driven this second phenotype of blue and I will be watching this thread with bated breath so please don't get to technical.
Hi Paul,

Did you check those birds to know if both blue types were alleles of the same locus?

Regards

Recio
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Hi everybody,

Thank you Johan for your explanation about the independency of wavelength respective to the refractive index (I must think about it since my first perception is that the wavelength is affected). In this case we could conclude that the apparent change in fluorescence probably depends on a change on psittacin type. Me too I prefere the very simple model of two psittacins (patched and even) one fluoorescent and the other not .... but we must consider the other facts we know now.

Let's approach the problem differently: let's analyse how Emerald behaves in a Blue bird, that is in a bird with the null mutation of the Blue-1 gene. In this situation the changes we see are dependent only on the Blue-2 gene and we can stablish that:
1. Wild-2Wild-2 does not show any yellowness (either pigmentary or structural) .... blue phenotype
2. EmeraldWild-2 show an even yellowness ...... SF Emerald phenotype.
3. EmeraldEmerald ..... we do not know its expression in Blue series birds, since the DF Emeralds so far produced probably are green series birds (they are highly fluorescents).

We can also stablish that Emerald behaves dominant over Wild-2 (or that Wild-2 behaves recessive over Emerald, since it is exactly the same).

As you can see, in the case of Blue-2 we have the same situation than for Blue-1:
1. An homozygous allele combination avoiding any yellow colour expression: BlueBlue (for Blue-1 gene) and Wild-2Wild-2 (for Blue-2 gene).
2. An heterozygous allele combination producing yellow colour: Wild-1Blue (for Blue-1 gene) and Wild-2Emerald (for Blue-2 gene)

What I am meaning is that what we call the Wild-2 allele is the counterpart of the Blue mutation. Both are the null mutation for each gene. and both behave recesive respective each heterozygous form. This is the reason why there is not any yellow colour let in Blue birds: the Blue-2 gene dysplays already the null mutation in the wild birds.

How could this happen from an evolutionary point of view? Maybe in the early times a fluorescent brillant bird (an Emerald bird) was successfull for breeding but with the time passing, predators evolved and were able to easierly detect those birds, so that they were eliminated from nature and only the mutants not expressing the gene were selected, leading to the presence of the nul mutation as the most prevalent one in nature (the actual Wild-2 gene).

This explanation is easier than a master gene regulating both Blue-genes and I think it is also closer to reality.

What do you think?

Recio
Indian Ringneck Vic
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Re: Blue-1 and Blue-2 in IRN

Post by Indian Ringneck Vic »

Recio I've had this question before and my answer is they are allec . My rational for believing that they are allec ( as well as being two locas ) is due to both blues being split or forked from the original blue locas therefore this being the case they share the same DNA and being cloned therefore it would be a reasonable assumption that they would be allec to each other this of cause my theory that has been based on visual observation which has no theoretic basis . I look at these two locas as being identical in make up yet still able to reflect slight variation in expression thats ocured due to thier separation . I'm here to learn I will be gratefull to hear your take on my unlearned theory.
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Johan S wrote:[The refraction index will not affect the wavelength/frequency, only the velocity of the wave propagation. Notice along the grey line in the image that the spacing (wavelength) between the blue wavefronts are the same in both mediums.

Image
Hi Johan,

I know what you mean and it accords to what I have read. Anyway, my first perception is that the shorter distance between 2 wavelengths is not the same at both sides of the grey line. Just follow the red line, at 90° of each wavefront, and it appears quite clear that the distance between 2 waves is shorter after the grey line than before the grey line. What am I missing?

Recio
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Hi Johan,

I do not need any answer. I have catch it !!!
The key is the change in velocity of the wave propagation. The apparent wavelength changes when there is a change in the refraction index, but velocity changes in the same degree, so that the frequency is not affected and neither the real wavelength (1/frequency).

Regards

Recio
Mikesringnecks
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Re: Blue-1 and Blue-2 in IRN

Post by Mikesringnecks »

Hi Recio
I'm afraid you have me confused and I suspect a lot of others. There are very real definition problems in this arena for me and I suspect a lot of others. It is not that we are necessarily incapable of understanding, it results from multiple writers world wide using both different terms for the same thing and the same terms for different things. Net result is I need you to be patient with me and answer some questions.

1.Terry Martin, in his book, talks about a range of alleles at the b locus in budgerigars giving rise to different phenotypes in combination with each other, not a second b locus. Is that still current thinking ?
2. You seem to actually be talking about a second locus, but not so much a "blue" locus, rather an "emerald" locus. Which is it?
3.I always assumed the blue locus was where yellow pigment was produced and the paired blue gene stopped production/delivery whilst various other alleles in combination with blue or each other caused partial disruption of one sort or another. Is that correct.
4.I would assume simply by the terminology that a second blue locus would be a second site where yellow pigment was produced. I don't think that is correct but, if it is not, why use the term second blue locus.
5.In principal, why can't an "emerald" locus or any other as yet unnamed locus for that matter, have an impact on yellow pigment products just like several loci have impacts on the production of eumelanin?

That is probably enough for now, but I will surely have more. In the meantime, I will go and read up on B1 and B2 and probably get myself even more confused.
Kind regards
Mike
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Hi Mike,

I will try to answer your questions step by step ... but I need your collaboration.
Let's see a standard model of a very simple metabolic pathway adapted to the synthesis of any mollecule. Let's call yellow psittacin to such final mollecule.

Image

Since each transformation depends on the presence of a specific enzyme, and that each enzyme is specifically coded by a gene .... how many possible "blue genes" (located in different "blue loci") can produce a blue bird through a null mutation?

Regards

Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Hi,

I guess that everybody has got the idea: each step concerning the pathway for the synthesis of any final product can be affected by a mutation blocking the production of the specific enzyme concerned at such step. That is: if there is a null mutation of the gene coding for the enzyme 1 we will get a blue bird, if there is a null mutation of the gene coding for the enzyme 2 we will also get a blue bird ... and so on. That is, there are n possible blue genes or blue loci concerned in this single and simple metabolic pathway.

This means that there can be as many "blue genes" (or "blue loci") as steps concerned for a single metabolic pathway. The fact that there is not only one "blue gene" but many possible "blue genes" should be the rule in our minds and not the exception.

Questions?

Recio
Mikesringnecks
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Re: Blue-1 and Blue-2 in IRN

Post by Mikesringnecks »

Hi Recio
OK you have lost me right at the start. My obviously incorrect understanding was that the yellow pigment was synthesized as a result of a set of instructions emanating from one site and that site was the blue locus. I then thought that, if any one of the steps involved in the synthesis was altered either completely or partially, we had a mutation.
What I didn't understand and can't comprehend, is that each such "mutation" is occasioned at different a blue locus site.
For what little it is worth, my understanding was that such "mutations" were sourced either from alleles located at the blue locus or from a locus at another site (IE cinnamon interrupting the development of black pigment at the brown stage of development).
Kind regards
Mike
Mikesringnecks
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Re: Blue-1 and Blue-2 in IRN

Post by Mikesringnecks »

Hi Recio
Its me again, I have been feeding the birds which gives time for quiet thinking and I think I may have solved one of my definitional understanding problems re alleles and loci.
I am still assuming that the b locus, as I understand it, is the site from where instructions for synthesis of yellow pigment are issued. Am I correct in assuming that loci b1, b2 etc are sites within the broad compass of the b locus where alleles have their effect?
So, when you talk about a second b locus, are you are talking about a site within the extent of the existing b locus and in fact the site where the action of what I would know as a blue series allele is having its impact?
Kind regards
Mike
Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Mikesringnecks wrote: I am still assuming that the b locus, as I understand it, is the site from where instructions for synthesis of yellow pigment are issued. Am I correct in assuming that loci b1, b2 etc are sites within the broad compass of the b locus where alleles have their effect?
So, when you talk about a second b locus, are you are talking about a site within the extent of the existing b locus and in fact the site where the action of what I would know as a blue series allele is having its impact?
Hi Mike

The blue locus is the place, in the DNA, where is located one gene coding for one specific enzyme acting on the pathway leading to the production of yellow psittacin. If this gene is completelly blocked (no synthesis of the enzyme) or produces an alterated enzyme without any biological activity we call it a null mutation and it completelly blocks the production of yellow psittacins, and thus, produces a blue bird. This is what we call a blue mutation.
If the enzyme is produced in a lower amount or with only a partial biological activity, the system will still produce some psittacin but at a lower level. In this case we say that it is a partial mutation (or parblue) and the "altered" gene (coding for the "altered" enzyme), which is always located at the same locus, is what we call an allele. In a wider meaning an allele is any DNA sequence which holds at a specific locus, either the most prevalent in the population (wild gene) or the less prevalent (what we call mutants: blue and parblues), but the degree of prevalence is not related to the activity/quantity of the produced enzyme (null, partial or total).

What I have described above for a single gene coding for one specific enzyme (let's call it enzyme 1), is also valid for any enzyme (enzyme 2, enzyme 3, .... enzyme n) in the same metabolic pathway leading to yellow psittacin synthesis. Each one of those enzymes is coded by a different gene, located in a different locus, and able to mutate and produce null or partial mutations, producing blues or parblues. To differentiate each one of those possible Blues and Parblues we call each specific gene (locus) Blue-1, Blue-2, ... Blue-n.

Let me know if I have explained it in an comprehensive way.

Regards

Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

molossus wrote:Recio et al..
assuming the Emerald is a parble(ok Willie :o ) and that it has a close relationship with other parblues eg turq ,indigo etc..
Why are the feather irridiscense so unlike each other...viz adult emerald and adult turq feathers are noway near close ... ?
Why does the underwing not bear a resemblence even remotely?Johan get your a## down here and collect some pics and do the same... you guys are frustrating slow... :evil:
Hi Lee,

Those are some of the reasons why I think that Emerald is not a parblue. Every parblue should show some similarities when it only affects to the total amount of psittacin produced (Ex Turquoise and Indigo), but whenever you find some effects at others levels (different iridescence, different fluorescence, different pattern distribution, different action on red psittacin ...) you should look for a different gene being involved.

Regards

Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

molossus wrote:Recio ... was it Terry or Deon who stated that if they are alleles from the same locus ,,, when mated together the parblue (allele) closest to the wildcolor will dominate over the partner allele (parblue)...
will this hold true in all cases?
Not, not at all. It depends, at least, on two factors:

1. Which is the wild allele? Ex: ara hyacinthe ... the wild allele of the Blue locus is the null mutation and this is the reason why the bird is blue. In the hypothesis of Emerald as a different mutation, the wild allele of this locus (Wild-2Wild-2) would also be the null mutation. In this case the corresponding parblue2 (Emerald) is behaving as dominant over the wild type ... but if you imagine a close isolated population in an island where the most prevalent allele combination is EmeraldEmerald, then you would say that the mutant Wild2Wild2 (less prevalent and thus we call it mutant) behaves as recessive respective to the wild phenotype (DF Emerald in this case).

2. The way that allele behaves in the heterozygous and the homozygous bird:
Ex: In IRN the homozygous Turquoise shows more psittacin than the heterozygous TurquoiseBlue, but in other species (I do not remmeber exactly which one but it was refered by Peter in the yahoo forum 2-3 years ago) the homozygous parblue shows less psittacin than the heterozygous BlueParblue. What does all this means? It means that the two genes producing Blue birds are not the same in those species. In one of them (IRN) the partial activation of the gene allows for a partial production of psittacins, increasing in the homozygous form. In the other one there is not a partial activation but a partial inhibition of the psittacin synthesis in the heterozygous form, so that the homozygous bird will show a higher inhibition and produce far less psittacin.
Let's quantify this:
IRN ... BlueBlue (0% psittacin), BlueTurquoise (30% psittacin) and TurquoiseTurquoise (60% psittacin). This is a partially activatory mechanism.
Other psittacidae ... BlueBlue (0% psittacin), BlueParblue (30% psittacin) and ParblueParblue (9% psittacin: 30% of 30%). This is a partially inhibitory mechanism. This kind of regulation depends on a colateral inhibitory pathway.

So, as you can see, even if there is only one Blue locus detected in a species it does not mean that it is the same than in other species.

... and now you understand that it is non sense to say that "if they are alleles from the same locus ,,, when mated together the parblue (allele) closest to the wildcolor will dominate over the partner allele (parblue)..." Far more: let's analyse this sentence: let's say that the "parblue (allele) closest to the wildcolor " is Turquoise, and that the "partner allele (parblue)..." is Indigo. In this situation "when mated together" a TurquoiseIndigo will show an intermediary phenotype between homozygous Turquoise and homozygous Indigo, and you will not find any dominance. The apparent dominance (not real) is only found when the system of psittacin production is at saturation (Ex: considering homozygous Turquoise, homozygous Wild and heterozygous TurquoiseWild).

Sorry for the long speech.

Regards

Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Mikesringnecks »

Hi Recio
I do understand this time thank you very much but what you say is not what I thought I understood from my readings.
I always thought that the blue locus was an identical site on a pair of autosomal chromosomes that carried the genetic instructions for the production and distribution of yellow pigment. I never read it to mean the location of an individual gene that had changed in some way to alter the nature of a chain of instructions (par blue) and/or cause that chain to fail entirely to deliver is outcome (blue).
Given the foregoing, why do some of the experts talk about the blue locus being duplicated "by accident" as a possible means of creating a second blue locus?
From what you are saying, a second blue locus is simply the site of a second gene that has been altered in some way to cause another change in the chain of instructions necessary for the production of yellow pigment?
Kind regards
Mike
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Mikesringnecks wrote:I always thought that the blue locus was an identical site on a pair of autosomal chromosomes that carried the genetic instructions for the production and distribution of yellow pigment. I never read it to mean the location of an individual gene that had changed in some way to alter the nature of a chain of instructions (par blue) and/or cause that chain to fail entirely to deliver is outcome (blue).
Hi Mike,
As you say ..."The blue locus is an identical site on a pair of autosomal chromosomes that carries the genetic instructions for the production of ..." not really the yellow pigment, but for the production of one protein (enzyme) which participates, with many others which are not dependent on this specific blue locus, in the final production of yellow psittacin. Then there are other genes which will control psittacin deposition.
I will make a similarity with melanin: SL-ino and NSL-ino could be the equivalent of Blue-1 and Blue-2 loci, each acting on different enzymes leading to the synthesis of melanin. We are able to make the difference easily because its different inheritance pattern, but if both genes were located in autosomes (or even in the same chromossome) I bet you anything that we would still be discussing if they are alleles of the same mutation or different mutations. Others mutations producing ino birds, like DF dom pied, do not act on the synthesis of melanin, which is not disturbed, but on the melanocytes migration/functionality, so that melanin is not transfered to the feathers. As you can see we can get ino birds without acting on melanin synthesis ... similar to what I propose to explain that a structural mutation (Emerald?) could act on the final psittacin expression.
Given the foregoing, why do some of the experts talk about the blue locus being duplicated "by accident" as a possible means of creating a second blue locus?
From what you are saying, a second blue locus is simply the site of a second gene that has been altered in some way to cause another change in the chain of instructions necessary for the production of yellow pigment?
Please, read here about the biochemical mechanisms producing duplicated genes: http://fr.wikipedia.org/wiki/Duplicatio ... 3%A9tique)
Respective to Emerald as an allele of the Blue-2 locus located in the same chromossome than Blue-1, the invoqued mechanism is a direct intrachromossomic duplication (tandem duplication).

The evolutionary aspects of duplicating genes are very well defined in the neofunctionalization paragraph here: http://en.wikipedia.org/wiki/Gene_duplication
"Gene duplications are an essential source of genetic novelty that can lead to evolutionary innovation. Duplication creates genetic redundancy, where the second copy of the gene is often free from selective pressure — that is, mutations of it have no deleterious effects to its host organism. If one copy of a gene experiences a mutation that affects its original function, the second copy can serve as a 'spare part' and continue to function correctly. Thus duplicate genes accumulate mutations faster than a functional single-copy gene, over generations of organisms, and it is possible for one of the two copies to develop a new and different function"

Regards

Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Mikesringnecks »

Hi Recio
Thanks again, I will read the references but I still have one perception problem with what I thought I understood.

If I have a simple turquoise bird, I was taught that it has a blue gene on one chromosome and a par blue gene on the other side of the pair, both located at the blue locus.

Why should the par blue mutation occur at exactly the same address as the blue mutation, given that there are innumerable possibilities in the chain of genes it takes to code for production of yellow pigment?
Kind regards
Mike
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Re: Blue-1 and Blue-2 in IRN

Post by madas »

Mikesringnecks wrote: If I have a simple turquoise bird, I was taught that it has a blue gene on one chromosome and a par blue gene on the other side of the pair, both located at the blue locus.
Not wrong at all.

Normal body cells are build with chromosome pairs and germ cells not. The chromosome pair consists of two exactly the same chromosomes.
Each chromosome consists of two DNA strands which are connected in the middle (not exactly the middle but within this area). Each DNA strand
is build of the same gen sequence. Each gen could have a specific makeup which is then called allele or gen expression. The specific location of such
an allele with in this gen sequence is called locus.
So for the b-locus you could have a blue allele or turq allele or wildtype allele or aqua allele on each of these two DNA strands. Means the germ cells
could contain b+/b+ or b+/tq or b+/b or b/tq or b/b or tq/tq at the b-locus. For the body cells you have b+/b+ b+/b+ or b+/tq b+/tq or b+/b b+/b
or b/tq b/tq or b/b b/b or tq/tq tq/tq.

Image Image

madas
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Re: Blue-1 and Blue-2 in IRN

Post by Mikesringnecks »

Hi Madas
I do understand all of that thank you very much. What I am having trouble with is the the size/length of the "address" on the chromosome pair we define as the blue locus. As I understand it, Recio has just told me that such an address is only the length of a single gene within the genetic sequence that codes for the production of yellow pigment.
Given that fact, I could not understand why the mutation that gives rise to a par blue phenotype should occur exactly opposite the the blue mutation. I had always assumed that both mutations occurred within the chain of instructions that code for yellow pigment production, but not necessarily directly opposite one another.
At least I'm only slightly confused now and I have Recio to thank for the improvement.
Kind regards
Mike
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Re: Blue-1 and Blue-2 in IRN

Post by madas »

Hi Mike,

each gen can have a specific length resp. count of DNA chains. Each chain is build by base pairs in which each pair is a AT, TA, CG or GC kombination. The order of 'A-T' and 'G-C' base pairs and the specific shaping of a base pair (means AT or TA) builds the makeup of a gen.

So lets assume the unmutated blue allele of the b-locus looks like: AT-GC-TA-GC
then the mutated blue allele could look like: AT-CG-TA-GC
and the mutated turq allele could look like AT-GC-AT-GC.

So the b-locus within the chromosom where gen for blue is located could look like this:

wildtype (top = left side of chromosome; bottom right side of chromosome):

...AT-GC-TA-GC...
...AT-GC-TA-GC...

blue (homozyguos):

...AT-CG-TA-GC...
...AT-CG-TA-GC...

turq (homozyguos):

...AT-GC-AT-GC...
...AT-GC-AT-GC...

wild split blue (hetereozyguos):

...AT-GC-TA-GC...
...AT-CG-TA-GC...

wild split turq (hetereozyguos):

...AT-GC-TA-GC...
...AT-GC-AT-GC...

turqblue (hetereozyguos):

...AT-CG-TA-GC...
...AT-GC-AT-GC...

But this description is very basic. In real a gen could be build of up to 2,5 mio base pairs.

madas
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Re: Blue-1 and Blue-2 in IRN

Post by Mikesringnecks »

Hi Recio
I learned my avian genetics from a part of a zoological degree course offered by an American uni years ago. It was written by an Alan Mason and has been very helpful to me in setting up my ringneck pairs over the years, but I always thought I remembered loci involving chains of several genes.
I have now revised my mental model with single point gene loci, thanks again so much Recio and also Madas for your help.
Kind regards
Mike
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Re: Blue-1 and Blue-2 in IRN

Post by Johan S »

Recio wrote:I will make a similarity with melanin: SL-ino and NSL-ino could be the equivalent of Blue-1 and Blue-2 loci, each acting on different enzymes leading to the synthesis of melanin. We are able to make the difference easily because its different inheritance pattern, but if both genes were located in autosomes (or even in the same chromossome) I bet you anything that we would still be discussing if they are alleles of the same mutation or different mutations.
Recio, it is interesting that you should mention the ino example. Tienie and I have discussed on a number of occasions that the IRN NSLino locus may not be the same as the a-locus NSLino as seen in Fischers lovebirds, where 4 different alleles exist. This discussion stemmed from the results currently seen from experiments done with 'bronze fallow' and NSLino in IRN that produced double split offspring, and not the intermediate coloured birds as for Fischers. So we may also end up having NSLino1 and NSLino2 locii.
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Johan S wrote:
Recio wrote:I will make a similarity with melanin: SL-ino and NSL-ino could be the equivalent of Blue-1 and Blue-2 loci, each acting on different enzymes leading to the synthesis of melanin. We are able to make the difference easily because its different inheritance pattern, but if both genes were located in autosomes (or even in the same chromossome) I bet you anything that we would still be discussing if they are alleles of the same mutation or different mutations.
Recio, it is interesting that you should mention the ino example. Tienie and I have discussed on a number of occasions that the IRN NSLino locus may not be the same as the a-locus NSLino as seen in Fischers lovebirds, where 4 different alleles exist. This discussion stemmed from the results currently seen from experiments done with 'bronze fallow' and NSLino in IRN that produced double split offspring, and not the intermediate coloured birds as for Fischers. So we may also end up having NSLino1 and NSLino2 locii.
Hi Johan,

I am aware of Tienie's results and I agree with your conclusions: his ino birds show an autosomic recessive inheritance pattern like the NSL-ino described in other species, but since this mutation is not allelic with bronze fallow ... we have two possibilities to consider:
1. This NSL-ino is not an allele of the a-locus.
2. His bronze fallow is not an allele of the a-locus.
It would be great to pair those SA birds to european NSL-ino and bronze fallow respectivelly, to know which one is really an allele of the a locus. Another possibility would be to produce hybrids of IRN and another related species owing for sure those mutations of the a-locus, looking for complementarity in the homozygous hybrids.

As we can see with this exemple we are only able to detect different mutations producing the same phenotype whenever there is a different inheritance pattern, a different crossing over rate, a different "allele set" for that locus, ... but if we do not own these tools it would be really by chance that we detect such specific mutations. If you google melanin and metabolic pathway you will find that there is not a single possibility to produce melanin, and that there are a lot of enzymes in such a pathway. Each one of those enzymes (and others regulating the expression of those enzymes) can mutate totally or partially, and produce ino and par-ino birds. With this idea in mind I agree with you that probably there are NSL-ino1, NSL-ino2, ...

@Tienie: Where are you about with those birds?

Regards

Recio
Last edited by Recio on Thu Dec 19, 2013 1:32 pm, edited 2 times in total.
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Re: Blue-1 and Blue-2 in IRN

Post by Johan S »

Recio wrote:1. This NSL-ino is not an allele of the a-locus.
2. His clearhead fallow is not an allele of the a-locus.
It would be great to pair those SA birds to european NSL-ino and clearhead fallow respectivelly, to know which one is really an allele of the a locus. Another possibility would be to produce hybrids of IRN and another related species owing for sure those mutations of the a-locus, looking for complementarity in the homozygous hybrids.
Recio,

1. We wouldn't know for sure if it is an a-locus allele. Also, the NSLino in SA and Europe is the same. They all get transferred as a recessive gene in cleartail bloodlines. Very few NSLino exist that isn't from cleartail. They do exist though, and I believe Tienie has shown that they are the same as the one in the cleartail line.
2. Clearhead fallow hasn't been tested to my knowledge. I was talking about 'bronze' fallow. :wink:

I think the only somewhat compatible hybrid would come with a fallow moustached parakeet, where a fallow mutation also exists. Not sure if their offspring would be fertile, and there isn't any proof that we are actually dealing with a bronze fallow mutation and not another fallow.

Further to the above, I have also been paying a lot more attention to blue birds in a couple of collections I've been visiting. It looks as if we have two different blue phenotypes this side of the ocean as well, similar to what Paul has been describing. I'll be studying these birds more closely, but will wait until they moult to be able to compare them better.
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Hi,

Mind away :oops: :lol:
Previous post reedited for correction

Thanks

Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Recio »

Johan S wrote:Further to the above, I have also been paying a lot more attention to blue birds in a couple of collections I've been visiting. It looks as if we have two different blue phenotypes this side of the ocean as well, similar to what Paul has been describing. I'll be studying these birds more closely, but will wait until they moult to be able to compare them better.
Hi Johan,

Some thoughts about two different blues. Blue mutation consists in a lack of psittacin. If you have two different blue birds, both completelly lacking psittacin, you are not facing two blue mutations, but probably a normal blue and a minor structural mutation, changing the normal hue of blue (similar but distinct to Dark). Do you know if there are intermediate phenotypes between both "blues"? ... has anybody bred the homozygous bird? Anyway the first question is to know which is the "normal" blue (the darker or the ligther bird) since the possible minor structural mutation could be a darkening or ligthening mutation.

Regards

Recio
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Re: Blue-1 and Blue-2 in IRN

Post by Johan S »

All very valid points, gents. And even those are incomplete to all the possibilities. It will keep us guessing for many years to come. :)
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