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PostPosted: Mon Dec 22, 2014 1:51 pm 
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shairlyn wrote:
If my random musings and bad photography entertain people then so much the better!


Shairlyn... I don't suppose you could include more "bad photography" in some of your updates? I would love to follow some of your genetic colour descriptions, but it would be so much more helpful if a representative picture were thrown in. Of course it's easy for me to do the asking - I don't have to do any of the work to take the pics, then upload them, etc., but I would most certainly come over and help if you lived about 500kms closer to me :nuts

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PostPosted: Mon Dec 22, 2014 4:49 pm 
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Smallflock, if some more photos would please people then I will do my best to take some! It probably won't be until after Christmas that I will have time, but I shall try to illustrate my genetic ramblings with some examples.

Assuming of course that the gang are willing to cooperate and pose which is always a challenge in itself. :D

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PostPosted: Mon Dec 22, 2014 6:22 pm 
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If people are interested in genetics I can give some examples with pictures. I'll see what I can do with some I've already taken, and then take some more to illustrate to recent blathering.

As I'm sure everyone knows, our genes are what dictates everything about us. You'll have heard that volume-wise we're 90% water (or something like that). But what makes us up functionally is protein. Genes are the instructions for making proteins. Different versions of a gene make slightly different proteins which can in turn have slightly different properties. Sometimes they have very different properties. Some times these properties are beneficial, sometimes they are detrimental, and in the case of chicken colours, sometimes they look cool.

Animals (including us) have two copies of each gene. They inherit one copy from each parent. Which of the parent's two copies they inherit is random (there are some exceptions to the rules but you have to know the rules before you can break them). For any given gene there may be more than one version (called an 'allele') floating around in the population; sometimes there are many. The different alleles of the same gene are usually denoted by the same letter with different additions (this is one of those rules to which there are exceptions).

An animal may have two copies that are the same (and are said to be homozygous) or two copies that are different (heterozygous). If they have two different copies or alleles, then which allele is expressed is governed by how the gene is expressed, and this is where we talk about Dominant and Recessive. If one allele is Dominant and one is Recessive then the Dominant allele will express. Two copies of a recessive allele must be carried before the recessive allele will express. Most genes are inherited independently, and a bird may possess several different colour alteration genes.

Colour Bases

In chickens there are five basic colours on which all the other variations are built. These are all different alleles of the 'E' gene, so they all start with 'e' and a bird can only have two of them. Most of the colours that we try to breed have two copies of the same allele, i.e. they are homozygous for one E 'allele'. The E alleles are:

E: Extended Black
ER: Birchen
e+: Wildtype
eWh: Wheaten
eb: Brown/Partridge

Note the plus on the Wildtype E gene. 'Wildtype' simply means the animal as it occurs in the wild. In chickens this is considered to be the Red Jungle fowl. All genes that are expressed in this bird are denoted with a plus sign. The plus does not mean that they are dominant or recessive, only that they are found in the Red Jungle Fowl.

It's important to understand that chickens make only two types of pigment: gold and black. Every 'colour' that you see is a variation on these two pigments. The E alleles dictate the basic layout of these pigments, then other genes modify them.

Without other modifiers, Extended Black birds are, funnily enough, mostly black. The hens have a small amount of gold in their hackle and the cocks have a gold hackle and saddle but a black wing. These are often called 'red brown'. If certain melanising genes are added, this produces a completely black bird. Black is a base that a lot of other colours are built on.

So, extended black E. This is Black Forest Cake, and she is Black (E/E. (+melanisers)):
Image

Note the 'penguin suit' chick next to Forest. This is what Extended Black chicks look like, except that they should have a black head. This chick has a white spot, and I will explain the spot in a minute.

Depending on how many melanisers they carry, the chicks can be very black:
Image

As I mentioned, chickens have two pigments, gold and black. Modifying genes may affect one pigment or both. They may affect where the pigment is expressed on the body as 'restricting genes' or 'extending genes' or how much pigment is expressed as 'diluting genes' or 'enhancing genes'.

Recessive White

An easy one to start with is the gene Recessive White. As the name suggests, this gene, denoted 'c', is a pigment restrictor; it restricts pigment from the feathers completely. When no pigment is expressed the feathers are white. Note that it is not an albino gene; pigment is still expressed in the eyes and internally. There is an albino gene that produces pink-eyed chickens and apparently they don't see very well.

As the name of the gene also suggests, it is recessive. A bird must carry two copies in order to be white. The other allele is C+, which causes pigment expression. Because it is the Dominant allele it is denoted with a capital letter. So, if a bird is C+/C+, they express pigment. If it is C+/c, it will express pigment. Only if a bird is c/c will it be white. This gene will turn a bird of any base colour white, as it restricts all pigment expression.

Interestingly, Black Forest Cake carries one copy of Recessive White. So she is E/E, C+/c. We discovered this because she had a white son. Here he is with two of his black sisters.
Image

The cockerel is E/E, c/c. The pullets could be either E/E C+/C+ or E/E C+/c. Note that I only know the cockerel's E genes because I bred him. If you handed me a white bird at random I would have no idea what E allele was underneath the Recessive White, so complete is the colour restriction. It will turn any bird white.

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PostPosted: Mon Dec 22, 2014 7:12 pm 
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Deluxe Drake
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Extended Black is unusual in the E alleles because the hen and cock look virtually the same. Once the melanin enhancers are added they are both pure black. This is actually the exception rather than the rule; in most base colours the male and female are different.

Wheaten

Most of my birds are eWh: Wheaten. I used to breed blacks and blues so I have useful photos but I don't breed them any more. I'm not going to talk about the other three E alleles as much because I have no experience with them, but the principles are the same.

A wheaten hen is, I think, one of the prettiest birds, but then I am terribly biased. Chelsea Bun is a very good example. Note that she is missing her long tail feathers as Pekins are silly creatures that must be trimmed for breeding. I love them. :)
Image

She has a ginger hackle, a 'wheat' coloured body and a black tail and wingtips. She also has some black tipping on her hackle and a dusting of tiny black flecks on her body. This is pretty close to the basic Wheaten. When showing, black on the hackle and body are considered undesirable and genes that restrict black are used to 'clean up' the bird. Chelsea doesn't have many of those restrictors as you can see if you look closely.

Here is an image I've found on the internet of an unmodified wheaten rooster, this one is a Wheaten Old English Game:
Image

Note the black body, the gold hackle and saddle and the gold 'wing triangle'. It is one of the ironies of breeding to show that a show-quality rooster like this one will not father a show quality pullet; she will have too much black on her. To get a 'clean' hen or pullet, with little to no black on the body or hackle, you need to use a 'pullet breeding' rooster. These are full of melanin restrictors, and look like my Red Rooster:
Image

Red cannot be shown, he is for breeding purposes only. Silly, isn't it? You cannot find a single black feather on his body. I think he's incredibly handsome. Hopefully he will make pretty babies for me. The genes he has are Columbian (Co) and Dark Brown (Db), both of which are black restrictors.

Columbian

Columbian is a dominant gene that restricts the expression of black to just the tail, the wing flights and the 'necklace' on the hackle. It does not affect the expression of gold. This can cause confusion as white birds with this pattern are usually called 'Columbian', however these also have the Silver gene and would be more correctly called 'Silver Columbian'. The 'Buff Columbian' is what happens when you restrict black with this gene and no other modifiers:
Image

Dark Brown

Dark Brown is an interesting gene to talk about as it shows 'partial dominance'. This means that one copy gives an effect, but two copies gives more of an effect. Dark Brown restricts black to just the tail and wings:
Image

However, where it shows partial dominance is that one copy of the gene will leave black spangles on the breast of the male, two copies removes them.

Here is my first wheaten cockerel Crackers. He is eWh/eWh, Db/db+. He has only one copy of Dark Brown:
ImageImage

Those particularly observant might also notice the grey tail-feathers; he also had one copy of blue (which I will talk about later). He was a lovely little chap and is missed.

These two genes tend to be cumulative with each other; the more copies you have the less black you have. Red Rooster will be eWh/eWh, Co/Co, Db/Db, which results in his pure red colour.

Image

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PostPosted: Mon Dec 22, 2014 7:44 pm 
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Blue

Blue (Bl) is a colour that is very popular but also unfortunately causes a lot of confusion. This is mostly because Blue, like Dark Brown, shows 'partial dominance'. So one copy has some effect, two copies have more. What I think causes a lot of confusion is that the two copy effect looks quite different to the one copy effect.

So, to make things easy lets start with a black bird, E/E. Blue is a diluter of black, so it causes the amount of black expressed to be reduced. It has no effect on gold. One copy of the Blue gene will turn a black bird into that familiar grey colour. There is no actual change in the pigment, just less of it.

A bird with a black base and one copy of the blue gene is E/E Bl/bl+.
The chick looks like this:
Image

The youngster looks like this:
Image

The cockerel at the front is black. The one behind him is blue. The one behind him is cuckoo, and we'll talk about cuckoo later.
Image

Where things get interesting (and confusing) is when a bird has two copies of Blue. On a black base this produces a white bird with black splotches. This is Puddle. She was a black bird with two copies of blue; this colour is called 'Splash'. The genetics are E/E, Bl/Bl.
Image

With a black rooster, she would give 100% blue offspring.

But what about blue on different backgrounds? Remember that blue only affects the black pigment, not the gold pigment. You can, for example, use it on wheatens. Remember that Black-Red wheaten rooster? You can turn him into a Blue-Red. The fellow on the right is a classic example. The one on the left has some melanin restrictors as well. They are both eWh/eWh, Bl/bl+. The boy on the left will also have at least one copy of Db.
Image

It has a similar effect on the hens. Unfortunately this was shortly before poor Biscuit died, but it's the best photo I can find of her blue hackle. Without the Blue gene she would have had a lot of black in her hackle.
Image

This is a very young Crumble (right) and Cobbler (left). If you look carefully you can just see the tip of Crumble's blue tail feathers in the middle of her bustle. Crumble is eWh/eWh, Bl/bl+. Cobbler does not have the blue gene.
Image

If a wheaten bird has two copies of the blue gene then the black turns to white with the odd black mark. In the roosters this is one of two ways to make a 'Pile' bird (the other being Dominant White - later). In a clean wheaten hen there is little visible effect, other than a white tail.

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PostPosted: Mon Dec 22, 2014 9:15 pm 
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OK, I'm feeling a little dizzy ... I'll come back after a night's rest and read through everything again - maybe it will find a rested brain cell that's working

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PostPosted: Tue Dec 23, 2014 12:30 pm 
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Sorry, I should take breaks between brain-dumps. Or at least warn people that genetics is my passion as well as my job.
:nuts

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PostPosted: Tue Dec 23, 2014 1:10 pm 
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This is terrific! Thanks so much for taking the time to write it up and post photos :hiya:


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PostPosted: Tue Dec 23, 2014 1:41 pm 
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You're very welcome Trillian, it's my pleasure. Hopefully some people find them helpful.

Look! I found a blue-tailed wheaten hen butt. Bottom right.
Image

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PostPosted: Tue Dec 23, 2014 11:21 pm 
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I'm with Trillion - Terrific work Shairlyn!

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PostPosted: Wed Dec 24, 2014 11:43 am 
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Wow, fantastic Sharilyn! I actually think I may be getting the hang of this so thank you for explaining in such a clear way. I am looking at my own little flock and I will sit down and try and map out what genes they are in there. There are some pretty funky colours, so this is a great challenge for the Xmas break. Thanks for inspiring me!!

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PostPosted: Wed Dec 24, 2014 2:03 pm 
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Lavender

This is for Bronze. :laughing

Lavender is actually a very simple gene. It is a recessive gene, like Recessive White, so a bird needs two copies to be Lavender. In action it is more like Blue, in that it is a diluter gene; however where Blue only affects the black pigment, Lavender affects both gold and black. It turns black to the familiar very pale grey, and gold to cream. Lav+ is the wildtype version of the gene (allele) that allows full pigment expression. 'lav' is the version that causes the dilution.

Lets start with a black base (E/E Lav+/Lav+), like Black Forest Cake on the left:
Image

If you then add two copies of the Lavender gene (lav/lav), you get a Lavender bird (E/E, lav/lav), like this one here:
Image

Now, if we start with a gold bird, like Red Rooster (eWh/eWh, Co/Co, Db/Db, Lav+/lav):
Image

We can make a cream bird with two copies of Lavender (eWh/eWh, Co/Co, Db/Db, lav/lav):
Image

If you look at Red's 'genotype' - the string of letters detailing what genes he has - you will note that he actually has one copy of 'lav'. I know this because the cream cockerel above is his son. Because Lavender is recessive one copy of the gene has no effect and he has his lovely red-gold colour. But his son, who would otherwise be identical, is made cream by having two copies of the gene. In genetics we would say that Red Rooster is 'carrying' Lavender. In poultry breeding some people would say that he is 'split for' Lavender.

It is important when buying for particular genetics to know whether the gene you are interested is dominant or recessive. I have heard of a case where black birds were sold as being 'split for' blue. Because Blue is (partially) Dominant, any bird carrying the gene must show it, and a black bird cannot have the gene. I can only hope that the breeder in question was ignorant of the genetics involved, rather than deliberately misleading people.

So the fun thing about Lavender is that, because it is a diluter and not a restrictor, like Blue it can be applied to any other colour. 'Porcelain' is Lavender Mille Fleur, for example.
ImageImage

You can certainly take a Wheaten pullet, like this:
Image

And make a Lavender Wheaten pullet (and enormous pile of sass) like Elsie here:
Image

You can take a Furness (melanised wheaten), like the one here:
Image

And make a Lavender Furness like Scalpie:
Image

You can take a Buff or Wheaten Columbian Rooster, like this:
Image
and make a Lavender Wheaten Columbian like Flash (eWh/eWh, Co/Co, db+/db+, lav/lav). The lavender in his hackle tells us that he does not have Dark Brown.:
Image

One of the things about recessive genes is that they can be hidden in a line, where birds only carry one copy, but a few offspring will carry two and surprise you! This is what happened with my Lavender wheatens, they were a complete surprise. Obviously my wheaten hens carried Lavender, and Phil also did!:
Image

You wouldn't think it to look at him, would you?

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PostPosted: Wed Dec 24, 2014 4:14 pm 
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Cuckoo

I kept promising to talk about Cuckoo so I'd better make good on it. I've been avoiding it because Cuckoo is one of those rule exceptions, specifically the rule that says that ever animal has two copies of every gene.

In Humans we have 23 pairs of chromosomes, each member of the pair being a match for the other in size, shape and gene content. The first 22 pairs are referred to by number, and we have two of Chromosome One, two of Chromosome Two, etc. This is why we have two copies of every gene, because there is one on each of the pair of chromosomes.

The exception is the 23rd pair, the sex-determining chromosomes. In Humans and other mammals, a female has two large chromosomes, called X chromosomes. This means that she has two copies of every gene that is on those chromosomes. However a male has one X and one small chromosome called a Y. This chromosome is very important because it contains the male master gene, the one that turns on all the other male genes and tells the organism to be male. If you don't get this gene, you're female, and female is the default for mammals.

The Y chromosome is actually quite small. There are a few genes that are on the X that are also on the Y, but there is a whole section that is missing, so males only get one copy of the genes in that section, whilst females get two. This means that for males there is no question of dominant and recessive, they only get one allele and that's what they express. These genes are called 'sex linked'. Normally this is fine but it can be a problem if the allele that they get has a mutation that doesn't work properly. The Haemophilia bleeding disorder genes are a classic example, and the reason that most Haemophiliacs are male. There is also a section of the Y chromosome that is not duplicated on the X. The male master gene is here. This is a system that has been in place for millions of years and works very well as it gives you a 50:50 male to female ration.

Here's a pretty scanning electron micrograph that I found of the Human sex chromosomes. X on the left, Y on the right:
Image

Now that you've got that straight in your head I'm going to confuse everyone, because birds are the opposite way around. In birds the large chromosome is dubbed Z and the male has two copies, ZZ. The small chromosome is called W and has the female master gene. So in birds, male is the default and they need the W chromosome to be female. Hens are ZW.

What has this got to do with Cuckoo? Cuckoo is a sex-linked gene. That means that it is on the long section of the Z chromosome that is not duplicated on the W gene. It is a Dominant gene, more correctly termed Sex-Linked Barring, and the allele is B. The non-barring allele is b+. Because it is sex-linked, a hen can only ever have one allele of the gene; she is either B or b+, Cuckoo or Not Cuckoo.

A rooster on the other hand can be B/B homozygous Cuckoo, B/b+ heterozygous Cuckoo or b+/b+ not Cuckoo. Because the gene is Dominant, both B/B and B/b+ show the cuckoo patterning. In fact there is a slight cumulative effect, where the B/B rooster has more white on him than the B/b+ rooster, and they are called Light Barred and Dark Barred in, for example, Plymouth Rocks. The terminology is a bit confusing. Do not confuse Cuckoo with Autosomal Barring such as in Campines, which is the result of several, very different genes. If I'm feeling brave I might tackle that one later.

So, what is Sex-Linked Barring/Cuckoo and what does it do? It is a pigment restricting gene, and causes the pigment to be layed down on the feather in bands, interspersed with white bands. It affects both black and gold pigments.

On a black base, it looks like this. Cockerel on the left is E/E, B/b+ and Cuckoo, cockerel on the right is E/E, b+/b+ and black:
Image

You can do the same thing to any other colour. 'Crele' is Cuckoo Partridge. From the net, here is the Partridge Rooster:
Image
Here is the Crele:
Image

Likewise here is a Buff bird:
Image
And here is the Buff Cuckoo:
Image

One of the interesting things about the Cuckoo gene is that it affects the chick down; it puts a white spot on the chick's head. Note the three penguins with headspots in the middle, compared to those around them without:
Image

All of these chicks have only one Cuckoo allele, either because they are female or they're males but their mothers were black (I only had a cuckoo rooster). In boys with two copies, the white head spot is much bigger. This makes breeds like Plymouth Rocks auto-sexing at hatch, as although all chicks have spots, the boys have bigger head-spots than the girls.

The Colonel, my old (dark) Cuckoo rooster. A truly magnificent bird, and the most expensive I ever bought. He is missed.
Image

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PostPosted: Wed Dec 24, 2014 6:14 pm 
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shairlyn wrote:
Lavender

It is important when buying for particular genetics to know whether the gene you are interested is dominant or recessive. I have heard of a case where black birds were sold as being 'split for' blue. Because Blue is (partially) Dominant, any bird carrying the gene must show it, and a black bird cannot have the gene. I can only hope that the breeder in question was ignorant of the genetics involved, rather than deliberately misleading people.



And make a Lavender Wheaten pullet (and enormous pile of sass) like Elsie here:
Image



Regarding the hypothetical breeders and the "split for blue" - I would give them the benefit of the doubt, just because of how the black/blue/splash ratios fall out, eg Blue x Black = 50% Blue, 50% Black, so the person could easily think all the chicks from such a black/blue pairing would be "half blue" whether the chicks were showing blue or not.

Regarding Elsie ... how would you write that?
eWh/eWh, Lav+/Lav+, Sass/Sass++?

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PostPosted: Wed Dec 24, 2014 6:25 pm 
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Smallflock wrote:

Regarding the hypothetical breeders and the "split for blue" - I would give them the benefit of the doubt, just because of how the black/blue/splash ratios fall out, eg Blue x Black = 50% Blue, 50% Black, so the person could easily think all the chicks from such a black/blue pairing would be "half blue" whether the chicks were showing blue or not.

Regarding Elsie ... how would you write that?
eWh/eWh, Lav+/Lav+, Sass/Sass++?


Exactly, that's what someone with no understanding of genetics might think with regards to blue, which is one of the reasons I'm writing these explanations. Genetically a bird who looks blue is 'half blue' because they have one blue gene and one not, as two blue genes is a Splash. I aim to enlighten! :-D

The great thing about genetics is that once you know what you're looking for, you can often deduce some of the bird's genes just by looking at them.

Elsie would have to be homozygous sass! :rofl: The sass seems to go with being lavender, they're all a little highly strung and make vicious broodies, even more so than the wheatens. Scalpie is the exception but then she's proven to be a rotten mother. Elsie is an excellent broody and is currently drawing blood from anyone who tries to inspect her golf balls.

She may be in for a shock in a few weeks, there are peahen eggs in the incubator... :laughing

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