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PostPosted: Tue Jan 06, 2015 1:39 pm 
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Following a request for some pictures and explanations, I've started posting somewhat rambling genetics lessons in my At Home with my Pekins blog, to try to help explain some of what I've been talking about with my own birds. Due to the positive responses I've had, I though I might tidy the lessons up a bit and re-post them here in the hope that others might find them useful.

I'm a geneticist by training, profession and conviction; the subject is something of a passion of mine. Fortunately I get paid to do this stuff with Humans, with chickens it is simply a hobby/mild obsession. I'm indebted to the breeders and researchers who over the years took the time to document their investigations and conclusions, and hope that I have interpreted their work correctly.

(Please note: Some of the photos I use are mine - most of the Pekins. Others I have scavenged from the web in order to correctly demonstrate a colour that I don't keep. If you see a picture of your bird here and you would prefer that it wasn't there or you would like credit for the photo, please let me know and I will adjust accordingly. On the flip side, if you see a picture and think 'I have a better shot of that in my Gallery', then by all means please volunteer it!)

Dottensilk has very kindly started a Feedback Thread for comments and questions; please feel free to head over there and ask/comment/ramble/throw things. It's always nice to hear how people are finding the material, and it helps me work out what to talk about next.

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Last edited by shairlyn on Tue Jan 13, 2015 5:09 pm, edited 3 times in total.

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PostPosted: Tue Jan 06, 2015 1:43 pm 
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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, or one letter capitalised (this is one of those rules to which there are exceptions).

An animal may have two copies of that gene 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, i.e. there is no competing allele and the recessive is the only option available. 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 later post.

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 because C is dominant. 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: Tue Jan 06, 2015 3:45 pm 
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Awesome information! I'm looking forward to the next edition.

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PostPosted: Tue Jan 06, 2015 3:54 pm 
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Great Shairlyn! Keep it coming :biggrin:

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PostPosted: Tue Jan 06, 2015 5:56 pm 
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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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Last edited by shairlyn on Sun Mar 19, 2017 4:48 pm, edited 1 time in total.

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PostPosted: Tue Jan 06, 2015 7:14 pm 
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What a good idea. I'm looking forward to it too.


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PostPosted: Wed Jan 07, 2015 7:50 am 
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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

Here is a better shot of a blue-tailed wheaten butt; bottom right. This one is a very pale blue.
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, which we will look at later). In a clean wheaten hen there is little visible effect, other than a white tail.

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PostPosted: Wed Jan 07, 2015 8:36 am 
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Hi Shairlyn - Thank you so much for all of this, it's just fantastic.

May I please ask a question on Blue. For your Blue chick picture you state:
A bird with a black base and one copy of the blue gene is E/E Bl/bl+

What does the /bl+ mean or signify?

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PostPosted: Wed Jan 07, 2015 8:57 am 
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Smallflock wrote:
Hi Shairlyn - Thank you so much for all of this, it's just fantastic.

May I please ask a question on Blue. For your Blue chick picture you state:
A bird with a black base and one copy of the blue gene is E/E Bl/bl+

What does the /bl+ mean or signify?


Hi Smallflock! The 'bl+' is the wild-type allele for that gene, the one that does not dilute the black pigment on the bird. All the blue birds have one copy of the Blue allele 'Bl' and one copy of the wild-type allele 'bl+' for that gene, remembering that there are two copies of each gene, one on each of the pair of chromosomes. Writing the '/bl+' is to show what is on the other chromosome. This is important for this gene because a bird with two copies of the 'Bl' allele is splash.

The little string of letters is called a 'genotype', and it's a representation of the genes that the bird in question carries. Assuming we're starting with a black base:
bl+/bl+ = Black (normal pigmentation)
BL/bl+ = Blue
BL/BL = Splash

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PostPosted: Thu Jan 08, 2015 12:12 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?

Interestingly, the mutation that causes Lavender in poultry has a homologue (similar gene) in many other animals, including humans! It's called Griscelli Syndrome and there are three forms of it. Unfortunately Type 1 involves mental retardation (might explain why my lavender wheaten chooks are flightly) and Type 2 with immune problems. Type 3 just has the colouring:
Image
Unfortunately Types 1 and 2 are much more common and often fatal at a young age.

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PostPosted: Thu Jan 08, 2015 4:42 pm 
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Hi Shairlyn,

Sorry to always be the slow one... could you explain melanisers? I read back through your posts and can't see it (although I did find where you'd explained the + wildtype :oops: )

Why is a Furness a melanised wheaton? :read

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PostPosted: Thu Jan 08, 2015 8:07 pm 
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Hi Smallflock! Sure, no problem. :)

Another word for colour is pigment or melanin. A 'melaniser' is a gene which increases the amount of pigment expressed. This is the opposite effect to that of diluters like Blue and Lavender.

Generally when we talk about melanisers we mean enhancers of the black pigment. There is a gene called Melanotic - which I will talk about later - which enhances the expression of black. A Furness is a Wheaten with Melanotic.

The Furness cocks look oddly impressive to my eye: http://www.kevinkrisadams.com.au/images/bestfurness.jpg

Hope that helps.

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PostPosted: Fri Jan 09, 2015 11:50 am 
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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: Tue Jan 13, 2015 1:21 pm 
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Predicting the next generation

I can go on for ages about various genes (and no doubt will over time) but I thought I'd divert slightly for a couple of posts and talk about genetic prediction, because people often ask 'if I cross this bird with that, what will I get?'. The answer is relatively simple, whilst at the same time not particularly intuitive. As such people who don't understand genetics usually get it wrong, but once you have the right tools it's not particularly difficult. Hopefully I can explain it properly so that everyone can do it. :)

Gregor Mendel was a scientist and and priest who lived in the 1800s and had a deep interest in the inheritance of characteristics. He spent an unhealthy amount of time cross-breeding pea plants, and divised his rules of inheritance, which are still used today. He is considered the father of modern genetics.

Unfortunately the importance of Mendel's work wasn't understood until after his death. Like many ground-breaking scientific discoveries, his work was rejected at the time. The generally held theory at the time was that of 'blending inheritance' whereby the offspring receives all the traits of the parent, but at half strength. Many observations seemed to uphold this theory, and even after it was debunked scientifically it stayed in the popular consciousness. A prime example is that dreadful piece of genocide-by-dilution that was promoted as part of the White Australia Policy, where the idea was that if Australian Aborigines had children by Europeans, then eventually everyone would be white. It was supported by things like this:
Image

As you can see, each generation becomes more European-looking; people thought that each generation had a dilutional effect. What's actually happening is that traits such as skin colour and the shape of facial features are not governed by one gene, but by many. Each generation only inherits one copy of each gene from the mother, and one from the father, so each time there is a smaller and smaller chance of inheriting an allele that gives a more Aboriginal phenotype.

Another piece of nomenclature: 'Genotype' is what the instructions in your genes say you should look like and how you should function, 'Phenotype' is what you actually look like and function. They are not always the same! A simple example is a sister and brother with the genes for blonde hair. By the time they are middle aged their genes still say 'have blonde hair' but you might find that, due to some other, unrelated genes, the brother is actually bald. This is also a nice example where you can tell the hair colour genes carried by the female, but not the male. :)

Things like height, weight, hair colour, eye colour, skin colour, shape of facial features etc are all governed by multiple, complex genes which makes them difficult to predict. Then again the Red Jungle fowl looks very different to the Green Jungle Fowl, when one meets them for the first time, due to the large number of genes that are different between them.
ImageImage.

I would just like to say that I want a Green Jungle Fowl. Those combs look awesome.

Now if we were to try to guess the genetics of these birds above, we'd all probably be as lost as each other. Fortunately Humanity has a long and enthusiastic heritage of chicken breeding and the experience and genetic heritage that goes with it. We have many breeds of particular colours and patterns which have been standardised and whose inheritance is well understood, and we have researchers who have dedicated a lot of time and work to sussing out the genetic basis of various traits. This then makes it relatively easy to determine a single genetic trait and predict it's inheritance.

If you're still with me after that giant ramble, here's the pointy end of the post.

The tool used for predicting inheritance is something that Gregor Mendel invented, and it's called the Punnet Square. It looks like this:
Image

Yep, that's right, four empty boxes. That's all it is.
Cool story, how do we use them?

First of all I need to explain a little more on chromosomes, genes and inheritance.

As I've mentioned before, Humans have 23 chromosome pairs, for 46 in total (and I'm too lazy to look up how many chickens have). Every cell in your body (exception rule) has these chromosomes, and they tell your body how to be what it is. One of the exceptions is your sex cells. Sperm and egg cells have only one copy of each of the 23 chromosomes, they don't have a pair. This is because the sperm and the egg will join together and their respective chromosomes will pair up, giving the resulting baby it's own set of 23 pairs. In each pair one chromosome came from mum and one from dad. Which one of mum or dad's two chromosomes gets incorporated into the sperm/egg and inherited by baby is random. This is important.

So whilst Dad has two copies of a particular gene, baby only inherits one of his. Same goes for mum. Same goes for chickens. And whilst your daughter or son might look like a clone of one of their parents, they are also half the other one! In there, somewhere...

One final note: It is important not to confuse inheritance with expression. If an allele is Dominant that means that it expresses over a recessive allele. It does not mean that all the offspring will inherit the dominant allele, only that those that do inherit it will show it.

Predicting single gene inheritance

Most of the time when we're asking what the offspring will look like, we're asking about the results of a single gene, with the birds being identical for all other genes. Lets make up a gene here, and I'm going to call it 'A'. A has two alleles, they are A1 and A2. Now remember that ever bird has two copies of each gene. This means that a bird can be homozygous A1 (A1,A1), heterozygous (A1,A2) or homozygous A2 (A2,A2).

Lets start with a Rooster who is homozygous A1. So his genotype is A1,A1.
Lets put him with a Hen who is homozygous A2. So her genotype is A2,A2.
Note the two alleles in each bird's phenotype. Each bird will pass one of those alleles onto their offspring.

Lets take our punnet square:
Image

What we do is we grid out the parent's genes. So lets start with Dad and what he will contribute to the offspring. We will put him at the top of the square and each allele above each column.
Image

Then we will take Mum and do the same at the side of the square.
Image

Now each box gives you the potential offspring combinations, and has a probability of 25%. What we do next is combine the alleles in the squares.
Image

As you can see, every box says 'A1/A2'. This means that 100% of the offspring will be heterozygous A1/A2. This is called the F1 or First Cross.

But what happens if we then cross the offspring together, brother to sister? This is called the F2. It is rather more interesting.
Image

Note that this time each parent can contribute either an A1 or an A2, as they carry both. When we fill in the squares we get some interesting combinations.
Image

The results are as follows:
1 x A1/A1
2 x A1/A2
1 x A2/A2

Since each square has a probability of 25%, that gives us the following ratios:

A1/A1: 25%
A1/A2: 50%
A2/A2: 25%

These are called the Mendelian ratios, and are universal for single-gene inheritance. What that means for the resulting bird is dependant on the nature of the alleles' expression.

I shall let folks digest that, and then give some practical examples in the next post.

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PostPosted: Wed Jan 14, 2015 10:21 am 
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Recessive/Dominant inheritance

Now that we have our Punnet Square and know how to use it, we need to know how to interpret it. This is where knowing how the alleles are expressed, i.e. Dominant or Recessive, comes into play.

Lets look at the first colour-change gene we talked about, Recessive White. This one is nice and easy as it's a clear dominant vs recessive relationship, and even helpfully says so in the name. So 'C', which causes a bird to express colour, is Dominant and 'c', which causes them to suppress colour (and thus be white) is Recessive.

If we take a white bird and cross them to a black bird from a line with no history of white, it looks like this:
Image

This results in 100% C,c offspring. Here is where we need to interpret. This is what we know:
C,C = Coloured bird.
C,c = Coloured bird, carrying white
c,c = white bird.

So from this square we can work out that all the offspring will be coloured, but all will carry Recessive White. Assuming that the white bird is from a black background, all the offspring will be black.

Then we ask, what happens if we cross the offspring together?
Image

From this we get the following genotypes:
25% C,C
50% C,c
25% c,c

We know from above that both C,C and C,c are coloured birds, so we get the following phenotypes:
75% Coloured
25% White

There is no way to determine, of the 75% coloured offspring, which ones carry recessive white, except by crossing them to a white bird and looking at the offspring.

Investigative Cross

Unfortunately our birds don't come with a little tag detailing their genotype; life would be much easier if they did! Sometimes we need to do some investigative crosses. So lets say that I gave you a coloured bird from the above cross, telling you that they came from a line that had Recessive White in it. How would you determine whether or not the bird that I gave you actually carried Recessive White?

Given the above cross, there are two possible options for the bird that I have given you. One is that it carries Recessive White, and is C,c and the other is that it doesn't carry it and is C,C. You can't use the punnet square ratios to predict the actual genetics of an individual bird, only the possible combinations that it could carry. To see those ratios you have to hatch a few chicks; seven is the minimum to be certain.

Now the easiest way to see whether the bird carries Recessive White is to cross it with a Recessive White bird. Here is where we do a little predicting. We say 'If my bird carries Recessive White, the Punnet Square will look like this':
Image

This will give me:
50% C,c = 50% Coloured Birds (carrying white)
50% c,c = 50% White birds.

But, if my bird does not carry Recessive White, the Punnet Square will look like this:
Image

100% C,c = 100% Coloured Birds (carrying white).

Then what you do is you perform the cross, you breed your new bird to your white bird and hatch some chicks. The statistically significant number is seven. If you get even one white chick, you know that your new bird carries Recessive White. However if all seven are coloured, you can be 95% certain that your bird does not carry Recessive White.

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