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PostPosted: Fri Dec 26, 2014 12:34 pm 
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Phoenix
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Brilliant explanations Shairlyn :thumbs:

Thanks for taking the time and sffort to write such excellent explanations , and providing clear photos along with the genetics info - makes it much easier to understand .
I agree with you about the wheatens - they are a beautiful soft colour - love the hens with the ginger hackle particularly.

Im looking forward to setting some of my new pekins eggs in the Autumn.....purely to see what genetics may be hiding there ....and to get more of these enchanting little birds.

cheers


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PostPosted: Sun Jan 04, 2015 1:11 pm 
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Deluxe Drake
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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
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. When I've had my lunch.

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Last edited by shairlyn on Tue Jan 06, 2015 7:49 am, edited 1 time in total.

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PostPosted: Sun Jan 04, 2015 1:13 pm 
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Deluxe Drake
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Okaaaay, the boards don't like formatting. I will do something to fix that, probably draw them myself. Watch this space.

In the meantime, I found an awesome list of all the known genes affecting appearance in Poultry: http://sellers.kippenjungle.nl/page3.html

Also, 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: Mon Jan 05, 2015 12:41 am 
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Junior Champion Bird
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You go Girl! Excellent.
By the way that poor young girl's hair is a great example of Lavender (more grey than blue).

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Struggling with Lav**


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PostPosted: Mon Jan 05, 2015 6:11 am 
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Gallant Game
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Poor Shairlyn. I don't think your Punnet squares made it through customs. The Green Jungle Fowl ... I'm glad that comb didn't make it over to the domestic side - it's a beauty, but can you imagine it on top of (say) a Speckled Sussex? It might work with some of the pom-pom breeds, but beyond that ....


Attachments:
Jungle Pekin.png
Jungle Pekin.png [ 129.49 KiB | Viewed 2712 times ]

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PostPosted: Mon Jan 05, 2015 2:12 pm 
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Deluxe Drake
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If you want to try things for yourself, here is a useful Punnet Square calculator. It only lets you enter one letter for each allele, but you can use it for multiple genes as well.

http://scienceprimer.com/punnett-square-calculator

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PostPosted: Tue Jan 06, 2015 12:06 am 
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Junior Champion Bird
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It's all very interesting, and easily understood with your explanations Shairlyn. I think I've learnt a "reasonable but not enough" amount about Genetics, and have learnt a few interesting points from reading your posts. Thank you! Will be watching this space

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PostPosted: Tue Jan 06, 2015 8:09 am 
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Deluxe Drake
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Aw Smallflock, I think that photoshopped Pekin looks awesome! Couldn't you see Flash with a comb like that? I shall keep dreaming. :)

I'm glad you're finding it useful Bronze. If there's something that you want to know or I can try to clear up, please just ask!

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 it 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.

Making sense so far?

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PostPosted: Tue Jan 06, 2015 2:09 pm 
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Deluxe Drake
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Dominant White

I thought that it was time to mention that there are two 'white' genes, the second being 'Dominant White'. It is a completely different gene to that which gives us Recessive White. The gene is the I gene, and the recessive allele 'i+' is that which is most common and causes normal colouration. The dominant allele 'I' restricts the black pigment, turning black to white.

Back when many breeds were being created, there would have been no way for breeders to know for certain that there were two different types of white, and I imagine that conflicting observations on inheritance might have caused a few punch-ups down at the pub.

Leghorns, we now know, are made white by Dominant White.
Image

However the allele is a little leaky and Dominant White bird on Extended Black will have some black flecks on their feathers. It also shows a small amount of incomplete dominance, whereby a bird that is heterozygous I/i+ will show more black flecks than a bird that is homozygous I/I. In leghorns the pure white colour is achieved by adding genes like Columbian Co and Dark Brown Db which further restrict the black pigment.

In the days before commercial hybrids there was a popular egg-producing cross in Australia called an 'Austra White'. It was made by putting a Leghorn (E/E, I/I) rooster over an Australorp (E/E, i+/i+) hen. I know that there is some work being done to produce these lovely birds again. This produces the genotype E/E, I/i+ and also reduces the other black pigment restrictors from the Leghorn. The Austra Whites look like this. Pretty aren't they?:
Image

Interestingly, Dominant White I is not the only allele for this gene. There are two others and they both dilute black to a lesser extent. One is Dun 'Id', and one is Smokey 'Is'. Both produce birds with a delicate grey shade and I confess I'm not up on the subtleties of the colours myself, but I understand they are quite different. This is a Dun bird:
Image

Both Smokey and Dun are dominant over the wildtype 'i+' and I believe that work is being done to determine how they relate to each other and Dominant White in terms of which is most dominant.

So whilst there are four possible alleles for this gene, any given bird can only have two of them, and we usually breed so that they have two copies that are the same. Remember that Recessive White 'c' is an allele of a completely different gene. It is possible for a bird to have both Dominant and Recessive White!

What is interesting about Dominant White is that it only affects the black pigment, whilst Recessive White affects both. What this means is that on a bird that has a pattern with both black and gold pigments, you can use Dominant White to turn the black sections white. This is used to great effect in several breeds.

We can turn the Wheaten bird:
Image

Into a Pile bird:
Image

Or we can take a Laced Wyandotte:
Image

And turn it into a Buff, white Laced (probably the wrong nomenclature):
Image

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Last edited by shairlyn on Thu Jan 15, 2015 12:47 pm, edited 1 time in total.

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PostPosted: Fri Jan 09, 2015 12:26 pm 
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Deluxe Drake
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I figured it’s probably time for an update on the bird front.

Mr Shairlyn has built me a lovely three storey grow-out pen, though due to a slight miscalculation I do need a step to get up to the penthouse! The young quail think it’s marvellous though, and are often to be found standing at the mesh doors, enjoying the view. They are all very hand tame and will come up to the front for pats when I open the doors. Being quail of course I have to keep one forearm across the opening to stop the silly things from jumping out.

Under them there are eight youngsters; five lavender wheaten – three are boys and little clones of their dad Flash – one wheaten boy, one buff girl and a white girl. They were raised by Ellie who has gone back to the lavender wheaten pen.

The bottom level houses Chelsea Bun and her ten chicks which are at the ‘feathered beetle’ stage of development. Again a majority of the lavenders, two whites, a couple of wheatens both of which look to be boys as well. A wheaten pullet would be nice!

I have separated out the quail that I want to keep into a pen in the Quail Condo; three Pharoah hens and a Tibetan pair. There will be some shuffling around between them and Old Yellow with his three Yellow hens. I’m offering the rest of the quail for sale, I figure most of the hens will go and we’ll eat the cocks.

Still in the Quail Condo is Lacey with her seven chicks, which are again lavenders and wheaten boys. There are three youngsters in the lavender pen, one of which is a lovely lavender-cream pullet, and there’s a small lavender pullet that Goldie raised who went into the Wheaten pen with her mother; I’m still waiting for her colour patterning to finalise.

I will probably keep one or two Lavender Wheaten pullets if I get a couple with the colouration that I want, and sell the remainder. I will be able to offer pairs and trios this year if someone is interested in breeding the colour.

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PostPosted: Mon Feb 16, 2015 9:23 am 
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Deluxe Drake
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As people have probably already worked out, I have decided to continue the genetics lessons over in Breeds and Breedings, since so many people seemed to be interested in them. Shairlyn's Genetics Lessons.

On the home front things are busy! The wedding is only five weeks away.

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PostPosted: Mon Feb 23, 2015 9:02 am 
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Deluxe Drake
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We have thirteen fresh, cheepy nuggets! Probably the last hatch of the season, but Ellie who has been broody for ages (third time this season) now has a baker's dozen of fuzzy little chicks to care for, for her sins.

A friend of mine gave me a chicken as a wedding present (best present ever!) and Pumpkin (the name she came with) is now settling into the wheaten pen. She's a really pale girl, virtually a cream wheaten, and so very pretty.

Four weeks till the wedding; eek!

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PostPosted: Thu Apr 09, 2015 8:38 pm 
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Deluxe Drake
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So, we survived the wedding, had an absolute blast, and an awesome honeymoon!

We are finally back to reality: the chook pens are badly in need of a dig-out. XD Nothing like a big pile of chicken s*** to bring you back down to earth. On the other hand it brings the veggies up a treat and we have had an awesome pumpkin harvest and are now bringing in sweet, juicy corn. Also I made sundried tomatoes with the excess cherry tomatoes and they are disturbingly delicious if I do say so myself. The pickled quail eggs worked well too. It's so nice to be able to produce some of our own food.

None of the wheaten breeding flock are laying now, although Pie and Goldie are still brooding with great determination and refusing to be broken. I may have to resort to the bucket. Only the lavender wheatens are laying but I'm not planning on hatching any more chickens this season. We may yet do a quail run; haven't decided yet.

Ellie's thirteen nuggets are now at the awkward, lanky stage and are every colour of the rainbow. I have finally got two wheaten pullets in the mix, although they're quite dark (almost clay) so I hope that they will lighten up as they develop. There are buffs, lavender wheatens, lavender columbian wheatens and one very odd looking pullet whose feathers sprouted with wheaten tips, but the remainder if the feather is white. She has a few orangy-coloured feathers on her head, and I am hoping against hope that she is a cream-wheaten like Pumpkin (who is not her mother as I was given her after those eggs were laid). That would be awesome as it would suggest that the relevant genetics are already in my flock.

We did incubate one more setting after Ellie's chicks, all eggs from the wheaten pen in the hopes of getting some more wheaten pullets, but Red Rooster was moulting, only four of the eggs were fertile and only three hatched. They were two buffs and a white. :doh However that and the fact that the white cockerel who is growing out in another pen shows small flecks of buff on his feathers narrows down the carriers of the Recessive White considerably. It has to be Red Rooster and either Wendy or Apricot Tart, both of whom are Buff x Wheaten and Goldie's daughters. If the two young wheaten pullets prove acceptable I might sell these girls on as I want to get more wheatens and those two have white on their earlobes (no idea why, neither parent did).

I am keeping the lavender wheaten pullets to grow out at the moment as I want to select for ones with good cream bodies and lavender hackles to breed from; it's nice to be at the point where I can select from the best rather than just breeding with whatever I have. The colour is becoming more consistent too, the down side of which is that I can't always tell the hens apart now. I may have to band them, or just call them all 'hey you'.

It also means that I am up to the eyeballs in cockerels. Unfortunately we have had a bit of the feather issue sometimes associated with Lavender, although it only seems to show up in the cocks. The ratty looking ones are destined for the cooking pot, the nice ones will be up for sale. I am getting Lavender wheaten and lavender columbian wheaten, both of which are proving very pretty in the boys. I can't wait until I have girls to offer with them as well.

Bruce the quail cock (name courtesy of Mr Shairlyn) and his girls are going strong, although their laying has dropped off. Hopefully they will pick up again as the chickens stop. They are such funny things but are at least much tamer than Old Yellow was, Bruce and the younger hens were hand reared and will let you pat them.

The quadrupeds are well, dogs are deliriously happy that we are back and the cats are being super-affectionate and wanting lots of attention. As fun as the honeymoon was, it is good to be home!

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PostPosted: Thu Apr 09, 2015 8:55 pm 
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Welcome back Shairlyn. Glad you enjoyed your honeymoon.

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Shane.


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PostPosted: Fri Apr 10, 2015 8:15 pm 
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I'm so glad you both had a great time- welcome back! :hiya:


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