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 Post subject: Re: Barnevelders
PostPosted: Thu Jul 09, 2015 2:06 am 
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Thank you everyone. In the 2 weeks since I started this thread, more things have fallen into place for me than in the past 10 years of 'messing with Barnies' by myself.

As Dotte said, "The resources are starting to come together"


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 Post subject: Re: Barnevelders
PostPosted: Thu Jul 09, 2015 2:11 am 
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I can see you are very interested in the egg colour side of things so i will go through that article and do my best to translate it into barnie terms shortly.

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 Post subject: Re: Barnevelders
PostPosted: Thu Jul 09, 2015 12:44 pm 
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I have nothing helpful to add other than a) it would be sad to lose the dark egg colour from our barnies, and b) DottesnSilk, I wish you would breed some lavender laced red Wyandottes!! Hah.


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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 12:36 am 
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Been out most of today so still haven't had a good read of the article on egg colour but the table of genes has been playing on my mind while i was out today (more sadness Sue) so i thought i'd start there because that's the bulk of what we need to know from the article anyway. This is the article the table was taken from http://www.maranschickenclubusa.com/files/eggreview.pdf and here is the table from the article with certain sections highlighted
Attachment:
egg shell colour gene table.jpg
egg shell colour gene table.jpg [ 329 KiB | Viewed 2520 times ]
The left hand column is the range of shades and colours that the suggested possible genes are said to create. The second column is the main gene that i believe is commonly called the blue egg gene. The next three columns are the proposed genes that in combination with the blue egg gene create all the different shades of blue, green, brown and white. I've put a border around (using a poor choice of colour) the non blue parts of the spectrum and further segregated the white from the brown parts of the spectrum (bordered in blue). So what does this mean?

First i'll try my hand at explaining the genetics in general terms. Who knows, a watered down version presented a different way may help others start to get a handle on the fundamentals of genetics. OK, here goes (deep breath), wish me luck.

The first thing i remember short circuiting my brain when i first started learning about genetics were the terms dominant and recessive. I found this really confusing. It's not about how powerful a gene is but more to do with a balance between the on and off state and how that displays.....stay with me. Take dominant white for example. If you didn't know better and you had heard of dominant and recessive white you would think that they have some sort of relationship and dominant white has some sort of power over recessive white. The fact is they are not related and recessive white could be considered more powerful (powerful being a subjective term) than dominant white..........stay with me, it's coming.

So what does dominant mean then? Each gene has two possible states, a bit like on and off as i eluded to earlier and each bird carries two copies/doses of the given gene. For dominant white the symbol is I. The two possible states are represented as I and i. So the possible combinations are I/I, I/i, i/I and i/i. The first and last combination is referred to as homozygous and the two in the middle are referred to as heterozygous. The two heterozygous combinations are essentially the same apart from which gene came from which parent. So the first and last combinations would be homozygous for dominant white (I/I) and homozygous for 'not dominant white' (i/i - anything not dominant white). The ones that are heterozygous would all be white in appearance but maybe leaky. This is why it is called a dominant gene, it only needs one dose to display.

So what about recessive white? Recessive white is denoted as c. The possible combinations are C/C, C/c, c/C and c/c. Because it is recessive, the only combination that will produce a white bird is c/c. All the others will be 'not white'. Their colour will be determined by what other genes they carry. As i mentioned earlier, there is no relationship between dominant and recessive white. That is to say that C/I etc. are not possible combinations.

So how could recessive white be regarded as more 'powerful' than dominant white? Red can leak through dominant white but recessive white in it's homozygous state will cover everything.....see, i got there in the end.

Moving along.....The string of genetic letters given to represent a bird is called the genotype. What the bird looks like is called it's phenotype. I'm more interested in genotype for this bit. It is important to understand that these genotypes are only details of what we understand at this point in time and only represents an incredibly small amount of the total genes that makeup the bird and most of those relate to colour. Even then the stuff that is understood is not complete and there are many other colour genes that are yet to be mapped. The genotype does give us a recipe on what creates their appearance though and with a little understanding of some fundamentals they can be helpful.

The other article i quoted some info from earlier had part of a genotype in the document, here it is eb/eb, Pg/Pg, Ml/Ml. We have been talking about eb base for a while now so hopefully that one stands out at you. If you go back to the article (in blue text) it talks more about Pg and Ml but what i wanted to point out is that if you think of each of these genes as having the potential to be on, off or in between (heterozygous) then you can get a bit of a handle on why things happen the way they do. You will notice that eb is recessive. The E locus (where the base colour genes live) is a bit different in that there are several known possible combinations on this one. Any one of (trying to remember them all off the top of my head and should be looking it up) E, Er, eWh, eb and e can go on the E locus. I'm sure there are more but these are the main ones (notice they all start with e) and in order of dominance. That is an E/eWh will look more like an E/E than a eWh/eWh as a chick and so on down the line, E being most dominant and e being most recessive.

I promised to translate to barnie so let's talk about eWh and eb bases. eb is less dominant (or more recessive depending on your viewpoint) than eWh. So how does eb 'float around' in a line for so long? Take this scenario and remember that because eb is considered recessive to eWh, a chick will have to carry two doses of the eb gene to look like an eb chick.

Scenario: One hen in a flock of eWh based barnevelders is unknowingly carrying one dose of eb (eWh/eb). It is the only one in the whole flock but she is pretty and lays dark eggs so the breeder uses her. The outcomes from this are half the offspring from this particular pairing will be also carrying one dose of eb. You can see from there that there is potential for more and more hens to be carrying eb and hiding it. Let's cut to the chase and say then the breeder keeps a cockerel that is also carrying eb and breeds it with some of the hens that are carrying eb. Now we have eWh/eb x eWh/eb. The possible outcomes are eWh/eWh, eWh/eb, eb/eWh and eb/eb (the brown chicks). From this pairing you would expect equal amounts of each combination but only one of the combos give eb phenotype so three quarters of them would look much the same (eWh) and only a quarter will be eb due to the dominance of eWh. You can see now how a recessive gene can hide in a line and seemingly come from nowhere. The exact same scenario could be applied to any recessive gene. Single combs in wyandottes for example. White sports in many lines are a result of recessive white hiding in the line.

Getting back to the genotype, what was quoted all related to plumage colour, eb base, pattern gene and melanised. The Ml is about the black pigment in the pattern and the Pg is about the ordering of the pattern. The article where the genotype came from doesn't talk about any of the genes for egg colour so what i want to do is try devise a genotype based on that table of genes and present it in an understandable way......hopefully.

From the table you can see that if the blue egg gene is present in it's O state, brown eggs don't happen so the first thing we can lock in is o/o. Then there are three proposed genes that don't have a name so let's call them x,y and z. X is a dominant brown egg shell enhancer, we want that so lock in X/X. Y is a brown shell inhibitor and it is recessive so we don't want that, lock in Y/Y. Z is a dominant brown shell inhibitor and we also don't want that so lock in z/z.

So for a genotype of desired egg colour we have o/o, X/X, Y/Y, z/z. So what do we do with this? Well, there's not a lot we can do but at least we have some idea that there is at least four genes at play and two of them appear to be required in their dominant state and as such have the potential to hide the recessive state. The o gene is insignificant because one copy would make blue or green and is therefore easily culled for. The dominant brown inhibitor that is required to be in it's recessive state could easily be lost track of being a recessive, unless it's affect could be identified.

Now, you have probably heard genes talked about in doses or copies before reading this post but you may never have thought of them as switches. If you think them as having an on, off or in between state then understand the influence of dominant and recessive on the 'in between' state then you understand fundamentally what has to be done. You don't even need to know what genes cause a particular desirable trait that appears, you just have to breed with it and see what the outcomes are to determine whether it is dominant or recessive if not already known and then work to an appropriate plan. The trick with the dark eggs though is it seems we are talking about three genes (aside from o) that have similar effects so pinpointing them is extremely difficult.

So how can we plan for this kind of genetic interaction without being able to identify which of the three significant genes are on, off or in between? The best suggestion i can offer is that if you have a hen that lays a particular darker egg than all the others, breed to her and treat it like it is a single recessive gene that is responsible. Keep a son and put him back over her and half of the next generation might have the dark egg combination that you are after. Do it again each season until you produce a high percentage of dark egg layers and you should have yourself some roosters that carry the right combination.........then you are away.

I think i'll leave it there for now. This is intended to be a very watered down view of my understanding of genetics and how it applies to this discussion but hopefully by presenting it in a different manner might just help some of you get a basic but fundamental idea of how it all works. I haven't touched on sex linkage, incomplete dominance, wildtype or other facets of genetics because i feel it would only cloud what i am trying to convey and there is no evidence to suggest that sex linkage is at play. I would love to present things as beautifully as Shairlyn does and have lot's of pics to explain things or even be able to bullet point things more but it's already a long enough post. Hopefully it helps some people and hopefully the watered down approach doesn't create any misconceptions......there is a lot to understand in the details but first you need some sort of framework of fundamental understanding to avoid suffocating in the details and climbing out (so to speak).

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 2:22 am 
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WOW Well done Dotte Thank You. Some of my old understanding of genetics (from a previous life without chooks - where is wasn't relevent) is waking up. With you doing all the hard work for me.

You stated that "there is no evidence to suggest that sex linkage is at play" this appears to refute the theory that the roo controls the egg colour.


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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 2:53 am 
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Not quite Sue, i was inferring that the article where the table comes from (although i have only skimmed it so far) didn't suggest that there was sex linkage inheritance in relation to the egg colour studies. This is more to do with a small group of genes that can only be carried in one dose by hens.

The rooster certainly needs to carry all the same genes for egg colour as the hens. That's why i suggested using a son of a good dark egg layer to increase the odds of getting two doses of genes in the offspring to produce cockerels carrying the right combination of genes. The only way you can estimate the genes the cockerels in a hatch are carrying is by going off the colours of eggs their sisters lay. If 100% of the sisters are good dark layers then you know dad has picked up the right stuff and so will all of his sons.

I will endeavor to clear up sex linkage for you another time.

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 8:46 am 
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D&S - great information. I need to go back and read it again. Thanks for contributing that for us. It's certainly food for thought.

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 9:06 am 
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Top read and good point about breeding a cockerel that carry the brown egg gene. :thumbs:

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 11:02 am 
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I'm glad you all approve. It is the first time i have attempted to convey the junk that floats around in my head and i don't have a lot of experience at preparing and presenting documents being a boilermaker by trade. I have just re read it myself (was very late when i finished) and have noticed a few bits that may cause some confusion.........we'll see what kind of question crop up and go from there. Next time i think i will prep it in a separate document and then paste it into the thread when it is ready and i might have a better chance of structuring it a little better and making it a little more concise. My brain tends to run off on tangents thinking about scenarios and then i often get off track and have to digress. If it sparks enough basic understanding to entice a few people to learn more then it has been well worth it.

Particularly happy to get your approval Cathy, thanks.

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 11:29 am 
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Sooo - The introduction of eb (to enhance patterning) possibly introduced the brown shell inhibitors. eb may be desirable to retain so long as the inhibitors can be eliminated.


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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 11:55 am 
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Thank you, DottesnSilk.
The specifics of your explanation convey more than merely the egg colour context. You also give a lesson in general terms. I am very grateful for the detail, it has propelled my interest and my comprehension.
If there are recessive genes involved, does that suggest a male input is present to egg shell colour? For it to be turned on the male would also have to pass on the recessive gene?
On a different topic, I usually sex my chicks using several phenotypes (using the speak here - did you notice). If the male doesn't display something the female does display, would that indicate a sex-linked gene at play? The most obvious is the dark eye stripe in females and its absence in males. Would this indicate that all the males have a melaniser inhibitor for that particular genetic characteristic that is present on their 78th chromosome their "Z" sex chromosome? Would this have to be dominant in males to always be expressed as the phenotype?

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 11:58 am 
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In lines other than the George Childs line yes, it is most likely that some of the genes have been lost assuming the eb base came from outside barnies. Even if a eb cockerel carrying tinted egg gene combo was used with a dark egg producing eWh hen, some of the genes would be lost or broken. The quickest way to repair or recover these genes is to breed back to the dark egg laying eWh hen, but then you lose eb again. So it becomes a real art to segregate eb without losing the combination of egg colour genes.

How eb got in the George Child's line i am not qualified to speculate but i would assume it was always floating around in the background. That's why this line presents an opportunity to siphon off some eb birds that have the desired egg gene combo and breed them together. Why the George Childs line is eWh when documentation suggests that barnevelders are traditionally eb is also something i'm not really qualified to speculate on but the reputation for outstanding cockerels may just be the reason.

I can't help but feel we are heading toward double mating. My speculation is that eb bases hens will prove superior but eWh bases cockerels will remain the superior males......just my prediction.

The biggest risk to barnies in my view is actually the show scene. Because egg colour isn't scored a breeder hell bent on winning prizes (for ego or profit) may ignore these genes and they risk being lost. I should re phrase that and say that it's not exactly the show scene that poses the risk but the competitive spirit that the show scene promotes. It's not really the show scene but more certain people. A bit like the argument that guns don't kill people, people kill people. It's very comforting to know that there are still people out there that put ego and profit aside and take the noble approach of preserving what we have.

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 12:52 pm 
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BarnieRaiser wrote:
If there are recessive genes involved, does that suggest a male input is present to egg shell colour? For it to be turned on the male would also have to pass on the recessive gene?
On a different topic, I usually sex my chicks using several phenotypes (using the speak here - did you notice). If the male doesn't display something the female does display, would that indicate a sex-linked gene at play? The most obvious is the dark eye stripe in females and its absence in males. Would this indicate that all the males have a melaniser inhibitor for that particular genetic characteristic that is present on their 78th chromosome their "Z" sex chromosome? Would this have to be dominant in males to always be expressed as the phenotype?
Great to see you have been studying hard BanieRaiser..........78th chromosome, Z, sex chromosome.......wow, you have been hard at it.......and using the speak :thumbs: .

Put simply, males and females generally look different anyway unless the male carries a hen feathered gene (another potential can of worms) so phenotype is not exclusively an indicator of sex linkage. I will try to expand but still keep it minimal.

The two main questions that seem to be popping up already are; 1) Does the male have anything to do with egg colour? 2) What the heck is sex linkage then and why does it not seem to apply?

The male has exactly the same influence on egg colour as the female. The only difference is that males don't lay eggs so there is no way to evaluate egg colour in males. Just like if the male were to be carrying only one copy of the pattern gene (Pg/pg), the pattern wouldn't come out right. As i mentioned earlier, the only way to estimate the combination of genes a cockerel is carrying (other than breeding against a known combination and evaluating outcomes) is to look at the female siblings and evaluate the depth and consistency of egg colour. If you start with a dark egg laying hen and she produces all lighter layers then you know the rooster used wasn't carrying the right combination and as suggested you would treat it like half the offspring are carrying the right combination and if luck is in your favour and you choose a son of the dark egg layer and breed back to her, you should produce a higher ratio of the correct combination for dark eggs thereby increasing the odds of selecting a cockerel with the right combo and not relying so much on luck. It's still guesswork, but calculated guesswork.

Sex linked (another deep breath - i hope i've got this all right in my head and it conveys correctly). There is one difference in males and females that is the Z chromosome. This chromosome only exists in males. There is a small group/class of genes that attach to this chromosome called sex link genes. The most obvious example to illustrate it verbally is the silver/gold gene. Silver and gold are actually the same gene. If you use my switch analogy you could think of it as on is silver and off is gold. Silver is the more dominant so when it is in the in between state a bird will look silver but some gold may leak through. In the normal (non sex linked) scenario you would expect if you crossed a silver bird (S/S) with a gold bird (s/s) you would get 100% silver carrying gold (S/s or s/S).......heterozygous silver to use 'the speak'. This is not the case. Hens don't have the Z chromosome so a silver hen will be denoted as S/- and a gold hen will be denoted as s/-. So if silver is dominant over gold does this mean that i will always get silver hens if i cross a silver and a gold? This is where the linkage comes in. It's about mode of inheritance. Normally an offspring will inherit one dose of each gene from each parent. With sex linked genes the hen can only inherit one dose and by default that comes from it's dad. So if a silver rooster (S/S) is bred to a gold hen (s/-) that pairing will produce all silver hens (S/-) and heterozygous silver cockerels (S/s). The inverse is similar but slightly different. Gold cockerel (s/s) over silver hen (S/-) produces all gold pullets (s/-) and heterozygous males (S/s or s/S) as before due to the dominance of the silver gene.

I'm getting into too much detail that i feel may start to cloud things if i go further but hopefully that illustrates that sex linkage is more about the way genes are inherited and only applies to a small group of genes. The article referenced didn't appear that the results suggested sex linkage inheritance in any of the relevant genes so that's why i felt i didn't need to go into it any further in the interests of keeping it as simple as possible and relevant to barnies and the goals of this thread. I hope that's just enough detail to clear up those two main questions.

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 2:43 pm 
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"Sex linkage is more about the way genes are inherited and only applies to a small group of genes".
Starting to make sense to me now. :think:

I have read a little bit about silver and gold lacing.
So that example was really helpful.
Slowly working my way through all the material referenced above.

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 Post subject: Re: Barnevelders
PostPosted: Fri Jul 10, 2015 5:19 pm 
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Keep at it BarnieRaiser, you are doing really well. I found at first that there was so much detail to decipher that it was very messy for a while in my head. Over time things started to fall into place and a fundamental understanding of some simple principles started to emerge from the fog. Then i started to get interested in a lot of the questions that come up in the forums asking what will i get if i cross x with y? Trying to get my head around these scenarios and offer some advice (mistakes were made on occasions but lessons were learned) really helped me clarify that fundamental understanding.

The best way i can describe it is it's a bit like learning a skill such as touch typing. First you need to get to know where everything is (a very boring process), then you need to string together words, sentences and paragraphs.......one character at a time. Before you know it, your hands are moving without too much thought and you have developed fluency. The hardest part is getting through the learning/practicing (boring/frustrating) phase and then it gets easy and can actually be enjoyable. Learning a musical instrument is another analogy that could be used. You don't just pick up a guitar and play a brilliant solo without first going through the really tedious learning phase. As with music, many people learning about genetics i feel get disheartened or lost along the way in the learning phase. From the outside looking in it can appear as though it takes a special talent or intelligence. It's the ones with a strong passion that persist and prevail.

There is certainly plenty of passion for this breed shown by certain members and you (BarnieRaiser) appear to have plenty of passion as well as intellect to work with and i have noticed you are extremely observant so i'm sure with persistence the big picture will reveal itself before long. I can't wait for your excited posts when it does. You, Sue, NEP and i can all skip the dinner parties and keep each other company with our boring (to most) discussions ;-) . Would you like to join us one evening David? We would love to have you.

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