Never Encourage a teacher -What I know about color genetics Lesson #2A

[tadkerson]

Quote:
I will answer this question and that will be it.


The dominant white gene is found in the white leghorn and will pass on one dominant white gene to the california white offspring. Callifornia white only carry one dominant white gene; one dominant white gene will sometimes allow for the the expression of black in the down or in the plumage of the adult bird.

The easiest way to explain the difference between dominant white and recessive white is that dominant white has a packaging problem, the cell makes the black pigment but the cell can not properly package the black pigment; the black pigment must be packaged in order to be placed into the feather.

The recessive white gene normally prevents the production of pigments. In order to make pigments the cell needs a special enzyme (tyrosinase). The recessive white gene prevents the production of this special enzyme- no pigments are produced- no color in the feather.

Include one dominant white gene and include sex linked barring- your California whites have sex linked barring under the white. The California white is also sex linked silver.

Your blue bird could be silver or gold.

Tim

 

[KDailey]

Quote:
Thank you so much for continuing. This is exactly what I need and I completely understand that some things will not be completely true in the begining but we must have somewhere to start. I've tried many a time to learn this stuff and rarely get past the first paragraph because I get too overwhelmed and can't make sense of any of it.

I've printed each lesson and will continue to do so so i can make my little notes and reference back to what you've said directly. (I have to use my work computer because I have no access at home so I wouldn't be able to log on to study.)

Thank you!!

 

[mamaKate]

Your topic line made me giggle. My kids were laughing the other day about never going through the "Why?" phase. They said they dared not ask.

 

[KDailey]

I have a question for mibirder. No one else.

I've having a hard time distinguishing the difference between genotype and genes. Genes make up the genotype?

 

[Henk69]

A few little remarks.
Birchen chicks do not typically have white chins.
e^b is independant of yellow shanks. But E and E^R tend to cover the yellow skin up with black, thus e^b is suitable for making a yellow shanked black for instance.

 

[mibirder]

KD -

Here is the generalized answer. There are three "words" that go together - gene, allele, and genotype. A gene is a chunk of DNA instructions that have the ability to make something happen (For example eye color). The Alleles for a gene are what those might specific make (think, blue eyes, or brown, or green, etc). Remember that most genes come in pairs. So the genotype will be the type of alleles that a specific pair might be - Both dominant, both recessive, of one of each. (Sometimes genotype will be used to mean what are all of the alleles for all of the genes in an individual, but more properly that is called the genome.) Also remember that a lot of genes will interact with other genes to slight change the specifics of what you see (which is the phenotype).

BTW as some one else pointed out, human eye color is often used in teaching beginning genetics, but it is much more complicated with lots of interacting genes actually going into the make-up, but the different eye colors are common enough so that most people will "get it". For those that continue to study it (say a doctor or genetist) , they'll learn/see down the road that its a lot more complicated than the simple explanation that's used in the beginning.

Hope that helps.

Dave

 

[mibirder]

Lesson #3A This is ending up to be a two part post

I think part of what makes genetics look so complicated is the amount of the vocabulary that is used in it. Another is that there are a lot of variations that can happen because of the total set of genes present. Another is that some traits are or can be affected by one gene or multiple genes and some genes control are or can have affect on one trait or multiple traits. I’m hoping you get a few of ideas so that you can look at all of this complexity and understand it is in fact complicated and not always cut and dried. If you really are interested in having a good understanding of genetics, you’re going to have to continue on from these posts, ask lots of questions, and “get it” bit by bit. I hope you’ll get started by these posts, but you’ll have to continue on your own it more fully grasp these subjects. This lesson will have more vocabulary in it. It may take going over it a couple of times!

The more genes you know the that make-up a particular chicken pair (genotypes) , the more you will know about what it will likely looks like (phenotype) and what its offspring can look like. Unfortunately, the reverse is NOT necessarily true – know what its phenotype may not tell you everything about all of its genes.

Let’s review: The e-series gene creates kind of a template upon which other genes for color and/or patterns to build upon. The e-series alleles (there are five) can be found in matched pairs (homozygous) where both are the same or where the pair are different from each other (heterozygous). While the e-series creates a general template, the appearance (phenotype) can be altered depending upon other gene pairs that may be present on other genes for a particular chicken.

Remember that different genes control different traits, sometimes multiple genes are needed for a single trait, and sometimes one gene may influence several related traits.

Before moving on, let’s build on some of things already present. Previously mentioned, some alleles for a gene can be dominant; some can be recessive; and sometimes the two may form an intermediate appearance. This intermediate business is called Incomplete Dominance. It doesn’t happen with every gene, but it does happen in some.
A chicken example of this is the genetic color Blue. You many have heard that this gene can produce, blue, black, or splash looking offspring. This is due to Incomplete Dominance. If the two alleles of the gene pair are both the recessive allele (symbol bl/bl) the chicken looks “black”. If one of the pair is dominant (Bl) and the other in the pair is recessive (bl) you’ll have a blue (or “gray”) looking chicken. Lastly, if the pair of alleles are both Dominant (Bl/Bl) you end up with splash looking chicken. These can vary from lighter to darker depending upon other gene pairs present. Remember, not all genes have incomplete dominance but there are some that do.

Besides alleles being described as dominant, recessive, and incomplete dominant, there are other vocabulary that might be used with genes. Words (and variations) like dilute, enhance, extend, reduce, prevents, inhibits, penetrate, incompletely penetrate, completely penetrate, leaky, autosomal, sex linked, and others. Sometimes, these words are used to mean slightly (or greatly) different things – so when you encounter them, if you aren’t sure about what is meant, be sure to dig deeper.

Also, let’s mention something about symbols. Some genes will just have two alleles, unlike the e-series that has five (or maybe more). They are sort of like an “off-on” (has-doesn’t have) switch – either the affect is present or its not. In some of these the “on” allele can be dominant and in others it can be recessive. The “off” allele often has the + (wild type symbol) used for clarity.

Some genes (and their alleles) are well studied and understood and some are not. In fact some are still “under study” and the “facts” are just proposals at this point. When this last type of gene is discussed the symbol(s) used may be just a “?” (Question mark) or the symbol letter(s) in single quotes (‘).

Sex-linked genes only have one allele for the females. When using the symbol short-hand a minus sign is often used for the “missing” allele in females (S/- or s/- for example).

Let’s begin to look at the Uniform Color or Body Color group or family and things may get another step more confusing – not because of what is known, but because of what isn’t known or known fully. Some genes in this group are fairly well know in terms of what they do and others are still in the “under-study” stage and so we don’t know everything about them at this time. Some produce changes that are more widespread and others may not be very widespread. Some have been scientifically proven and well studied; a few others are proposed or not scientifically understood and/or clearly studied at this time. Regardless, what the genes in this family or group all have in common is that they will change the appearance more or less uniformly over the template or body of the chicken(from the e-series gene).

The member genes of the Uniform Color group or family include:

Dominant White and its alleles (more than one other) symbol I
Dull Black (understudy) no set symbol at this time, some think it is maybe an allele of I
Recessive White symbol c (other allele C+)
Silver symbol S (the other allele produces gold symbol s+. It is also sex linked – see note)
Blue symbol Bl (other allele bl+)
Lavender symbol lav (other allele lav+)
Cream symbol ig (other allele ig+)
Recessive sex linked (see note) Chocolate symbol choc (other allele choc+)
Recessive black (understudy) symbol ? or ‘rb’ used often (so they other “allele” = ‘rb+’) Likely multiple genes
Champagne blond (understudy) symbol ‘Cb’ (other “allele” = ‘Cb+’)
Charcoal (understudy) symbol ‘cha’ (other “allele” = ‘cha+’)

NOTES: Remember back when it was mentioned that many genes come in pairs of alleles, but some only have one allele? These are called sex linked genes. The one sex will have the usual pair, but the sex will only have one. In humans you may have heard males have an XY (chromosomes) and females have an XX(chromosomes) . (Chromosomes are the physical cell parts where the genes (alleles) are located in an organism. Usually they are in pairs each member having the same genes on it. One pair, Sex Chromosomes, are a little different – they can be a matched pair like other chromosomes or one of one set of genes and the other has different genes on it.) Well it’s different in birds. Male birds have ZZ and the females are Z- (or Zw sometimes is used). If a particular gene is on the Z then males get to have a pair, but females (having only one Z) only get to have one. These are sex linked genes.

Because this post has covered a lot and is getting long, the next post will talk a bit about these genes and their alleles in this group.

 

[mibirder]

(Continuing from last time.)

There was lots of added vocabulary last time, but let’s review some of the high lights:

Genes, usually have a pair of alleles in them – except for Sex Linked genes – these genes are on the Sex Chromosomes and so in chickens, the males get a pair of alleles, but the females only have one allele. For example, the S gene or the choc gene from the Uniform Color group.

With a pair of alleles for one gene, they can be the same or one can be of one type and the other different. With a dominant allele, it only takes one of the pair for the affect to be seen. For the recessive allele it takes both alleles being recessive to see it – Unless the gene happens to have Incomplete Dominance. In those cases, when the allele pair are different from each other there is some kind of intermediate affect seen. For example, the Bl gene from the Uniform Color group.

Much of the time we’re lucky and a particular gene and its affects are well studied and there is lots known about what it does and what changes may come about. But sometimes new genes are found and they are still under study. For example, dull black or the cha proposed gene. Sometimes that study may lead toward more than one genes/gene interaction that causes something specific such as with proposed ‘recessive black’. Regardless of the specifics for any of the genes in this grouping, they all have in common that their effects are generally seen across the whole chicken.

White is a color that brings up a lot of questions, so let’s look at a little deeper. White can be a confusing color in that there are two genes that individually and/or collectively can cause a chicken to look “white”. These are Dominant White and recessive white. Dominant White has a few known alleles and a few others that are still under study. Dominant White inhibits mainly Black pigment from the feather. With just one Dominant White allele in a pair (I/i+), black pigment is affected, but red is not. With both in the pair being Dominant White (I/I), both red and black are affected, but there may often be flecks of black and/or red on the feathers. Some other genes in a chicken can have an affect on the flecking. Because Dominant White is dominant, there could be other recessive colors “hidden under it” which you can’t see, but the genes that make them are still in the chicken.

Recessive white can inhibit both the black and red pigment when the allele pair for the gene is both recessive white (c/c). If the pair is mixed (C+/c) and certain other genes are also in the chicken, it can appear to be white. Recessive white by itself isn’t as affective as Dominant White in hiding other colors under it.
Some white chickens may have just the I gene present, some may have just the c gene present, and others still may have both I and c present. The “whitest of the whites” usually has both present. In addition to these two genes, there may be some other genes in a chicken (white enhancers) that can affect white.
So what this mean for white chickens? If Dominant White is present as heterozygous allele pair (I/I+) for both parents and another color(s) is being “hidden” by the Dominant White in both, these other colors may show up in the offspring. The problem is that just because a chicken looks to be white, we can’t easily tell by just looking at it if it’s Dominant White(I), recessive white(c ), or both (I and c) nor can we easily tell if it is heterozygous (I/I+ or C+/c) or homozygous (I/I or c/c)for the allele pairs that are present.

There’s a great tool available on the Internet to help visualize how this works call the Chicken Calculator. As a beginner, when I first looked at the Chicken Calculator, I couldn’t figure out how to use it and was very confused by it all. That’s when I knew I had lots more to start learning. The folks who really understand chicken genetics may have years and years of experience, and may have experience with lots of different gene situations – that isn’t and wasn’t me (and it still isn’t!). So I had to rely on what I generally knew from biology, what I could learn from other resources and by asking questions /reading answers (and I still have to do these things). But at this time, let’s take what has been mentioned and look at a simple example with some white colored chickens.

There are a few versions of the calculator “out there” as those who are responsible for it have improved and expanded its functions. (In fact one of the BYC members is that person – Henks69. All our thanks go to him for all the hard work!)

Here’s the address of the one for our example: http://kippenjungle.nl/kruising.html

There are a few features that pop up right away. There’s one side for the male chicken (left) and one side for the female (right). Listed of each are a bunch of genes that have drop downs to select different allele pairs for the different genes. Each of these has a little drawing at the top that can change as you change gene and allele pairs. (For example, for one parent, go to the E-series gene drop down and select the different possibilities and see how the drawing changes).

For this simple example, let’s select the follow for both male and female: Select the E/E choice from the E-series gene. Go down the list to the I gene and select I/I+ (heterozygous Dominant White). (note the changes in the drawing as you make selections.). And lastly for the Bl or Blue gene also select the Bl/bl+. From the drawing even though we added some of the blue gene to our chicken it still looks white (Because of the other genes we selected). Leave all of the other gene choice as they are. To make it easier for this example, down at the bottom is a check box for “Hide Genotypes. Go ahead and check that box. Also down at the bottom is a button for “Calculate Crossing”. Click that button and look at what appears at the bottom! Here are the possible offspring that might be the results from our two white looking chicken parents!

As you learn more and more about individual genes and their allele pairs, you can come back to the Chicken Calculator and check out your understanding and get some idea about what different combinations can produce in their offspring.

The genes in this group are a varied collection. I don’t have much experience with many of them and (from readings) some are not well studied at this time so not everything is known. There are a number of good resources that do a good job explaining what is known about these genes and you should seek out those if interested.

 

[KDailey]

Thanks so much! I'm really enjoying the lessons

 

[mibirder]

Lesson #4 - Starting to make "colored patterns" on chickens

(For those interested in the Blue gene and its actions, Chris09 started a nice thread with lots of photos and names for different “blue” chickens and some discussion of them. Check it out! Here’s the link: https://www.backyardchickens.com/forum/viewtopic.php?id=583263 )

The next group of genes – Color Restricting or Color Distributing Group – contains several different genes that can change where the red and/or black pigments are added to or taken away from on the chicken – red may be extended (or black restricted), it can be made lighter (diluted) or made darker (intensified). Depending upon the other gene allele pairs that may be present, the effects can vary a bit. Regardless of the specifics for a gene combination, the genes in this group make changes based upon changing where the red and/or black pigments will be found on the chicken.

The genes listed in this group include:

Columbian symbol Co (other allele co+) restrict black from some areas, & extend red, dilute red
Dark Brown symbol Db ( other allele db+) similar to Co
Red Diluter symbol Di (other allele di+) Lightens or dilutes red
Mahogany symbol Mh (other allele mh+) Darkens red, restricts black
Melanotic symbol Ml (other allele ml+) Extends black

These genes often interact with other genes present and with each other so that the specific appearances can vary from chicken to chicken, e-series to e-series based what other genes are. Some of the color patterns, such as single lace (think Silver Laced Wyandotte) relies on Co and Ml along with the Pg gene from the (next group) Pattern Group.

In very general terms Co restricts black to the "ends" of the adult chicken – neck/head end and tail end. Co can vary depending on which e-series gene is involved as well as other genes present.

Db can act like “super-charged Co” and can be easily confused with Co. One difference is that Db may restrict black such that black will only be on the tail and wings (like with Black-Tailed White Jap Bantams) Another way to think of this is to remove black from the hackle (which Co does not do). As always the specific actions of Db depends upon the other genes present and can vary based upon which of the e-series are involved.

Di is kind of fairly straight forward in that it lightens the red pigment so that red can become orange, dark red can become light brown , gold can become straw yellow, etc.

Mh can represent a few different affects that involve darkening red, extending red, and restricting black.(Think Rhode Island Red).

Ml is sometimes described as the opposite of Db in that Ml can extend black into the hackle, shoulders and/or saddle areas. As noted, Ml (along with Co and Pg) are needed to make single laced birds.

Because this group of genes tends to commonly interact with the other genes present, it’s a bit complicated to go into details about what every combination of genes might look like. However, these genes are fairly well known and so there are lots of resources that can go into greater details about these genes and their affects in combinations with other genes.

(PS At the end of these "lessons" I'll put a list of resrouces (books and Interent) that can go into more details as well as to give someone else's take on the general information. Hopefully, everyone can feel free to mention their resources as well.)

Dave