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#76 2012-02-13 21:22:08

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

A couple of comments -
Miller's inbreeding coeffcieints are correct ONLY if the two individuals being mated aren't themselves inbred. That is, the offspring of a father-daughter mating has an F (inbreeding coefficient) of .25 only if the father wasn't himself inbred and wasn't related to the daughter's mother. If either of those conditions are not true (which is quite likely), then F will be higher than .25.

He says:
"Mendelian Inheritance: States that both dominant and recessive qualities of the parent stock are inherited by their offspring pre-dominately through sex chromosomes and sub-dominately through autosomes (or non sex related chromosomes)."
I can't imagine where he got this from; it makes almost no sense. Mendelian traits are generally considered to be those that are governed by one locus (or a fairly small number of loci), and that exhibit dominance, recessiveness, etc. (e.g. barring, blue eggshell colour). This is in comparison to so-called quantitative inheritance, or quantitative traits, that are under the control of many loci acting together and which exhibit a continuous range (e.g. brown egg shell colour, growth rate)

He says:
"Sex-Linked Inheritance: With chickens, the cock carries two chromosomes for sex while the hen carries only one. So any gene located on the cock chromosome will be passed to both his sons and daughters; while any gene on the hen's sex chromosome will only be passed on to her sons. "

If you substitute "Z chromosome" for "sex chromosome", you get
Sex-Linked Inheritance: With chickens, the cock carries two Z chromosomes while the hen carries only one. So any gene located on both of the cock's Z chromosomes will be passed to both his sons and daughters; while any gene on the hen's Z chromosome will only be passed on to her sons.
which is clearer and more accurate.

Last edited by ipf (2012-02-13 21:23:23)

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2012-02-13 21:22:08

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#77 2012-02-15 19:01:37

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

And here's Batch 3:
Original version:
Linkage - When relationships between different characteristics are observed, they are said to be linked or tend to be inherited together. The relationship implies the characteristics are located on the same chromosome. The linkage can be loose or tight depending on where they are located on the chromosome. The closer together they are on the chromosome the tighter the linkage the farther apart they are on the chromosome the looser the linkage. Refer also to crossovers and linkage value.

Discussion
Many characteristics that are related to each other are not linked.

I would suggest:
Linkage - Genes that lie on the same chromosome are said to be linked; traits governed by these genes tend to be inherited together. The linkage can be loose or tight, depending on where they are located on the chromosome. The closer together they are on the chromosome, the tighter the linkage; the farther apart they are on the chromosome the looser the linkage. Linkage is measured in “map units”, which reflect the likelihood of the genes being separated by crossing over during gamete formation.
This is useful, in that the appearance of one trait can be used to predict a second trait, if the genes governing the traits are linked.

Example: The blue egg locus (O, o) is linked to (on the same chromosome as) the pea comb locus (P, p). The distance between them is about 4.3 map units. A purebred Ameraucana will have genotype OP/OP. If mated to, say, a barred rock (genotype op/op), the genotype of the offspring (for these loci) will be OP/op. Gametes produced by this bird will be mostly OP or op, but 4.3% of the gametes will be Op or oP (due to crossing over).
Thus, if the granddaughter of a pure Ameraucana has a pea comb, there is a (100-4.3=) 95.7%  probability that she will lay blue eggs. (How cool is that?!?)

Original version:
Locus (Loci) - The specific physical location of a gene or genes, or sequence of genes on a chromosome. (The plural of locus is Loci)

I would suggest:
Locus - The specific physical location of a gene (or DNA sequence) on a chromosome. (The plural of locus is loci)

Original version:
Modifier or Modifying gene - A gene that alters or influences the expression or function of another gene. Rather than masking the effects of the other gene (dominance) it modifies or alters the phenotypic expression of the other gene.

Discussion:
Dominance only applies to single locus effects, where one allele suppresses the effect of the other allele at that locus (e.g., O, the blue egg allele, is dominant to o, the non-blue egg allele, so a bird with genotype O/o will lay blue (or green) eggs).

I would suggest:
Modifier or Modifying gene - A gene at one locus that alters or influences the expression or function of another gene at a different locus. This effect is called epistasis.

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#78 2012-02-16 00:48:16

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

Thanks ipf!

What would be an example of characteristics that are related to one another but not linked? Just so I understand what you mean.


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#79 2012-02-16 15:34:10

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

You do ask the good questions. Well, in my mind, the  main reason not to use the term "related" in this context is that it is rather vague in meaning. "Linked" (in genetic terms) has a very simple and precise meaning - i.e. on the same chromosome; two genes are either linked, or they are not, while relationship has a continuous range. Also, I think of related things as somehow similar, like, perhaps, genes for comb shape, or genes for different aspects of feather structure, but such genes are no more likely to be on the same chromosome that two completely random genes.

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#80 2012-02-16 17:41:11

gubi
Member
From: Walton
Registered: 2011-06-30
Posts: 1344
Website

Re: Topic 2: Genetics Terms and Definitions

Why does a modifier gene have to be on a different locus then the gene which it alters or influences the expression off?


Herd of Brown Swiss, a few sheep, red cuckoo basque, Silverspangled Appenzeller Spitzhauben, ameraucanas(EE), Welsummer, broodie silkies and a few more heritage hens

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#81 2012-02-16 17:49:54

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

If it's at the same locus, it is simply an allele, or variant of that gene.

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#82 2012-02-23 02:13:10

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

More definitions Please ipf! =D


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#83 2012-02-28 21:20:50

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

Batch 4 (sorry I'm so slow; work is very busy these days)

Original version:
Mutation - A permanent structural alteration in DNA. These changes occur naturally and randomly. In most cases, DNA changes either have no effect or cause harm, but occasionally a mutation can improve an organism's chance of surviving and passing the beneficial change on to its descendants. Most mutations are recessive to the wild type and will not express itself until two birds are mated which carry the recessive mutation. One quarter of the offspring will show the mutation. Visible changes are referred to as sports and natural selection will affect their survival in the genetic pool.

discussion: nothing is permanent. . .

I would suggest:
Mutation: A sudden structural alteration in DNA. These changes can be either spontaneous (natural) or induced, by mutagenic chemicals or radiation. In most cases, DNA changes either have no effect or cause harm, but occasionally a mutation can improve an organism's chance of surviving and passing the beneficial change on to its descendants. Most mutations are recessive to the wild type and will not be expressed unless two birds are mated which carry the recessive mutation. One quarter of the offspring can be expected to express the mutation. Birds expressing the changes are referred to as sports; natural and artificial selection will likely affect their survival, as well as the persistence of the mutated gene (allele) in the gene pool.

Original version:
Outcross - The act of breeding together animals that are members of the same breed, variety or strain, but not closely related in pedigree.
Or the progeny of an outcross. Outcrossing is one of the three main types of breeding, the other two being linebreeding and inbreeding.

Discussion: linebreeding is one form of inbreeding. All line breeding is inbreeding, but there are other forms of inbreeding as well. 

I would suggest:
Outcross – Mating of birds that are unrelated (or, more realistically, quite distantly related). It is a relative term, since all birds are related to each other. It is generally applied to the breeding together of animals that are members of the same breed, variety or strain, but not closely related in pedigree.
The term “outcross” can also refer to the progeny of an outcross.

Original version:
Phenotype- Phenotype is the physical appearance of the chicken. It is what we 'see', but it also includes structure (body shape and size), function (egg laying abilities, meat qualities, fertility) and behavior (friendliness, self preservation skills). The phenotype along with the pedigree are the main methods of judging the chicken's genetic input.

Discussion – this is really good, and captures the essence of what phenotype is. Other things, like disease resistance, are also part of the phenotype.

I would suggest:
Phenotype- Phenotype is what we 'see' when we look at a chicken, but it also includes structure (body shape and size), function (egg laying abilities, meat qualities, fertility) physiology, disease resistance, and behavior (friendliness, self preservation skills). It includes all expressed traits. The phenotype and the pedigree are the main methods of judging the chicken's genetic makeup.

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#84 2012-02-29 01:57:06

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

Thanks ipf. Did you see the newest quiz =D?


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#85 2012-02-29 01:59:58

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

Yes! I answered it? I think?

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#86 2012-02-29 02:07:15

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

Maybe you did it is hard for me to tell who responded. But only 3 brave responders so far. Either that means we lost everyone or not everyone is :Crazy: like me and thinks quizzes are fun :oops:


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#87 2012-02-29 02:39:40

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

Well, I thought it was great! And it made me think, which is always a good thing.

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#88 2012-02-29 02:47:17

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

Well that's great ipf I'm glad you enjoyed it, they are fun to create. And no one has used the "other" category which makes me think I avoided mucking up any of the questions and there is actually a correct answer choice for each one :thumbsup:


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#89 2012-02-29 03:05:07

Lindy Lou
Member
From: Priceville, Ontario
Registered: 2011-07-03
Posts: 999

Re: Topic 2: Genetics Terms and Definitions

I haven't given it a shot yet. I'm struggling to get over a cold before i leave for Virginia but to date my head isn't working too good yet. :sad: I need a headache smilie


Some of us are driven by the need to make animals a part of our lives. We are soothed by their presence, fascinated by their behavior, and amused by their antics.

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#90 2012-02-29 12:29:35

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

In response the the statement that mutations are usually recessive to the wild type. That statement struck me as a bit odd. Deleterious mutations perhaps are almost always recessive as that is how they remain in the population but I don't know about mutations in general?

Looking at this website http://www.ncbi.nlm.nih.gov/pubmed/3165529 I see a significant number of mutations that are dominant (wild type is marked with a +, for example non barred (b+) is the wild type.)


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#91 2012-02-29 15:39:57

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

It's more an empirical observation than a theoretical "truth". However, I think it's accepted that most mutations are deleterious, with some being neutral, and a few being weakly advantageous. This makes sense - when you have a complex set of coding instructions, it seems reasonable that a random change in the structure of the instructions is more likely to mess up function than improve it. Think about your car, or your computer, or the blueprint for your house - if you open it up and make a random change, is it likely that it will improve function? No. Not impossible (in theory), but not likely. Same wih DNA.

Then, dominant deleterious mutations will be eliminated almost immediately, as they will be expressed. This leaves lots of recessive mutations, and a few dominant ones.

Or, looking at it from another angle, it could be argued that at the instant the mutation happens, it is equally likely to be dominant as recessive, and then (because most are deleterious) most of the dominants get weeded out. Is this where you'r coming from, PG? We could change it to "Most mutations that persist in populations are recessive to the wild type".

There's also the argument that, for coding genes, mutations are likley to interrupt functionality. But because there are two alleles at each locus, if there is one normal (wild type) allele and one mutant, often the normal one will code for enough product for the organism to function - so that the phenotype is that of the normal gene. This is, in effect, dominance of the normal allele.

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#92 2012-03-01 01:39:05

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

Realizing that most of the alleles for poultry I know of (the ones listed on the site I referenced) are ones you can see visually and are far from representative of all the mutations that exist I would say that:

I agree that a mutation as equal likelyhood of being dominant or recessive when it occurs.
I agree that most mutations are deleterious.
I agree that a dominant recessive mutation will fairly quickly be eliminated from the population.

I don't agree (yet, feel free to convince me ;)) that most mutations that persist in the population are recessive.
I would agree that "most deleterious mutations that persist in the population are recessive".

Perhaps what i am trying to ask is why would non deleterious mutations not have an equal chance of being dominant or recessive? Or are most mutations deleterious and therefore most are recessive?

When I look at the list of alleles on that website for visual traits they are roughly 50% recessive wild type. Perhaps the percentage is influenced by the fact most of those listed are visual traits that humans have retained in the population artificially. Maybe because one of the greatest selection pressures on chickens (domesticated for thousands of years) has been humans so mutations that would be deleterious in nature become neutral or an advantage?

I understand exactly what you are saying ipf and if selection pressure we're natural I would agree. Since for poultry for some traits humans have shifted or altered selection pressure by picking the "pretty" chickens, using vaccines and antibiotics, incubating eggs instead of letting the hen do the work etc. maybe we have also shifted the ratio of recessive to dominant mutations?


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#93 2012-03-01 03:38:31

Maggiesdad
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From: Louisa County, Virginia
Registered: 2011-10-05
Posts: 1980

Re: Topic 2: Genetics Terms and Definitions

poplar girl wrote:

Well that's great ipf I'm glad you enjoyed it, they are fun to create. And no one has used the "other" category which makes me think I avoided mucking up any of the questions and there is actually a correct answer choice for each one :thumbsup:

I used the other category to be able to let you know how my logic was working (plus be able to plug my name in there!), not to be critical of the question or structure. I really appreciate the time you all are devoting to this. :surfing:

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#94 2012-03-01 03:43:58

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

You bet MD! It's great you wrote out your thoughts :thumbs:


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#95 2012-03-01 17:52:10

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

poplar girl wrote:

Realizing that most of the alleles for poultry I know of (the ones listed on the site I referenced) are ones you can see visually and are far from representative of all the mutations that exist I would say that:

I agree that a mutation as equal likelyhood of being dominant or recessive when it occurs.
I agree that most mutations are deleterious.
I agree that a dominant recessive mutation will fairly quickly be eliminated from the population.

I don't agree (yet, feel free to convince me ;)) that most mutations that persist in the population are recessive.
I would agree that "most deleterious mutations that persist in the population are recessive".

Perhaps what i am trying to ask is why would non deleterious mutations not have an equal chance of being dominant or recessive? Or are most mutations deleterious and therefore most are recessive?

When I look at the list of alleles on that website for visual traits they are roughly 50% recessive wild type. Perhaps the percentage is influenced by the fact most of those listed are visual traits that humans have retained in the population artificially. Maybe because one of the greatest selection pressures on chickens (domesticated for thousands of years) has been humans so mutations that would be deleterious in nature become neutral or an advantage?

I understand exactly what you are saying ipf and if selection pressure we're natural I would agree. Since for poultry for some traits humans have shifted or altered selection pressure by picking the "pretty" chickens, using vaccines and antibiotics, incubating eggs instead of letting the hen do the work etc. maybe we have also shifted the ratio of recessive to dominant mutations?

If most mutations are deleterious, and (for the sake of argument), we assume that dominant and recessive mutations are equally common, and we agree that dominant deleterious mutations will be quickly eliminated, a bit of algebra might help:
Frequency of advantageous mutations (Adv) =a
Frequency of deleterious mutations (Del)=>a (i.e. greater than a)
Frequency of dominant mutations( Dom) =b
Frequency of recessive mutations (Rec)=b
We have:
frequency of Dom&Adv=ab
frequency of Rec&Adv=ab
frequency of Dom&Del=0
frquency of Rec+Del=>ab

So, total frequency of recessives =ab+(>ab)=>2ab
total frequency of dominants =ab
and for any positive values of a and b, the former is greater than the latter.

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#96 2012-03-02 01:51:25

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

:shock: what if I just agree to agree?

....But I only agree this holds true for mutations that are deleterious :chairhide:


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#97 2012-03-03 16:07:20

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

Well, if you're not convinced, PG, you can simply remove those sentences. They aren't intrinsic to the definition, but were included in the definition proposed by a forum member, and I left them in because
a) I try to minimise tweaking,
b) I believe them to be true, and
c) they add information.

Last edited by ipf (2012-03-03 16:07:45)

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#98 2012-03-03 16:44:20

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

I posted the definition in the sticky yesterday with the wording "most mutations that persist in populations are recessive to the wild type".

A minor point as you say...I'm ready to move on!


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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#99 2012-03-05 03:39:58

ipf
Member
From: Salt Spring Island, BC, Canada
Registered: 2011-08-29
Posts: 168

Re: Topic 2: Genetics Terms and Definitions

Batch 5:

Original version:
Quantitative - Of, relating to, or susceptible of measurement. A quantitative trait is a phenotype that is influenced by multiple genes.

Discussion:
Although the dictionary  says quantitative=measurable, the genetic definition is distinct. Quantitative traits are traits displaying a continuous range of values.

I would suggest:
Quantitative - A quantitative trait is one that exhibits a continuous range of values, and is known to be under the control of multiple genes. Examples of quantitative traits: Brown egg colour, body size, egg weight.

Recessive - Of, or pertaining to, a gene (or allele) whose phenotypic expression is masked by a dominant gene (or allele).

I would suggest:
Describes an allele (variant of a gene) whose expression is suppressed by the other allele at the same locus in the given individual; the other allele is said to be “dominant” over the first.
Example: o (non-blue egg) is recessive to O (blue egg); a bird carrying one O and one o allele (so genotype is O/o) will lay blue (or green) eggs.

Original version:
Hybrid vigor - The extra vigor, exceeding that of their parent stocks, frequently shown by the hybrids from the crossing of such genetically dissimilar parents as different species, breeds, strains, or inbred lines. It may be expressed as more rapid growth, larger size, greater viability, or otherwise.

I would suggest:
Hybrid vigor - The extra vigor, exceeding that of their parents, frequently shown by the crosses (hybrids or outcrosses) between genetically dissimilar parents. Parents can be from different species, breeds, varieties, strains, or inbred lines. Hybrid vigour may be expressed as more rapid growth, larger size, better viability, higher fertility, disease resistance, and/or other traits we think of as related to survivability and productivity.
Many consider hybrid vigour to be merely the absence of inbreeding depression, particularly when applied to crosses between more closely related parents (e.g. from different inbred lines, strains, breeds and varieties).
Examples: production strains of chickens, such as Cornish crosses and white leghorns, are four-way crosses between highly inbred lines of the same (in the case of leghorns) or different (in the case of Cornish crosses and brown production layers) breeds or varieties.
References: Hutt, Genetics of the Fowl (pg 552-553)
Previous thread on this topic: http://forums.euskaloiloas.com/viewtopic.php?id=332

Original version:
Heterosis. Generally thought to be synonymous with hybrid vigor.

I would suggest:
Heterosis. Generally considered to be to be synonymous with hybrid vigor.

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#100 2012-03-10 18:41:52

poplar girl
Administrator
From: Athabasca, AB, Canada
Registered: 2011-06-30
Posts: 3159

Re: Topic 2: Genetics Terms and Definitions

Batch 5 stickied ipf. Sadly i had no questions to ask or controversial comments to make :oops:


Raising red cuckoo (marraduna) Euskal Oiloak and self blue (lavender) & black Belgian Bearded d'Uccles.

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