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So, I'm currently attending a basic level genetics course where I have encountered some problems with crossing and chi-square. Please bear in mind that I'm completely new to this, so the question might even come across as stupid for some.

I'm having trouble determining when I'm supposed to "use" one or two loci. As far I know, it's simply one loci for one trait (on the most basic level). My exercise handout seems to confuse me further, however. I'll write to examples to show you:

1. When a plant was self-fertilized the offspring was as following: 94 green and 21 yellow plants. How does this result relate to the hypothesis that the parent was heterozygote for a recessive chlorophyll-defective gene?

It's a chi-square problem, but first you have to determine the ratios of the offspring. In this particular problem, I concluded that it's a matter of A/a crossing table. Made the table (AA+Aa+Aa : aa = 3:1 ratio) and calculated chi-square and got the correct answer.

The next problem is as following:

When crossing a plant bearing blue fruit, and a plant bearing white fruit, the offspring-plants bore blue fruits. When the F1-plants were self-crossed, the F2-plants yielded 158 plants with blue fruits and 8 plants with white fruits.

And then again use chi-square. Problem is, in this one, there are apparently 16 (4x4 table) different genotypes, meaning there are four alleles distributed among two different loci. Why? They way I see it it's a matter of blue/white, one or the other. Two alleles makes sense to me, why introduce another loci without actually introducing a second trait?

I'm missing something here, but I don't know what.
MrJules
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### Re: Question about basic crossing.

MrJules wrote:
I'm having trouble determining when I'm supposed to "use" one or two loci. As far I know, it's simply one loci for one trait (on the most basic level). My exercise handout seems to confuse me further, however.

No, trait and locus are not the same. Locus refers to the position of the gene on chromosome. Trait refers to characteristic responsible for phenotype.

I will try to explain it better using your 2nd example.

1. Blue and white are phenotypic traits.
2. Blue fruit color is probably caused by anthocyanins (blue/purple/red pigments).
3. Anthocyanins are metabolites, which means they are NOT gene products. Thus, to produce them, plant needs to produce various enzymes to synthesize the pigment. To produce proteins you need genes.
4. Let's say there are 2 pathways to produce anthocyanin. Think of it in simple terms.

For example:

Let's say you have only 1 way to have serial in the morning:
You need a bowl, milk and serial. If you don't have any bowls you cannot have your serial!
Now, say you have some plastic containers which you can use instead of the bowl. So, now you have 2 ways to have you serial.

Back to anthocyanin - two ways to produce Blue means at least 2 different key genes are involved (like bowl and plastic container). As long as you have one, you don't need the other. If you have both, the outcome is the same. If you have neither, the color is white (no pigment).

5. Now, these 2 genes can be located close together of far apart. When they are located close together, they cannot be inherited separately and, usually, said to belong to the same locus. When they are far apart, like in this case, either one can be inherited independently. In this case they belong to two loci.

As to how to decide how many loci to use:

for self-pollination: divide F2 dominant by F2 recessive (158/8=19.75). The standard ratios are:
single is 3:1,
double = 15:1,
triple = 63:1.
You just pick the closest number and use chi-squared test to verify…
Cat
King Cobra

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if the two genes are close enough, they are said to be linked, but not on the same loci
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

JackBean
Inland Taipan

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Not true. Locus can contain a cluster of related genes. Like Hox locus C contains genes HOXC4, HOXC5, HOXC6, HOXC8, HOXC9, HOXC10, HOXC11, HOXC12, HOXC13. Here is one of the random papers I pulled up to illustrate this point: http://www.nature.com/onc/journal/v22/n ... 6808a.html
Cat
King Cobra

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Joined: Thu Feb 14, 2008 7:40 pm

I'm still a bit confused about the two ways, Cat. How were you able to come to the conclusion that there are two ways you can gain blue colour?
How can you discern from the provided information that white is actually a product of a separate loci, and not a result from the "absence" of blue-allele dominance?

I thought I could also ask another quick question (not related to this specific topic) here instead of creating a new thread. Does complete penetrance imply dominance? If an affected woman mates with a healthy man and the trait she carries the genes for are subject to complete penetrance, will the offspring be affected regardless if she is homo/heterozygote? (I.e. dominant).
MrJules
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Joined: Fri Dec 02, 2011 6:26 pm

### Re:

MrJules wrote:I'm still a bit confused about the two ways, Cat. How were you able to come to the conclusion that there are two ways you can gain blue colour?

How many loci to use? You need to self-cross F1 of two pure breed individuals and look at F2 ratios:

for self-pollination: divide F2 dominant by F2 recessive (158/8=19.75).

The standard ratios are:
single is 3:1 (one loci),
double = 15:1 (two loci),
triple = 63:1 (three loci), etc.
You just pick the closest number and use chi-squared test to verify… In this case 19.75 is closest to 15:1 ratio and that means two loci.

Next question:

How can you discern from the provided information that white is actually a product of a separate loci, and not a result from the "absence" of blue-allele dominance?

I did not say that "white" is a different locus. I said that there are two loci for blue: call them "blue1" and "blue2". For every phenotype there is a default one. "Blue1" or "Blue2" gene = blue color and NO "Blue" gene (called null mutation) = default phenotype. This means that in absence of this gene, color is X (in theory can be any color). However, this color will come out in the F2 generation (do the cross to see what I mean). So, some of the progeny will be of default color. As only white color is present - it must be the default phenotype. Thus "white" is null allele of "blue" gene.

Lastly,

Does complete penetrance imply dominance? If an affected woman mates with a healthy man and the trait she carries the genes for are subject to complete penetrance, will the offspring be affected regardless if she is homo/heterozygote? (I.e. dominant).[/i]

"Complete penetrance" refers to a dominant allele of the gene. So, if she is heterozygous, then progeny can be either affected or normal.
Cat
King Cobra

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Joined: Thu Feb 14, 2008 7:40 pm