All language subtitles for 37031x_PR_DNA_Markers_05_Plotting_SNP_Freq_C1_v1-en

PETER REDDIEN: But now let's come to our chromosome one

graph.

OK.

So now, I'll depict chromosome one.

OK?

And then we'll have the same y-axis here,

the frequency of reads that are blue type.

OK?

And let's say gene X exists right here.

OK.

What should this graph look like?

So we're considering this chromosome, chromosome one,

where we know gene X is.

And we're looking at these individuals.

We're sequencing them.

We're asking, along this chromosome, what

are the frequency of the reads that are white type SNPs

and blue type SNPs.

So what do you think?

Any predictions.

Yeah.

STUDENT: Blue SNPs would be less frequent towards gene X.

PETER REDDIEN: OK.

So the blue type SNPs would be less frequent towards gene X.

So pretty low down here, near here.

Maybe on both sides pretty low.

And as you go away from gene X?

STUDENT: It would go up.

PETER REDDIEN: And what would be the theoretical maximum?

STUDENT: 0.25

PETER REDDIEN: 0.25.

OK, so this might go up on both sides in some way towards 0.25.

OK.

So chromosome one data would look very different

from the other chromosomes.

And we'd know gene X is here.

OK?

Now-- yeah, question.

STUDENT: Could you say one more time

why decreasing one is closer?

PETER REDDIEN: OK, because this is just

straight recombinant frequency logic.

So when you think about the likelihood

of a crossing over event between gene X and a polymorphism,

if the polymorphism is further away,

there's a larger region of DNA where that crossover

could have happened.

If it's really close, that crossover

had to happen in a very close little window.

So the probability of crossing over

goes down as two things get closer.

So that's why it goes down.

So something that's like two nucleotides away from gene X,

we'll say, you need a huge sample size to ever

get lucky enough to see that.

So that's why.

Yeah.

STUDENT: Why is it 0.25 is, like, the maximum?

PETER REDDIEN: Same idea, that if the chromosome is

large enough, you can have the distance be

so great that it appears unlinked, even though it's

on the same chromosome.

That would be the theoretical maximum.

If you had a very small chromosome,

you may never get to 0.25.

So what we do, then--

now, we went through this example,

which you would have to do this with an organism in the lab.

But a lot of this idea, a lot of this way of thinking,

where you can now look at all these things globally,

are the concepts you kind of need

to understand more applications of genetics

with non-laboratory organisms or with humans or in agriculture

and so on.

So you'll see variations on this kind of approach

as we go through the class.

And we have to think about things

differently if we don't have sort of true breeding strains.

We can control the crosses, and so on.

OK.

So and if you think about what we're doing,

when you made a map of the X chromosome,

you took gene pairs, you maybe got up to a three-factor cross,

where you're getting recombinant frequencies.

And that's great for getting this logic down.

And now what we're doing is essentially the same thing.

So our recombinant frequency here

will be two times our frequency of the blue SNPs.

OK?

Two times because I just walked you

through why it's 0.25 instead of 0.5.

So you can refer back to that to understand

why I multiply by two here.

And so you could, in principle, make a map,

hand draw out your recombinant frequency for every SNP

in the genome, thousands and thousands of them,

and draw out a map with this like you've been doing.

Same kind of logic.

But because we have this reference sequence assembly,

we know where all these SNPs are.

We can map them to the reference sequence.

And so the position, the relative position

of all these SNPs and their actual distance between one

another is all known.

So we're instantly getting the position of this thing

on that actual sequence map.