All language subtitles for 17031x_PR_LOD_Scores_01_Review_v2-en

PETER REDDIEN: Really, all we're trying to do

here is apply everything you've learned so far about linkage,

recombinant frequency, independent assortment.

We're just trying to apply it to real-world scenarios, where

we have data from pedigrees.

And when we do that, just to recap,

we don't always have the ideal scenario.

We have to work with whatever historically happened.

And so because of that we have to look and evaluate

each meiosis that we can see in the pedigree

and see if we can get information out of it

and what kind of information.

That's where these two topics we've been

discussing become relevant.

Where we talked last time about this topic

of an informative meiosis, where we have two alleles of a marker

and two alleles for a trait gene, and meiosis

is informative in our pedigree when

we can determine which were transmitted together.

OK.

So if we have some individual, K,

she's transmitting gametes for fertilization

to generate offspring.

And it is these meioses we're referring to,

to address whether they're informative.

OK.

So we're assessing the transmission of gametes

from K to produce the offspring.

Now, we also talked about this topic

of phase, which helps us infer whether the gametes that

would be coming from K would be recombinant or nonrecombinant.

So to understand whether K's gametes were

recombinant or nonrecombinant, we might

want to know the phase of the alleles that were

in K that made those gametes.

And we know the phase from K's parents.

OK.

We can assess whether we do know the phase or not.

So this is the stage where we'd have data here from something

that got transmitted to K that allowed us to know

the phase in individual K. OK.

Question?

OK.

So the question is, do these meioses

have to be informative to know the phase in K?

STUDENT: Or does K have to be an informative?

PETER REDDIEN: OK.

So we could have like this.

Let's see, AA, BB.

And then we have AB OK.

This is going to work.

So if we know that K is D over plus,

then we didn't get any information from this meiosis.

But we do know the phase of D and individual K--

so if this is individual K.

We know the D allele had to come with B--

sorry, with A-- if this parent was the one transmitting

the trait to K from here.

So I'm to erase my ABs because that was not working.

So this is a scenario where we have

no information about the meiosis from this individual.

But we do know the phase of K. OK?

STUDENT: Doesn't that make K an informative meiosis, though?

PETER REDDIEN: We can then evaluate the meioses

that individual K undergoes.

So that's kind of what I'm trying to emphasize here

with what I've depicted, that we're looking at the meioses--

if we're looking at the meioses from K,

we can evaluate whether those meioses were informative.

Some might be, some might not be.

And then if we want to know about the phase of K,

we have to have some information from K's parents.

We could ask if K's parents had informative meioses.

And that's a separate question from whether K

had informative meioses.

And if we wanted to know something

about the phase in K's parents, we'd

need to know about information from K's grandparents.

OK?

Are there questions about that?

The phase is going is sort of intuitively

going to be helpful in knowing which gametes are recombinant

and not recombinant.

There's one thing that's going to require

a little extra consideration, which is a phase is unknown.

Can you get any information about probability of linkage?

We're going to deal with that in the second part of the lecture.

But if you want to definitively know

whether a gamete is recombinant or not recombinant,

you need to know the phase.

It's not the only situation where

you can have data that contributes to a LOD score,

as I'll come to in that second part.

But the phase allows you to infer what's

recombinant or nonrecombinant.

Now that, if you recall-- so if you just think about it.

So if you have an individual that

has some genotype like this, and you

do a test cross where you want to infer

was a recombinant a nonrecombinant gamete, well,

how do you know what the configuration

of this individual is?

Was it A with B?

Little a with little b?

Or A with little b, little a with big B?

Does it matter if we want to figure out

which gametes come from this individual

are recombinant or not recombinant?

Yes, right?

Can anyone say why it matters?

We can tell which gametes are recombinant or not.

It will be different gametes, the recombinant ones,

depending upon the configuration.

So for this configuration, the recombinant gametes

are a B A with little b and little a with big B.

Whereas, in this configuration, the recombinant gametes

are big A with big B and little a with little b.

So that configuration matters.

Well, how do we know if we're just

given some genotype like this?

How would we know which of these configurations is right?

You have to look at the parents.

OK.

And the way we did that originally, when we could do

crosses by design with organisms in the lab,

is we cross parents of known genotypes.

We cross true breeding strains.

So we crossed-- well, let's do it this way.

OK.

So if we did that cross, what is our correct configuration?

This one.

That's the type of thing we did in the past.

But you could imagine different kinds of crosses

that would lead to the other configuration.