Original subtitles

MICHAEL HEMANN: How do we use SNPs to do mapping?

OK, so let's just look at--

here, let's look again at a repeat length polymorphism,

so an SSR.

In a sense, we can use them interchangeable.

We'll talk for convenience sake about an SSR.

So, again, we have a gel and on this agarose gel

we have three lanes, and say we have some marker--

we have two markers--

marker lengths.

So we have a length A, we have a length B.

And so you can start with a homozygous individual that

has two copies of A, so they only show one band.

And another individual that has two copies of B

and so they only show that B band,

and they can have offspring that are AB.

So with markers-- and this is actually going to carry forward

into lectures next week--

there are a couple critical requirements

for getting what we call informative data from crosses.

So if we think about requirements for mapping

with DNA markers.

OK?

So the first requirement is the parent

with the phenotype has to be heterozygous for the marker.

So there's some phenotype that we care about

that we want to map, and that parent has to be heterozygous

because we're going to look for the segregation

of a particular marker with the phenotype of interest.

And the only way we can do that is

if there are two different alleles of that marker

so that we can actually see, is it segregating with one

of these alleles or the other.

If they're the same allele, we don't get any information.

And the second is that we need to know

the marker or the marker allele, that each parent contributed.

So let's think of a couple crosses here.

So here we'll have two parents and two kids.

Same thing over here.

We have an affected mother and this affected mother is AB.

So already that satisfies the first criteria

that I set up, that the person that has the phenotype that we

care about is heterozygous for a marker that we're looking at.

And so say we cross with male that's AA--

this is a little bit like a test cross--

and we have two kids.

So in this case, for both of these kids,

do we know that the--

do we know the allele that they're

getting from each parent?

Do we know the marker allele that they're

getting from each parent?

Yes.

We do.

We know that this child--

both children, actually, inherited B

from the mother and A from the father.

So we'll call these informative.

And this is going to become really important when we're

talking more about human genetics, inheritance,

and start talking about LOD scores,

but they're informative.

So in this case, say we cross to an AB

and we have a child that is AA and a child that is AB.

In the case on the left, do we know

which allele came from each parent,

or which allele each parent contributed?

No?

Yeah.

So this gets a little bit more complicated.

So basically here we're seeing that we

don't know the identity of these A's, and in essence they're

identical to each other.

But we do know that each parent gave an A,

and so there we're going to say it's informative.

In this case, AB, it's noninformative.

And it's noninformative because we

have no idea which parent gave the A

and which parent gave the B, so there

we're a little bit clueless.