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MICHAEL HEMANN: How do we use SNPs to do mapping?
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OK, so let's just look at--
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here, let's look again at a repeat length polymorphism,
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so an SSR.
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In a sense, we can use them interchangeable.
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We'll talk for convenience sake about an SSR.
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So, again, we have a gel and on this agarose gel
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we have three lanes, and say we have some marker--
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we have two markers--
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marker lengths.
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So we have a length A, we have a length B.
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And so you can start with a homozygous individual that
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has two copies of A, so they only show one band.
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And another individual that has two copies of B
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and so they only show that B band,
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and they can have offspring that are AB.
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So with markers-- and this is actually going to carry forward
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into lectures next week--
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there are a couple critical requirements
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for getting what we call informative data from crosses.
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So if we think about requirements for mapping
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with DNA markers.
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OK?
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So the first requirement is the parent
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with the phenotype has to be heterozygous for the marker.
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So there's some phenotype that we care about
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that we want to map, and that parent has to be heterozygous
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because we're going to look for the segregation
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of a particular marker with the phenotype of interest.
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And the only way we can do that is
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if there are two different alleles of that marker
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so that we can actually see, is it segregating with one
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of these alleles or the other.
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If they're the same allele, we don't get any information.
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And the second is that we need to know
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the marker or the marker allele, that each parent contributed.
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So let's think of a couple crosses here.
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So here we'll have two parents and two kids.
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Same thing over here.
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We have an affected mother and this affected mother is AB.
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So already that satisfies the first criteria
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that I set up, that the person that has the phenotype that we
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care about is heterozygous for a marker that we're looking at.
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And so say we cross with male that's AA--
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this is a little bit like a test cross--
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and we have two kids.
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So in this case, for both of these kids,
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do we know that the--
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do we know the allele that they're
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getting from each parent?
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Do we know the marker allele that they're
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getting from each parent?
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Yes.
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We do.
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We know that this child--
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both children, actually, inherited B
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from the mother and A from the father.
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So we'll call these informative.
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And this is going to become really important when we're
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talking more about human genetics, inheritance,
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and start talking about LOD scores,
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but they're informative.
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So in this case, say we cross to an AB
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and we have a child that is AA and a child that is AB.
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In the case on the left, do we know
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which allele came from each parent,
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or which allele each parent contributed?
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No?
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Yeah.
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So this gets a little bit more complicated.
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So basically here we're seeing that we
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don't know the identity of these A's, and in essence they're
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identical to each other.
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But we do know that each parent gave an A,
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and so there we're going to say it's informative.
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In this case, AB, it's noninformative.
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And it's noninformative because we
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have no idea which parent gave the A
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and which parent gave the B, so there
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we're a little bit clueless.
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