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PETER REDDIEN: So now what I'm going to do
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is instead of drawing the genotype like this,
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I'm going to draw an individual chromosome.
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I've drawn two chromosomes here.
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And let's say this is a particular chromosome
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in our organism.
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I'll call it chromosome one.
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So we're diploid here.
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We have two copies of chromosome one,
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and let's just say it turns out that gene X exists
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on chromosome one.
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We don't know that yet but I'm just
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going to say that turns out to be where it is.
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So I'll just draw a gene X in some position
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on chromosome one.
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OK, so this is our starting strain,
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and we're going to now cross it to some other individuals,
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our gene X plus homozygotes.
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So this is individual one, this is individual two.
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And I'm going to say that these individuals will
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vary not just at their gene X, but also
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at many other locations in the genome.
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Like I said, we vary every thousand nucleotides or so,
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so let's say these individuals vary every thousand nucleotides
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or so.
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They have polymorphisms.
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I'm going to indicate these polymorphisms
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with little tick marks scattered across the chromosome.
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All right, so let me try to be a little explicit about what
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I'm drawing here just so it's clear.
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So if we zoom in on this chromosome here,
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that's just shorthand notation for double-stranded DNA
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sequence of a chromosome.
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And then these tick marks are polymorphisms.
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Let's take this one polymorphism that's
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right to the right of gene X. So let's
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say we'll call that polymorphism SNP1.
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So let's say this is the sequence of SNP1 where SNP1
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is this nucleotide so we could say
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it has an A at this position.
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Again, it's double-stranded DNA sequence, so when I say an A
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I'm just referring to this 5 prime to 3 prime A here.
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OK, so then SNP1 and this individual is right here.
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So if we look at the white individual chromosome,
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say SNP1 has a G, so maybe its sequence would be like this.
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OK?
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So if we look at this position, the same position
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in the genome in these two individuals,
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they differ where this individual has an A,
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this individual has a G. But the rest
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of the sequence surrounding it would be identical.
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Maybe every thousand nucleotides or so,
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we find one of these scenarios.
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OK, so this is chromosome one in this individual,
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this is chromosome one in the other individual.
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All right, so now we get an F1 where we have one chromosome
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one from this parent and one chromosome one
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from this parent like that.
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So now let's do a cross where what we're going to do
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is mapping.
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In the past, you did crosses with heterozygotes
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to look at recombinant gamete frequencies to do mapping,
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to get some measure of distance.
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OK?
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And in this case, what we're going to be mapping
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are not two genes that are causing phenotypes,
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but are one gene that causes the phenotype, gene X, which
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respect to all of these polymorphisms
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all at the same time.
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OK.
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OK, so we'll do a test cross for this.
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Let's cross to a-- could be the original parent,
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or this could be from some true breeding strain.
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Cross back to an individual that has these white type
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polymorphisms that is homozygous mutant for gene X.
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Then we'll go to the next generation,
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and it's this next generation where we're going
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to try to collect some data.
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And what we're going to do is we're
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going to select the individuals with the phenotype
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and we're only going to be looking at those.
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We know they're gene X homozygous by the phenotype.
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All right, so we know that these progeny are all
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going to get one of these chromosomes from this parent.
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OK?
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Then we know that they're going to get at least this region
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of this chromosome from this parent
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because we're only looking at the gene X homozygotes.
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So we on the other chromosome we're at least
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going to have that region.
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And the rest of the region depends on whether there was
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any recombination in the meiosis that produced the gamete
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carrying gene X between this chromosome,
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this homologue of chromosome one, and this homologue.
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So let's just say that there happened
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to be a crossing over event that produced the gamete is going
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to be in this individual I depict at this location
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that I depict with an x.
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So let's just say then, and in some given individual,
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the chromosome that came looked like this.
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So it has lots of white SNP, white type SNPs,
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and some blue type SNPs.
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So now what we're going to do is we
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are going to collect DNA from many individuals that
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have the gene X phenotype and we're going to pool it.
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So if this was one individual, we take the DNA,
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we take the individual from another-- oh wait,
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you take the DNA from another individual
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that had this phenotype and another individual and so on.
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Could do dozens and dozens of these if we want.
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We pool all that DNA together in a tube, then we sequence it.
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We make a sequencing library and we sequence it.
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OK, and then we're going to map these reads.
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We're going to basically do what we did at the beginning, align
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these reads to some reference.
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8974
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