All language subtitles for 17031x_PR_DNA_Markers_03_Mapping_SNPs_v1-en

PETER REDDIEN: So now what I'm going to do

is instead of drawing the genotype like this,

I'm going to draw an individual chromosome.

I've drawn two chromosomes here.

And let's say this is a particular chromosome

in our organism.

I'll call it chromosome one.

So we're diploid here.

We have two copies of chromosome one,

and let's just say it turns out that gene X exists

on chromosome one.

We don't know that yet but I'm just

going to say that turns out to be where it is.

So I'll just draw a gene X in some position

on chromosome one.

OK, so this is our starting strain,

and we're going to now cross it to some other individuals,

our gene X plus homozygotes.

So this is individual one, this is individual two.

And I'm going to say that these individuals will

vary not just at their gene X, but also

at many other locations in the genome.

Like I said, we vary every thousand nucleotides or so,

so let's say these individuals vary every thousand nucleotides

or so.

They have polymorphisms.

I'm going to indicate these polymorphisms

with little tick marks scattered across the chromosome.

All right, so let me try to be a little explicit about what

I'm drawing here just so it's clear.

So if we zoom in on this chromosome here,

that's just shorthand notation for double-stranded DNA

sequence of a chromosome.

And then these tick marks are polymorphisms.

Let's take this one polymorphism that's

right to the right of gene X. So let's

say we'll call that polymorphism SNP1.

So let's say this is the sequence of SNP1 where SNP1

is this nucleotide so we could say

it has an A at this position.

Again, it's double-stranded DNA sequence, so when I say an A

I'm just referring to this 5 prime to 3 prime A here.

OK, so then SNP1 and this individual is right here.

So if we look at the white individual chromosome,

say SNP1 has a G, so maybe its sequence would be like this.

OK?

So if we look at this position, the same position

in the genome in these two individuals,

they differ where this individual has an A,

this individual has a G. But the rest

of the sequence surrounding it would be identical.

Maybe every thousand nucleotides or so,

we find one of these scenarios.

OK, so this is chromosome one in this individual,

this is chromosome one in the other individual.

All right, so now we get an F1 where we have one chromosome

one from this parent and one chromosome one

from this parent like that.

So now let's do a cross where what we're going to do

is mapping.

In the past, you did crosses with heterozygotes

to look at recombinant gamete frequencies to do mapping,

to get some measure of distance.

OK?

And in this case, what we're going to be mapping

are not two genes that are causing phenotypes,

but are one gene that causes the phenotype, gene X, which

respect to all of these polymorphisms

all at the same time.

OK.

OK, so we'll do a test cross for this.

Let's cross to a-- could be the original parent,

or this could be from some true breeding strain.

Cross back to an individual that has these white type

polymorphisms that is homozygous mutant for gene X.

Then we'll go to the next generation,

and it's this next generation where we're going

to try to collect some data.

And what we're going to do is we're

going to select the individuals with the phenotype

and we're only going to be looking at those.

We know they're gene X homozygous by the phenotype.

All right, so we know that these progeny are all

going to get one of these chromosomes from this parent.

OK?

Then we know that they're going to get at least this region

of this chromosome from this parent

because we're only looking at the gene X homozygotes.

So we on the other chromosome we're at least

going to have that region.

And the rest of the region depends on whether there was

any recombination in the meiosis that produced the gamete

carrying gene X between this chromosome,

this homologue of chromosome one, and this homologue.

So let's just say that there happened

to be a crossing over event that produced the gamete is going

to be in this individual I depict at this location

that I depict with an x.

So let's just say then, and in some given individual,

the chromosome that came looked like this.

So it has lots of white SNP, white type SNPs,

and some blue type SNPs.

So now what we're going to do is we

are going to collect DNA from many individuals that

have the gene X phenotype and we're going to pool it.

So if this was one individual, we take the DNA,

we take the individual from another-- oh wait,

you take the DNA from another individual

that had this phenotype and another individual and so on.

Could do dozens and dozens of these if we want.

We pool all that DNA together in a tube, then we sequence it.

We make a sequencing library and we sequence it.

OK, and then we're going to map these reads.

We're going to basically do what we did at the beginning, align

these reads to some reference.