Mapping with molecular markers

Question 1

Why would we use SNPs for mapping vs just visible phenotypes?

Answer 1

Millions of SNPs vs a few thousand visible phenotypes. Get a more precise location with SNPs

Question 2

What do we look for when mapping with SNPs?

Answer 2

Linkage between the SNP and the mutation

Question 3

What criteria needs to be met when choosing 2 strains to cross for SNP mapping?

Answer 3

The SNP has to be able to be differentiated, so the two strains need to have different SNP alleles to map with

Question 4

What individuals do you start with for SNP mapping?

Answer 4

True breeding strains. One will be hermaphrodites that are homozygous for the mutant allele and homozygous for SNP allele A, and the other are males that are homozygous WT at mutant gene and homozygous for SNP allele B

Question 5

What do you cross the F1 generation to if working with worms? Working with anything else?

Answer 5

Would self the worms, since they are hermaphrodites. Anything else would need to be test crossed

Question 6

How many progeny of the F2 will show the mutant phenotype if the SNP and the mutations were unlinked? Linked?

Answer 6

25% of the progeny show the mutant phenotype, regardless if the SNP is linked or unlinked, because the SNP doesn’t have a visible phenotype

Question 7

What is the phenotype of the F2 progeny we would look at to determine the SNP allele present?

Answer 7

Mutant phenotype and a few controls

Question 8

What would be the ratio of SNP alleles present in F2 progeny displaying a mutant phenotype if the mutation and SNP were unlinked?

Answer 8

1 A/A homozygote, 2 A/B heterozygotes, 1 B/B homozygote

Question 9

What would be the ratio of SNP alleles present in F2 progeny displaying a mutant phenotype if the mutation and SNP were linked?

Answer 9

Way more homozygotes of the SNP allele that the parental strain with the mutation has

Question 10

What do you do with the F2 individuals displaying the mutant phenotype?

Answer 10

Extract DNA from every single individual with the mutant phenotype

Question 11

What do you do with DNA extracted from F2 progeny displaying the mutant phenotype?

Answer 11

PCR of the SNP locus

Question 12

What do you do with the PCR products of the F2 progeny to determine which SNP allele is present?

Answer 12

Restriction digest and run on a gel if the SNP is a Snip SNP

If it’s not a Snip SNP, then do ASO hybridization

Question 13

If we were using flies instead of worms, what would the genotype of the tester be?

Answer 13

Recessive for the mutant gene, but can have either SNP allele as long as it’s homozygous

Question 14

What type of dominance is displayed by SNP alleles and other molecular markers?

Answer 14

Codominance

Question 15

What tools do we need to have to do deletion mapping?

Answer 15

A collection of Df mutants, with all the deletions characterized

Question 16

What is a Df chromosome?

Answer 16

Chromosomes that carry a deletion in a region that we want, but everything else outside of that is WT

Question 17

What are the 2 parental stocks used for deletion mapping?

Answer 17

Individual carrying the mutation and is also homozygous recessive for gene a. The other one is the Df stock and one chromosome is carrying the deletion but everything else is WT, and the other chromosome is mutant for every gene

Question 18

How do we know if our mutation is in a particular region with deletion mapping?

Answer 18

If one chromosome has a deletion in the region where the mutation is, the individual is hemizygous and we get the mutant phenotype with only one copy of the allele

Question 19

After crossing the 2 deletion mapping parental stocks, what progeny do we select from the F1?

Answer 19

Select individuals that are WT for gene A, which means it has the deletion chromosome. Then score those ones for the mutant phenotype

Question 20

What does it mean if F1 individuals with WT gene A phenotype shows the mutant phenotype as well when doing deletion mapping?

Answer 20

The mutation is within a deleted region

Question 21

What does it mean if F1 individuals with WT gene A phenotype does not show the mutant phenotype as well when doing deletion mapping?

Answer 21

The mutation is not within that deleted region