Mapping with molecular markers Flashcards
Why would we use SNPs for mapping vs just visible phenotypes?
Millions of SNPs vs a few thousand visible phenotypes. Get a more precise location with SNPs
What do we look for when mapping with SNPs?
Linkage between the SNP and the mutation
What criteria needs to be met when choosing 2 strains to cross for SNP mapping?
The SNP has to be able to be differentiated, so the two strains need to have different SNP alleles to map with
What individuals do you start with for SNP mapping?
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
What do you cross the F1 generation to if working with worms? Working with anything else?
Would self the worms, since they are hermaphrodites. Anything else would need to be test crossed
How many progeny of the F2 will show the mutant phenotype if the SNP and the mutations were unlinked? Linked?
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
What is the phenotype of the F2 progeny we would look at to determine the SNP allele present?
Mutant phenotype and a few controls
What would be the ratio of SNP alleles present in F2 progeny displaying a mutant phenotype if the mutation and SNP were unlinked?
1 A/A homozygote, 2 A/B heterozygotes, 1 B/B homozygote
What would be the ratio of SNP alleles present in F2 progeny displaying a mutant phenotype if the mutation and SNP were linked?
Way more homozygotes of the SNP allele that the parental strain with the mutation has
What do you do with the F2 individuals displaying the mutant phenotype?
Extract DNA from every single individual with the mutant phenotype
What do you do with DNA extracted from F2 progeny displaying the mutant phenotype?
PCR of the SNP locus
What do you do with the PCR products of the F2 progeny to determine which SNP allele is present?
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
If we were using flies instead of worms, what would the genotype of the tester be?
Recessive for the mutant gene, but can have either SNP allele as long as it’s homozygous
What type of dominance is displayed by SNP alleles and other molecular markers?
Codominance
What tools do we need to have to do deletion mapping?
A collection of Df mutants, with all the deletions characterized