Midterm 1 - Notes 2 (Part 2) Flashcards
What is an example of a genetic marker?
Microsatellites
What can microsatellites generate?
Genetic maps
How many repetitive motifs in a genomic DNA?
10-100 repeats
What can be different between the locus?
The number of repeats
What is a typical size of a repeat?
2-6 nucleotides
Are microsatellites very abundant?
Yes
- they spread through the genome
What are 3 advantages to microsatellites?
- Very abundant
- Unaffected by the environment or development
- Easy to detect
What do microsatellites have a high rate of?
Mutations
- resulted from a lot of variation
When do most mutations occur?
During DNA replication
- slipped strand misparing
- mutations add or subtract one repeat unit at a time
What do microsatellites rarely influence?
Phenotypes
- they are neutral markers
What happens in uninformed markers?
There is no variation
- is only homozygous
What is an informative marker?
There is variation
- contains both homozygous and heterozygous
What can a microsatellite inheritance (paternity test) do?
It can follow alleles from one generation to another
Why would you need to look at more than one marker when testing for paternity (DNA)?
Because it is likely that another man in the population has the same allele
What kind of marker pattern would you expect if the markers are not linked/ not related?
2-1-2 segregation pattern
What happens to the recombinant combination as the alleles get further apart?
You will get a higher percentage of recombinant combination (and a lower maternal combination)
Cente morgan
Is the probability of recombination occurring
- measures genetic distances
Recombinant
When you have an A allele in one segment and a B allele in the other segment
- mis-matched pairing
Why do you need many different markers when creating a linkage map?
Because if you only have a few all the markers might be on different chromosomes and you will not have any linkages
- the more markers you have the better the results will be
- the markers need to be spread out
What happens when the linkage group is 50/50?
The linkage will not be included in the linkage map, but it will start a new one
Why was a radioactive (GT)15 probe used?
Because CA repeats are very common so it increases the chance of finding a microsatillite
- GT is the complement of CA
What did the radioactive probe allow?
It allowed specific stuff to bind to it and light up in order to identify it
Polymorphic
Are the differences between two organisms
What was the genetic map based on?
Genotypes
What is the reason that markers are not equally distributed?
Because they are randomly selected
Why could a genetic map have so many gaps?
Because the markers could not be equally distributed the genetic distance between them vary and could over count a linkage
If you have 12 linkage groups, how many chromosomes should you have?
12
Why would you have more linkage groups than chromosomes?
Because the linkage groups could have a large region and overlap and therefore be counted more than once
What is the average genetic distance for a marker?
1 marker per 4cM
How do you asses the quality of the marker?
You would look at the average genetic distance between any 2 markers
What is 1 marker per 4cM suitable for mapping?
Morphological traits
What does it mean when you have more linkage groups than chromosomes?
That the linkage groups were too large to connect
- they overlapped
Spine present or spine absent is an example of what?
Qualitative trait
Variation in spine length is an example of what?
Quantitative trait
Qualitative traits
Traits that can be described
Quantitative traits
Traits that can be represented by a numerical value
What kind of phenotypes are in qualitative traits?
2-3 define phenotype variants only
What kind of phenotypes are in quantitative traits?
The phenotypes vary along a gradient
What are qualitative traits caused by?
A single gene
What are quantitative genes caused by?
Multiple genes
How are qualitative and quantitative traits mapped?
The same way as any genetic marker
QTL
Quantitative Trait Loci
What did it mean when 2 genes were completely independent?
The 2 groups would be the same with no significance difference
What if the marker was close to the gene that effected the phenotype?
Then the 2 groups should be a significant difference
How can you determine the significance?
By finding out the p value
- the smaller the p value the more significant it is
What is a big factor on effecting phenotype?
Distance
- the further away the more likely it will recombinant
LOD
Logarithm of odds
Logarithm of odds
Is the ratio of probability that 2 traits are linked over the probability that they are not
- (linked/not linked)
What does LOD > 3 mean?
That the chance of no-linkage is less than 1 in 1,000
- it is 1000x more likely that they are linked than that they are not linked
What does LOD = 0 mean?
That it is equally likely that they are linked or not linked
When would you have a high LOD score and a low LOD score?
- High = closer to the gene that contributes to the phenotype
- Low = further away from the gene that contributes to the phenotype
What does a high LOD score mean?
That there is high linkage to the gene causing the phenotype
What does a genetic map not tell you?
Doesnt tell you what the genes are
What can a genetic map let you do?
It can let you use the genes as a predictor
