Genomic markers Flashcards
What are genomic markers used for?
To carry out genetic analysis to identify a specific locus on the DNA
Which genetic markers are more used?
DNA polymorphisms
Minisatellites
Region of the DNA that is repeated: forensic genetics
Microsatellites
More frequent than minisatellites: shorter length than minisatellites
Advantages of using microsatellites
- Easy to detect via PCR
- present in high numbers in the genome
- co-dominant in nature
Disadvantages of using microsatellite
- initial identification
- DNA sequence information necessary
Which projects were involved with SNPs?
International HapMap Project
1000 genomes
What does recombination mapping do?
Allows us to estimate the genetic distance between loci
Independent assortment regarding loci
Loci which are on separate chromosomes or on the same chromosome but are so far apart that they segregate independently
What happens when 2 loci are very close to each other?
They co-segregate: never separated by recombination
How do we establish the relationship between the loci?
In terms of the genetic relationship and distance as a function of the genetic relationship
If 4 types of gametes are observed what is the case?
Independent segregation: NOT LINKED
If we observe 2 parental combinations and 2 recombinant what is the case, between 0% and 50%?
The 2 loci are not independently segregating but are not fully co-segregating
When does crossing over take place?
At the 4-chromatid stage of propahse I meiosis
What happens if you have double crossing over?
Creates parental combinations of these 2 alleles
How do we measure the distance between 2 loci?
In terms of recombination frequency
1% recombination is 1cM
What is the maximum number of recombination that we can measure in a genetic analysis?
50%
How do we calculate recombination frequency?
Recombinants/ number of gametes
How many meioses are needed to be statistically significant?
10
Linkage analysis
Analysis in which we establish if there is linkage hence genetic association between the 2 loci
What does it mean if the % recombination is lower than 50%?
The genes must be on the same chromosome
What is the cis arrangement?
wt alleles on one homologous chromosome and both mutants on the other
What is the trans arrangement?
Arrangement has one mutant and wt on each homolog
What does a crossover in the cis arrangement result? and in the trans arrangement?
cis arrangement–> trans arrangement
trans arrangement–> cis arrangement
How is a genetic map established?
From estimating the crossover rate in a particular segment of the chromosome
What does crossover do?
reduce formation of other chiasmata nearby
What does crossover produce?
Interference
What is interference?
Total interference with no other crossovers in the region
Coefficient of coincidence
double crossing over observed/ double crossing over expected
Interference equation
1- coefficient of coincidence
Mapping functions
Mathematical formulas used to define the relationship between map distance and recombination frequency
Haldane’s mapping function
p= 1/2 (1-e^-2d)
For which window is the estimator distance between 2 genes precise
7cM
Which quantity is additive and which is not?
Map distance is additive; frequency of recombination is not
Which factors influence genetic distance?
- Gender: more recombination in females than in females
- Chromosome structure: where the centromere is located, recombination is the lowest
