Lectures 11 & 12: Gene Mapping Flashcards
Define a linkage map
This is a genetic map of a species or experimental population that shows the position of its known genes or genetic markers relative to each other in terms of recombination frequency (cM), rather than specific physical distance along each chromosome.
What is association mapping also known as?
Linkage disequilibrium mappinng
What is association mapping?
This is a map that required the mapping of quantitative trait loci taking advantage of historic linkage disequilibrium to link phenotypes to genotypes.
When does recombination occur?
Meiosis - zygotene
What is the main determinant of haplotype patterns?
Recombination frequency
T/F: Genes that are far apart on a chromosome will exhibit less crossover events thus recombination compared to those that are closer together
False
Which two phenotypes did Morgan use in his linkage experiments?
Red vs purple eyes and normal vs vestigial wings
T/F: Morgan performed a backcross experiment?
True
What is the formula for recombination faction?
Number of recombinant progeny/ total number of progeny
What are syntenic loci?
Loci that are on the same chromosome
1% recombination corresponds to how many cM
1 cM
What is the range for recombination faction?
0.0-0.5
What does a recombination frequency of 0.0 imply?
That the two loci are so close together that recombination does not occur between them
What does a recombination frequency of 0.5 imply?
That the two loci are unlinked and this is equivalent to independent assortment which occurs for alleles of loci that are on different chromosomes
Define Linkage phase
The arrangement of alleles on each chromosome
Define Haplotype
The combination of alleles on each chromosome
What is a genetic marker?
A DNA sequence with a known location on a chromosome; primers
What are RFLPs?
Restriction Fragment Length Polymorphisms
What are VNTRs?
Variable Number Tandem Repeats
What are SNPs?
Single Nucleotide Polymorphisms
T/F + explain: Marker loci can infer information on the causation of a genetic disease?
False; a marker locus simply designates which chromosome is being transmitted by the parent which has nothing to do with the actual causation of the disease.
T/F: Linked markers can be typed at any age?
True
Name three factors that influence crossover rates
Oogenesis, telomeric regions and recombination hot spots
Name a situation of an informative pedigree.
Where a homozygous dominant mates with a homozygous recessive or a heterozygous mating with a homozygous recessive
Give an example of a non-informative pedigree
Two heterozygotes or two homozygous recessive matings
Does informative/ non-informative pedigrees show they are homo/heterozygous for the disease locus?
No, there is either one or two copies of a two-allele RFLP, SNP, VNTR or microsatellite which are closely linked to the disease locus.
Name three characteristics that make marker loci useful.
Codominance to determine linkage phase, numerous and highly polymorphic
Why is polymorphic loci useful in linkage mapping?
This increases the probability that matings will be informative as it ensures that most parents will be heterozygous for the marker locus, making it easier to establish linkage phase in families.
How can marker loci help build a recombination map?
They help narrow down the size of the region that contains the disease causing locus.
What statistical measure is used to ensure that linkage was not observed by chance?
The Logarithm of the Odds score; LOD (Z)
Define LOD.
The common logarithm of the ratio of the likelihood of linkage at a specific recombination fraction to the likelihood of no linkage.
What does an LOD score of 3.0 indicate?
3.0 indicates that the likelihood in favour of linkage is 1000 times greater than the likelihood against linkage.
Which LOD score indicates no linkage?
-2.0; the odds are 100 to 1
If Theta = 0.5 then…
this supports Mendel’s second law; that there is an independent assortment of alleles
T/F: Linkage peaks can be followed by association mapping using SNPs
True
Define polygenic inheritance.
The traits/ disorders which are associated with the effects of multiple genes which are termed polygenes
What is multifactorialism?
Where traits/disorders result from a combination of multiple genetic and environmental causes.
Why doesn’t every marker on the chromosome show association or co-segregation with disease?
Linkage disequilibrium
What is Linkage Disequilibrium?
This is where there are locations on the chromosomes which exhibit a higher or lower rate of recombination. - Recombination hot/ cold spots
Why is linkage disequilibrium important?
Understanding LD patterns across the genome is critical for accurate localisation of disease causing genetic mutations
What is the difference between linkage and LD?
Linkage measure co-segregation of a chromosomal region whereas LD measures co-segregation in a population
Why are LD studies small?
They use data from historic recombination
Why are LD studies useful?
They offer fine mapping of disease genes
When are association mapping studies useful?
When we are interested in narrowing down a large region that has previously been identified by linkage or when one has restricted range of candidate genes for studying.
What are the two reasons for association mapping studies?
1) The locus is a functional variant and 2) the locus is in LD with a functional variant
