Linkage and Chromosome Mapping Flashcards
linked genes
alleles at different loci travel together
they do not assort independently
complete linkage
when genes are close together and no crossing over occurs between them
What allows recombinant types to be produced?
crossing over
crossing over
- occurs between non-sister chromatids of homologous chromosomes
- occurs in pachytene
- allows recombinant types to be produced
recombinant gamete types
gametes that arose due to a crossover
parental gamete types
gametes that are not a product of crossing over
Which type are more frequent: parental or recombinant?
parental
coupling phase
when one chromosome contains the dominant alleles for both loci and the other contains the recessive alleles for both loci
repulsion phase
when each chromosome contains both a dominant and recessive allele - heterozygous for both
recombination frequency
the frequency of crossing over between two genes
it is proportional to the distance between the genes
are there more crossovers between genes that are further apart or closer together?
far apart
map distance
numerically equal to the percentage of recombination between the loci
= (recombination frequency)(100)
1% recombination = 1 centimorgan
2 point mapping experience
you are trying to determine the distance between two linked loci
Steps to 2 point mapping
- mate 2 pure-breeding individuals opposite in phenotype for the two loci in question
- test cross F1
- classify the testcross progeny into parental types and recombinant types
- determine the map distance as percentage of progeny that were due to a recombination event between the two loci
If independent assortment occurs, then there should be…
an equal number of parental and recombinant types
Which would you expect when genes are linked?
- # parental > # recomb
- # parental < # recomb
- # parental = # recomb
parental > # recombinant
Interpret a map distance of 13
- there are 13 centimorgan between A and B loci
- the probability of a crossover between the A and B loci is 0.13
- 13% of the gametes from the heterozygous individual are expected to be the recombinant type
For map distances <25…
there is a nearly linear relationship between recombination frequency and actual distance
For map distances >25…
the percent recombination underestimates map distance
What is the map distance that will show for independently assorting loci?
50 cM
mapping function
a graph that shows the relationship between the percent recombination that we observe in an experiment and the actual map distance between genes
Creighton and Morgan
- crossing over does involve physical exchange between homologous chromosomes
3 point map
looks at 3 genes on a chromosome
Steps to 3 point mapping
- create an individual heterozygous for 3 genes
- test cross
- pair up the data based on opposite characteristics - crossovers in the same location
- Identify the NCO and DCO
- determine gene order
- rewrite F1 gametes in correct order
- classify progeny based on type of cross over
- determine map distance
Testing for linkage in a 3 point test
- complete chi square between each loci for independent assortment
- find the parental types - those that are pure breeding and those that have the same phenotype combination as the pure breeding
- if fail to reject with more parental, can assume linkage
classes of crossover with 3 gene types
- NCO - no crossing over
- SC1 - cross over in left region of map
- SC2 - cross over in right region of map
- DCO - double crossover
Determining gene order with 3 genes
- Find NCO and DCO
- write down both NCO
- write down one DCO
- circle the DCO alleles in the NCO
- the allele circled alone is in the center of the map
- rewrite both NCO with the correct allele in the center
- put one NCO on the top and the other on the bottom
coefficient of coincidence
determine if a cross over in one region affects the change of getting a simultaneous cross over in the other region or if the crossing overs are independent of each other
C = (Observed # DCO)/(Expected # DCO)
interference
when number of observed DCO is less than expected, something “interfered” with crossing over
I = 1-C
NCO
=1-any crossover
=1-SCO1-SCO2-DCO
=1-r1-r2+DCO
SCO1
=r1-DCO
SCO2
=r2-DCO
DCO
=r1r2C
ascus
the sac containing all products from the meiotic and mitotic divisions of Neurospora crassa
describe how an ascus is form
- Fertilization of haploid female and male occurs
- both divisions of meiosis occur
- a mitotic division occurs
- all products are held together in one sac
1st division segregation
when no crossover occurs in meiosis of Neurospora crass
4/4 pattern
2nd division segregation
a crossover between gene and centromere occurs in meiosis of Neurospora crassa
there are 4 types of these patterns
pedigree analysis
observe multiple families to find traits that are associated with each other by tracing them on pedigrees
sendai virus
used to fuse mouse and human cells for synteny testing
synteny test
used to locate human genes to their chromosomes
cell culture test so looking at enzymes, proteins not phenotypes
performed by fusing mouse and human cells
synkaryon line
stabilized cell lines in synteny tests
contain a few human chromosomes and most if not all of the mouse chromosomes
heterokaryon
a cell that has two nuclei
GWAS
- genome wide association studies
- used to map human genes based on associations between phenotypic characteristics and molecular markers
- can help identify small region of the chromosome to look for genes that have biological significance for our phenotype
SNPs
single nucleotide polymorphisms
molecular marker most commonly used in GWAS
variations at a single base pair
What do GWAS look at?
populations of individuals
not pedigrees or parent-child-family relationships
