Linkage and Chromosome Mapping

Question 1

linked genes

Answer 1

alleles at different loci travel together

they do not assort independently

Question 2

complete linkage

Answer 2

when genes are close together and no crossing over occurs between them

Question 3

What allows recombinant types to be produced?

Answer 3

crossing over

Question 4

crossing over

Answer 4

• occurs between non-sister chromatids of homologous chromosomes
• occurs in pachytene
• allows recombinant types to be produced

Question 5

recombinant gamete types

Answer 5

gametes that arose due to a crossover

Question 6

parental gamete types

Answer 6

gametes that are not a product of crossing over

Question 7

Which type are more frequent: parental or recombinant?

Answer 7

parental

Question 8

coupling phase

Answer 8

when one chromosome contains the dominant alleles for both loci and the other contains the recessive alleles for both loci

Question 9

repulsion phase

Answer 9

when each chromosome contains both a dominant and recessive allele - heterozygous for both

Question 10

recombination frequency

Answer 10

the frequency of crossing over between two genes

it is proportional to the distance between the genes

Question 11

are there more crossovers between genes that are further apart or closer together?

Answer 11

far apart

Question 12

map distance

Answer 12

numerically equal to the percentage of recombination between the loci

= (recombination frequency)(100)

1% recombination = 1 centimorgan

Question 13

2 point mapping experience

Answer 13

you are trying to determine the distance between two linked loci

Question 14

Steps to 2 point mapping

Answer 14

• 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

Question 15

If independent assortment occurs, then there should be…

Answer 15

an equal number of parental and recombinant types

Question 16

Which would you expect when genes are linked?

• # parental > # recomb
• # parental < # recomb
• # parental = # recomb

Answer 16

parental > # recombinant

Question 17

Interpret a map distance of 13

Answer 17

• 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

Question 18

For map distances <25…

Answer 18

there is a nearly linear relationship between recombination frequency and actual distance

Question 19

For map distances >25…

Answer 19

the percent recombination underestimates map distance

Question 20

What is the map distance that will show for independently assorting loci?

Answer 20

50 cM

Question 21

mapping function

Answer 21

a graph that shows the relationship between the percent recombination that we observe in an experiment and the actual map distance between genes

Question 22

Creighton and Morgan

Answer 22

• crossing over does involve physical exchange between homologous chromosomes

Question 23

3 point map

Answer 23

looks at 3 genes on a chromosome

Question 24

Steps to 3 point mapping

Answer 24

• 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

Question 25

Testing for linkage in a 3 point test

Answer 25

- 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

Question 26

classes of crossover with 3 gene types

Answer 26

- NCO - no crossing over - SC1 - cross over in left region of map - SC2 - cross over in right region of map - DCO - double crossover

Question 27

Determining gene order with 3 genes

Answer 27

- 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

Question 28

coefficient of coincidence

Answer 28

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)

Question 29

interference

Answer 29

when number of observed DCO is less than expected, something "interfered" with crossing over I = 1-C

Question 30

NCO

Answer 30

=1-any crossover =1-SCO1-SCO2-DCO =1-r1-r2+DCO

Question 31

SCO1

Answer 31

=r1-DCO

Question 32

SCO2

Answer 32

=r2-DCO

Question 33

DCO

Answer 33

=r1*r2*C

Question 34

ascus

Answer 34

the sac containing all products from the meiotic and mitotic divisions of Neurospora crassa

Question 35

describe how an ascus is form

Answer 35

- Fertilization of haploid female and male occurs - both divisions of meiosis occur - a mitotic division occurs - all products are held together in one sac

Question 36

1st division segregation

Answer 36

when no crossover occurs in meiosis of Neurospora crass | 4/4 pattern

Question 37

2nd division segregation

Answer 37

a crossover between gene and centromere occurs in meiosis of Neurospora crassa there are 4 types of these patterns

Question 38

pedigree analysis

Answer 38

observe multiple families to find traits that are associated with each other by tracing them on pedigrees

Question 39

sendai virus

Answer 39

used to fuse mouse and human cells for synteny testing

Question 40

synteny test

Answer 40

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

Question 41

synkaryon line

Answer 41

stabilized cell lines in synteny tests | contain a few human chromosomes and most if not all of the mouse chromosomes

Question 42

heterokaryon

Answer 42

a cell that has two nuclei

Question 43

GWAS

Answer 43

- 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

Question 44

SNPs

Answer 44

single nucleotide polymorphisms molecular marker most commonly used in GWAS variations at a single base pair

Question 45

What do GWAS look at?

Answer 45

populations of individuals | not pedigrees or parent-child-family relationships