Deck 5: Genetic Linkage and Mapping in Eukaryotes

Question 1

A geneticist is mapping the chromosomes of the newly captured gremlin. Stripe is heterozygous for linked genes with alleles Bb, Ee, and Hh that determine if gremlins have biting teeth (B), are evil (E), have hair (H). In order to determine if the three genes are linked, a standard testcross was done, and 1000 offspring had the following genotypes: $$\begin{array} { l l } 48 & \text { bb ee } \mathrm { Hh } \\36 & \text { Bb ee hh } \\400 & \text { Bb ee } \mathrm { Hh } \\4 & \text { Bb Ee Hh } \\426 & \text { bb Ee hh } \\46 & \text { Bb Ee hh } \\38 & \text { bb Ee Hh } \\2 & \text { bb ee hh }\end{array}$$ What is the recombination frequency between genes E and B?

A) 9.0%
B) 8.4%
C) 42.6%
D) 10.0%
E) 9.4%

Answer 1

10.0%

Question 2

Assuming three genes are linked, how many recombinant genotypes would you expect and at what frequency?

A) four recombinant genotypes, more frequent than expected by independent assortment
B) six recombinant genotypes, less frequent than expected by independent assortment
C) six recombinant genotypes, more frequent than expected by independent assortment
D) four recombinant genotypes, less frequent than expected by independent assortment
E) two recombinant genotypes, more frequent than expected by independent assortment

Answer 2

B

Question 3

In sweet peas, the genes for flower color and pollen grain shape are 11 cM apart. A pure- breeding purple flowering plant with round pollen grains is crossed to a pure- breeding red flowering plant with long pollen grains. The resulting F1 offspring are all purple flowering plants with long pollen grains. What percent of offspring from a test cross analysis of the F1 individuals would you expect to be red flowering plants with long pollen grains?

A) 5.5
B) 89
C) 44.5
D) 39
E) 11

Answer 3

C

Question 4

Genetic linkage leads to the production of a significantly greater than expected number of gametes containing chromosomes with _ _.

A) dominant alleles
B) recessive alleles
C) allele combinations that are different from parental combinations
D) mutant alleles
E) parental combinations of alleles

Question 5

You perform a test cross of the dihybrid AaBb and score the phenotypes of 1000 progeny. Assuming independent assortment, how many of the progeny do you expect to display the dominant phenotype for both the A and B genes?

A) 500
B) 750
C) 250
D) 100
E) 200

Question 6

Incomplete genetic linkage of three genes in a trihybrid produces eight genetically different gamete genotypes. How many different gamete genotypes are produced in a four- gene cross with incomplete genetic linkage?

A) 16
B) 8
C) 4
D) 24
E) 20

Question 7

In fruit flies, red eyes (pr+_) are dominant to purple eyes (prpr) and normal wings (vg+_) are dominant to vestigial wings (vgvg). The genes are located on the same chromosome. A pure breeding red- eyed fly with vestigial wings was crossed with a pure- breeding purple- eyed fly with normal wings. All of the F1 progeny had a WT phenotype. Which of the following represents the arrangement of alleles on the F1's chromosome?

A) pr+vg+/pr+vg+
B) prvg/prvg
C) prvg/pr+vg+
D) pr+vg/prvg+
E) prpr+/vgvg+

Question 8

The alleles of linked genes tend to _ .

A) experience a higher rate of crossing over
B) be mutated more often than unlinked genes
C) assort independently
D) assort independently and show a higher rate of crossing over
E) segregate together during gamete production

Question 9

If you are given a recombination frequency of 34% between genes X and Y and 27% between X and Z, can you predict the order of the three genes?

A) No; based on this data alone, the order could be X- Z- Y or Z- X- Y.
B) No; based on this data alone, the order could be Z- Y- X or X- Y- Z.
C) Yes; the order is Z- X- Y.
D) Yes; the order is X- Y- Z.
E) Yes; the order is X- Z- Y.

Question 10

In an individual that is dihybrid for completely linked genes, which alleles would you expect in the gametes?

A) only recombinant gametes
B) one parental allele combination occurring more frequently than another
C) one parental allele combination occurring more frequently than another and no recombinant gametes
D) two equally frequent gametes containing only parental allele combinations
E) two equally frequent gametes containing only parental allele combinations and no recombinant gametes

Question 11

What organism exhibits complete genetic linkage, meaning there is no recombination between homologous chromosomes?

A) Female Drosophila
B) Female Homo sapiens
C) Male Drosophila
D) Male Homo sapiens
E) Zea mays (corn)

Question 12

Syntenic genes can assort independently when .

A) they are located on different chromosomes
B) they are far apart on a chromosome and crossing over occurs very rarely between the genes
C) they are far apart on a chromosome and crossing over occurs frequently between the genes
D) they are very close together on a chromosome
E) crossing over occurs rarely between the genes

Question 13

William Bateson and Reginald Punnett were not able to detect genetic linkage in sweet peas. Which of the following explains why Thomas Morgan was able to detect autosomal genetic linkage?

A) He performed Lod score analysis to determine the distance between the genes he was studying.
B) He crossed two heterozygous individuals and was able to determine offspring genotypes from their phenotypes.
C) He crossed a heterozygous individual with a homozygous recessive individual and was able to determine progeny genotypes from their phenotypes.
D) He sequenced the DNA and was able to determine the distance between the genes.
E) He performed a three- point test cross.

Question 14

What is a two- point test cross, involving a dihybrid F1 fly, used for when mapping genes?

A) to determine if the F1 fly is homozygous dominant or heterozygous
B) to determine the allele combinations that a homozygous recessive fly can create
C) to determine which alleles are dominant and which are recessive
D) to determine the recombination frequency between two genes
E) to determine the allele combinations that the F1 fly can produce

Question 15

What type of test would you use to determine whether observed data constitute evidence of genetic linkage or are simply a case of chance variation from expected values?

A) recombination frequency (r) calculation
B) chi- square analysis
C) two- point test cross
D) three- point test cross
E) test cross

Question 16

The syntenic genes B and T are linked. A cross between two parents, with genotypes BBtt and bbTT, produces F1 progeny with the BbTt genotype. What are the possible arrangements of alleles on the F1 progeny's chromosomes?

A) Bb/Tt
B) BT/Bt or bt/bT
C) BT/bt
D) Bt/bT
E) B/T or b/t

Question 17

Genes A and B are 7.5 map units apart on one chromosome. Genes C and D are 8.0 map units apart on a second non- homologous chromosome. The recombination frequency between A and C is .

A) 0.003
B) 0.851
C) 0.155
D) 0.006
E) 0.500

Question 18

In sweet peas, the genes for flower color and pollen grain shape are 11 cM apart. A pure- breeding purple flowering plant with round pollen grains is crossed to a pure- breeding red flowering plant with long pollen grains. The resulting F1 offspring are all purple flowering plants with long pollen grains. What percent of offspring from a test cross analysis of the F1 individuals would you expect to be purple flowering plants with long pollen grains?

A) 11
B) 44.5
C) 39
D) 5.5
E) 89

Question 19

In fruit flies, red eyes (pr+_) are dominant to purple eyes (prpr) and normal wings (vg+_) are dominant to vestigial wings (vgvg). The genes are located on the same chromosome. A pure- breeding red- eyed fly with vestigial wings was crossed with a pure- breeding purple- eyed fly with normal wings. All of the F1 progeny had a WT phenotype. The recombination frequency between the two genes is 15%. If an F1 individual were test crossed, what percentage of the progeny would you expect to have the WT phenotype?

A) 85%
B) 50%
C) 7.5%
D) 92.5%
E) 15%

Question 20

A geneticist is mapping the chromosomes of the newly captured gremlin. Stripe is heterozygous for linked genes with alleles Ee, Hh, and Bb, that determine if gremlins are evil (E), have hair (H), and b teeth (B). In order to determine if the three genes are linked, a standard testcross was done, and the offspring had the following genotypes: $$\begin{array} { l l } 48 & \text { ee Hh bb } \\36 & \text { ee hh Bb } \\400 & \text { ee Hh Bb } \\4 & \text { Ee Hh Bb } \\426 & \text { Eehh bb } \\46 & \text { Eehh Bb } \\38 & \text { Ee Hh bb } \\2 & \text { ee hh bb }\end{array}$$ What is the recombination frequency between genes E and H?

A) 40%
B) 8%
C) 92%
D) 8.4%
E) 7.4%

Question 21

What is the highest possible frequency of recombination between linked genes that can be generated by any type of crossover event?

Question 22

Genes A and B are located 10 cM from each other on a chromosome. Gene C is located 25 cM from gene A and 15 cM from gene B. Assuming that I = 0, what is the probability that the trihybrid ABC/abc will produce an AbC gamete?

A) 25%
B) 3.75%
C) 63.75%
D) 76.5%
E) 1.5%

Question 23

Construct a map of the chromosome, with the most accurate map distances, from the follow recombination frequencies between individual pairs of genes:
C - F 13%, V - F 20%, V - C 8%, S - F 4%, C - S 9%,

Question 24

Two genes, A and X, exhibit incomplete linkage. The frequency of each parental gamete (AX and ax) is 45%. What is the approximate frequency of the Ax gamete?

Question 25

Incomplete genetic linkage is far more common than complete linkage. What is the term for gametes produced when recombination shuffles the alleles of linked genes?

Question 26

Genes associated by GWAS studies have all of the following characteristics except?

A) They have a specific group of alleles that co- occur with a specific trait.
B) They have a significant probability value statistic.
C) They have a specific group of alleles that are usually identified by SNPs.
D) They are most useful when they include both genes that contribute to disease and nearby genetic markers.
E) They are all located in the same chromosomal region.

Question 27

For a given cross, the expected number of double recombinants is 18 and the observed number of double recombinants is 12. What is the coefficient of coincidence (COC)?

A) 1.50
B) 0.50
C) 0.67
D) 0.33
E) 0.30

Question 28

What is the term for chromosomes that do not reshuffle the alleles of linked genes?

Question 29

Recombination frequencies between genes can be altered by all the following except?

A) addition of a chromosomal segment outside of the two genes being studied
B) evolution
C) being the homogametic rather than the heterogametic sex
D) concentration of cofactors for DNA binding proteins
E) temperature

Question 30

Which of the following is true regarding comparison of the physical maps and recombination maps?

A) Only with recent genome sequence analysis, which compares physical and recombination maps, has it been possible to determine that recombination hotspots are distributed evenly throughout the Drosophila genome.
B) Map distances calculated by recombination frequencies can underestimate the physical distance between two genes.
C) There is a linear relationship between recombination frequency and physical distance if the genes are separated by more than 50 cM.
D) Two genes with a coldspot between them have larger recombination frequencies than predicted by their physical distances.
E) Two genes with a hotspot between them have smaller recombination frequencies than predicted by their physical distances.

Question 31

For a given cross, the expected number of double recombinants is 18 and the observed number of double recombinants is 12. What is the interference (I)?

A) 0.30
B) 1.50
C) 0.50
D) 0.67
E) 0.33

Question 32

Which of the following contributes to maintaining linkage disequilibrium in a population?

A) recombination
B) migration of individuals with new SNP haplotypes into the population
C) mutation
D) natural selection
E) having a very small distance between genes and their syntenic genetic markers

Question 33

For a given haplotype, the frequencies of alleles for gene Y are Y = 0.55 and Y' = 0.45, and the frequencies at gene Z are Z = 0.15 and Z' = 0.85. What is the predicted frequency of the YZ haplotype in a population in linkage equilibrium?

A) 0.1275
B) 0.3825
C) 0.9175
D) 0.2475
E) 0.4000

Question 34

What is observed when syntenic genes are close enough to one another that they are unable to assort independently?

Question 35

After analysis of 100 pedigrees, the Zmax from the analysis of linkage between a disease gene D and the DNA marker P was found to be - 2.5 at 0 = 0.01. Which of the following is the best interpretation of these results?

A) The evidence supports linkage of D and P at 1.0 cM.
B) The evidence indicates that D and P are not linked.
C) The evidence supports linkage of D and P at 10 cM.
D) No conclusion can be made regarding linkage of D and P.
E) The evidence supports linkage of D and P at 0.1 cM.

Question 36

After analysis of 100 pedigrees, the Zmax from the analysis of linkage between a disease gene D and the DNA marker P was found to be 3.5 at 0 = 0.25. Which of the following is the best interpretation of these results?

A) The evidence indicates that D and P are not linked.
B) The evidence supports linkage of D and P at 0.25 cM.
C) The evidence supports linkage of D and P at 2.5 cM.
D) No conclusion can be made regarding linkage of D and P.
E) The evidence supports linkage of D and P at 25 cM.

Question 37

The order of genes on a plant chromosome is A, B, and D, where A and B have a recombination frequency of 0.2, and B and D have a recombination frequency of 0.3. A pure- breeding plant that has the dominant A and D phenotypes with a recessive b phenotype is crossed to a pure- breeding plant that has the recessive a and d phenotypes with the dominant B phenotype. The resulting hybrid is crossed to a plant that has all three recessive phenotypes. Under the assumption that the value for interference in this region is zero, what percentage of each progeny type would result from a single crossover between B and D?

A) 50% AbD/ abd; 50% aBd/ abd
B) 24% ABd/ abd; 24% abD/ abd
C) 7% ABD/ abd; 7% abd/ abd
D) 12% Abd/ abd; 12% aBD/ abd
E) 9% ABD/ abd; 9% abd/ abd

Question 38

The order of the genes on a plant chromosome is A, B, C, where A and B are located 10 cM apart and B and C are located 3 cM apart. What is the probability that the trihybrid ABC/abc will produce any kind of recombinant gamete?

A) 0.30%
B) 87.30%
C) 1.27%
D) 8.73%
E) 12.70%

Question 39

What unit of physical distance between genes on a chromosome provides a convenient way to relate the recombination frequencies for linked genes with their positions and order along a chromosome?

Question 40

The Zmax from the analysis of a disease gene N and the DNA marker H was 2.5 at 0 = 0.1. Which of the following is the best interpretation of this result?

A) N and H are separated by 10 cM.
B) N and H are separated by less than 10 cM.
C) N and H are separated by more than 10 cM.
D) N and H are not linked.
E) No conclusion can be made regarding the linkage of N and H.

Question 41

Recombination frequency differs between males and females. Which sex has a higher rate of recombination, heterogametic (males) or homogametic (females)?

Question 42

The pedigrees below are for a dominant disease where individuals with the dominant disease allele (D) are affec Individuals that were alive were also screened for a polymorphic DNA marker that has six alleles identified as P P4, P5, and P6.
a) In Family B, explain why the P1 marker cannot be assumed to be transmitted with the dominant allele given there is no haplotype data for the first generation.
b) In Family A, how does the information regarding the haplotype of individuals in the first generation allow y determine the allelic phase of the disease?
"Use Figure 5.15 in Chapter 5, page 169 from main title."

Question 43

What is the Lod score?

Question 44

A chromosome with a different combination of alleles than parental that is created by crossing over between homologous chromosomes is termed .

Question 45

What would a Lod score of 3.2 tell you about genetic linkage? What information does the 0 value tell you?

Question 46

In most tests of genetic linkage, the number of double crossovers is LESS than the number expected due to what effect, which limits the number of crossovers that can occur in a short length of chromosome?

Question 47

A geneticist is mapping the chromosomes of a new fish species. These fish have genes for the dominant traits non- bioluminescent (B), ventral eyes (D), and short spikes (L) with corresponding recessive traits bioluminescent (b), dorsal eyes (d), and long spikes (l). He test- crosses one of these fish who is dominant at all th loci to determine if the three genes are linked resulting in the data shown below: a) Why are these data consistent with genetic linkage among the three genes?
b) Perform a chi- square test to determine if these data show significant deviation from the expected phenotype distribution.
c) Determine the recombination frequencies between each pair of genes.
d) Determine the coefficient of coincidence (COC) and interference (I) values for this data set.

Question 48

The specific array of alleles making up a set of linked genes on a single chromosome is called a .

Question 49

Alleles of linked genes usually segregate together during meiosis. When they don't, it is because has occurred between them.

Question 50

What is the relationship between linked genes and syntenic genes? Are syntenic genes always linked?Are linked genes always syntenic? Describe what is meant by each term.

Question 51

If there is a maximum Lod score of 4.2 at 0 = 0.31, what can you say about the linkage and the distance between two genes?

Question 52

Instead of creating a gene map along a chromosome, is a method of analysis that detects and locates the genes that, as a group, influence form or appearance.

Question 53

A geneticist is mapping the chromosomes of the newly captured gremlin. Stripe is heterozy for three linked genes with alleles Ee, Hh, and Bb, that determine if gremlins are evil (E), ha (H), and biting teeth (B). In order to determine if the three genes are linked, a standard testc was done, and the 1000 offspring had the following genotypes: Diagram the alleles on the homologous chromosomes of the heterozygous individuals with correct gene order.

Question 54

5% recombination is equal to map unit(s) (m.u.) or centimorgan(s) (cM) of distance between linked genes.

Question 55

If too little time has passed for crossing over to randomize haplotypes or if natural selection favors certain haplotypes, what would you expect to see?

Question 56

When constructing a genetic map of Zea mays, Creighton and McClintock used genetic markers as well as structural differences in the homologous copies of chromosome 9 that can be seen under the microscope. What are these structural differences called?

Question 57

How is Newton Morton's statistical method (Lod score analysis) helpful for calculating the overall probability of genetic linkage when allelic phase is unknown?

Question 58

Compare and contrast the following three DNA genetic markers: variable number tandem repeats (VNTRs), single nucleotide polymorphisms (SNPs), and restriction fragment length polymorphisms (RFLPs).

Question 59

Genes A, B, and C lie at map positions 2.5, 7.5, and 17.5, respectively. In a three- point test cross, you observed 2 double crossovers in a total of 1000 progeny. What is the interference in this region?

Question 60

Refer to this map to answer the questions:
a) What is the distance between gene E and gene F?
b) Assuming I = 0, what is the probability of no crossovers between gene D and gene E?
c) Assuming I = 0, what is the probability of no crossovers between gene E and gene F?
d) Considering both gene pairs, what is the proportion of nonrecombinant gametes?
e) What is the predicted frequency of each parental gamete (DEF/def )?
f) What is the recombination frequency between gene D and gene E?
g) What is the recombination frequency between gene E and gene F?
h) What is the frequency of two single recombinant gametes between genes D and E?
i) What is the frequency of two single recombinant gametes between genes E and F?
j) What is the frequency of each of the double- recombinant gametes, DeF and dEf?
k) Fill in the blanks below to prove that the sum of the frequencies of the eight predicted gamete genotypes is e 1.0: