Chapter 5 - Genetic Linkage and Mapping in Eukaryotes

Syntenic genes can assort independently when

A) they are very close together on a chromosome.

B) they are located on different chromosomes.

C) crossing over occurs rarely between the genes.

D) they are far apart on a chromosome and crossing over occurs frequently between the genes.

E) they are far apart on a chromosome and crossing over occurs very rarely between the genes.

D) they are far apart on a chromosome and crossing over occurs frequently between the genes.

The alleles of linked genes tend to

A) segregate together during gamete production.

B) assort independently.

C) be mutated more often than unlinked genes.

D) experience a higher rate of crossing over.

E) assort independently and show a higher rate of crossing over.

A) segregate together during gamete production.

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

A) allele combinations that are different from parental combinations.

B) parental combinations of alleles.

C) mutant alleles.

D) dominant alleles.

E) recessive alleles.

B) parental combinations of alleles

4) 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) BT/bt

B) Bt/bT

C) Bb/Tt

D) BT/Bt or bt/bT

E) B/T or b/t

B) Bt/bT

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

A) one parental allele combination occurring more frequently than another

B) two equally frequent gametes containing only parental allele combinations

C) only recombinant gametes

D) one parental allele combination occurring more frequently than another and no recombinant gametes

E) two equally frequent gametes containing only parental allele combinations and no recombinant gametes

E) two equally frequent gametes containing only parental allele combinations and no recombinant gametes

6) 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 the F1 fly can produce

C) to determine the allele combinations that a homozygous recessive fly can create

D) to determine the recombination frequency between two genes

E) to determine which alleles are dominant and which are recessive

D) to determine the recombination frequency between two genes

7) 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) 0.851

B) 0.003

C) 0.006

D) 0.500

E) 0.155

D) 0.500

8) 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) prvg/pr+vg+

B) pr+vg/prvg+

C) prpr+/vgvg+

D) prvg/prvg

E) pr+vg+/pr+vg+

B) pr+vg/prvg+

9) 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) 7.5%

B) 15%

C) 50%

D) 85%

E) 92.5%

A) 7.5%

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

A) Male Drosophila

B) Female Drosophila

C) Zea mays (corn)

D) Male Homo sapiens

E) Female Homo sapiens

A) Male Drosophila

11) 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 sequenced the DNA and was able to determine the distance between the genes.

B) He performed a three-point test cross.

C) He crossed two heterozygous individuals and was able to determine offspring genotypes from their phenotypes.

D) He crossed a heterozygous individual with a homozygous recessive individual and was able to determine progeny genotypes from their phenotypes.

E) He performed Lod score analysis to determine the distance between the genes he was studying.

D) He crossed a heterozygous individual with a homozygous recessive individual and was able to determine progeny genotypes from their phenotypes.

12) 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) 44.5

B) 11

C) 5.5

D) 89

E) 39

A) 44.5

13) 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) 44.5

B) 11

C) 5.5

D) 89

E) 39

C) 5.5

14) 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) Yes; the order is X-Z-Y.

B) Yes; the order is X-Y-Z.

C) Yes; the order is Z-X-Y.

D) No; based on this data alone, the order could be Z-Y-X or X-Y-Z.

E) No; based on this data alone, the order could be X-Z-Y or Z-X-Y.

E) No; based on this data alone, the order could be X-Z-Y or Z-X-Y.

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) test cross

B) two-point test cross

C) three-point test cross

D) chi-square analysis

E) recombination frequency (r) calculation

D) chi-square analysis

16) 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) 100

B) 200

C) 250

D) 500

E) 750

C) 250

17) A geneticist is mapping the chromosomes of the newly captured gremlin. Stripe is heterozygous for three linked genes with alleles Ee, Hh, and Bb, that determine if gremlins are evil (E), have hair (H), and biting teeth (B). In order to determine if the three genes are linked, a standard testcross was done, and the 1000 offspring had the following genotypes:

48 ee Hh bb

36 ee hh Bb

400 ee Hh Bb

4 Ee Hh Bb

426 Ee hh bb

46 Ee hh Bb

38 Ee Hh bb

2 ee hh bb

What is the recombination frequency between genes E and H?

A) 8%

B) 92%

C) 7.4%

D) 8.4%

E) 40%

A) 8%

18) A geneticist is mapping the chromosomes of the newly captured gremlin. Stripe is heterozygous for three linked genes with alleles Bb, Ee, and Hh that determine if gremlins have biting teeth (B), are evil (E), and have hair (H). In order to determine if the three genes are linked, a standard testcross was done, and the 1000 offspring had the following genotypes:

48 bb ee Hh

36 Bb ee hh

400 Bb ee Hh

4 Bb Ee Hh

426 bb Ee hh

46 Bb Ee hh

38 bb Ee Hh

2 bb ee hh

What is the recombination frequency between genes E and B?

A) 9.4%

B) 10.0%

C) 9.0%

D) 8.4%

E) 42.6%

B) 10.0%

19) 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) 4

B) 8

C) 16

D) 20

E) 24

C) 16

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

A) two recombinant genotypes, more frequent than expected by independent assortment

B) four recombinant genotypes, more 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) six recombinant genotypes, less frequent than expected by independent assortment

E) six recombinant genotypes, less frequent than expected by independent assortment

21) 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) 0.33

B) 0.50

C) 0.30

D) 0.67

E) 1.50

D) 0.67

22) 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) 0.33

B) 0.50

C) 0.30

D) 0.67

E) 1.50

A) 0.33

23) 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) 76.5%

B) 63.75%

C) 25%

D) 1.5%

E) 3.75%

D) 1.5%

24) 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) 1.27%

C) 8.73%

D) 87.30%

E) 12.70%

E) 12.70%

25) 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) 24% ABd/ abd; 24% abD/ abd

B) 7% ABD/ abd; 7% abd/ abd

C) 12% Abd/ abd; 12% aBD/ abd

D) 50% AbD/ abd; 50% aBd/ abd

E) 9% ABD/ abd; 9% abd/ abd

C) 12% Abd/ abd; 12% aBD/ abd

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

A) There is a linear relationship between recombination frequency and physical distance if the genes are separated by more than 50 cM.

B) 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.

C) Map distances calculated by recombination frequencies can underestimate the physical distance between two genes.

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.

C) Map distances calculated by recombination frequencies can underestimate the physical distance between two genes

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

A) temperature

B) concentration of cofactors for DNA binding proteins

C) being the homogametic rather than the heterogametic sex

D) evolution

E) addition of a chromosomal segment outside of the two genes being studied

E) addition of a chromosomal segment outside of the two genes being studied

28) 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) 0.2475

B) 0.1275

C) 0.9175

D) 0.3825

E) 0.4000

D) 0.3825

32) 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 specific group of alleles that are usually identified by SNPs.

C) They have a significant probability value statistic.

D) They are all located in the same chromosomal region.

E) They are most useful when they include both genes that contribute to disease and nearby genetic markers.

D) They are all located in the same chromosomal region.

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

A) migration of individuals with new SNP haplotypes into the population

B) mutation

C) recombination

D) natural selection

E) having a very small distance between genes and their syntenic genetic markers

C) recombination

29) 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 θ = 0.25. Which of the following is the best interpretation of these results?

A) No conclusion can be made regarding linkage of D and P.

B) The evidence supports linkage of D and P at 25 cM.

C) The evidence supports linkage of D and P at 2.5 cM.

D) The evidence supports linkage of D and P at 0.25 cM.

E) The evidence indicates that D and P are not linked.

B) The evidence supports linkage of D and P at 25 cM.

30) 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 θ = 0.01. Which of the following is the best interpretation of these results?

A) No conclusion can be made regarding linkage of D and P.

B) The evidence supports linkage of D and P at 10 cM.

C) The evidence supports linkage of D and P at 1.0 cM.

D) The evidence supports linkage of D and P at 0.1 cM.

E) The evidence indicates that D and P are not linked.

E) The evidence indicates that D and P are not linked.

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

A) N and H are not linked.

B) N and H are separated by 10 cM.

C) N and H are separated by more than 10 cM.

D) N and H are separated by less than 10 cM.

E) No conclusion can be made regarding the linkage of N and H.

E) No conclusion can be made regarding the linkage of N and H.

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

genetic linkage

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

parental chromosomes

3) 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?

nonparental or recombinant gametes

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

50%

5) 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?

5%

6) Construct a map of the chromosome, with the most accurate map distances, from the following recombination frequencies between individual pairs of genes:

C - F 13%, V - F 20%, V - C 8%, S - F 4%, C - S 9%,

(V)-----8 cM-----(C)------9 cM------(S)---4 cM---(F). Due to interference, the map distances calculated between genes that are far apart are less accurate than those for genes that are closer together. Therefore, smaller recombination frequencies must be used to find all of the distances for the most accurate map.

7) 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?

map unit (m.u.) or centimorgan (cM)

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?

60%

9) A geneticist is mapping the chromosomes of the newly captured gremlin. Stripe is heterozygous for three linked genes with alleles Ee, Hh, and Bb, that determine if gremlins are evil (E), have hair (H), and biting teeth (B). In order to determine if the three genes are linked, a standard testcross was done, and the 1000 offspring had the following genotypes:

48 ee Hh bb

36 ee hh Bb

400 ee Hh Bb

4 Ee Hh Bb

426 Ee hh bb

46 Ee hh Bb

38 Ee Hh bb

2 ee hh bb

Diagram the alleles on the homologous chromosomes of the heterozygous individuals with the correct gene order.

hEb

10) 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?

interference

11) 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?

cytological markers

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

homogametic (females)

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

linked and 31 cm apart

14) 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?

linkage disequilibrium

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

recombinant chromosome

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

crossing over

3) 5% recombination is equal to ________ map unit(s) (m.u.) or centimorgan(s) (cM) of distance between linked genes.

5

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

haplotype

5) 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.

genome-wide association studies (WAGS)