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Genetics: An Integrated Approach (Sanders) Chapter 5 Genetic Linkage and Mapping in Eukaryotes 5.1 Multiple-Choice Questions 1) 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. Answer: D Section: 5.1 Skill: Knowledge/Comprehension 2) 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. Answer: A Section: 5.1 Skill: Knowledge/Comprehension 3) 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. Answer: B Section: 5.1 Skill: Knowledge/Comprehension 4) The syntenic genes A and Z are linked. A cross between two parents, AAZZ and aazz, produces F1 progeny with the AaZz genotype. What are the possible arrangements of alleles on the F1 progeny's chromosomes? A) AZ/az B) Az/aZ C) Aa/Zz D) AZ/Az or az/aZ E) A/Z or a/z Answer: A Section: 5.1 Skill: Knowledge/Comprehension

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5) In a dihybrid cross exhibiting complete genetic linkage, what would you expect? 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 Answer: E Section: 5.1 Skill: Knowledge/Comprehension 6) In a two-point test-cross analysis, a dihybrid F1 fly is crossed to a A) pure-breeding mate with a dominant phenotype (AABB). B) pure-breeding mate with a recessive phenotype (aabb). C) heterozygote mate (AaBb). D) mate that is dominant for one gene and recessive for the other (AAbb or aaBB). E) second dihybrid F1 fly (sibling cross). Answer: B Section: 5.1 Skill: Knowledge/Comprehension 7) 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. Answer: E Section: 5.2 Skill: Application/Analysis 8) 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 Answer: D Section: 5.2 Skill: Knowledge/Comprehension

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9) Incomplete genetic linkage of three genes in a trihybrid produces eight genetically different gamete genotypes. How many genotypes are produced in a four-gene cross with incomplete genetic linkage? A) 4 B) 8 C) 16 D) 20 E) 24 Answer: C Section: 5.2 Skill: Application/Analysis 10) 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 chance B) four recombinant genotypes, more frequent than expected by chance C) six recombinant genotypes, more frequent than expected by chance D) four recombinant genotypes, less frequent than expected by chance E) six recombinant genotypes, less frequent than expected by chance Answer: E Section: 5.2 Skill: Knowledge/Comprehension 11) For a given cross, the expected number of double recombinants is 20 and the observed number of double recombinants is 15. What is the coefficient of coincidence (c)? A) 0.25 B) 1.33 C) 20 D) 0.75 E) 15 Answer: D Section: 5.3 Skill: Application/Analysis 12) For a given cross, the expected number of double recombinants is 20 and the observed number of double recombinants is 15. What is the interference calculation (I)? A) 0.25 B) 1.33 C) 20 D) 0.75 E) 15 Answer: A Section: 5.3 Skill: Application/Analysis

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13) Where does crossing over occur? A) at the centromeres B) at the telomeres C) at nodules that occur randomly at "hotspots" along the synaptonemal complex D) at nodules that occur in specific, evenly spaced locations along a chromosome E) at both the centromeres and telomeres Answer: C Section: 5.4 Skill: Knowledge/Comprehension 14) When does recombination occur? A) before DNA replication B) at the two-strand stage, when each member of a homologous chromosome pair is composed of two sister chromatids, and before DNA replication C) at the four-strand stage, when each member of a homologous chromosome pair is composed of two sister chromatids, and before DNA replication D) at the two-strand stage, when the sister chromatids have been separated, and after DNA replication E) at the four-strand stage, when each member of a homologous chromosome pair is composed of two sister chromatids, and after DNA replication Answer: E Section: 5.4 Skill: Knowledge/Comprehension 15) Which type of crossover event produces no recombinant chromosomes? A) single-strand crossover B) two-strand double crossover C) three-strand double crossover D) four-strand double crossover E) None of the above; all crossover events produce recombinant chromosomes. Answer: B Section: 5.4 Skill: Knowledge/Comprehension 16) Which type of crossover event produces two parental and two recombinant chromosomes in gametes? A) single-strand crossover B) two-strand double crossover C) three-strand double crossover D) four-strand double crossover E) None of the above; all crossover events produce only recombinant chromosomes. Answer: C Section: 5.4 Skill: Knowledge/Comprehension

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17) Which type of crossover event produces all four recombinant chromosomes? A) single-strand crossover B) two-strand double crossover C) three-strand double crossover D) four-strand double crossover E) None of the above; all crossover events produce a combination of parental and recombinant chromosomes. Answer: D Section: 5.4 Skill: Knowledge/Comprehension 18) For a given haplotype, the frequencies of alleles for gene Y are Y = 0.65 and Y' = 0.35, and the frequencies at gene Z are Z = 0.25 and Z' = 0.75. What is the predicted frequency of the Y'Z' haplotype? A) 0.16 B) 0.26 C) 0.74 D) 0.84 E) 1.1 Answer: B Section: 5.4 Skill: Synthesis/Evaluation 19) Intragenic recombination can be detected A) based on recombination between homologs carrying different mutant alleles. B) by the recovery of 100% double-mutant chromosomes. C) by the recovery of both wild-type and double-mutant chromosomes. D) based on recombination between homologs with different mutant alleles and recovery of 100% double-mutant chromosomes. E) based on recombination between homologs with different mutant alleles and recovery of both wildtype and double-mutant chromosomes. Answer: E Section: 5.4 Skill: Knowledge/Comprehension 20) The Huntington disease (HD) allele was discovered A) by mapping it to blood enzyme genes, based on Lod scores of -2. B) through pedigree analysis alone. C) by linkage to a DNA genetic marker, D4S10 with a Lod score of 8.53. D) through mapping to known homologs in other organisms such as mice. E) through direct sequencing of mutations identified by SNPs. Answer: C Section: 5.8 Skill: Knowledge/Comprehension

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5.2 Short-Answer Questions 1) What is observed when syntenic genes are so close to one another that they are unable to assort independently? Answer: genetic linkage Section: 5.1 Skill: Application/Analysis 2) Chromosomes that do not reshuffle the alleles of linked genes are identified as what? Answer: parental chromosomes Section: 5.1 Skill: Application/Analysis 3) Recombination analysis allows for the mapping of genes because the frequency of crossing over is proportional to what? Answer: distance between genes Section: 5.1 Skill: Knowledge/Comprehension 4) What organism exhibits complete genetic linkage, meaning there is no recombination between homologous chromosomes? Answer: male Drosophila or Diptera Section: 5.1 Skill: Knowledge/Comprehension 5) Incomplete genetic linkage is far more common than complete linkage. Recombination between the homologs produces what type(s) of gametes? Answer: parental and nonparental Section: 5.1 Skill: Knowledge/Comprehension 6) 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? Answer: 5% Section: 5.1 Skill: Application/Analysis 7) There are three genes located in the gene order A-B-C on a chromosome. Would you expect the recombination frequency to be higher between A and B or A and C? Answer: higher from A to C (farther apart) Section: 5.1 Skill: Application/Analysis 8) Bateson and Punnett saw early evidence of gene linkage. What terms did they use to describe genes that remained together frequently and the loss of parental alleles in favor of new, nonparental phenotypes in the F2 progeny? Answer: coupling and repulsion Section: 5.1 Skill: Knowledge/Comprehension 6 Copyright © 2013 Pearson Education, Inc.

9) Morgan realized that Bateson and Punnett had detected genetic linkage but couldn't explain their results because they performed the wrong cross. What type of cross did Morgan use for the analysis of genetic linkage of autosomal genes in Drosophila? Answer: two-point test-cross analysis Section: 5.1 Skill: Knowledge/Comprehension 10) In a two-point test-cross analysis, what are the "two points" being tested? Answer: the two genes Section: 5.1 Skill: Knowledge/Comprehension 11) What unit of physical distance between genes on a chromosome provides a convenient way to link the recombination frequencies for linked genes with their positions and order along a chromosome? Answer: map unit (m.u.) or centimorgan (cM) Section: 5.2 Skill: Knowledge/Comprehension 12) What type of test would you use to determine the relative order of more than two genes? Answer: three-point test-cross Section: 5.3 Skill: Knowledge/Comprehension 13) 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? Answer: interference (I) Section: 5.3 Skill: Knowledge/Comprehension

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14) Refer to this map to answer the following 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 equal to 1.0: _______ + _______ + _______ + _______ + _______ + _______ + _______ + _______ = 1 DEF def Def dEF DEf deF DeF dEf Answer: a) 12 cM b) 92% c) 88% d) (0.92)(0.88) = 0.8096 e) (0.5)(0.8096) = 0.4048 f) 8% g) 12% h) (0.08)(0.88)(0.5) = 0.0352 i) (0.12)(0.92)(0.5) = 0.0552 j) (0.08)(0.12)(0.5) = 0.0048 k) 0.4048 + 0.048 + 0.0352 + 0.0352 + 0.0552 + 0.0552 + 0.0048 + 0.0048 = 1 Section: 5.3 Skill: Synthesis/Evaluation 15) 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? Answer: cytological markers Section: 5.4 Skill: Knowledge/Comprehension

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16) What is the highest possible frequency of recombination between linked genes that can be generated by any type of crossover event? Answer: 50% Section: 5.4 Skill: Knowledge/Comprehension 17) Does recombination frequency between linked genes increase as the distance between genes gets larger or smaller? Answer: larger Section: 5.4 Skill: Knowledge/Comprehension 18) Recombination frequency differs between males and females. Which sex has a higher rate of recombination, heterogametic (males) or homogametic (females)? Answer: homogametic (females) Section: 5.4 Skill: Knowledge/Comprehension 19) If there is a maximum Lod score of 4.2 at = 0.31, what can you say about the linkage and the distance between two genes? Answer: linked and 31 cM apart Section: 5.5 Skill: Application/Analysis 20) If too little time has passed for crossing over to randomize haplotypes or if natural selection favors certain haplotypes, what type of linkage would you expect to see? Answer: linkage disequilibrium Section: 5.6 Skill: Knowledge/Comprehension 21) Ascospores in yeast are not arranged in a particular order. Thus, the four haploid ascospores contained within a yeast ascus are known as what? Answer: unordered tetrad Section: 5.7 Skill: Knowledge/Comprehension 5.3 Fill-in-the-Blank Questions 1) The alleles of syntenic genes can be reshuffled by crossing over between homologous chromosomes to produce ________. Answer: recombinant chromosomes Section: 5.1 Skill: Knowledge/Comprehension 2) The tendency of alleles of linked genes to segregate together during meiosis can be broken by ________. Answer: crossing over Section: 5.1 Skill: Knowledge/Comprehension 9 Copyright © 2013 Pearson Education, Inc.

3) Genetic linkage can be spotted by comparing the observed frequencies of ________ with the frequencies expected (assuming independent assortment). Answer: gamete genotypes/progeny phenotypes Section: 5.1 Skill: Knowledge/Comprehension 4) In early genetic analysis, 5% recombination is equal to ________ map unit(s) (m.u.) or centimorgan(s) (cM) of distance between linked genes. Answer: 5 Section: 5.2 Skill: Application/Analysis 5) The specific array of alleles making up a set of linked genes on a single chromosome is called a ________. Answer: haplotype Section: 5.6 Skill: Knowledge/Comprehension 5.4 Essay Questions 1) What is the relationship between linked genes and syntenic genes? Are syntenic genes always linked, or are linked genes always syntenic? Describe what is meant by each term. Answer: Linked genes are always inherited together with no independent assortment. Syntenic genes are genes found on the same chromosome. Linked genes are always found on the same chromosome, but they are unable to sort independently because there is no crossing over observed between these two genes. Syntenic genes can be unlinked, and their alleles will assort independently, if they are far enough apart on the chromosome for crossing over to generate independent assortment of the alleles. Section: 5.1 Skill: Synthesis/Evaluation 2) The mapping of the human genome in the mid-1980s was integral for identifying new human genetic markers because of the identification of what types of polymorphic DNA markers? Answer: SNPs and restriction fragments Section: 5.5 Skill: Synthesis/Evaluation Gene-mapping methods that have been successfully used in model organisms are difficult to apply to human gene mapping, due to the fewer number of offspring and the lack of controlled matings. 3) Describe why allelic phase is a major obstacle in mapping human genes. Answer: Allelic phase is the arrangement of different alleles of linked genes on homologous parental chromosomes. Allelic phase is required for genetic linkage analysis because you need to know which alleles are unique to "parental" and "recombinant" gametes. Section: 5.5 Skill: Synthesis/Evaluation

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4) How is Newton Morton's statistical method helpful for calculating the overall probability of genetic linkage when allelic phase is unknown? Answer: Morton's method determines whether genetic linkage exists between genes for which allelic phase is unknown by comparing the likelihood of obtaining the genotypes and phenotypes observed in a pedigree if two genes are linked versus the likelihood of getting the same pedigree structure if the genes assort independently. This approach assesses the probability of genetic linkage between two genes at a time and compares the probability of genetic linkage to the probability of independent assortment of the genes. Section: 5.5 Skill: Synthesis/Evaluation 5) What is the Lod score? Answer: The ratio of these two likelihoods gives the "odds" of genetic linkage, and the Logarithm of the odds ratio generates the Lod score, a statistical value representing the probability of genetic linkage between two genes. A Lod score is a statistic that can attain significance favoring genetic linkage if the probability of genetic linkage is sufficiently greater than the probability of independent assortment, or significance against genetic linkage if the probability of independent assortment is sufficiently greater than the linkage probability. Lod scores can be interpreted for individual families, or they can be added together for as many families as are analyzed. Section: 5.5 Skill: Synthesis/Evaluation 6) What would a Lod score of 3.2 tell you about genetic linkage? What information does the Θ value tell you? Answer: Scores of greater than 3.0 provide evidence of genetic linkage. Θ values that correspond to a significant Lod score indicate an approximate distance (in cM) between linked genes. Section: 5.5 Skill: Synthesis/Evaluation 7) Describe the three types of tetrads. Answer: Parental ditypes (PD) contain four haploid cells with the same alleles seen in the parental class. Nonparental ditypes (NPD) contain four recombinant haploid cells because the two parental alleles have recombined to form a nonparental combination of alleles. Tetratype tetrads (TT) contain four different kinds of haploid cells: two parental spores and two recombinant spores. When two genes are not linked, tetratypes arise when a crossover occurs between one of the two genes and its centromere. Section: 5.7 Skill: Synthesis/Evaluation

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Tetrad analysis can be used to identify genetic linkage in haploid eukaryotes. Parental and recombinant gametes contained in an ascus can be analyzed to map genes. 8) What ratios of these three tetrads would you expect to see if two genes are linked or unlinked? Why is one type of tetrad more or less common? Answer: If two genes are linked, you will see that PD > TT > NPD. PD tetrads are most common; they are produced when no crossover occurs between genes and when two-strand double crossover takes place. TT tetrads are less frequent than PD; they occur when single crossovers or three-strand double crossovers take place. NPD tetrads are least frequent; they form only when four-strand double crossover occurs. If PD = NPD, then the two genes are unlinked. This ratio indicates that either the genes are located on different chromosomes or they are syntenic but very far apart. Section: 5.7 Skill: Synthesis/Evaluation 9) The products of meiosis yield the following results: PD = 1200 TT = 750 NPD = 50 What is the recombination frequency? Answer: RF = [(NPD + 1/...