Gene mapping: genetic and physical MCQs With Answer

Introduction: Gene mapping—both genetic and physical—is a cornerstone of modern bioinformatics and pharmacogenomics. For M.Pharm students, understanding how genes are localized on chromosomes and how physical DNA maps are constructed is essential for drug target identification, elucidating genetic causes of adverse drug reactions, and for translational research. This collection of multiple-choice questions (MCQs) covers mapping principles (recombination, centiMorgans, LOD scores, interference), mapping functions (Haldane, Kosambi), experimental approaches (linkage analysis, radiation hybrids, FISH, restriction and clone-based mapping), and marker systems (SNPs, SSRs, RFLPs). Answers are included to aid focused revision for exams and research-driven problem solving.

Q1. What is the correct definition of a genetic map?

• A physical representation of DNA sequence in base pairs
• A map based on recombination frequencies that shows relative positions of loci
• A schematic of chromatin folding in the nucleus
• An alignment of assembled contigs to chromosomes

Correct Answer: A map based on recombination frequencies that shows relative positions of loci

Q2. How is recombination frequency (RF) calculated in a two-point genetic cross?

• Number of parental progeny divided by total progeny × 100
• Number of recombinant progeny divided by total progeny × 100
• Number of double crossovers divided by total progeny × 100
• Number of linked progeny divided by total progeny × 100

Correct Answer: Number of recombinant progeny divided by total progeny × 100

Q3. Which statement best describes the Kosambi mapping function?

• It converts recombination fractions to map distances assuming no interference
• It converts recombination fractions to map distances while accounting for crossover interference
• It provides a physical to genetic distance conversion in base pairs
• It is used exclusively for sex-linked loci mapping

Correct Answer: It converts recombination fractions to map distances while accounting for crossover interference

Q4. One centiMorgan (cM) is best defined as:

• The physical length of 1,000 base pairs on a chromosome
• The distance over which 1% of meiotic products are recombinant
• The average size of a bacterial artificial chromosome (BAC)
• The probability of mutation per generation at a locus

Correct Answer: The distance over which 1% of meiotic products are recombinant

Q5. Approximately how many base pairs correspond to 1 cM in the human genome on average?

• About 1 kilobase (1 kb)
• About 1 megabase (1 Mb)
• About 100 megabases (100 Mb)
• About 1 gigabase (1 Gb)

Correct Answer: About 1 megabase (1 Mb)

Q6. What is the main advantage of a three-point cross over multiple two-point crosses?

• It eliminates the need to score recombinants
• It allows simultaneous determination of gene order and double crossover frequency
• It provides direct physical distances in base pairs
• It measures mutation rates between loci

Correct Answer: It allows simultaneous determination of gene order and double crossover frequency

Q7. Which physical mapping technique can localize a DNA sequence to a chromosomal band using fluorescently labeled probes?

• Restriction fragment length polymorphism (RFLP) mapping
• Fluorescence in situ hybridization (FISH)
• Two-point linkage analysis
• Bulk segregant analysis

Correct Answer: Fluorescence in situ hybridization (FISH)

Q8. Which molecular marker is most abundant and commonly used for high-resolution association studies?

• Restriction fragment length polymorphism (RFLP)
• Short tandem repeat (STR/SSR)
• Single nucleotide polymorphism (SNP)
• Isozyme polymorphism

Correct Answer: Single nucleotide polymorphism (SNP)

Q9. Radiation hybrid (RH) mapping determines marker order by:

• Measuring recombination frequencies in meiosis
• Assessing co-retention of markers in irradiated cell hybrids
• Sequencing overlapping clones for contig assembly
• Using restriction enzyme digestion patterns

Correct Answer: Assessing co-retention of markers in irradiated cell hybrids

Q10. In positional cloning (map-based cloning), the initial step after linkage mapping is typically:

• Whole-genome sequencing of the organism
• Construction and screening of genomic clones to build a physical contig around the candidate region
• Measuring gene expression by microarrays
• Performing GWAS on an unrelated population

Correct Answer: Construction and screening of genomic clones to build a physical contig around the candidate region

Q11. Which approach primarily leverages linkage disequilibrium across unrelated individuals to map disease-associated variants?

• Classical linkage analysis using pedigrees
• Genome-wide association study (GWAS)
• Radiation hybrid mapping
• Chromosome walking with BACs

Correct Answer: Genome-wide association study (GWAS)

Q12. Contig assembly in physical mapping refers to:

• Ordering genes by recombination frequency
• Joining overlapping cloned DNA fragments to form a continuous stretch of sequence
• Measuring crossover interference across the genome
• Labeling chromosomes for FISH analysis

Correct Answer: Joining overlapping cloned DNA fragments to form a continuous stretch of sequence

Q13. A LOD score of 3.0 indicates approximately what odds in favor of linkage?

• 10:1
• 100:1
• 1,000:1
• 10,000:1

Correct Answer: 1,000:1

Q14. Crossover interference is quantitatively defined as:

• The ratio of single crossovers to double crossovers
• 1 minus the observed number of double crossovers divided by the expected number of double crossovers
• The recombination fraction between adjacent markers
• The physical distance between two genes in base pairs

Correct Answer: 1 minus the observed number of double crossovers divided by the expected number of double crossovers

Q15. What is the maximum recombination frequency observed between two independently assorting loci?

• 25%
• 50%
• 75%
• 100%

Correct Answer: 50%

Q16. Which mapping approach produces a map that reflects recombination distances rather than physical nucleotide distances?

• Genetic linkage mapping
• Optical mapping
• BAC-based physical mapping
• Whole-genome shotgun assembly

Correct Answer: Genetic linkage mapping

Q17. Which physical mapping method provides long-range ordered restriction maps by imaging single DNA molecules stretched on a surface?

• Fluorescence in situ hybridization (FISH)
• Optical mapping
• Sanger shotgun sequencing
• RNA-seq based mapping

Correct Answer: Optical mapping

Q18. Compared to YACs, bacterial artificial chromosomes (BACs) are generally preferred in physical mapping because:

• BACs can carry much larger inserts than YACs
• BACs have lower rates of chimerism and greater stability in bacteria
• BACs are eukaryotic and replicate in yeast
• BACs are single-stranded vectors used for FISH

Correct Answer: BACs have lower rates of chimerism and greater stability in bacteria

Q19. Which statistic is commonly used to quantify linkage disequilibrium and is preferred for power in association tests?

• Recombination frequency (RF)
• D’ (Lewontin’s D prime)
• r² (squared correlation coefficient)
• LOD score

Correct Answer: r² (squared correlation coefficient)

Q20. The Haldane mapping function differs from Kosambi because Haldane:

• Accounts for crossover interference explicitly
• Assumes no interference between crossovers
• Converts physical distance directly to base pairs
• Is only valid for sex chromosomes

Correct Answer: Assumes no interference between crossovers

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