Unit 10: PCR & Molecular markers - Practice Quiz

1 What does the abbreviation PCR stand for?

2 Which enzyme is commonly used in PCR to synthesize new DNA strands?

3 What is the correct order of the three main steps in a single PCR cycle?

4 During the denaturation step of PCR, the temperature is typically raised to about:

5 What are primers in a PCR reaction?

6 What does the abbreviation RAPD stand for in molecular marker analysis?

7 What does the abbreviation RFLP stand for?

8 Which technique is used to separate DNA fragments based on their size?

9 In gel electrophoresis, DNA molecules move towards which electrode?

10 Which stain is commonly used to visualize DNA bands in an agarose gel?

11 What does the abbreviation SSR stand for in molecular markers?

12 What does the abbreviation AFLP stand for?

13 Which of the following molecules provides the building blocks for new DNA strands during PCR?

14 Which instrument is used to carry out PCR by rapidly cycling through different temperatures?

15 A DNA molecular marker is best described as:

16 Which molecular marker technique requires prior knowledge of the DNA sequence to design specific primers?

17 The annealing step in PCR allows which of the following to occur?

18 What is loaded alongside DNA samples on a gel to indicate fragment sizes?

19 The term polymorphism in molecular marker analysis refers to:

20 Which of the following is a PCR-based molecular marker?

21 A researcher uses RAPD markers to analyze genetic diversity among plant accessions. Which feature makes RAPD suitable when no prior sequence information is available?

22 During RFLP analysis of plant DNA, a point mutation removes a restriction site. What is the expected effect on the resulting banding pattern?

23 Two plant varieties show SSR (microsatellite) alleles of 180 bp and 192 bp at the same locus. If the repeat unit is a dinucleotide, what is the difference in repeat number between them?

24 Which property of SSR (microsatellite) markers makes them preferred for cultivar identification over RAPD?

25 In AFLP analysis, plant genomic DNA is first digested and then adaptors are ligated. What is the immediate purpose of ligating adaptors to the restriction fragments?

26 A dominant marker such as RAPD cannot distinguish between which two genotypes at a locus?

27 While designing a PCR to amplify a plant marker region, the melting temperatures of the two primers differ by . What is the most likely consequence?

28 A plant DNA sample gives smeared, non-specific bands in RAPD even after repeating the reaction. Which adjustment is most appropriate to improve specificity?

29 SCAR markers are often developed from RAPD markers. What is the main advantage of converting a RAPD band into a SCAR marker?

30 In agarose gel electrophoresis of amplified plant DNA markers, smaller DNA fragments migrate:

31 A study compares 50 plant genotypes and requires markers spread across the whole genome, generated quickly and cheaply without prior sequence data. Which marker system best fits these constraints?

32 If a marker is described as codominant, what can be directly inferred from its banding pattern in a plant?

33 A PCR reaction for a plant SSR marker produces no band, but the positive control works. The template DNA has an ratio of 1.4. What is the most likely problem?

34 Which step of the PCR cycle is directly responsible for separating the double-stranded plant template DNA?

35 For phylogenetic analysis of plant genetic distance, marker data are often converted into a similarity matrix. A Jaccard coefficient of 0 between two accessions indicates:

36 Why are SNP markers increasingly favored for high-throughput genotyping of plant DNA?

37 In a RAPD gel, one primer amplifies 8 bands across the sample, of which 3 are polymorphic among genotypes. What is the percentage polymorphism for this primer?

38 A researcher wants to fine-map a disease-resistance gene and needs a marker tightly linked to it and easily transferable across labs. Which marker type is most appropriate?

39 During AFLP, the use of two restriction enzymes (a rare cutter and a frequent cutter) primarily helps to:

40 A dendrogram built from plant marker data groups two accessions on the same terminal branch with a very short branch length. This indicates that the two accessions are:

41 A researcher performs RAPD analysis on two plant cultivars using a single 10-mer primer. Cultivar A shows a band at 800 bp that is absent in Cultivar B. Upon repeating the reaction with a slightly lower annealing temperature, several new faint bands appear in both cultivars. What is the most likely explanation for the new bands?

42 In an RFLP analysis of a plant population, a restriction enzyme recognition site is lost in some individuals due to a point mutation. On a Southern blot with a probe spanning the region, what banding change would you expect in individuals homozygous for the mutation compared to wild type?

43 A codominant SSR (microsatellite) marker is scored in an F2 plant population. A given locus in the parents shows alleles of 150 bp and 160 bp. Which banding pattern in an F2 individual indicates heterozygosity?

44 During AFLP analysis, genomic DNA is digested with a rare cutter (EcoRI) and a frequent cutter (MseI), followed by adapter ligation and selective amplification. Why are two enzymes of differing cutting frequency used together?

45 A dominant marker (e.g., RAPD) and a codominant marker (e.g., SSR) are compared for mapping a recessive disease-resistance gene in an F2 population. Why is the codominant marker generally more informative?

46 You genotype 4 SSR loci that are all unlinked, each with 2 alleles at equal frequency in a random-mating plant population. What is the probability that two unrelated individuals share the identical genotype at all four loci? (Assume each locus genotype probability follows simplification with match probability of per locus.)

47 A SCAR marker is developed from a polymorphic RAPD band. What is the primary advantage of converting a RAPD marker into a SCAR marker?

48 In a CAPS (Cleaved Amplified Polymorphic Sequence) analysis, a 500 bp region is PCR-amplified from two alleles and then digested with a restriction enzyme. Allele 1 is cut into 200 bp + 300 bp fragments; allele 2 is uncut. This pattern indicates that the polymorphism is:

49 A researcher observes that an SSR locus amplifies a main allele band accompanied by a ladder of smaller bands (stutter bands). What is the molecular cause of these stutter bands?

50 Two plant DNA samples give identical RAPD profiles across 15 primers. A colleague concludes they are genetically identical clones. What is the most valid criticism of this conclusion?

51 In marker-assisted selection, a molecular marker is 5 cM from the target gene. What is the approximate probability that a recombination event separates the marker from the gene in a single meiosis?

52 A dominant AFLP marker segregates in an F2 population. In a 3:1 (band present : band absent) ratio, what fraction of the band-present individuals are expected to be heterozygous?

53 When analyzing plant DNA, ISSR markers use primers targeting the region between two microsatellites. Why do ISSR primers not require prior sequence knowledge of the target genome, unlike SSR markers?

54 A genetic diversity study computes Jaccard similarity from binary marker data. Why is the Jaccard coefficient often preferred over simple matching for dominant markers like RAPD and AFLP?

55 A CAPS marker fails to distinguish two alleles even though a SNP is known to exist between them. The SNP does not fall within any available enzyme's recognition site. Which technique best rescues this situation without sequencing every sample?

56 In a bulked segregant analysis (BSA) for a plant disease resistance gene, DNA from resistant and susceptible individuals is pooled into two bulks and screened with markers. A marker showing a band only in the resistant bulk most likely indicates the marker is:

57 A polymorphism information content (PIC) value is calculated for two SSR loci. Locus X has 2 alleles at frequencies 0.5/0.5; Locus Y has 4 alleles at 0.25 each. Which locus is more informative and why?

58 During PCR of plant DNA for marker analysis, no amplification occurs despite good template quality. Adding PVP or BSA to subsequent reactions restores amplification. The original failure was most likely caused by:

59 A phylogenetic dendrogram built from AFLP data shows one accession clustering far from morphologically similar accessions. Before concluding it is genetically distinct, what is the most important check?

60 SNP genotyping is increasingly favored over SSRs for large-scale plant analysis. Which combination of properties best explains this shift?