DNA fingerprinting techniques for herbal identification MCQs With Answer

Introduction: DNA fingerprinting techniques are essential tools in modern herbal identification, ensuring authenticity, safety, and quality of herbal medicines. This blog offers focused multiple-choice questions tailored for M.Pharm students studying Herbal and Cosmetic Analysis (MPA 204T). The questions cover core molecular methods—PCR-based markers (RAPD, ISSR, SSR), DNA barcoding (rbcL, matK, ITS), SNP analysis, AFLP, RFLP, and next-generation sequencing approaches—along with practical issues like DNA extraction from processed herbal materials, primer design, data interpretation, and database use. These MCQs reinforce conceptual understanding and analytical skills needed for forensic identification, detection of adulteration, and research applications in phytopharmacognosy.

Q1. Which DNA marker system is most prone to reproducibility issues due to sensitivity to PCR conditions, yet is simple and inexpensive for screening herbal samples?

• Simple Sequence Repeat (SSR)
• AFLP (Amplified Fragment Length Polymorphism)
• RAPD (Random Amplified Polymorphic DNA)
• Single Nucleotide Polymorphism (SNP)

Correct Answer: RAPD (Random Amplified Polymorphic DNA)

Q2. Which barcode region is most commonly recommended as a core plastid marker for plant identification and widely used in herb authentication databases?

• COI (cytochrome oxidase I)
• matK
• ITS2
• 16S rRNA

Correct Answer: matK

Q3. Which technique combines restriction digestion with PCR-amplified fragments to reveal polymorphisms and is useful when sequence variation creates restriction site differences?

• PCR-RFLP (Restriction Fragment Length Polymorphism)
• ISSR (Inter Simple Sequence Repeat)
• RAPD
• SSR genotyping

Correct Answer: PCR-RFLP (Restriction Fragment Length Polymorphism)

Q4. What is the principal advantage of SSR (microsatellite) markers for herbal authentication compared with RAPD?

• SSR markers require no prior sequence information
• SSR markers provide co-dominant, highly reproducible, and multi-allelic data
• SSR markers are cheaper and faster than RAPD
• SSR markers work best on highly degraded DNA

Correct Answer: SSR markers provide co-dominant, highly reproducible, and multi-allelic data

Q5. Which DNA region is most suitable for differentiating closely related plant species and often used as an internal transcribed spacer barcode?

• rbcL
• matK
• ITS (Internal Transcribed Spacer)
• trnL intron

Correct Answer: ITS (Internal Transcribed Spacer)

Q6. AFLP is particularly valuable in herbal identification because it:

• Requires species-specific primers for each target
• Generates a large number of reproducible polymorphic markers without prior sequence data
• Is based solely on single nucleotide changes measurable by sequencing
• Is less labor-intensive than standard PCR

Correct Answer: Generates a large number of reproducible polymorphic markers without prior sequence data

Q7. Which factor is most critical when extracting DNA from processed herbal materials (e.g., powders, extracts) for fingerprinting?

• Ensuring high RNA content
• Removal of secondary metabolites and inhibitors that interfere with PCR
• Maximizing protein content
• Using only organic solvents for extraction

Correct Answer: Removal of secondary metabolites and inhibitors that interfere with PCR

Q8. In DNA barcoding of plants, a two-locus combination often recommended for improved resolution is:

• COI + 16S
• rbcL + matK
• ITS + COI
• trnH-psbA + 16S

Correct Answer: rbcL + matK

Q9. Which technique provides single-base resolution and is increasingly used for high-throughput herbal genotyping and discovery of SNP markers?

• RAPD
• Capillary electrophoresis fragment analysis
• Next-Generation Sequencing (NGS) / Genotyping-by-Sequencing (GBS)
• ISSR

Correct Answer: Next-Generation Sequencing (NGS) / Genotyping-by-Sequencing (GBS)

Q10. Interpreting band patterns from gel-based markers requires careful scoring. Which is a common limitation when using dominant markers like RAPD or ISSR for population-level inference?

• They show co-dominant inheritance and thus require sequencing to resolve alleles
• Dominant markers cannot distinguish heterozygotes from homozygous dominant individuals
• They always require fluorescent labelling for visualization
• They provide exact allele sizes comparable across labs without standards

Correct Answer: Dominant markers cannot distinguish heterozygotes from homozygous dominant individuals

Q11. Which database is primarily used for the DNA barcode reference library of plants and supports herb authentication?

• GenBank only
• BOLD (Barcode of Life Data System)
• Protein Data Bank (PDB)
• KEGG

Correct Answer: BOLD (Barcode of Life Data System)

Q12. Which approach is best when you need species-level identification of a multi-component herbal product containing degraded DNA fragments?

• Standard full-length barcoding using long amplicons (>800 bp)
• Short or mini-barcode sequencing (short amplicons) and NGS-based metabarcoding
• RAPD profiling only
• SSR genotyping with large allele ladders

Correct Answer: Short or mini-barcode sequencing (short amplicons) and NGS-based metabarcoding

Q13. Which marker type is most useful for identifying maternal lineage in plants and is often used to trace seed or maternal origin in herbal studies?

• Nuclear SSR markers
• Chloroplast DNA markers (cpDNA)
• SNPs in nuclear genes only
• ISSR markers

Correct Answer: Chloroplast DNA markers (cpDNA)

Q14. Multiplex PCR in herbal authentication is advantageous because it:

• Requires separate reactions for each target locus
• Allows simultaneous amplification of multiple loci, saving time and sample
• Is incompatible with fluorescent detection methods
• Reduces primer design complexity

Correct Answer: Allows simultaneous amplification of multiple loci, saving time and sample

Q15. When validating a DNA-based method for herbal identification in a regulatory setting, which parameter is least relevant?

• Specificity and discriminatory power
• Repeatability and reproducibility across labs
• Cost of raw herbal material in the market
• Limit of detection for adulterants or contaminants

Correct Answer: Cost of raw herbal material in the market

Q16. Which electrophoretic technique provides high resolution and automated sizing of fluorescently labelled SSR fragments commonly used in herbal genotyping?

• Agarose gel electrophoresis with ethidium bromide
• Capillary electrophoresis with fluorescent detection
• Vertical polyacrylamide slab gel without size standard
• Two-dimensional gel electrophoresis

Correct Answer: Capillary electrophoresis with fluorescent detection

Q17. In designing primers for plant DNA barcoding, which criterion is most important to maximize cross-species amplification while retaining discriminatory power?

• Target highly conserved flanking regions with variable internal sequences
• Design primers that anneal to hypervariable regions only
• Use primers with very high GC content (>80%) for stability
• Always avoid universal primers and design species-specific ones

Correct Answer: Target highly conserved flanking regions with variable internal sequences

Q18. Which of the following best explains why PCR inhibitors from herbal extracts affect DNA fingerprinting outcomes?

• Inhibitors increase polymerase fidelity leading to false positives
• Inhibitors bind DNA or polymerase, reducing amplification efficiency and causing dropouts or biased profiles
• Inhibitors improve primer specificity, enhancing results
• Inhibitors only affect sequencing platforms, not PCR

Correct Answer: Inhibitors bind DNA or polymerase, reducing amplification efficiency and causing dropouts or biased profiles

Q19. Which statement about SNP markers in herbal authentication is correct?

• SNPs are multi-allelic and therefore less informative than SSRs
• SNPs provide high-throughput, co-dominant, and easily standardizable data suitable for population and forensic analyses
• SNP discovery does not require sequence information
• SNP assays cannot be multiplexed for plant samples

Correct Answer: SNPs provide high-throughput, co-dominant, and easily standardizable data suitable for population and forensic analyses

Q20. For quality control of an herbal drug suspected of substitution, which combined approach offers the most robust identification?

• Visual botanical inspection only
• Chemical fingerprinting (HPTLC/LC-MS) combined with DNA-based identification (barcoding/SSR/SNP)
• RAPD profiling alone without chemical data
• Measuring moisture content and ash values only

Correct Answer: Chemical fingerprinting (HPTLC/LC-MS) combined with DNA-based identification (barcoding/SSR/SNP)

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