Transgenic plants: methods, gene identification, localization and sequencing MCQs With Answer

Introduction

This quiz collection on transgenic plants is designed for M.Pharm students specializing in medicinal plant biotechnology. It focuses on practical and theoretical aspects of creating and analyzing transgenic plants: transformation methods (Agrobacterium, biolistics, protoplast electroporation, floral dip), strategies for gene identification and confirmation (PCR, Southern blot, junction PCR), approaches to determine gene localization (GFP fusions, in situ hybridization, immunolabeling) and sequencing techniques used to characterize transgene insertion and integrity (Sanger, NGS, long-read sequencing). Each multiple-choice question tests conceptual understanding and applied knowledge crucial for designing, validating and interpreting transgenic experiments in medicinal plant research and regulatory contexts.

Q1. What defines a transgenic plant?

• A plant that has undergone natural mutation without foreign DNA
• A plant that contains and expresses a gene transferred from another species integrated into its genome
• A plant that is hybridized conventionally between two cultivars
• A plant treated with chemical mutagens to induce trait changes

Correct Answer: A plant that contains and expresses a gene transferred from another species integrated into its genome

Q2. Which method is most commonly used for stable nuclear transformation of many dicotyledonous plants?

• Polyethylene glycol (PEG) mediated DNA uptake of intact seeds
• Agrobacterium tumefaciens-mediated transformation
• Microinjection into leaf epidermal cells
• Topical application of DNA to stems

Correct Answer: Agrobacterium tumefaciens-mediated transformation

Q3. What is the T-DNA region in Agrobacterium-mediated transformation?

• The chromosomal region encoding virulence genes
• The transfer DNA segment within the Ti plasmid that is integrated into the plant genome
• The bacterial ribosomal DNA used for plasmid replication
• The bacterial cell wall component required for plant attachment

Correct Answer: The transfer DNA segment within the Ti plasmid that is integrated into the plant genome

Q4. Which selectable marker gene is commonly used to select transformed plant cells using kanamycin?

• bar (phosphinothricin acetyltransferase)
• uidA (GUS)
• nptII (neomycin phosphotransferase II) conferring kanamycin resistance
• GFP (green fluorescent protein)

Correct Answer: nptII (neomycin phosphotransferase II) conferring kanamycin resistance

Q5. Which reporter gene is most widely used for live-cell subcellular localization studies in plants?

• GUS (β‑glucuronidase)
• LacZ (β‑galactosidase)
• GFP (green fluorescent protein)
• nptII (neomycin phosphotransferase II)

Correct Answer: GFP (green fluorescent protein)

Q6. Which transformation method delivers DNA-coated particles into plant tissues using high-velocity microprojectiles?

• Agrobacterium-mediated transformation
• Electroporation of intact plants
• Biolistic or particle bombardment (gene gun)
• Agroinfiltration of fruits

Correct Answer: Biolistic or particle bombardment (gene gun)

Q7. Which technique is considered the classical method for determining transgene copy number and integration pattern?

• Northern blot analysis
• Southern blot analysis
• Western blot analysis
• RT-qPCR for transcript quantification

Correct Answer: Southern blot analysis

Q8. Which sequencing technology provides long reads that are particularly useful for resolving complex insertion sites and structural variants?

• Illumina short-read sequencing
• Sanger dideoxy sequencing
• PacBio SMRT long-read sequencing
• Mass spectrometry-based peptide sequencing

Correct Answer: PacBio SMRT long-read sequencing

Q9. For determining the subcellular localization of a transgenic protein in planta, which approach is most direct?

• Quantitative RT-PCR of transcript levels
• GFP fusion protein observed by confocal microscopy
• Southern blot to check copy number
• Antibiotic selection on culture media

Correct Answer: GFP fusion protein observed by confocal microscopy

Q10. The floral dip transformation method is most commonly applied to which model plant?

• Zea mays (maize)
• Oryza sativa (rice)
• Arabidopsis thaliana
• Triticum aestivum (wheat)

Correct Answer: Arabidopsis thaliana

Q11. What does junction PCR specifically detect in transgenic plants?

• Presence of selectable marker transcripts
• Integration junctions between transgene sequences and flanking plant genomic DNA
• Protein-protein interactions of the transgene product
• Methylation status of promoter regions

Correct Answer: Integration junctions between transgene sequences and flanking plant genomic DNA

Q12. CRISPR-Cas9 genome editing in plants most commonly results in which primary molecular outcome at the target site?

• Precise insertion of a large donor sequence without DSBs
• Double-strand break followed by error-prone repair producing small insertions or deletions (indels)
• Immediate transcriptional upregulation of off-target genes
• Conversion of RNA into DNA at the target locus

Correct Answer: Double-strand break followed by error-prone repair producing small insertions or deletions (indels)

Q13. The “position effect” in transgenic plants refers to which phenomenon?

• The impact of growth position in a greenhouse on phenotype
• Variation in transgene expression caused by the genomic context of insertion
• Localization of proteins to a specific cellular compartment
• Positioning of selectable marker genes within the T-DNA

Correct Answer: Variation in transgene expression caused by the genomic context of insertion

Q14. Which high-throughput approach can be used to map transgene insertion sites genome-wide and detect structural rearrangements?

• Targeted PCR only
• Whole genome sequencing (WGS) with read mapping
• Simple staining of chromosomes
• Transient expression assays in protoplasts

Correct Answer: Whole genome sequencing (WGS) with read mapping

Q15. In situ hybridization on plant tissue sections is principally used to detect what?

• Subcellular localization of proteins by fluorescence
• Presence and spatial distribution of specific DNA or RNA sequences in tissues
• Total genomic DNA quantity per cell
• Metabolite concentration gradients

Correct Answer: Presence and spatial distribution of specific DNA or RNA sequences in tissues

Q16. Which recombinase system is widely used to excise selectable marker genes from transgenic plant genomes?

• Zinc finger nuclease system
• Cre-lox site-specific recombination
• Agrobacterium vir gene deletion
• RNA interference (RNAi)

Correct Answer: Cre-lox site-specific recombination

Q17. Which promoter is commonly employed to drive strong constitutive transgene expression in many plant species?

• RbcS (small subunit of Rubisco) tissue-specific promoter
• CaMV 35S promoter (Cauliflower mosaic virus 35S)
• Heat-shock promoter used only under stress
• Root-specific promoter from a legume

Correct Answer: CaMV 35S promoter (Cauliflower mosaic virus 35S)

Q18. One major advantage of plastid (chloroplast) transformation over nuclear transformation is:

• Lower protein expression levels but higher stability
• Higher transgene expression and predominantly maternal inheritance reducing pollen-mediated gene flow
• Easier transformation of monocots using Agrobacterium
• Guaranteed single-copy integration only

Correct Answer: Higher transgene expression and predominantly maternal inheritance reducing pollen-mediated gene flow

Q19. To comprehensively assess potential off-target mutations induced by CRISPR editing in a transgenic plant, the best approach is:

• Only sequencing the target amplicon
• Whole genome resequencing and comparative analysis with the parental genome
• Southern blot for copy number of the guide RNA
• Measuring phenotype without molecular analysis

Correct Answer: Whole genome resequencing and comparative analysis with the parental genome

Q20. Small RNA (sRNA) sequencing in transgenic plants is primarily used to detect which phenomenon?

• Transgene insertion loci in the nuclear genome
• Expression profiles of siRNAs/miRNAs indicating gene silencing and RNAi activity
• Protein abundance of the transgene product
• Chloroplast genome copy number changes

Correct Answer: Expression profiles of siRNAs/miRNAs indicating gene silencing and RNAi activity

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