The following could represent probable reasons for the observed variability in transgene expression levels
(A) Position effects on passenger gene
(B) Transgene silencing of the marker gene
(C) Variation in copy number of passenger gene
(D) mRNA instability of marker gene
Which one of the following combinations of above statements is correct?
(1) A and C   (2) C and D
(3) B and D  (4) A and B

The correct answer is (1) A and C – position effects on the passenger gene and variation in copy number of the passenger gene are the most plausible causes of the variable expression pattern of gene “Y” in independent transgenic plants.

Understanding the question setup

Agrobacterium-mediated transformation produced 8 independent transgenic plants carrying:

• a selection marker gene X, and

• a passenger gene Y (whose protein expression is plotted).

All lines survived selection (so marker X is functional), but Y protein levels vary widely. This is classic for independent insertion events and usually reflects position effects and copy-number differences of the passenger gene.

Evaluating each statement

(A) Position effects on passenger gene – TRUE and relevant

• Each T-DNA insert lands at a different chromosomal position with distinct local chromatin structure, nearby enhancers/silencers, and DNA methylation status.

• These position effects strongly influence promoter activity and transgene expression, causing some lines to show high, moderate, or low Y levels even with the same construct.

• Therefore A is a correct and central explanation.

(B) Transgene silencing of the marker gene – NOT explaining the pattern

• If the marker gene X were silenced, those plants would lose resistance and typically be eliminated during selection or show no growth, not just altered Y levels.

• The graph concerns Y expression, and all 8 plants passed marker-based selection, so widespread marker silencing is unlikely to be the main cause of Y variability.

• Hence B is not an appropriate explanation here.

(C) Variation in copy number of passenger gene – TRUE and relevant

• Different transformants can carry different copy numbers of the passenger gene Y (single copy, multiple tandem copies, etc.).

• More copies often (though not always) produce higher transcript and protein levels; fewer copies give lower expression.

• Copy-number variation is therefore another major contributor to the range of Y expression, making C correct.

(D) mRNA instability of marker gene – Not the key factor

• Instability or poor expression of marker-gene mRNA would compromise selection but would not directly create the graded pattern of Y expression across independently transformed lines.

• The variability described is about the passenger gene Y, not about losing marker function, so D is not the best explanation.

Why option (1) A and C is correct

The observed bar-graph pattern (some lines low, some medium, some very high for Y) is exactly what is expected from:

• Position effects (A) – different insertion sites affecting promoter activity.

• Copy-number variation (C) – different numbers of Y copies per line.

Options that rely on marker silencing or marker mRNA instability (B, D) do not logically account for the uniform survival under selection and specifically variable Y expression. Therefore, the best combination is A and C.

SEO‑oriented introduction (for article use)

In Agrobacterium-mediated plant transformation, independent transgenic lines that carry the same construct often show widely different expression levels of the passenger gene. This variability is mainly due to genomic position effects—where in the chromosome the T-DNA integrates—and differences in transgene copy number, rather than problems with the selectable marker gene. Consequently, when analyzing variable expression of a passenger gene like “Y,” the most appropriate explanations are position effects on the passenger gene and variation in its copy number, corresponding to options A and C.