Which part of the plant is typically free of viruses and can be used…

The correct answer is Option (3) → Meristem (apical and axillary)

A virus spreads through an infected plant, but it does not reach every part. The meristem, the actively dividing tissue at the shoot tip (apical) and in the leaf axils (axillary), stays free of virus. Scientists cut out the meristem and grow it in vitro, under sterile conditions in a nutrient medium, to obtain healthy, virus-free plants. Meristems of banana, sugarcane and potato have been cultured in this way.

Option (1) Roots — Incorrect. Roots of an infected plant can carry the virus. They are not the part used to raise virus-free plants.

Option (2) Leaves — Incorrect. Leaves of an infected plant usually carry the virus. A plant grown from them would be infected too.

Option (3) Meristem (apical and axillary) — Correct. The apical and axillary meristems remain free of virus even in an infected plant, so they are cultured to get virus-free plants.

Option (4) Flowers — Incorrect. Flowers are reproductive organs of the plant and can carry the virus. They are not used for this method.

NCERT Extract:
Biotechnological Applications in Agriculture – “Another important application of the method is the recovery of healthy plants from diseased plants. Even if the plant is infected with a virus, the meristem (apical and axillary) is free of virus. Hence, one can remove the meristem and grow it in vitro to obtain virus-free plants. Scientists have succeeded in culturing meristems of banana, sugarcane, potato, etc.”