But, why then we take P.D=0 in a wire assuming $R=0 $. Will electrons
not accelerate here?
They would accelerate accelerate in the wire if there was no other resistance in series with the wire. If there is resistance in series with the wire that resistance controls the current and prevents the electrons from accelerating. Since the no resistance wire is in series with the resistor, the current is constant in the wire as well.
The potential difference, $V$, between two points is defined as the work per unit charge required to move the charge between the points. Since no work is required to move the charge between any two points of a wire with zero resistance, the potential difference between any two points of the wire is zero.
A mechanical analogy involving friction might help.
Imagine you are pushing a box at constant velocity with a constant force a distance $d$ on a floor having friction.
The box is analogous to the electric charge, $Q$ moving at constant velocity (analogous to constant current).
The floor with friction is analogous to the resistance
The force you apply to the box is analogous to the force applied by the electric field, $F=QE$
The work you do moving the box the distance $d$ is analogous to the work done by the electric field moving the charge through the resistor, $W=QEd$.
The work you do per unit mass the distance $d$is analogous to the work done per unit charge by the field through the resistor , namely the voltage $V=\frac{W}{Q}=Ed$.
The equal negative work done by kinetic friction that dissipates heat in the floor is analogous to the negative work done by the resistor due to collisions. The collisions dissipate the energy provided by the field as resistance heating.
Now imagine after pushing the box the distance $d$ the floor becomes frictionless. This is analogous to encountering the zero resistance wire in series the resistor. You (the electric field) no longer needs to do work to keep the box (charge) moving at constant velocity (constant current) since there is no longer friction (resistance) to overcome. Since no work is required to move the charge through the zero resistance wire, the potential difference between any two points of the wire is zero.
Hope this helps.