Count:
what should I use instead of ethernet controller then to accept the data from RJ45 jack? and which things I should know about the existing system?
The RJ45 is just a connector. You need to find out if the protocol is being sent using ethernet or RS232 or RS485.
You need to find out everything about the existing system. What PLCs are being used, what are they being used for, where are they located, why do they need replaced, why is a wirless LAN required.
Research the exisitng system. What is the DTU is it a PLC card if so what make and model. Likewise what is the RTU is it a PLC card if so what is the make and model. If you then lookup these cards you will find out whether they are using ethernet or RS232/RS485
Count:
the DTU should connect to PC through RJ45 and accept the queries in MODBUS RTU only. That's what I have been asked to develop
What you have been asked to develop is unclear and does not really make sense.
Modbus RTU is normally a serial protocol let's say it is using RS232, why on earth would somebody specify that it has to connect to a PC using an RJ45 connector? You would connect to the PC using a USB to RS232 converter. These typically have a male 9 way 'D' type connector, so you would connect with a cable fitted with a female 9 way 'D' type connector.
The existing system does not have a PC does it. So what software are you going to be running on the PC, is it a package you are going to buy or something you are going to write yourself, what does it do?
You seem to be planning on translating characters from one format to another and back again. That sounds like a completely needless and complicated step.
What does the Arduino do, why is it there?
Nobody can help you without a clear understanding of the existing system, what you want to replace it with and why.