Whether annual return is to be signed by the company secretary

If CS is appointed, it should also be signed by Company Secretary. If CS is not appointed, it should be signed by PCS.

But i had submitted form without PCS and side was accepted the form and generate SRN 

In your case then the Compay may be a small company and there may be not be any CS appointed.For small comp annual return is to be singed only by the director of the company, if CS is not appointed.

Company having Turnover more than 50CR and share capital 5 Lac. so status of comapny is not a small company 

How it is possible?? Kindly check the form again. Whether the form was signed by PCS . If uploaded without PCS sign, kindly write to MCA helpdesk and inform your ROC in order to avoid difficulties in future.