Hello Mohit. Khalsa was associated with GNDU some years ago but now it has opened its own university. According to studies and reviews, khalsa is better than gndu but its quite expensive too for bsc honors in agriculture. The best universities for studying your course in India are: 

• Tamil Nadi Agriculture University, tamil nadu
• Acharya NG Ranga Agriculture University, hyderabad
• Parul university, vadodara
• Pujab Agriculture University, ludhiana
• Govind Ballabh pant Agriculture University, pantnagar
• Mahatma phule krishi vidyapeeth, pune
• Birsa Agriculture University, ranchi
• Dr. Rajendra prasad Agriculture University, samastipur
• Dr dy patil Agriculture University, pune
• Sam Higginbottom Agriculture University, allahabad
• Mahatma jyoti rao phule university, jaipur
• Jawaharlal nehru krishi vishwa vidyalaya, jabalpur
• Indira gandhi krishi viswa vidyalaya, raipur