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Since being from a college, not affiliate by ICAR you cannot go with ICAR AIEEA PG exam. You have to appear for state PG entrance exam so that you will get admitted for M.Sc. Agriculture in government colleges. You cannot take admission in government agricultural University as they demand graduation in B.Sc. Agriculture from government University i.e ICAR.
Take admission in private universities as there are many universities who give admission in PG agriculture like amity university, LPU, Indian Agricultural Research Institute - [IARI], Tamil Nadu Agricultural University - [TNAU] and many more. Go for MBA in agri business by CAT as there are two Iims who give admission in ABM means agribusiness management I e, IIM Ahmedabad and IIM Lucknow. B.Sc. Agriculture from a non ICAR affiliated college makes them ineligible for appearing in exams held for government jobs. But it is not so. Students can appear for exam such as UPSC (IFS), SSC IBPS (AO), FCI, NABARD NDDB, etc. After completing B.Sc. Agriculture from any college affiliated to a recognised university. Students must understand that just like JEE entrance exam, ICAR also conducts an entrance exam. By qualifying ICAR entrance exam, students get admission in ICAR affiliated colleges or government colleges. But it does not have any concerned with government job.