Science

It may be different in different universities but mainly, the Selection Process is based on the marks obtained in the qualifying examination and interview.

Where do you wish to apply?

Both are good, It totally depends upon how much knowledge you gain.

The basic eligibility criteria for BE/ B.Tech in Agricultural Engineering is 10+2 or equivalent with Physics, Chemistry, Mathematics and preferably Biology. Duration of bachelors course in agricultural engineering is 4 years. Besides the required educational qualification, the candidates have to appear for the entrance examination conducted at the State level, National level or University level. Indian Council of Agricultural Research (ICAR), New Delhi conducts an All India Examination for admission to Agricultural colleges for B.Tech. courses all over the country.

Admission is through university level online counseling based on the rank obtained in Banaras Hindu University Postgraduate Entrance Test (BHU-PET).
Please check for your eligibility to pursue M.Sc in Plant Biotechnology at BHU from the link provided below.
https://www.shiksha.com/science/course/m-sc-in-plant-biotechnology-banaras-hindu-university-rajiv-gandhi-south-campus-uttar-pradesh-other-272603