Your son is definitely eligible for agriculture because many agricultural colleges give admission to the candidates who took Mathematics, Physics and Chemistry in 12th. Also the students who has took Biology Physics and Chemistry are also eligible. Some colleges in South India need Biology Physics and Chemistry..eligibility criteria and admission process vary from college to college.

It would have been better if you have mention which college you are interested in. I can assure you that your son is totally eligible for taking agriculture course.

All the best