hi,

yes, definitely it will have effects, since jee main consists of three subjects, mathematics, physics and chemistry.  and each of the subjects has equal portion in questions. if you only prepare for one of the subject you may only able to answer from only 100 marks question. and it may not possible for you to answer all of the questions from that area even if you studied hard, now to get a tier one college you need to score atleast 150+ marks or even more in jee main.

hope you get my point.