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I feel that the communication between me and my supervisor is not clear enough to discuss my future career plans with him. Also, while discussing my progress in half-yearly meetings, he expresses subtle dissatisfaction with my work and efforts. Now that I am applying for postdoc positions, I have put his contact as a referee for my applications but I don't feel the trust in him that he will be completely just to my active efforts and skills.

So I would like to know what does it imply to a potential employer if they see that the primary supervisor of the applicant is not a referee for the application.

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The absence of a letter of reference from your current supervisor will almost certainly lead to questions with a hiring committee, leaving them to wonder why no such letter was provided. Of course, there can be a number of legitimate reasons for the absences of such a letter and therefore a committee cannot conclude anything from it. But what they will fear is that the letter is absent because your supervisor is dissatisfied with you.

Moreover, typically for fresh PhDs the committee is expecting the letter of the PhD supervisor to be the most useful because they are expected to be in the best position to judge your qualities as a researcher. So unless somebody else can provide an equally significant reference for you, the absence of a letter from your PhD supervisor is going to hurt your application simply because the committee may find that they simply do not have enough information to evaluate your strengths and weaknesses.

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