The important limitations of mutation breeding are:
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They are sometimes harmful to organism.
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The frequencies of the mutants which are desirable are usually low.
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The absence of detailed information of the mutagens is not good method of crop improvement.
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Screening the large population must be done for selecting the desirable mutation.
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Certain desirable mutations are sometimes associated with the undesirable side effects.
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The detection of the recessive mutation in the clonal crops is difficult. Since most of the mutations are recessive.
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The mutation breeding in the polyploidy species is difficult and large doses of mutagens must be applied.