Is there any specific temperature for annealing because I have done gradient temperature several time for amplification but found that only few species were amplified with matk primer.
Although matK is highly conserved across many plant species, there are always subtle differences in sequences perhaps in primer binding sites as well. So, first try to design species specific primers instead of universal primers ( I don't know whether you use species specific primers or universal primers). If you want to design species specific primer, you can try to download the template sequence for the species (millet, if it is available or choose cloely related species) from public database like NCBI. Also, you can check the ideal annealing temperatures usign online softwares and try to use Gradient PCR to find ideal annealing temperature.
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