Bacillus thuringiensis (Bt) is a spore-forming bacterium which produces insecticidal crystal protein in the sporulation phase.
Polymerase chain reaction (PCR)-based identification of Bacillus thuringiensis toxin genes has become a routine step in most B.
thuringiensis isolation and characterization initiatives. In the present study, eighteen native Bt isolates from diverse habitats of
North India were taken for the presence of cry1 type genes. The distribution of cry1 gene families in native Bt isolates was examined
by PCR amplification of genes with three sets of corresponding PCR primers. In native Bt isolates many variant bands were also
observed in addition to expected bands on PCR amplification. Different sets of primers for the same gene give different results due
to different sites of primer binding. Maximum number of isolates showed expected bands when primers designed by Ceron were
used compared to other primers. However, with other primers, the numbers of variant bands was larger. The isolates, SK-13, 63
and 105 showed the maximum number of cry1-type genes, followed by SK-20, 28, 48, 88, 94, 301, 304 and 307, whereas SK-3
showed the presence of only 3 cry1-type genes. RFLP analysis of 1.6 kb fragment indicated the presence of variant bands from the
reference strains. Several promising isolates with predicted toxicity towards lepidoptera have been observed in this study.