Intra-specific genetic variation was studied in 28 genotypes of Cleome viscosa L. growing in Swat district, Khyber Pakhtunkhwa, Pakistan. It was found that genotypes showed the utmost allelic variation for leaf upper and lower surface with emerald green (75%), and yellow green (75%) respectively, other leaves lower and upper surfaces were (25%) green and yellow green (26%) respectively. The majority of C. viscosa genotypes were (50%) yellow flowers while others were with (29%) white yellow colour and (21%) dull yellow. Most of the seeds were with black (46%). The protein profiling was carried out on 12% gel electrophoresis; seven reproducible bands with molecular weight ranges from 180 to 10 KDa were detected in C. viscosa, the locus contribution toward genetic disagreement (LCTGD) of C. viscosa was 57%. Notably, L-3, L-4 L-5, was monomorphic in C. viscosa and was treated as species specific. L-1, L-2, L-7 were polymorphic. These bands showed 79%, 4%, 14% and 79% variation respectively. In the current investigation the intra-specific variation was observed limited and alone SDS-PAGE did not determine the high level of intra-specific variation; however, diverse germplasm were suggested to be acquired from various sources.
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