Assessment of Genetic Diversity in Cotton (Gossypium spp.) Varieties Using RAPD Markers

Abstract

Background: Genetic diversity assessment is essential for the effective characterisation and utilisation of cotton germplasm in breeding programmes. Random amplified polymorphic DNA (RAPD) markers provide a simple and rapid approach for detecting variation without prior sequence information. Aim: This study assessed genetic diversity and relationships among five cotton (Gossypium spp.) varieties using RAPD markers. Method: Genomic DNA was isolated from Phule Rukumai, Phule Yamuna, Phule Anmol, Phule Dhanwantary, and Phule-688 using a modified rapid extraction protocol. Ten RAPD primers were initially screened, of which five produced reproducible amplification. The amplified fragments were resolved by agarose gel electrophoresis and scored as present or absent. Polymorphic information content (PIC) was calculated to evaluate primer informativeness. Genetic similarity was estimated using Jaccard’s coefficient, and cluster analysis was performed using the unweighted pair-group method with arithmetic mean. Results: The five primers generated 23 scorable bands, with an average of 4.6 bands per primer. Thirteen bands were polymorphic and ten were monomorphic, representing 56.52% and 43.48%, respectively. PIC values ranged from 0.016 to 0.384, with a mean of 0.150. Jaccard’s similarity coefficients ranged from 0.133 to 0.466. Phule Yamuna and Phule Anmol showed the highest similarity, whereas Phule Rukumai was comparatively distinct. Conclusion: RAPD markers effectively differentiated the evaluated cotton varieties and provided preliminary evidence of their molecular relationships. The findings may support initial germplasm characterisation and parent selection, although wider validation using more genotypes and marker systems is required.