SSR and RAPD-Based Genetic Diversity in Cotton Germplasms

Abstract

This study aimed to evaluate the genetic diversity and to characterize 11 Gossypium hirsutum L. (cotton) germplasms by RAPD and SSR markers. The genomic DNA from the 11 cotton germplasms was amplified with 10 oligonucleotide primers and five microsatellite primer pairs for RAPD and SSR assay, respectively. The 10 RAPD primers generated 335 distinct bands with 100% polymorphisms indicated highly diversed nature. In addition to polymorphism, 29 unique RAPD sequences were identified in 11 cotton germplasms. The five SSR primer pairs generated 69 distinct bands of which 39 were considered as polymorphic (56.52% polymorphisms). Moreover, four unique SSR sequences were identified in three germplasms, namely CB-1, CB-5 and CB-9. The combined RAPD and SSR dendrogram made CB-11 germplasm distinct from the rest and placed alone in a separate cluster that correlated with its phenotypic and agronomic features. Thus, by means of RAPD and SSR markers the genetic diversity was assessed and the 11 cotton germplasms could be characterized authentically.