Development and Application of Random Amplified Polymorphic DNA (RAPD) for the Improvement of Cotton Crops

Random amplified polymorphic DNA (RAPD) markers have played a significant role in accelerating cotton (Gossypium spp.) improvement by enabling rapid genome-wide assessment of genetic variation without the requirement for prior sequence information. RAPD has been widely applied in cotton germplasm characterization, cultivar identification, hybrid confirmation, and the early development of molecular linkage maps. Its simplicity, low cost, and the ability to amplify multiple polymorphic loci in a single reaction made RAPD particularly valuable during the early phases of cotton molecular breeding. The successful implementation of RAPD depends strongly on high-quality genomic DNA, and optimized extraction protocols, such as those designed specifically for cotton tissues, ensure reliable amplification. Although more advanced marker systems such as SSRS and SNPS have since become dominant, RAPD continues to be a useful tool for preliminary screening and for breeding programs operating in resource-limited environments. This chapter highlights the workflow, development, and applications of RAPD in cotton improvement, supported by the evidence from key studies that established its relevance in molecular plant breeding.