Molecular markers have been a valuable tool in cotton breeding investigations. Various marker techniques used in cotton include Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeats (SSR), Inter Simple Sequence Repeats (ISSR) and Sequence Related Amplified Polymorphism (SRAP).They have large number applications like characterization of gene pool, DNA fingerprinting, phylogenetic analysis, molecular dissection of complex traits, and characterization of genome organization . Several challenges have been overcome in cotton genomic research and now genetic linkage maps of cotton have been developed based on both intraspecific (intrahirsutum) and interspecific (Gossypium hirsutum x Gossypium barbadense) population and the QTLs responsible for leaf shapes, plant trichomes, photopheriodism, stomatal conductance, disease resistance, yield and fibre quality traits have been mapped. This article would give an overview of genomic research on cotton.
Key words: Cotton, DNA markers, diversity studies, QTL mapping