Sequence information and high-throughput methods such as cDNA micoarray to measure gene expression abundances open the door to integrating gene expression with regulatory machineries in plants. Most of the genome is non-coding sequences with important potential effects in gene regulation and plant development. In our efforts to design molecular marker systems to search polymorphism associated with fiber yield and quality, we have attempted to develop methodologies that more specifically target regulatory regions of the genome in cotton. In this study we designed degenerate primers based on conserved core promoter sequences for DNA amplification. We used 8 or 40 genotypes with diverse genetic backgrounds and geographical origins to test our hypothesis. The marker system will be used to identify QTLs that are associated with fiber quality and agronomic traits in a BIL (backcross inbred line) population.