Understanding the genetic basis of complex traits is vital for meeting the challenge of increased fiber quality and yield in this period of global climate change. Minor genes or QTLs control most of the agronomic traits in cotton with small contributions to the overall phenotypic effect. Identifying marker-trait associations for the QTLs would enable genomics based cotton improvement. Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for detection and fine mapping of QTLs underlying such complex traits. Our research will support the construction of the largest immortal mapping population in cotton, which will ultimately help to bridge genomics and plant breeding through the dissection of complex traits and laying the foundation for genome-wide selection in breeding programs.