This study investigates the structure of linkage disequilibrium (LD) and its association with phenotypic traits in the maize genome. It analyzes 102 maize inbred lines representing a wide range of genetic diversity used in maize breeding. The research explores patterns of LD within and across genes, and its implications for association studies in maize. The study finds that LD generally declines rapidly with distance within genes, with rates of decline varying among genes. This rapid decline is likely due to large effective population sizes and high recombination rates in maize. SSR loci showed stronger evidence of genome-wide LD than SNPs in candidate genes. Grouping lines into three subpopulations reduced but did not eliminate LD. SSR data also suggested that artificial selection on flowering time may have contributed to population structure. The study suggests that association studies have great potential for identifying the genetic basis of important traits in maize with high resolution. The study also examines the relationship between LD and phenotypic traits. It finds that SSRs show stronger associations with flowering time traits than with morphological traits. The study suggests that selection on flowering time may have played a role in generating LD in the maize genome. The results indicate that LD decays rapidly in maize, which could be favorable for association testing of candidate genes near mapped QTLs. However, the rapid LD decay may make genome-wide association testing with SNPs challenging. The study highlights the importance of controlling for population structure in association studies and suggests that suitable methods are now available for this purpose. The study also discusses the implications of LD for mapping QTLs to the level of individual genes, which could provide new insights into the molecular and biochemical basis of quantitative trait variation. The study concludes that association studies have great potential for identifying the genetic basis of important traits in maize with high resolution.This study investigates the structure of linkage disequilibrium (LD) and its association with phenotypic traits in the maize genome. It analyzes 102 maize inbred lines representing a wide range of genetic diversity used in maize breeding. The research explores patterns of LD within and across genes, and its implications for association studies in maize. The study finds that LD generally declines rapidly with distance within genes, with rates of decline varying among genes. This rapid decline is likely due to large effective population sizes and high recombination rates in maize. SSR loci showed stronger evidence of genome-wide LD than SNPs in candidate genes. Grouping lines into three subpopulations reduced but did not eliminate LD. SSR data also suggested that artificial selection on flowering time may have contributed to population structure. The study suggests that association studies have great potential for identifying the genetic basis of important traits in maize with high resolution. The study also examines the relationship between LD and phenotypic traits. It finds that SSRs show stronger associations with flowering time traits than with morphological traits. The study suggests that selection on flowering time may have played a role in generating LD in the maize genome. The results indicate that LD decays rapidly in maize, which could be favorable for association testing of candidate genes near mapped QTLs. However, the rapid LD decay may make genome-wide association testing with SNPs challenging. The study highlights the importance of controlling for population structure in association studies and suggests that suitable methods are now available for this purpose. The study also discusses the implications of LD for mapping QTLs to the level of individual genes, which could provide new insights into the molecular and biochemical basis of quantitative trait variation. The study concludes that association studies have great potential for identifying the genetic basis of important traits in maize with high resolution.