This study investigates the structure of linkage disequilibrium (LD) and phenotypic associations in the maize genome, using 102 inbred lines representing a broad genetic diversity. The researchers found that intragenic LD generally declined rapidly with distance, but the rate of decline varied among genes. Intragenic LD was particularly strong in genes related to flowering time and plant height. Simple sequence repeat (SSR) loci showed stronger genome-wide LD compared to single-nucleotide polymorphisms (SNPs) in candidate genes. Grouping lines into three subpopulations reduced LD but did not eliminate it. The study also suggests that divergent artificial selection on flowering time may have contributed to population structure. Overall, the research indicates that association studies in maize have great potential for identifying the genetic basis of important traits with high resolution, provided that population structure effects are effectively controlled.This study investigates the structure of linkage disequilibrium (LD) and phenotypic associations in the maize genome, using 102 inbred lines representing a broad genetic diversity. The researchers found that intragenic LD generally declined rapidly with distance, but the rate of decline varied among genes. Intragenic LD was particularly strong in genes related to flowering time and plant height. Simple sequence repeat (SSR) loci showed stronger genome-wide LD compared to single-nucleotide polymorphisms (SNPs) in candidate genes. Grouping lines into three subpopulations reduced LD but did not eliminate it. The study also suggests that divergent artificial selection on flowering time may have contributed to population structure. Overall, the research indicates that association studies in maize have great potential for identifying the genetic basis of important traits with high resolution, provided that population structure effects are effectively controlled.