The article discusses the structure of linkage disequilibrium (LD) in plants, emphasizing its importance in association mapping and the identification of quantitative trait loci (QTL). LD, or nonrandom association of alleles at different loci, plays a crucial role in association studies by determining the resolution and number of markers needed. The mating system, population structure, and recombination hotspots significantly influence LD patterns. In plants, LD is more extensive in outcrossing species like maize compared to selfing species like Arabidopsis. The article reviews LD in various plant species, highlighting the rapid decay of LD in maize and the longer decay in Arabidopsis. It also discusses the impact of population structure on association studies, the role of recombination hotspots, and the future of LD-based genome dissection. The authors emphasize the need for a thorough understanding of LD across different species to design effective association mapping strategies.The article discusses the structure of linkage disequilibrium (LD) in plants, emphasizing its importance in association mapping and the identification of quantitative trait loci (QTL). LD, or nonrandom association of alleles at different loci, plays a crucial role in association studies by determining the resolution and number of markers needed. The mating system, population structure, and recombination hotspots significantly influence LD patterns. In plants, LD is more extensive in outcrossing species like maize compared to selfing species like Arabidopsis. The article reviews LD in various plant species, highlighting the rapid decay of LD in maize and the longer decay in Arabidopsis. It also discusses the impact of population structure on association studies, the role of recombination hotspots, and the future of LD-based genome dissection. The authors emphasize the need for a thorough understanding of LD across different species to design effective association mapping strategies.