Abstract text: Tomato (Solanum lycopersicum) is one of the most consumed horticultural crops worldwide, yet the study of stem lignification and the underlying genetic basis is poorly understood in this crop. To fill this knowledge gap, we conducted Genome-wide association studies (GWAS) with a diverse collection of 160 tomato genotypes to investigate the genetic architecture of lignification and other features of tomato plants. We successfully applied high-throughput imaging and a near-infrared spectroscopy (NIRs) model to characterize both the anatomical and biochemical features of lignification for a large population size. The results uncovered the diversity of lignification across genotypes. In parallel, plant height and stem width, as well as inflorescence and fruiting traits, were measured, given their potential correlation with lignification as suggested by previous studies. The association test on lignification revealed promising candidate genes involved in either lignin biosynthesis or secondary wall formation. Furthermore, the comparison across GWAS on different traits has identified possible colocalizations of the significant QTLs for lignification and other traits. These findings expanded our understanding of lignification in tomato and provided valuable insights into the interplay of multiple physiological processes.