Natural Variation and Association Analysis of Melatonin Synthesis Genes with Root-Related Traits in the Maize Seedling Stage

Root system architecture is pivotal for the acquisition of water and nutrients in maize, serving as an essential foundation for achieving high and stable yields. Identification of the genetic components and natural variations determining root traits may facilitate molecular breeding of maize varieties with better root traits. Melatonin plays an important role in plant physiology and development. In this study, nine melatonin biosynthesis genes were re-sequenced in 348 inbred lines, 68 landraces, and 32 teosintes to investigate variations related to maize root traits. The analysis of nucleotide diversity suggested that these genes may have undergone selection, particularly within their promoter regions. Marker–trait association analysis identified 26 variants significantly associated with six root traits. Five variations within the ZmTDC4 promoter were significantly correlated with both total root length (TRL) and lateral root length (LRL). Among these, SNP-1784 explained the most phenotypic variation of root traits, including TRL and LRL, that has undergone selection throughout maize domestication and improvement. Furthermore, knockout of ZmTDC4 in maize resulted in a pronounced reduction in root length, underscoring its critical role in root development. Collectively, these findings elucidate the role of melatonin synthesis genes in root development and identified favorable alleles, thus providing key loci for breeding maize varieties with superior root systems.