Genetic Mapping Identifies Stable QTL and Candidate Genes Regulating Internode Proportion for Maize Plant Architecture Improvement

Background: Ideal plant architecture is central to high-yield maize breeding. The proportional length of internodes above the ear plays a crucial role in determining plant architecture. Methods: In this study, we used an association panel comprising 288 maize inbred lines and performed genome-wide association studies (GWASs) with 1.25 M high-density single nucleotide polymorphism (SNP) markers under a Q + K mixed linear model. Results: A total of 821 significant SNPs associated with plant height (PH), height above ear (HAE), and internode-related traits were detected, which were further classified into 417 quantitative trait loci (QTL). Among these, 128 significant SNPs and 44 QTL were identified for the U1/HAE trait, and 37 significant SNPs and 27 QTL for the U1/PH trait. Four stable QTL (qU1–qU4) were identified through colocalization analysis. Two candidate genes, Zm00001d013222 (involved in gibberellin signaling) and Zm00001d021304 (involved in cell wall metabolism), were further supported by haplotype analysis. For the former gene, U1/PH values in Hap1 and Hap3 were significantly lower than those in Hap2 (p < 0.01). For the latter gene, Hap2 exhibited a significantly higher U1/HAE value compared to Hap1 (p < 0.001). Conclusions: These findings provide new genetic insights into the regulation of maize internode proportion and plant architecture, offering potential targets for molecular breeding.