Integrated GWAS and Transcriptome Analysis to Identify Genes Underlying Plant Height and Ear Height Plasticity in Maize Germplasm

Abstract

Background: Integrating tropical and temperate maize germplasm represents a pivotal strategy for driving genetic innovation, with phenotypic plasticity serving as a critical indicator of successful integration. Methods: We analyzed 155 inbred lines across 5 contrasting environments to investigate variation and plasticity in plant height (PH) and ear height (EH). Results: Genome-wide association studies (GWAS) identified 77 loci associated with phenotypic plasticity, while the transcriptome profiling of Mo17 and T32 in Zhangye and Sanya revealed 9 candidate genes potentially regulating these traits, including Zm00001d043110, Zm00001d053972, and Zm00001d010154. Conclusions: These results provide valuable genetic resources and theoretical foundations for germplasm improvement. The identified genes hold promise for molecular marker development, facilitating the breeding of elite lines with stable PH and EH across environments, thereby contributing to maize improvement and enhancing global food security.