Genome-Wide Association Study of Plant and Ear Height in Maize (Zea mays L.) and Identification of Candidate Genes

Maize is one of the most widely cultivated crops worldwide and is extensively used for animal feed and industrial applications. Plant height (PH) and ear height (EH) are critical determinants of lodging resistance and tolerance to high planting density, and coordinated regulation of these traits is essential for yield improvement. In this study, 479 maize inbred lines from Northeast and North China were genotyped using 7861 single-nucleotide polymorphism (SNP) markers to perform a genome-wide association study (GWAS). After controlling for population structure and relatedness, the mixed linear model (MLM) identified 20 loci significantly associated with PH on chromosomes 2, 4, 5, 6, 7, and 8, and 8 loci associated with EH on chromosomes 2, 3, 4, and 7. A total of 23 candidate genes were identified, including PLATZ8, pectin methylesterase 36, and leucine-rich repeat extensin 14. Gene Ontology (GO) enrichment analysis revealed significant enrichment in biological and molecular functions such as DNA binding, pectinesterase activity, zinc ion binding, ATP binding, and uniporter activity. Bioinformatic characterization of the two most likely candidate genes, Zm00001d002726 and Zm00001d015394, showed that both possess a typical compact four-exon structure. Functional prediction indicated that Zm00001d002726 encodes a pectinesterase/pectinase, potentially regulating cell elongation through pectin degradation and remodeling of the cell wall. Pectinesterase activity may influence PH and EH by mediating pectin demethylation within the cell wall. In contrast, Zm00001d015394 encodes a PLATZ family transcription factor that may regulate downstream gene expression through DNA-binding activity. These findings provide insight into the genetic architecture and potential molecular mechanisms underlying PH and EH in maize and offer a foundation for future breeding efforts.