A Novel Mutation in Maize D1 (Dwarf 1) Confers a Severe Dwarf Phenotype

Plant height is a fundamental quantitative phenotypic trait affecting maize (Zea mays) planting density and is an important focus in the breeding of varieties suitable for mechanical harvesting. In this study, we found a natural extreme dwarf mutant designated as d25, whose dwarf phenotype is controlled by a single recessive gene. The phenotype was restored by spraying with gibberellic acid 3 (GA3), which indicated that the mutant phenotype of the d25 mutant resulted from mutations in genes involved in the gibberellin (GA) metabolic pathway. Additionally, performing bulked segregant analysis on 30 extreme phenotypic plants in the F2 population (d25 × P002), we located one major quantitative trait locus (QTL) at chromosome 3 from 9.3 to 11 Mb. In combination with transcriptome sequencing analysis of d25 and WT plants, we identified the cloned typical plant height-related gene D1, whose expression was significantly higher in d25 mutant plants than that in WT plants. Further analysis revealed that a 275 bp structural variant spanning exonic and intronic regions of the D1 gene accounted for the dwarf phenotype in the d25 mutant. Protein prediction revealed that this variant site alters the translated protein sequence of this region, thereby modifying its function and impairing the critical pathway responsible for hormone synthesis, resulting in reduced plant height. These findings indicate that the d25 mutant may be a novel mutant allele of the D1 gene affecting maize plant development.