Candidate Gene Localization of ZmDLE1 Gene Regulating Plant Height and Ear Height in Maize

Plant height is one of the important target traits in maize plant type breeding, which is closely related not only to mechanized grain harvesting and lodging resistance, but also to maize yield. Therefore, it is of great theoretical and breeding value to isolate QTL/gene of maize plant height and analyze its function. This study aims to locate a novel maize dwarf gene ZmDLE1, clarify its biological function, and provide important theoretical basis and gene resources for accelerating the improvement of maize plant type.

A single recessive mutant was derived in maize inbred line LY8405, from Crop Research Institute of Gansu Academy of Agricultural Sciences, by chemical mutagenic agent Ethyl Methyl Sulfonate (EMS). A maize dwarf and low ear mutant was isolated from the M₂ progeny, and the M₃ and M₄ progeny could stably inherit, which was named dwarf and low ear mutant1 (Zmdle1). The F₂ population was constructed by hybridization with Mo17 and was identified by bulked segregate analysis-sequencing (BSA-seq) and target segment recombination exchange. Based on the Mo17 reference genome, the genes in the target region were obtained and functionally annotated to locate candidate genes.

Phenotypic identification of Zmdle1 was carried out, and the phenotype of Zmdle1 at seedling stage was not significantly different from that of the control LY8405. The plant height and ear height of Zmdle1 at mature stage were reduced by 87.2 cm and 55.4 cm, respectively, accounting for about 35.0% and 62.9%, difference is extremely significant. Morphological observation showed that the decrease of internode number and the shortening of internode cell length were the main reasons for the significant decrease of plant height and ear height of Zmdle1. The genetic analysis of the mutant gene was conducted by using the F_2:3 genetic populations. The Zmdle1 mutant is inherited in a 3:1 (χ²=2.854) ratio and is a single recessive gene. Therefore, according to the results of BSA-seq, the candidate gene ZmDLE1 was initially located in the 15 Mb region of Bin1.09-1.10 on chromosome 1 of maize. The polymorphism molecular markers were further developed using the re-sequencing results of Mo17 and Zmdle1, and the target gene was accurately cloned by map-based cloning. Finally, the candidate genes were mapped to the size range of 600 kb, and there were 16 candidate genes in this range. By comparing the re-sequencing data, it was found that Zm00001d033231 gene changed into A at the 2062 position G, which resulted in amino acid changing from glycine to serine, and the transcription level expression was significantly reduced compared with LY8405. Zm00001d033234 changed from T to C at the 223rd position leading to the 75th amino acid changed from serine to proline, and there was no significant difference in transcription level. Through association analysis of natural populations and the predicted genes for functional annotation, it was found that Zm00001d033231 and Zm00001d033234 were related to the growth and development of maize.

The candidate gene ZmDLE1 in the Bin1.09 region at the end of chromosome 1, was identified to effectively regulate maize plant height and ear height, and the target region was reduced to 600 kb by fine localization. Association analysis showed that Zm00001d033231 was genetic locus significantly associated with plant height within the target region.