Identification of Potential Candidate Dwarf Genes in Maize by BSA-Seq and Transcriptomic Analyses

Maize (Zea mays L.) is a globally important crop. Understanding plant height and the underlying dwarfing genes is of critical importance for improving lodging resistance and optimizing plant architecture. In this study, a dwarf mutant designated CM17-2 was obtained by exposing the maize inbred line B73 to carbon ion beam irradiation. The mutant exhibited markedly reduced plant height, internode length, and ear height. Segregation analysis in the F₂ population revealed a 3:1 ratio, indicating monogenic recessive inheritance. Using bulked segregant analysis (BSA), the causal locus was mapped to four intervals on chromosomes 2, 4, and 5. Exogenous GA₃ treatment rescued the dwarf phenotype and restored plant height to near-wild-type levels, indicating GA sensitivity. Transcriptomic analysis following GA₃ treatment identified 3292 differentially expressed genes (DEGs) between CM17-2 and B73. Among these, 1664 GA₃-responsive genes were significantly enriched in the plant hormone signal transduction pathway. Integration of BSA-seq and transcriptomic data pinpointed 18 candidate genes on chromosome 4. Through gene annotation, four potential candidate genes likely associated with dwarfism were identified, and the functions of these candidate genes need to be validated in future experiments. The identification of these potential candidate genes lays a theoretical foundation for the subsequent functional analysis, gene cloning, and mechanistic studies of maize dwarfism-related genes.