Identification of a novel dwarfing gene, Rht_m097, on chromosome 4BS in common wheat.

Plant height is a crucial agronomic trait in wheat, regulated by multiple genes, and significantly influences plant architecture and wheat yield. In this study, a novel dwarf mutant, designated as m097, was developed and characterized through the treatment of seeds from the common wheat cultivar Jinmai47 with ethyl methanesulfonate (EMS). Microscopic analysis revealed that the dwarf phenotype was attributed to a reduction in the longitudinal cell size of the stem. Similar to the wild type, m097 exhibited sensitivity to exogenous gibberellic acid (GA). Genetic analysis indicated that the reduced plant height in m097 was regulated by a semi-dominant dwarfing gene, Rht_m097. Through bulk segregant analysis (BSA) utilizing the wheat 660K SNP array, Rht_m097 was mapped and confined to a region of approximately 2.58 Mb on chromosome arm 4BS, encompassing 16 high-confidence annotated genes. In addition, transcriptome sequencing (RNA-seq) was conducted on the first internode below the panicle of JM47 and m097 at the jointing stage, leading to the identification of two potential candidate genes exhibiting differential expression. Furthermore, the analysis of gene ontology and metabolic pathways from RNA-seq data indicated that the down-regulated differentially expressed genes (DEGs) in m097 were biologically classified as regulating actin cortical patch organization and assembly. Concurrently, it was observed that the up-regulated DEGs were significantly enriched in various phytohormone metabolic pathways, including those involved in indole-3-acetic acid (IAA) biosynthesis, jasmonic acid biosynthesis, and gibberellin signaling. Overall, this study provides a novel genetic resource for the breeding of dwarf wheat and establishes a foundation for subsequent gene cloning.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01558-0.