Identification and physiological function analysis of a new dwarf spikelet Dwarf18 -allele mutant in rice

Plant height and panicle architecture are closely related agronomic traits that determine rice yield. In this study, a genetically stable dwarf spikelet mutant was isolated from the japonica cultivar “Taipei 309” through ethyl methanesulfonate mutagenesis. The mutant is mainly characterized by dwarfing, long grains, small width, and small panicle architecture. Genetic analysis revealed that the mutant phenotype was controlled by a single recessive nuclear gene, which was mapped to a 20-kb region between indel markers P4 and P5 on chromosome 1. Only one dwarf gene, Dwarf18 ( D18 ), has been cloned in this region, which encodes gibberellin 3β-hydroxylase (GA3ox2), suggesting that the mutant gene and D18 may be allelic. Sequence analysis of the mutant gene revealed the deletion of one base (G) in the second exon, causing a nonsense mutation. Quantitative real-time PCR results indicated that OsGA3ox2 expression in the mutant was significantly decreased. Therefore, we tentatively named the mutant gene “ d18-1 .” Tissue section observation revealed the mutant showed a markedly decreased length of longitudinal cells but an increased number of cells in the stem compared with the wild-type. A physiological function analysis revealed that the mutant was more sensitive to GA treatment but less sensitive to BR treatment than the wild-type. Expression analysis of genes related to GA and BR biosyntheses and signal transduction pathways revealed that GA-inactivating gene OsGA2ox3 and GA biosynthesis-related genes OsGA20ox2 and OsGA3ox2 were downregulated in the mutant; however, there were no significant differences in the expression of the key genes involved in the GA signaling pathway. In addition, downregulation was observed in most of the genes involved in the biosynthesis and signal transduction of BR in the mutant. These results indicate that the dwarf phenotype observed in the mutant was caused by abnormal GA synthesis and further impairment of the response pathway to exogenously active BR, resulting in a low-sensitivity response to BR. In addition, the microarray analysis of the wild-type and mutant panicles at the booting stage detected 1497 differentially expressed genes involved in phenylpropanoid biosynthesis and carbohydrate and carbon metabolisms. Therefore, the nonsense mutation of the OsGA3ox2 gene in the mutant was considered to affect the regulation of GA and BR biosyntheses and signal transduction pathways as well as panicle architecture development. This study provides new information for further research into the regulation of rice dwarfing and the genetic network of panicle architecture.