Phenotypic characterization and transcriptomic analysis of the semi-dwarf mutant sd3 in Tartary buckwheat

Plant height is a key agronomic trait in Tartary buckwheat, closely associated with lodging resistance, photosynthetic efficiency, and yield formation. Dwarfism is generally advantageous for enhancing lodging resistance and thereby improving yield. To explore dwarf stem gene resources, and to provide a theoretical basis for understanding plant height development and its application in breeding, we conducted phenotypic characterization and transcriptomic analysis of the semi-dwarf mutant <italic>sd3</italic>, previously generated through EMS mutagenesis. The results showed that compared with the wild type, the plant height of the <italic>sd3</italic> at the mature stage reduced 28.43%, and the number of nodes on the main stem decreased by 44.44%. The reduction in node number was the primary cause of the dwarfism in <italic>sd3</italic>. Cytological observations revealed enhanced lateral cell division at the stem nodes in <italic>sd3</italic>, which has led to significantly thickened stem walls and an increased basal internode diameter. <italic>sd3</italic> is sensitive to gibberellin, and exogenous GA₃ can restore its phenotype. Transcriptome analysis identified 3067 differentially expressed genes (DEGs), GO and KEGG pathway enrichment revealed 57 genes potentially involved in regulating plant height. Notably, <italic>GID1</italic> in the gibberellin signaling pathway was upregulated in <italic>sd3</italic>, while <italic>GID2</italic>, <italic>UNE10</italic>, and <italic>PIF1</italic> were downregulated, suggesting these genes may play a key role in the dwarf phenotype of <italic>sd3</italic>. Overall, our findings provide preliminary insights into the dwarfing mechanisms of <italic>sd3</italic> and offer valuable candidate genes for breeding lodging-resistant varieties and improving plant architecture through genetic approaches.