CRISPR/Cas9 Gene Editing of OsSD1 and OsDEP1 Improves Plant Architecture and Yield in Indigenous Black Rice Cultivar Chakhao Amubi

Abstract

Rice ( Oryza sativa L.) sustains over half of the global population. The black rice landraces of North-East India are agronomically limited by tall stature, lodging, and low yield. We employed CRISPR/Cas9 -mediated multiplex genome editing to improve the elite aromatic black rice cultivar Chakhao Amubi by targeting three key regulators of plant architecture and yield — SD1 (Semi-Dwarf 1) , DEP1 (Dense and Erect Panicle 1) , and GS3 (Grain Size 3) — with editing efficiencies of 26.5%, 46.9%, and 25.8%, respectively. Loss-of-function sd1 mutants displayed a pronounced semi-dwarf phenotype along with decreased panicle length, leaf area, and grain number; however, a compensatory increase in tiller number could overcome the yield penalty. Exogenous GA₃ application fully restored plant height in sd1 lines. Homozygous dep1 mutants exhibited significantly enhanced leaf area and grain number per panicle (~ 14.5%), with overall yield improvement (~ 7%). The GS3 mutants displayed no significant phenotypic variation, likely owing to their heterozygous state. Importantly, edited lines retained the cultivar’s speciality trait anthocyanin content, aroma, and cooking quality. Collectively, precise editing of SD1 and DEP1 effectively improved plant architecture and yield in black rice, offering a robust precision-breeding strategy for the genetic enhancement of traditional landraces.