Targeted disruption of OsBADH2 induces basmati aroma in the popular indica rice variety IR-64 using CRISPR/Cas9

Vacha Bhatt, Thakku R. Ramkumar, Vitthal Barvkar, Rupesh Deshmukh, Gunvant B. Patil & Altafhusain Nadaf

Theoretical and Applied Genetics; October 18 2025; vol. 138

Rice, a major staple food for half of the world’s population, has been a significant source of nutrition. India is the second-largest producer and consumer of rice globally. Rice aroma is considered one of the most important traits as it is a key factor determining market price and is related to local and national identity. The genetic basis underlying aroma synthesis is well-explored in rice, and it is controlled by a recessive mutation in the betaine aldehyde dehydrogenase 2 (OsBADH2) gene that results in the synthesis of 2-acetyl-1-pyrroline (2AP). However, the non-scented rice varieties such as IR-64 carry a functional OsBADH2 gene. Therefore, to induce aroma in IR-64, we employed CRISPR/Cas9 tool to knockout the OsBADH2 gene. The single guide RNA targeting OsBADH2 was cloned into pRGEB31 vector and transformed into IR-64 using Agrobacterium-mediated transformation. Several transgenic lines were developed and genotyped for targeted and untargeted (off-target) mutations in T₁ generation. No off-target activity was recorded in T₁ edited lines. Analysis of aromatic volatiles showed induction of 2AP in the grains of T₀ and T₁ edited lines. Moreover, a significant decrease in gamma-aminobutyric acid (GABA) content was observed, indicating a functionally successful gene editing. However, the agronomic characterization of OsBADH2 edited T₁ lines revealed a reduction in yield-related characteristics. In conclusion, this research has established a successful genome-editing approach to induce the commercially important trait of aroma in the IR-64 rice variety and assessed yield-related traits in gene edited IR-64 lines.

See https://link.springer.com/article/10.1007/s40502-025-00901-z