Black rice, a local Indonesian variety known for its high economic and nutritional value, owes its health benefits to anthocyanins, compounds with antioxidant properties.
Despite its advantages, black rice is classified as a recalcitrant cultivar, meaning it is extremely difficult to culture and regenerate outside of soil environments.
This has long hindered efforts to develop biotechnological applications such as genetic engineering or mass propagation through tissue culture.
A research team from Universitas Gadjah Mada (UGM) has recently made a major breakthrough by identifying the OsRKD3 gene as a crucial trigger for the formation of somatic embryos, which develop from non-reproductive cells during tissue culture, in black rice.
This discovery marks a significant advancement in plant regeneration techniques, particularly for local cultivars that have proven challenging to culture in vitro.
Led by Professor Yekti Asih Purwestri of the UGM Faculty of Biology (Biology UGM), the study was published in the internationally recognized Q1 journal BMC Plant Biology at the end of 2023 under the title “RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice.”
In collaboration with researchers from the University of Warwick, UK, the team introduced the OsRKD3 gene into black rice cells using Agrobacterium tumefaciens–based genetic transformation.
OsRKD3 is part of the RWP-RK domain gene family, previously known to be involved in embryogenesis in several plant species.
Although the gene’s mechanism in monocot plants, such as rice, was not yet fully understood, experimental results confirmed that OsRKD3 can reactivate the potential of somatic cells to develop into complete embryos.
This process occurs under controlled laboratory conditions, allowing new plants to grow from ordinary plant tissue.
Professor Purwestri described OsRKD3’s ability to induce somatic embryogenesis as a major step forward in plant biotechnology.
She explained that the gene plays a key role in reprogramming somatic cells into embryonic cells.
“This approach is vital for improving regeneration protocols, especially for cultivars like black rice that are difficult to regenerate,” she said.
“A plant’s ability to regenerate in vitro is a critical prerequisite for stable and efficient genetic transformation.”
The study further revealed that activating OsRKD3 not only triggers embryo formation but also stimulates the expression of transcription factors such as AP2/ERF, MYB, and COL, which are known to regulate hormone signaling and stress responses.
According to Professor Purwestri, the callus tissue formed during the experiment exhibited distinct morphological characteristics, indicating high regenerative potential, compact, non-watery, and easily differentiated into shoots and roots.
“These findings strengthen the hypothesis that OsRKD3 functions as a genetic switch, activating the embryogenesis program in plant tissues,” she noted.
Beyond demonstrating the effectiveness of OsRKD3, the research also established a system that could be adapted for other rice varieties or even monocot plants that are notoriously difficult to regenerate.
This has important implications for the development of high-yield cultivars through genetic transformation, where efficient regeneration remains a major bottleneck.
The system could also be used in germplasm conservation programs, particularly for high-potential local varieties that are increasingly threatened by the dominance of commercial strains.
“This approach can not only accelerate black rice regeneration but also create new opportunities for more efficient genetic transformation,” Professor Purwestri added.
The technique paves the way for developing black rice with new desirable traits, such as disease resistance, climate adaptability, or higher concentrations of beneficial compounds.
Moreover, this success could serve as the foundation for building genetic platforms for other strategic crops such as maize and sorghum.
She also emphasized the importance of interdisciplinary collaboration, integrating molecular genetics, tissue culture, and bioinformatics to advance research in this field.
“We hope this discovery can serve as a foundation for continued innovation in plant breeding, both in Indonesia and globally,” she said.
Through this research, UGM reaffirms its strategic role in scientific innovation, grounded in local potential and forward-looking approaches.
This commitment aligns with the university’s broader agenda to support national food security and self-sufficiency through sustainable life sciences and technology.
As a local variety with high nutritional value, black rice is believed to offer health benefits such as natural antioxidants and a low glycemic index, making it a strong candidate for development as a functional food.
In the near future, the research team plans to conduct limited field trials on regenerated black rice plants to assess genetic stability and agronomic potential.
This follow-up research is expected to involve partnerships with agricultural institutions and national genetic resource centers.
The discovery of OsRKD3’s role in overcoming regeneration barriers marks a critical step toward preserving and enhancing the quality of local rice varieties.
It also forms part of UGM’s ongoing efforts to support food security through local plant breeding and cutting-edge biotechnological approaches.
Author: Triya Andriyani
Post-editor: Afifudin Baliya
Illustration: Freepik