Inositol pyrophosphates in phosphate homeostasis: increasing nutrition value in rice

Project Information

P-use efficient rice

Grant agreement ID: 101107445

DOI

10.3030/101107445

Project closed

EC signature date 20 March 2023

Start date 10 November 2023

End date 9 November 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 189 687,36

Coordinated by

RHEINISCHE FRIEDRICH-WILHELMS-UNIVERSITAT BONN
Germany

Periodic Reporting for period 1 - P-use efficient rice (Inositol pyrophosphates in phosphate homeostasis: increasing nutrition value in rice)

Reporting period: 2023-11-10 to 2025-11-09

Summary of the context and overall objectives of the project

Phosphorus (P) is essential for plant growth and development, yet in most soils phosphate (Pi) is poorly available. To compensate, farmers apply excess P fertilizers, causing environmental pollution and depletion of finite phosphate reserves. In rice, a staple for over half the world’s population, low Pi availability limits growth, while seed phytate - an abundant P storage form - reduces micronutrient bioavailability for humans and animals. Enhancing phosphorus-use efficiency (PUE) and reducing seed phytate are therefore critical for sustainable rice production, improved nutrition, and environmental protection.
This project focuses on elucidating the roles of inositol pyrophosphates (PP-InsPs) and their associated kinases, ITPK and VIH, in regulating phosphate signaling and homeostasis in rice. PP-InsPs are emerging as central signaling molecules controlling Pi sensing, transport, and allocation. By investigating their biochemical, molecular, and physiological functions, this research aims to uncover how PP-InsPs influence phosphate use efficiency and seed nutritional value without compromising plant immunity or growth.
Specific Objectives:
The project was structured around four interrelated objectives:
1. Biochemical characterization of rice ITPK and VIH homologs to understand enzymatic properties and regulation.
2. Identification and stereo-isomeric characterization of rice PP-InsPs to map their diversity and functional relevance.
3. Generation of transgenic rice lines with modified ITPK/VIH expression for in planta functional analysis.
4. Molecular, biochemical, and physiological characterization of transgenic lines to assess impacts on Pi homeostasis and seed phytate content.
Pathway to Impact:
The project bridges fundamental signaling research with applied crop improvement. Expected outcomes include: enhanced phosphorus-use efficiency, improved nutritional quality, and generation of genome-edited resources. Insights gained will support sustainable agriculture, reduced fertilizer reliance, and breeding of nutrient-efficient, climate-resilient rice, addressing global food security and environmental sustainability.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The project advanced understanding of rice ITPK and VIH genes in phosphate homeostasis and seed phytate regulation. All ITPK genes were successfully cloned, and the kinase domains of VIH proteins responsible for inositol pyrophosphate synthesis were generated and established in yeast and bacterial expression systems. These constructs are being used for detailed biochemical and kinetic analyses. Stereo-isomeric profiling of PP-InsPs has been implemented using CE-ESI-MS, and NMR-based studies of enzyme activity and energy-dependent regulation are ongoing.
Multiple genome-edited rice lines were generated using CRISPR/Cas9 and Agrobacterium-mediated transformation. Independent transgenic lines were obtained in the lowland varieties Kitaake and Nipponbare, including single, double, and higher-order mutants. Hydroponic and soil-based trials have been initiated to standardize growth conditions and assess physiological and biochemical traits. In addition, genome-edited lines targeting ITPK, VIH, and symbiosis-related genes CASTOR and POLLUX were successfully developed in NERICA-4, an upland rice variety important for sub-Saharan Africa. A dedicated transformation protocol was established, enabling the generation of putative VIH1/2 and CASTOR/POLLUX edited lines, currently being propagated to obtain homozygous material.
Overall, the project has generated essential genetic, molecular, and biochemical resources, which will provide novel insights into PP-InsP-mediated phosphate signaling in rice, and will lay the foundation for developing rice varieties with enhanced phosphorus-use efficiency, reduced seed phytate content, and improved nutritional value.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project has generated significant advances in understanding the role of inositol pyrophosphate signaling in rice phosphate homeostasis and seed phytate regulation. Genome-edited rice lines targeting ITPK, VIH, and symbiosis-related genes (CASTOR and POLLUX) were successfully developed across both lowland and upland the transformation-recalcitrant NERICA-4 varieties, establishing a valuable platform for functional studies in previously challenging genotypes. These genetic and biochemical resources extend current knowledge by providing mechanistic insights into phosphate signaling pathways and their relationship with nutrient allocation, arbuscular mycorrhizal interactions, and seed nutritional quality.
The outcomes will have potential impacts for sustainable agriculture and crop improvement. They will enable the development of rice varieties with enhanced phosphorus-use efficiency and improved micronutrient bioavailability, supporting reduced fertilizer input and environmental sustainability. The project also provides tools for further research on nutrient signaling, stress adaptation, and symbiotic interactions, fostering international collaboration.
To ensure further uptake and maximize impact, key needs include advancing physiological and field validation studies, scaling up the use of genome-edited lines in breeding programs, and supporting intellectual property protection, commercialization, and regulatory compliance. Additionally, dissemination of methods and resources through open-science initiatives, standardized protocols, and FAIR data management will facilitate adoption by the wider plant science community.