Harnessing the genetic potential for arbuscular mycorrhizal (AM) symbiosis in rice

The broad aim of the PhD is to harness the genetic potential for arbuscular mycorrhizal (AM) symbiosis in rice. Recent establishment of the high coverage, 3000 Oryza sativa (rice) genome sequence dataset through international effort at the International Rice Research Institute (IRRI), Philippines, provides a unique opportunity to investigate genetic diversity in AM symbiosis. In addition, identification of a novel shoot metabolite marker of AM fungi-association- blumenols- allows for development of a high-throughput screening method to interrogate variation in AM outcome between accessions. This provides a strong basis for a Genome Wide Association Study (GWAS) aiming to identify candidate gene variants required for AM symbiosis in rice.

The project aim requires attention to the following objectives:
1. To develop a precise, robust protocol to give consistent, blumenol-derived AM colonisation phenotypes on infection of genetically and physiologically variable rice accessions with Rhizophagus irregularis.
2. To perform a GWAS at the International Rice Research Institute aiming to identify candidate gene variants required for AM fungal associations.
3. To characterise and validate the functional and ecological relevance of the identified gene variants.

The project will be co-supervised by Dr. Uta Paszkowski, Department of Plant Sciences, University of Cambridge and Dr. Amelia Henry, International Rice Research Institute (IRRI), Philippines. It will involve a first year at the University of Cambridge to establish a reliable protocol for characterisation of colonisation of diverse rice cultivars by R. irregularis. Variation can often be observed in progression and establishment of AM colonisation so this will ensure that the marker phenotype is consistent. In addition, the robustness of the 'blumenol detection' method for detecting variation in AM colonisation in rice plants will be confirmed through collaboration with Prof. Ian Baldwin at the Max Planck Institute for Chemical Ecology, Jena, Germany. The established protocol will then be taken to IRRI, Philippines to conduct the genetic screen during the second year. The final years will then be back at the University of Cambridge to characterise and validate gene variants identified.

The proposed studies will deliver donor materials, QTLs and associated marker systems for introgression of QTLs into upland breeding programs. Thus through use of marker-assisted-backcrossing approaches they will readily translate to products, which, once disseminated through IRRI's network with national partners, will have direct impact in upland farmers' fields, and will be evaluated for their utility in wider water-saving rice production systems.