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

PHD的广泛目标是利用水稻丛枝菌根(AM)共生的遗传潜力。最近菲律宾国际水稻研究所(IRRI)通过国际努力建立了高覆盖率的3000个水稻(水稻)基因组序列数据库，为研究AM共生中的遗传多样性提供了一个独特的机会。此外，AM真菌的一种新的地上部代谢物标记--缔合--blumenol的鉴定，使高通量筛选方法得以发展，以询问不同种质间AM结果的差异。这为一项旨在确定水稻AM共生所需的候选基因变异的基因组广谱联合研究(GWAS)提供了强有力的基础。该项目的目标需要注意以下目标：1.开发一种精确的、健壮的方案，以给出一致的、源于blumenol的AM定植表型，该表型在侵染具有遗传和生理变异的水稻材料时被不规则根噬菌侵染。2.在国际水稻研究所进行GWA，旨在确定AM真菌联合所需的候选基因变异体。3.鉴定和验证已鉴定的基因变异体的功能和生态相关性。该项目将由剑桥大学植物科学系的Uta Paszkowski博士和菲律宾国际水稻研究所(IRRI)的Amelia Henry博士共同监督。这将涉及剑桥大学的第一年，以建立一个可靠的协议，以确定不同水稻品种的不同水稻品种的定植特征。在AM定植的进展和建立过程中经常可以观察到变异，因此这将确保标记表型是一致的。此外，将通过与德国耶拿马克斯·普朗克化学生态研究所的Ian Baldwin教授的合作，证实“blumenol检测”方法在检测水稻植株AM定殖率变异方面的稳健性。然后，建立的方案将被带到菲律宾的IRRI，在第二年进行基因筛查。最后几年将回到剑桥大学，鉴定和验证已确定的基因变异。拟议的研究将提供供体材料、QTL和相关的标记系统，用于将QTL导入旱地育种计划。因此，通过使用标记辅助回交方法，它们将很容易转化为产品，一旦通过IRRI与国家合作伙伴的网络传播，将对旱地农民的田地产生直接影响，并将评估其在更广泛的节水水稻生产系统中的效用。

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.