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

博士学位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）通过国际合作建立了覆盖3000个水稻基因组序列数据集，为研究AM共生体的遗传多样性提供了一个独特的机会。此外，鉴定出一种新的AM真菌关联的芽部代谢物标记物- blumenols-允许开发一种高通量筛选方法来查询不同品种之间AM结果的差异。这为旨在确定水稻AM共生所需候选基因变异的全基因组关联研究（GWAS）提供了坚实的基础。项目目标需要注意以下目标：1。制定一个精确的，强大的方案，以提供一致的，布鲁美诺衍生的AM定植表型，遗传和生理上可变的水稻品种感染不规则根噬菌。2. 在国际水稻研究所进行GWAS，旨在确定AM真菌关联所需的候选基因变异。3. 表征和验证鉴定的基因变异的功能和生态相关性。该项目将由剑桥大学植物科学系Uta Paszkowski博士和菲律宾国际水稻研究所（IRRI） Amelia Henry博士共同监督。该项目将在剑桥大学（University of Cambridge）开展第一年的工作，建立一套可靠的协议，以确定不规则稻虱对不同水稻品种的定殖特性。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的一致性。此外，通过与德国耶拿马克斯普朗克化学生态学研究所的Ian Baldwin教授合作，将证实用于检测水稻植物中AM定植变异的“blumenol检测”方法的稳健性。然后将确定的方案带到菲律宾国际水稻研究所，在第二年进行遗传筛选。最后几年将回到剑桥大学，对已发现的基因变异进行表征和验证。提出的研究将提供供体材料、qtl和相关的标记系统，用于qtl的导入到陆地育种计划中。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，这些产品一旦通过国际水稻研究所与国家伙伴的网络传播，将对旱地农民的田地产生直接影响，并将评估它们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.