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

博士学位的主要目的是利用水稻中丛枝菌根（AM）共生的遗传潜力。最近建立的高覆盖率，3000水稻（水稻）基因组序列数据集，通过国际努力在国际水稻研究所（IRRI），菲律宾，提供了一个独特的机会，调查AM共生的遗传多样性。此外，一种新的芽代谢物标记AM真菌协会blumenols的鉴定允许开发一种高通量筛选方法，以询问加入之间的AM结果的变化。这为水稻全基因组关联研究（Genome Wide Association Study，GWAS）提供了强有力的基础，该研究旨在鉴定水稻AM真菌共生所需的候选基因变体。为了开发一个精确的，强大的协议，给一致的，blumenol衍生的AM定殖表型感染的遗传和生理可变的水稻品种与Rhizophagus irregularis。2.在国际水稻研究所进行GWAS，旨在鉴定AM真菌关联所需的候选基因变体。3.确认和验证已鉴定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的Uta Paszkowski博士和菲律宾国际水稻研究所的Amelia亨利博士共同监督。这将涉及在剑桥大学的第一年，以建立一个可靠的协议，表征不同的水稻品种的殖民由R。不规则的在AM定殖的进展和建立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，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，将确认“blumenol检测”方法用于检测水稻植株中AM定殖变化的稳健性。第二年，将把制定的方案带到菲律宾的IRRI进行遗传筛查。最后几年将回到剑桥大学进行鉴定和验证基因变异。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渗入高地育种计划。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，将对高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.