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Exploiting silenced genes to improve wheat breeding

Principal Supervisor: Dr. Marco CatoniLink opens in a new window

Co-supervisor: Dr Graeme Kettles

PhD project title: Exploiting silenced genes to improve wheat breeding

University of Registration: University of Birmingham


Project outline:

Wheat is the most extensively cultivated crop worldwide and it is used as a critical food resource for more than 2.5 billion people. To accommodate the food request of a growing population, it has been estimated that wheat production should increase by 60% by 2050. Recently, changes in DNA molecular modifications (also known as epigenetic marks) generated in model plants produced novel stable phenotypes without altering the DNA sequence itself. This epigenetic variation represents a promising resource to generate more productive crop varieties, in alternative to classical breeding or transgenic plants. However, compared to model plants, wheat has a larger genome and a more complex epigenetic regulation, which requires biological material and tools specifically designed to study epigenetic regulation in this crop.

Although wheat is a target of intense breeding programs, most of these strategies are based on the existing natural genetic variation. With this project, we aim to develop a tool to directly screen for conditions able to increase epigenetic variability in wheat, which is still largely unexplored in crops. Specifically, we will build a transgenic line able to report epigenetic alterations. In such a line, the expression of the reporter gene will be used to efficiently detect conditions where the transcriptional silencing is impaired, facilitating the generation of novel stable epigenetic phenotypes. This approach was initially established in Arabidopsis and used in other plants, significantly contributing to the discovery of new epigenetic factors and the characterization of epigenetic alleles. With the reproduction of such system, we will use such novel biological tool in wheat to investigate epigenetic alterations of and their effect on the phenotype directly in one of the most important crop important for human food production. Epigenetic variability can potentially add a completely new level of phenotypic variation to assist traditional breeding, contributing to improving wheat and increasing food production and sustainable agriculture, to meet the challenges related to feed a growing population and to adapt agriculture to global climate changes.

BBSRC Strategic Research Priority: Sustainable agriculture and food – Plant and crop science


Techniques that will be undertaken during the project:

It is expected that a student will apply many techniques including genome wide library preparation for next generation sequencing (RNAseq, BS-DNASeq, DNAseq), and analysis of the acquired datasets (genome alignments, DNA methylation call, differentially methylated regions identification, differential gene expression analysis). This may include the preparation of libraries for long read sequencing (Pac Bio), de novo genome assembly and genome comparison studies. Data analysis will make large use of command line tools developed for Linux environments and the programming language R. In addition, this project will require to design and perform experiment with crops in controlled conditions, classic molecular biology techniques (cloning, plant transformation) and might include other genomics (DNA blot, transposon display, PCR), transcriptomic (Northern blot, quantitative RT-PCR) and proteomic (protein extraction, Western blot) approaches.

 

Contact: Dr. Marco CatoniLink opens in a new window