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.
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 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.Techniques that will be undertaken during the project:
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 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.
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