Exploiting silenced genes to improve wheat breeding

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.

Techniques

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.

Improve genetic stability in regenerated crops

Project Outline

Genome stability is important in plants to maintain genetic uniformity of cultivated crop varieties. Recently developed methods applied to plant material, for example tissue culture for plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. LTR-TEs can proliferate in plant genomes by copying their DNA sequence by reverse transcription (RT) of an RNA intermediate molecule, with a process similar to mammal retroviruses. This activity results in uncontrolled genetic variation in propagated plant material, representing a serious threat to crop genetic stability and food security, particularly for non-model crops with limited genomics resources. For example, somaclonal variation generated by tissue culture propagation of banana (Musa spp.) material, can lead to major alteration at genomic level in the regenerated plants, causing lost or alteration of commercial relevant traits and strongly limiting the biotechnological application for this crop.

Taking advantage of the available molecules developed to contrast retrovirus infection in mammal models, in this project we will apply antiretroviral drugs as suitable approach to control the activation in LTR-TEs in plants. We developed new protocols for plant propagation based on this concept (patented by UoB - PBL Technology), able to inhibit the activation of LTR-TEs. We will test the effect of this new protocol on genome stability, both to investigate the LTR-TE role in plant genome stability, and to develop a new efficient approach to reduce genome instability in crop systems.

Specifically, we will use commercial systems provided by the company Tropic Biosciences, partner of this project, to develop new sustainable biotechnological approaches to generate valuable traits in banana and other tropical crops.

This project will:

Develop new tissue culture approaches in collaboration with an industrial partner, relaying on patented intellectual propriety of the University of Birmingham.

Apply molecular biology approaches and produce and analyse high-throughput genomics dataset (DNAseq and RNAseq) to identify and characterise active LTR-TEs, to determine their role in genome stability in both model plants and commercially important crop systems.

Quantify the impact of LTR-TEs activation on genome stability of different plant system, and develop new improved protocols of plant propagation on species critical for food security in development countries.

References

Brestovitsky, A., Iwasaki, M., Cho, J., Adulyanukosol, N., Paszkowski, J., Catoni, M.*, 2023. Specific suppression of long terminal repeat retrotransposon mobilization in plants. Plant Physiology kiac605. https://doi.org/10.1093/plphys/kiac605