Enabling population scale epigenomics for crop improvement

Aim

Develop and fully implement a new library preparation method, unmethyated region sequencing (UMR-seq), for extremely cost-effective profiling of DNA methylation in large genomes.

Brief project outline

The proposed project is a collaboration between GIH, SAFS and QAAFI to develop, implement and validate a novel approach for DNA methylation profiling in large genomes. The motivation is to enable effective large scale DNA methylation profiling projects to assess the role of DNA methylation in trait variation and leverage this for more efficient crop improvement strategies. If successful, the outcome would be the introduction of an extremely cost-effective method for comparative epigenomics. The method is also very useful for the rapid identification for regulatory regions in crop genomes as targets for agricultural improvement.

This project brings together an expert collaborative team across agricultural division at UQ including, investigators Peter Crisp (SAFS – Plant Science) with expertise in epigenomics, Lee Hickey (QAAFI – Centre for Crop Science) with expertise in wheat and barley crop breeding and genetics; and Kai Voss-Fels (QAAFI - Centre for Animal Science) with expertise in genomic selection.

Genomics-based innovative aspect of proposal

To address the inhibitory price of conventional whole genome bisulfite sequencing (WGBS), we have been working towards inventing a new, very cost-effective method called UMR-seq, to profile DNA methylation in crops with large genomes. For most crops, the majority of their genome is highly methylated with only a small fraction lacking methylation; for example, only 3-5% of the barley genome is unmethylated. While methylation can be categorised into different types depending on the sequence context or genomic location, when considering the effect on gene expression, the most important types of methylation are highly methylated and unmethylated, which repress and promote expression respectively. Building on our recent work studying unmethylated regions (Crisp et al. 2020), we hypothesised that a more efficient way to profile DNA methylation genome wide could be to focus on the functional important unmethylated fraction.

Broad applicability of the technique

We anticipate that this technique will be immediately of high interest to those in the plant epigenetic community as an alternative method for DNA methylation profiling, especially those working on plants with large genomes. There will be immediate applications for population level investigations and ecological studies. If our wheat epiGWAS results reveal that UMR-seq data improves accuracy in genomic prediction, then we expect there will interest from crop breeding companies and commercial opportunities. We also speculate that this same method could have exciting applications in animal genomes especially with regard to variation in DNA methylation during development, so this method may be broadly of interest to the research community.