Plant Epigenetics: An untapped molecular resource for crop improvement

Taking root over 23,000 years ago, agriculture triggered a monumental change in society and the way in which people lived, sweeping aside the traditional hunter-gatherer lifestyle. For generations breeders relied on transgressive segregation to improve their crops, crossing two varieties and then selecting offspring that were superior to the parent plants. Repeating this process times over, man has produced the elite crop varieties our global population now depends on. Relatively recently, developments in genotyping have enabled the large-scale predication of traits based on DNA markers. Alongside this, new traits can now be actively produced and introduced through direct genome editing using technology like CRISPR. Both strategies rely on exploiting changes in nucleotide sequence between individuals and the impact this has on phenotype.  

DNA methylation as a resource in crops 

There is now growing evidence that genomic changes may not be the only opportunity for enhancing traits in important plant species. Epigenetic phenomena such as paramutation, transgenic silencing, imprinting, and transposable element inactivation are prevalent in plants and potentially offer an untapped molecular resource for directed crop improvement. One form of epigenetic modification, known as DNA methylation, has attracted particular interest. Studies investigating the methylome of diverse accessions of key crop species have indicated that >99% of these modifications are conserved within a species. However, this still leaves up to thousands of differentially methylated regions (DMRs) between accessions. Crucially, for 10-20% of these DMRs, studies have indicated a negative association between methylation and gene expression, suggesting that some DMRs have the potential to directly influence phenotype by influencing gene expression. 

Advancing our understanding of plant epigenetics  

Further evidence for the potential role of DMRs in influencing plant phenotype has been generated through the analysis of epigenetic recombinant inbred line (epiRIL) populations in A. thaliana. These are generated by crossing two genetically identical plants that differ in DNA methylation levels, owing to one parent being a homozygous mutant for a gene required for the proper maintenance of DNA methylation. The selection of offspring with the wild-type copy of this gene followed by multiple generations of self-pollination results in a population with very similar genomes that vary only in methylation levels. Due to the stripping of methylation at particular chromosomal regions of some of these epRILs, they have the potential to express information that is typically silenced by DNA methylation in natural variants. To date, many quantitative traits including flowering time, plant height, and response to abiotic stress have been shown to be influenced in a heritable manner in epRILs. Some of which have now been mapped to DMRs. Checking against existing accessions of A. thaliana has revealed that many of these DMRs exist as natural variants and, could potentially be acted on by natural or artificial selection. So far, creating epRIL populations in other plant species has proven difficult, as they are much more sensitive to genome-wide changes in methylation levels. To drive this research forward, more precise or moderate techniques must be developed to influence epiallelic variation in more sensitive species. 

First steps taken toward epigenetically modified cotton 

With cotton prices low and, predictions indicating that they are likely to fall again to only 73 cents per pound in 2018 from the average 78 cent per pound expected across 2016-2017, farmers in the industry are struggling to cope. One researcher, Dr Z. Jeffrey Chen at The University of Texas at Austin has set out to develop more productive cotton by exploiting its epigenome. Building on the most complete genetic map of American Cotton he developed with his collaborators in 2015, Chen has now identified 500 genes that are epigenetically modified differently between wild and domesticated cotton. His group were able to trace how changes in DNA methylation occurred through hybridisation events in the wild, in response to environmental factors and finally, during domestication by humans. Excitingly, the team found that wild cotton contains a methylated gene that prevents it from flowering when daylight hours are long, a trait that makes it well suited to it’s natural, tropical environment. In domesticated cotton, the same gene has lost this methylation, allowing the gene to be expressed, an epigenetic change that has potentially had a huge impact on enabling cotton to go global. 

In a press statement, Chen said “Knowing how the methylome changed during evolution and domestication will help bring this technology one step closer to reality”.

Keeping pace with a growing population 

By 2050, the world will need to feed 9 billion people, 2 billion more than we struggle to feed today. To meet that requirement and ensure that the global population receive sufficient nutrition, global food production must increase by around 70% in just 30 years. Alongside this, globalisation and modernisation is increasing the demand for industrial crops like cotton, whilst pressures to decrease our reliance on fossil fuels increases our demand for better biofuel alternatives. Properly harnessing and understanding the stability of epigenetic variation may represent a key tool in meeting these ever-growing demands.