Inheritance of gene expression in polyploid wheat

Ensuring that we have a secure food supply is one of the biggest challenges facing humankind today. To be able to meet this challenge we will need to use a wide range of approaches to improve crop production.

Many of our major crops are polyploid, which means that all their DNA has been duplicated and they have multiple copies of each gene. Polyploidy is particularly common in plants and many of our most important foods come from polyploids. It is likely that you ate a polyploid for breakfast since these include the wheat which made your toast, oats in your porridge, potatoes in your hash browns or that healthy banana. The world's population is increasing rapidly, which means we will need to dramatically increase food production to make sure everyone has enough to eat. However, increasing the production of polyploid crops is complicated by the multiple copies of each gene in their DNA. In a non-polyploid plant we can work out the function of an individual gene, to be able to use that gene to improve the crop. For example we might want to identify a gene which can make more tomatoes per plant. However in a polyploid we don't just need to understand what the function of one gene is, we need to know what the other copies are doing too.

In our lab we are using wheat as an example to start understanding the multiple copies of genes in polyploids. The different organs and cells in a wheat plant all have the same DNA with three copies of each gene, but the gene copies can be switched on, switched off or dimmed independently, much like a room with three separate lamps. We recently found that about one third of the time the gene copies are turned on at different levels. Surprisingly in different wheat plants these gene copies can be turned on in different patterns. For example in one wheat plant copy number 1 might be turned on, but in a different wheat plant copy number 1 is turned off and copy number 2 is turned on.

To develop improved wheat plants we crossbreed different wheat plants to generate seeds that have some characteristics from the mother and some from the father, aiming for improved characteristics overall. We found that the offspring from such a cross may keep the same pattern of gene copies turned on as their mother or their father, or they may make a new pattern. In this project we will discover how often new patterns of gene activity are generated and how these patterns are controlled. The knowledge we obtain will be used to find ways to change the patterns of gene activity which will benefit the production of wheat and other polyploid crops.

Many of the world's major crops are polyploid including wheat, which is a staple crop for 2.5 billion people. The wheat genome contains three copies of most genes, known as homoeologs (copies of the gene from the A, B and D genomes, together constituting one triad). Homoeologs have been proposed to confer adaptive advantages in polyploids, for example through tissue specific expression. However to take advantage of the flexibility that homoeologs afford the wheat genome to increase food production, we need to understand how the three homoeologs are regulated.

Several major agronomic traits are controlled by changes in the expression level of one homoeolog including VRN1 and PPD1 that have been essential to adapt wheat flowering to a range of environmental conditions. These well-studied genes are not unique in showing differences in the expression levels of homoeologs. We recently found that homoeologs in ~30% of triads differ in their expression levels, i.e. one homoeolog is over or under expressed compared to the other two gene copies. Furthermore, ~30% of triads change their homoeolog expression between wheat varieties and our preliminary data shows that differences in homoeolog expression can be inherited. In this project, we will explore the genetic and epigenetic factors which influence the inheritance of homoeolog expression. We will discover fundamental information about the control of gene expression in polyploid wheat and identify potential routes to manipulate homoeolog expression that may also be applicable to other polyploid crops of agronomic importance.

This project contributes to the BBSRC's strategic priority area "Agriculture and food security"

Who will benefit from this research and how?
This research will benefit both public and private sector organisations involved in improving wheat and other polyploid crops. These organisations include plant breeding companies, multinational biotechnology companies and farmer-facing organisations such as the AHDB and NIAB. Another beneficiary will be CIMMYT (International Centre for Maize and Wheat Improvement, Spanish acronym) whose breeding programmes are responsible for over 70 % of wheat grown in the developing world. Ultimately this research will contribute to improved crop varieties which will benefit consumers by providing nutritious and affordable food.

How will they benefit from this research?
These organisations will benefit from improved understanding of gene regulation in wheat. This will influence the targeted approaches to crop improvement taken by biotechnology companies, for example informing how many gene copies need to be targeted for gene editing. This will also inform breeding programmes for wheat and potentially other polyploid species, about the importance of homoeolog expression levels, and enable the development of methods to manipulate homoeolog expression levels within breeding programmes which will unlock novel variation. In the longer term these organisations will benefit from this novel source of variation to develop improved wheat varieties and other polyploid crops.

What will be done to ensure they benefit?
The PI has a strong track record in ensuring that outputs from her research are taken up by industry (e.g. Finalist in BBSRC Innovator of the Year 2018). The PI has existing collaborations with commercial plant breeding companies and multinational biotechnology companies (e.g. RAGT, KWS, Limagrain and BASF) which will facilitate discussions about the latest results and their potential use in breeding programmes. The Monogram (UK small grain cereals) network presents an annual opportunity to discuss results with the UK wheat community which includes academics, wheat breeding companies, and farmer facing organisations such as NIAB and AHDB. In addition to these formal and informal activities, results will be deposited as pre-prints to ensure rapid open-access dissemination of information, followed by publication in peer-reviewed journals.