Dominant cis-regulatory variation to improve quantitative traits in polyploid wheat

Project Information

dcPolyWheat

Grant agreement ID: 866328

DOI

10.3030/866328

Project closed

EC signature date 6 March 2020

Start date 1 October 2020

End date 30 September 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 994,00

EU contribution

€ 1 999 994,00

Coordinated by

JOHN INNES CENTRE
United Kingdom

Periodic Reporting for period 4 - dcPolyWheat (Dominant cis-regulatory variation to improve quantitative traits in polyploid wheat)

Reporting period: 2025-04-01 to 2025-09-30

Summary of the context and overall objectives of the project

Crop production must increase to meet the food, feed, and fuel demands of a global population expected to exceed nine billion by 2050. Yet current rates of yield gain are not sufficient, and one in nine people already experience food insecurity. With limited scope to expand agricultural land, improving crop productivity is a major lever to reduce hunger risk. However, key agronomic traits are typically quantitative and controlled by many genes; in wheat, this is further complicated by polyploidy, where most genes occur in two or three copies with overlapping functions, masking the effects of single-locus variation.

dcPolyWheat addresses this bottleneck by combining trait biology, recent advances in wheat genomics and pangenomes, and genome editing to overcome functional redundancy and unlock otherwise inaccessible phenotypic variation. We created publicly accessible germplasm carrying novel regulatory alleles and established experimental and analytical pipelines to identify, engineer, and evaluate variants with potential to improve productivity traits. The project provides a framework that is transferable to other polyploid crops and demonstrates how targeted regulatory variation can contribute to future food security.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the project we (1) generated the data required for our analysis of wheat floral and grain development, (2) identified regions of the genome which could be amenable to genome editing to improve productivity traits, (3) developed proof-of-concept studies for the strategy, (4) implemented new bioinformatics approaches to access natural variation for productivity traits, and (5) performed an unprecedented, cellular-resolution view of gene activity along spike development using spatial transcriptomics.

These datasets enabled the prioritisation of genes and regulatory elements underpinning floral and grain traits that ultimately determine yield, quality and nutrition. In proof-of-concept experiments, we showed that targeted edits in regulatory regions can enhance traits such as grain size and weight. We progressed from controlled environment studies to the first European field trials of transgene-free genome edited wheat, and have now advanced germplasm for larger-scale evaluation, including farmer-led trials.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Our initial work has highlighted the complexity of gene expression profiles within wheat flowers and early developing grains. This insight has meant that we have to focus on specific cell types within these developing tissues to further understand how they work and hence ultimately breed to improve productivity traits. We have developed new open-access methods and protocols to make best use of the available genomic resources and to help understand the biology of early developing wheat flowers and grains. With these methods we have identified master regulators of gene expression in wheat which we will now aim to tweak with the use of genome editing approaches. The new regulatory landscape in the UK means that we can also tests these lines in the field for enhanced performance. We expect that these experiments will allow us to identify novel genetic variation which improves our biological understanding of fundamental processes central to food and nutrition security, while at the same time having the potential to be used within breeding programmes worldwide.

Field trials