Wheat has a very large and complex genome. Researchers have found that different varieties can use their genes in different ways. By studying RNA – the molecules that carry out instructions from DNA – researchers can see which genes are active and when. By mapping this gene activity for the first time, researchers are able to accelerate international wheat breeding programmes, developing new varieties of wheat which can adapt to the rapidly escalating climate emergency.
Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. To meet the demands of a growing global population, plant breeders face the challenge of increasing wheat production by an estimated 60 per cent within the next 40 years.
The wheat pan-transcriptome offers a powerful tool to help meet this challenge. It will enable plant breeders to accelerate yield improvements and develop more resilient wheat varieties – better equipped to cope with rising temperatures, water shortages, and poor soil quality. Importantly, this can be done without increasing reliance on fertilisers, which are linked to biodiversity loss and pollution.
“We’ve revealed layers of hidden diversity spanning our modern wheat variations. This diversity is likely to underpin the success of wheat over such a wide range of global environments,” said Dr. Rachel Rusholme-Pilcher, Senior Postdoctoral Researcher at the Earlham Institute and co-first author. “We discovered how groups of genes work together as regulatory networks to control gene expression. Our research allowed us to look at how these network connections differ between wheat varieties revealing new sources of genetic diversity that could be critical in boosting the resilience of wheat.”
Furthermore, this work has created an important resource for the worldwide wheat research community – a clear example of how national and international collaboration and new technologies can lead to scientific breakthroughs in global food security.
Much of the untapped genetic diversity may stem from how wheat has adapted to different environments over time, shaped by over 100 years of modern breeding and more than 10,000 years of cultivation.
“The new expression atlas allowed us to independently predict and compare the gene content of the wheat cultivars. We used those gene predictions together with the pan-transcriptome data to identify pronounced variation in the prolamin superfamily and immune-reactive proteins across cultivars,” said Dr. Manuel Spannagl, Deputy Group Leader in the Plant Genome and Systems Biology Group at Helmholtz Munich
Transcript isoform sequencing and de novo annotation was carried out by the Technical Genomics and Core Bioinformatics Groups at the Earlham Institute through the BBSRC-funded National Bioscience Research Infrastructure in Transformative Genomics.
“This work demonstrates the power of technology to reveal novel biology, in this case hidden functional diversity which had not been documented before. Wheat pangenomics resources are growing rapidly with more diversity yet to be discovered,” said Dr. Karim Gharbi, Head of Technical Genomics at the Earlham Institute.
Original Publication
White et al., 2025: De Novo Annotation Reveals Transcriptomic Complexity Across the Hexaploid Wheat Pan-Genome. Nature Communications. DOI: 10.1038/s41467-025-64046-1
Funding acknowledgement
The study was supported by the BBSRC-funded Decoding Biodiversity research programme and National Bioscience Research Infrastructure in Transformative Genomics at the Earlham Institute, as well as the BBSRC cross-institute Delivering Sustainable Wheat programme.
The study was conducted as part of the International 10+ Wheat Genome Project, and involved a global collaboration of scientists from countries including Australia, Japan, France, Germany, Switzerland, the United States, the United Kingdom, Saudi Arabia, and Canada.
