Uncovering DELLA protein targets in wheat

Understanding how Green Revolution genes regulate growth and development in wheat remains a key challenge in plant research. The gibberellin (GA) hormone influences critical traits such as cell elongation, nitrogen remobilisation, and disease resistance by triggering the degradation of DELLA proteins—growth repressors that indirectly modulate transcriptional networks.

During the Green Revolution, wheat breeders selected for mutant DELLA proteins resistant to GA-induced degradation, producing semi-dwarf plants with improved lodging resistance and higher yields. However, these mutations also introduced trade-offs, such as reduced nitrogen use efficiency (NUE) and poor seedling emergence. While studies in Arabidopsis and barley suggest that DELLA proteins regulate different biological processes through specific downstream targets, the identity of these targets and their regulatory mechanisms in wheat remain largely unknown. Identifying these genes could help breeders fine-tune GA responses to improve specific traits without compromising overall plant performance.

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THE QUESTION
How do DELLA downstream targets impact NUE and seedling emergence?
Let’s start by breaking up the root question, as answering smaller sets of questions can be simpler.
  • What are the downstream DELLA protein targets that regulate different developmental processes?
  • How do DELLA proteins control these targets within transcriptional networks?

  • How can identified DELLA targets be validated and utilised for improving wheat traits?
THE METHOD
Presence of DELLA genes in wheat cultivars
Understanding the presence-absence variation (PAV) and single nucleotide polymorphisms (SNPs) in DELLA genes across wheat cultivars is key to dissecting their role in growth regulation. Variations in these genes can influence traits such as nitrogen use efficiency, seedling emergence, and stem elongation. By integrating PAV and SNP data, researchers can identify genotypic differences that affect DELLA function and regulatory interactions. Using KnetMiner, they can explore these variations in the context of transcriptional networks and gene interactions, providing insights that support targeted breeding strategies for optimised GA responses.
AI-Assisted Search of DELLA Targets
Researchers investigating DELLA protein targets in wheat used KnetMiner to systematically explore gene interactions and their roles in seed germination and nitrogen use efficiency (NUE). Using the Concept Search feature, they identified wheat sequences containing DELLA domains and cross-checked presence-absence variation (PAV) data across eight wheat cultivars.

To understand regulatory interactions, they loaded DELLA gene interaction data, incorporating GENIE3 predictions from over 850 wheat expression studies and validated Arabidopsis interactions from BioGrid experimental data. Next, using the Refined Search feature, they selected over 100 DELLA target genes and searched for supporting evidence linking them to seed germination and NUE.

By exploring target evidence networks, they used the AI Summary feature to generate a literature review of 45 relevant publications. Finally, they saved and shared the resulting gene knowledge graphs and reports, enabling further validation, streamlining collaboration, and accelerating discovery.
Conclusion
By applying KnetMiner’s advanced knowledge graph capabilities, researchers can gain new insights into DELLA target genes and their roles in wheat development. This can accelerate breeding strategies aimed at fine-tuning GA responses for improved crop performance while minimising trade-offs. The ability to prioritise candidate genes for experimental validation enables a more targeted approach to breeding higher-yielding, resource-efficient wheat varieties.

Testimonial

Developed through a collaborative effort with Dr. Stephen Pearce from Rothamsted Research, this project leverages his extensive expertise in plant genetics and breeding. Dr. Pearce's insights have been instrumental in refining our approach to identifying DELLA protein targets, ensuring that our research is both innovative and grounded in practical application.

Dr. Stephen Pearce
Principal Investigator @ Rothamsted Research

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