Research Projects

Leaf rust, caused by Puccinia triticina, is a persistent threat to wheat productivity, leading to recurrent yield losses. While resistant cultivars have been deployed, the pathogen rapidly evolves to overcome resistance genes, making durable resistance a major challenge for sustainable wheat production. Two key genes, Lr34 and Lr28, confer contrasting yet complementary defense responses: Lr34 mediates adult plant, partial, non-race-specific resistance, whereas Lr28 provides strong seedling, race-specific resistance. However, the molecular orchestration of gene action and signalling underpinning these responses particularly the role of epigenetic regulation remains poorly understood in wheat at the functional genomics level. Scientific Objectives: 1. Map genome-wide DNA methylation and histone modification landscapes during Lr28 and Lr34-mediated resistance. 2. Integrate epigenomic profiles with transcriptomic data to identify defense pathways and regulatory nodes. 3. Construct a spatio-temporal atlas of defense gene expression and epigenetic modulation. 4. Validate key regulators and develop epigenetic markers to accelerate breeding of rust-resistant wheat. Hypothesis: We hypothesize that Lr28 and Lr34 activate resistance through dynamic, tissue-specific, and temporally regulated epigenetic modifications that fine-tune defense gene networks. These modifications may establish immune memory, contributing to durable resistance. Main Experiments: Using near-isogenic lines carrying Lr28 and Lr34, plants will be inoculated with P. triticina and sampled across developmental stages and time points. Whole-genome bisulfite sequencing (WGBS) and ChIP-seq will profile DNA methylation and histone marks, while ATAC-seq will reveal chromatin accessibility. Parallel RNA-seq will capture transcriptional dynamics. Integration of multi-omics data will identify differentially regulated genes and epialleles. Candidate regulators will be validated by qRT-PCR and ChIP-qPCR, and resistance-associated epigenetic markers will be tested across diverse germplasm. Significance: This project addresses a critical knowledge gap by uncovering how epigenetic mechanisms orchestrate wheat defense responses. The outcomes will provide the first spatio-temporal epigenomic atlas for Lr28 and Lr34, identify regulatory modules driving durable resistance, and deliver novel epigenetic markers for breeding. Achieving these objectives will not only advance fundamental understanding of plant immune regulation but also enable translational applications for developing wheat cultivars with broad-spectrum, long-lasting resistance contributing to global food security and sustainable agriculture.