Asymmetric expression of homoeologous genes in wheat roots modulates the early phase of iron-deficiency signalling

Abstract

Iron (Fe) limitation leads to significant changes in the gene expression in plants to induce iron uptake and mobilization with simultaneous restriction of Fe-dependent metabolism and growth. In our quest to unravel underlying molecular pathways and biochemical processes involved in this stress response, we performed RNA-seq studies of plants exposed to Fe stress. In the past, the wheat transcriptional response to Fe deficiency was studied in severely compromised seedlings showing confounding primary and secondary responses due to decreased photosynthesis and growth. Here, we clustered the transcriptional landscape of wheat roots across the early stages of the Fe deficiency response (4 & 8 days) integrated with Fe resupply conditions. Root growth was significantly inhibited on day 4, followed by visible apparent chlorosis on day 8. Transcriptional analysis revealed that the number of differentially expressed genes increased from 1386 to 3538 from day 4 to day 8, with an overlap of 2006 genes. Moreover, genes with dynamic changes in expression patterns encoded for membrane transporters and transcription factors reportedly contribute to Fe homeostasis in other plant species. Comparative analysis was performed for Fe deficiency response at 4, 8 and 20 days, revealing a core set of Fe-regulated genes. Further assessment of the homoeologs expression suggested an increased induction bias at day 8 compared to day 4. Particularly the A genome contributed significantly at day 4 and the A+D genomes at 8 days. Results revealed that prolonged duration of Fe stress resulted in compounding effects on the number and levels of gene expression. Overall, our work contributes towards fundamental knowledge of the Fe signalling networks in wheat and points to the interplay of the three sub-genomes in this hexaploid species to fine-tune the transcriptional response.