PLANTS - SPATIAL TRANSCRIPTOMICS

Dr. Scott Boden, ARC Future Fellow at the University ofAdelaide, leads research into the genetic regulation of wheat’s flowering structures, flowering time, and grain quality. His goal is to understand the developmental and genetic processes that set yield potential and resilience in cereal crops.

In earlier work, Dr. Boden’s team used bulk transcriptomics to identify and characterise key genes controlling flowering time and spike architecture. This approach revealed how these genes influence the timing of flowering, spikelet initiation, and final spike structure, and uncovered how environmental cues like day length and temperature interact with genetic pathways. The team also mapped regulatory hierarchies between genes, linked genetic variation to agronomic traits, and validated gene functions using mutant and transgenic lines.

While these studies provided valuable insight into which genes are important, they could not reveal where in the developing spike these genes were active or which cell types drove these processes. Identifying this gap led Dr. Boden to become interested in spatial transcriptomics. Among the spatial technologies available, Stereo-seq™ (STOmics) has the highest-resolution, species-agnostic platform for unbiased RNA detection in plant tissues.

By applying this technology at the SAGC and collaboratively work with Dr Boden’s team to optimise STOmics workflow on wheat spikelets at early and late developmental stages.

This enabled the generation of high-resolution spatial maps of gene expression, linking specific genes to distinct cellular functional groups. The ability to pinpoint where, and in which cells, genes are switched on provides an unprecedented view of wheat inflorescence development. This is particularly powerful in wheat, with its complex hexaploid genome, where different sub-genomes may contribute unequally to development. The project brought together expertise from Genomics, Histology, and Microscopy teams, along with Dr Boden’s lab to successfully implement the STOmics workflow on these wheat samples.

“The hexaploid wheat genome made processing these samples quite a challenge, being nearly 5x larger than the human genome, as well as causing read alignment issues due to homologs within the sub-genomes. Fortunately, we did manage to process all samples through the SAW pipeline after tweaking parameters to optimise memory usage and better handle multi-mapping reads.”

This important work has the potential to inform breeding strategies aimed at optimising inflorescence architecture, improving grain quality, and enhancing resilience to stresses such as heat and drought—critical steps towards the next generation of high-performance cereal crops.