Harnessing within-cultivar variation to identify hidden genetic resistance using single plant-omics

Redmond, E. J.; Li, M.; Holden, S.; Awan, M. J. A.; Zhang, Y.; Gill, J. S.; Virhia, J.; Hargreaves, J.; Danks, P.; Sleath, B.; Subramaniam, R.; Hicks, C.; Overy, D. P.; Brar, G. S.; Ezer, D.

doi:10.64898/2026.04.02.710456

bioRxiv · 10.64898/2026.04.02.710456

Harnessing within-cultivar variation to identify hidden genetic resistance using single plant-omics

Redmond, E. J.·Li, M.·Holden, S.·Awan, M. J. A.·Zhang, Y.·Gill, J. S.·Virhia, J.·Hargreaves, J.·Danks, P.·Sleath, B.·Subramaniam, R.·Hicks, C.·Overy, D. P.·Brar, G. S.·Ezer, D.

View original source ↗Export metadata ↓

Abstract

Fusarium graminearum is a fungal pathogen that causes scab or head blight in small grain cereals and threatens global cereal production. Disease progression varies widely among individual plants of the same cultivar, reflecting both genetic and environmental heterogeneity. This complicates the identification of early host responses, because each individual plant in a population is at a slightly different phase of disease progression. Here we apply single plant-transcriptomics to a population of 121 malt-barley exposed to F. graminearum, enabling us to reconstruct a temporal sequence of regulatory processes during early infection. We identified several disease-resistance associated genetic variants that are already endemic in this high-yielding cultivar, suggesting potential as breeding targets. These variants were within proteins involved in ROS-burst production, a lectin-kinase PRR, and enzymes with DON-detoxification activity. Single plant-transcriptomics offers a novel strategy for characterising early plant-pathogen interactions, turning intra-population heterogeneity from an experimental barrier into an asset.

Explore related subjects

plant biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Redmond, E. J., Li, M., Holden, S., Awan, M. J. A., Zhang, Y., Gill, J. S., Virhia, J., Hargreaves, J., Danks, P., Sleath, B., Subramaniam, R., Hicks, C., Overy, D. P., Brar, G. S., Ezer, D.. 2026-04-06. Harnessing within-cultivar variation to identify hidden genetic resistance using single plant-omics. https://doi.org/10.64898/2026.04.02.710456

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Ancestral polyploidy and non-linear dosage shifts define the photosynthetic transition in the Heliantheae alliance

Whole-genome duplications (WGDs) have played a central role in plant evolutionary innovation, yet their genome-wide influence on complex physiological traits such as carbon-concentrating mechanisms (CCMs) remains poorly resolved. Here, we present high-quality genome assemblies and annotations for 35 species within the Heliantheae alliance (Asteraceae), spanning the complex photosynthetic spectrum from C3 to C4. Ks-based analyses combined with gene tree-species tree reconciliation identified a shared paleopolyploid event (WGD-2) ~30 million years ago. Using phylogenetically informed association mapping with these species, we detected 451 functional MapMan BINs with copy number variation significantly associated with interspecific variation in the CO2 compensation point. Notably, 303 of these BINs contain greater than 10% WGD-2-derived genes, indicating a strong enrichment of duplicated loci within photosynthetically relevant functional modules. Effect-size analysis revealed that the C3-to-C4 transition is governed by threshold-dependent genomic architecture rather than gradual additive change. Substantial expansions in key transcription factor modules, including HD-ZIP, HSF, LOB, and TCP, were associated with strong non-linear physiological shifts, consistent with genomic tipping points. By integrating comparative genomics, physiological trait variation, and evolutionary analysis, this study establishes a mechanistic link between ancient polyploidy and contemporary photosynthetic diversification. These findings provide a framework for understanding the genetic basis of carbon concentrating mechanism evolution and inform future optimization of photosynthetic efficiency in Asteraceae crops such as sunflower.

plant biology↗

bioRxiv2026

Heat-induced increases in xylem vulnerability: Experimental evidence and possible mechanisms

Hotter droughts driven by global warming are increasing tree mortality worldwide. Here, we propose a theoretical framework that explains how dissolved gas affects the stability of bubbles in xylem sap, and shows that in the presence of gas, sudden increases in temperature can accelerate embolism formation. We then provide experimental evidence that heat exposure can change xylem vulnerability to drought. Using data from seven Australian and European tree species, we assessed how elevated temperature (+15 and +20 {degrees}C above ambient) affects both xylem embolism resistance, measured with the Optical Vulnerability Technique, and VPD-corrected drying times. We found evidence for reduced embolism resistance and accelerated dehydration in heat-exposed plants. On average, trees reached the water potential at 50% loss of xylem function at 0.73 MPa less negative water potentials and 7.8 kPa h earlier, though responses were highly species-specific, and credibly different from zero only in the Australian species. Our results are consistent with the proposed framework and suggest that embolism resistance may not be a static trait, which has important repercussions for studies of plant vulnerability to drought. Further studies are necessary to assess the potential effects of heat-induced reductions in embolism resistance on tree mortality during heatwaves.

plant biology↗

bioRxiv2026

Genome-wide latitudinal variation associated with defence and reproductive pathways linked to Norway spruce adaptation

Environmental cues modulate the natural variations in genes that outline local adaptation in plants for optimal survival. Genome-wide analysis using exome capture dataset in Norway spruce (Picea abies L. Kast) in Sweden revealed natural allelic variation in coding regions of genes associated with defence and reproductive pathways that follow a latitudinal cline, despite of the weak population structure with a low genetic differentiation. Steepest clines in the allele frequencies of missense SNPs from coding region (cSNPs) were detected in 60S RIBOSOMAL PROTEIN L18 (RPL18C), a gene involved in plant survival and defence/stress responses and LONG AFTER FAR-RED 3 (LAF3) that mediates light responses. This was closely followed by cline in ZINC 4 FINGER DNA 3'-PHOSPHOESTERASE (ZDP), involved in DNA repair and DNA demethylation pathways. Flowering genes that displayed latitudinal cline in cSNPs included BARELY ANY MERISTEM 1 (BAM1), REDUCED VERNALIZATION RESPONSE 1 (VRN1), FLOWERING CONTROL LOCUS A (FCA) and TERMINAL FLOWER 1 (TFL1) among few others. These variations may contribute to differential functioning of the defence/flowering genes, enabling the tree to thrive at its best under given local environmental conditions. The clines provide evidence towards local adaptation in these Norway spruce populations across Sweden; it coincides with the latitudinal variation in climatic conditions including temperature, day length and light quality, along with existing cline e.g. differential growth and defence response, and bud-burst/bud-set. The knowledge can be applied in forest industry to design future sustainable breeding strategies e.g. assisted migration, in the context of inevitable climate change.

plant biology↗