Anna Elisabeth Backhaus

Background and Aims: Plant functional traits link environmental conditions to plant performance and adaptation. Growing evidence suggests that intraspecific trait variation can be as important as differences between species, yet large intraspecific studies of in situ variation remain rare. Most studies have focused on plant morphological traits, whereas the concentrations of elemental nutrients in seeds have received much less attention so far. Methods: We conducted a large-scale in situ study of the widespread annual ruderal grass Hordeum murinum. We sampled 2070 individuals from 207 populations across a large part of its native range in Europe and North Africa. We measured seed ripening phenology and growth-related traits in situ and analysed concentrations of elemental nutrients in the seeds. Key Results: We found that H. murinum grew larger, produced seeds later and had heavier seeds in colder and wetter regions. Plants growing in denser vegetation were taller and produced heavier seeds but formed fewer spikes. Concentrations of elemental nutrients in the seed generally declined with seed weight and were driven primarily by climatic variables, whereas soil conditions had only minor effects on plant traits and seed nutrients. Population identity explained a substantial proportion of trait variation, indicating a possible genetic component. Conclusions: Our findings provide a comprehensive view of how H. murinum responds to environmental gradients across its European distribution. Climatic variables, particularly temperature, are key drivers of reproductive timing and concentrations of elemental nutrients in the seed, whereas local environmental conditions, such as biotic pressures, are more important for growth-related traits. Together, these patterns indicate that H. murinum modulates its growth and reproductive investment along environmental gradients, balancing phenology, stress tolerance and limited competitive capacity.

Genebanks have a vital role in safeguarding plant genetic resources and providing access to valuable genetic diversity that is absent from modern breeding gene pools. Yet, a major challenge for using genebank materials in crop improvement programs lies in selecting manageable subsets of accessions that maximize genetic diversity for traits of interest. The integration of genomic information is creating new opportunities to address this challenge. Recent studies have shown that k-mer-based bioinformatic approaches capture and reveal previously hidden functional diversity that is missing in elite cultivars. Here we present a perspective on how such approaches enable a precise identification of allele and haplotype diversity across large genebank collections that can guide the strategic selection of accessions for crop improvement. Incorporating this untapped genetic diversity from genebanks into crop improvement pipelines is increasingly recognized as a crucial strategy for developing climate-resilient cultivars.

Climate change and the degradation of natural habitats are forcing a fundamental re-evaluation of agricultural systems. As farming conditions shift, crops must deliver traits that were historically overlooked in breeding programs, such as nitrogen-use efficiency, drought tolerance, and contributions to soil and ecosystem health. These traits have been lost from modern, genetically narrow breeding pools but remain available in genebank collections. Interestingly, renewed interest in these traits is driven by government interests, rather than farmers, who increasingly shape each other’s agendas and, at times, funding streams.We argue that meeting these emerging needs requires revisiting the governance, mission, and access structures of genebanks so they can serve a broader and more diverse stakeholder community. Genebanks are largely funded by governments and NGOs as a public-good investment aimed at improving livelihoods. Yet the pathway from public investment to societal impact is indirect: genebanks supply genetic diversity to breeders; breeders develop improved germplasm; seed companies distribute these; and farmers, also supported by government incentives, ultimately adopt varieties that aim to deliver both environmental and social benefits. In this model, breeders, the only private-sector actors in the chain, become the primary direct beneficiaries of public investment, while farmers, citizens, and ecosystems benefit only downstream.To foster more just and equitable agricultural transitions, we propose that governments and genebanks collaboratively redefine genebank objectives with direct input from farmers and other marginalized stakeholders. This may include not only adjusted breeding priorities but also expanded opportunities for the direct use of genebank materials by farmers. Such an approach would better align public spending with societal expectations for sustainable landscapes and fair resource access. It would also benefit historically underused crop species that have low commercial value and are thus not bred directly, such as orphan crops.In an increasingly digitalized world, genebanks must therefore rethink how they engage with stakeholders, dismantle historical barriers to equitable seed access, and develop access models that extend beyond professional breeders. Modernizing these systems will position genebanks to contribute more effectively to environmental and social justice in future agricultural systems.

Plant functional traits link environmental conditions to plant performance and adaptation. Growing evidence shows that in-situ intraspecific trait variation can be as important as differences between species, yet large intraspecific datasets measured in situ are rare. While most studies focused on plant morphological traits, contents of elemental nutrients in the seeds received much less attention so far. We conducted a large-scale in-situ study of the widespread ruderal grass Hordeum murinum . We sampled 2070 individuals from 207 populations from a large part of the native range in Europe and Northern Africa. In-situ, we measured seed ripening phenology and morphological traits, and analyzed the content of elemental nutrients in the seeds. We found that Hordeum murinum grew larger, produced seeds later, and had heavier seeds in colder and wetter areas. Plants in denser vegetation were taller with heavier seeds but formed fewer spikes. Seed nutrient content generally declined with seed weight and was mainly driven by climate. Soil conditions had only minor effects on plant traits and seed nutrients. Population identity explained much of the variation, indicating a possible genetic component. Synthesis : Our findings provide a comprehensive view of Hordeum murinum responding to environmental gradients across its European distribution. Climatic variables, especially temperature, are key drivers for reproductive success and seed nutrient content, while local environments, such as biotic pressures, are more critical for growth-related traits. These patterns indicate that H. murinum modulates its growth and reproductive investment along environmental gradients, balancing phenology, stress tolerance, and limited competitive capacity.

The diversity of plant inflorescence architecture is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base, which form as a result of delayed spikelet and floral development compared with central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, gene expression patterns along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, we optimize Multiplexed Error Robust Fluorescence In Situ Hybridization, a spatial transcriptomics technique, in wheat inflorescence tissue, enabling transcript localization for 200 genes to cellular resolution across 4 stages of development. Cell segmentation and clustering of 50,000 cells identified 18 expression domains and their enriched genes, revealing the spatio-temporal organization of spikelet and floral development, and characterizing tissue-level gene markers. Using these domain- and cell-level maps, we characterize expression patterns of genes differentially expressed across the apical-basal axis. We identify distinct, spatially coordinated expression patterns distinguishing axillary meristems and their subtending leaf ridges across the apical-basal axis before visible spikelet formation, highlighting factors patterning meristem identity and transition. To support the broader research community, all raw and processed data are publicly available, including through an interactive WebAtlas interface (www.wheat-spatial.com).

The diversity of plant inflorescence architectures is specified by gene expression patterns. In wheat ( Triticum aestivum ), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base which initiate first but subsequently lag in development compared with central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, the spatio-temporal dynamics and gradients along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, using spatial transcriptomics, we profiled 200 genes across four stages of wheat inflorescence development to cellular resolution. Cell segmentation and unsupervised clustering identified 18 expression domains and their enriched genes, revealing dynamic spatio-temporal organisation along the apical-basal axis of the inflorescence. Along this axis, we uncovered distinct and spatially coordinated gene expression gradients patterning meristems prior to the visible delay in basal spikelet development. This study demonstrates the potential for spatial transcriptomics time-series to advance plant developmental biology.

Large differences exist in the number of grains per spikelet across an individual wheat (Triticum aestivum L.) spike. The central spikelets produce the highest number of grains, while apical and basal spikelets are less productive, and the most basal spikelets are commonly only developed in rudimentary form. Basal spikelets are delayed in initiation, yet they continue to develop and produce florets. The precise timing or the cause of their abortion remains largely unknown. Here, we investigated the underlying causes of basal spikelet abortion using shading applications in the field. We found that basal spikelet abortion is likely to be the consequence of complete floret abortion, as both occur concurrently and have the same response to shading treatments. We detected no differences in assimilate availability across the spike. Instead, we show that the reduced developmental age of basal florets pre-anthesis is strongly associated with their increased abortion. Using the developmental age pre-abortion, we were able to predict final grain set per spikelet across the spike, alongside the characteristic gradient in the number of grains from basal to central spikelets. Future efforts to improve spikelet homogeneity across the spike could thus focus on improving basal spikelet establishment and increasing floret development rates pre-abortion.

Wheat ( Triticum aestivum L .) breeding efforts have increased grain yield predominantly by raising grain numbers per spikelet, rather than grain weight or spikelet number. However, across a single spike large differences exist in the number of grains per spikelet. The central spikelets produce the highest number of grains in any given genotype while apical and basal spikelets are less productive. Basal spikelets are delayed in development just after initiation and are smaller and less advanced than central spikelets already by the glume primordium stage. However, basal spikelets continue to develop and produce florets until much later in the wheat growth cycle. The precise timings or the cause of their growth cessation, and subsequent abortion, is largely unknown. In this study we investigated the underlying causes of rudimentary basal spikelet abortion. We investigated basal spikelet development in four UK winter wheat varieties as well as a set of near-isogenic lines for VRT-A2 ( VEGETATIVE TO REPRODUCTIVE TRANSITION 2 ) using shading applications in the field. We propose that basal spikelet abortion is likely the consequence of complete floret abortion as both occur at the same time and have the same response to shading treatments. Furthermore, we found that the developmental age of florets pre-abortion is an important factor for their likelihood to survive and develop viable seed. Previously, it had been proposed that reduced assimilate availability in the base of the spike leads to increased abortion. Re-analysis of published data alongside data presented here, however, does not support this model. We found that rather than assimilate availability, it is the reduced developmental age of basal florets before abortion that correlates with increased abortion. Using the floret Waddington developmental stage pre-abortion, we were able to predict final grain set per spikelet across the spike, alongside the characteristic gradient in number of grains from basal to central spikelets. We found that advancing past Waddington stage 5.5 seems to be important for floret survival and that most florets in basal spikelets had not reached this stage at the onset of floret abortion. The abortion of all florets could therefore be the reason for their rudimentary appearance in the mature spike, suggesting that basal spikelet abortion is simply the consequence of all florets inside the spikelet being aborted and thus all other spikelet structures (e.g., lemma, rachilla, glume) also ceasing to develop. Future efforts to improve spikelet homogeneity across the spike could thus focus on improving basal spikelet establishment and increasing floret development rates pre-abortion.

Spikelets are the fundamental building blocks of Poaceae inflorescences, and their development and branching patterns determine the various inflorescence architectures and grain yield of grasses. In wheat (Triticum aestivum), the central spikelets produce the most and largest grains, while spikelet size gradually decreases acropetally and basipetally, giving rise to the characteristic lanceolate shape of wheat spikes. The acropetal gradient corresponds with the developmental age of spikelets; however, the basal spikelets are developed first, and the cause of their small size and rudimentary development is unclear. Here, we adapted G&T-seq, a low-input transcriptomics approach, to characterize gene expression profiles within spatial sections of individual spikes before and after the establishment of the lanceolate shape. We observed larger differences in gene expression profiles between the apical, central, and basal sections of a single spike than between any section belonging to consecutive developmental time points. We found that SHORT VEGETATIVE PHASE MADS-box transcription factors, including VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT-A2), are expressed highest in the basal section of the wheat spike and display the opposite expression gradient to flowering E-class SEPALLATA1 genes. Based on multi-year field trials and transgenic lines, we show that higher expression of VRT-A2 in the basal sections of the spike is associated with increased numbers of rudimentary basal spikelets. Our results, supported by computational modeling, suggest that the delayed transition of basal spikelets from vegetative to floral developmental programs results in the lanceolate shape of wheat spikes. This study highlights the value of spatially resolved transcriptomics to gain insights into developmental genetics pathways of grass inflorescences.

Spikelets are the fundamental building blocks of Poaceae inflorescences and their development and branching patterns determine the various inflorescence architectures and grain yield of grasses. In wheat, the central spikelets produce the most and largest grains, while spikelet size gradually decreases acro- and basipetally, giving rise to the characteristic lanceolate shape of wheat spikes. The acropetal gradient correlates with the developmental age of spikelets, however the basal spikelets are developed first and the cause of their small size and rudimentary development is unclear. Here, we adapted G&T-seq, a low-input transcriptomics approach, to characterise gene expression profiles within spatial sections of individual spikes before and after the establishment of the lanceolate shape. We observed larger differences in gene expression profiles between the apical, central and basal sections of a single spike than between any section belonging to consecutive developmental timepoints. We found that SVP MADS-box transcription factors, including VRT-A2 , are expressed highest in the basal section of the wheat spike and display the opposite expression gradient to flowering E-class SEP1 genes. Based on multi-year field trials and transgenic lines, we show that higher expression of VRT-A2 in the basal sections of the spike is associated with increased numbers of rudimentary basal spikelets. Our results, supported by computational modelling, suggest that the delayed transition of basal spikelets from vegetative to floral developmental programmes results in the lanceolate shape of wheat spikes. This study highlights the value of spatially resolved transcriptomics to gain new insights into developmental genetics pathways of grass inflorescences. One sentence summary: Large transcriptional gradients exist within a wheat spike and are associated with rudimentary basal spikelet development, resulting in the characteristic lanceolate shape of wheat spikes.