Plant Science Research Weekly: June 6, 2025
Review: Gene discovery, from Arabidopsis to crops
This year marks the 25th anniversary of the publication of the first genome sequence of a plant, Arabidopsis thaliana, (see https://doi.org/10.1038/35048692). As this review by Bevan et al. observes, this exciting accomplishment was met with some skepticism by those who felt that it was not likely to contribute to crop improvement, and would detract from traditional breeding approaches. However, with the benefit of hindsight, we can see that it was a critical first step. Today, we have a wealth of genomic data from a large number of plants including many crops, and an ever-evolving toolbox that enables us to bridge the gap between genome analysis and trait identification. This review discusses many of these critical tools that support sequencing, genome analysis, deconvolution of complex and polyploid genomes, and analysis and curation of pan-genome datasets. It quickly becomes evident that many of the tools and discoveries derived from Arabidopsis research directly support trait discovery in crops (for example, the genetic pathways that lead to flowering, and the hormone response networks and their effects on plant height). Thanks to the genomic revolution, trait analyses in crops and gene discovery in Arabidopsis are now integrated, facilitating the direct application of the latest advances in biology to crop improvement. (Summary by Mary Williams @PlantTeaching.bsky.social) Plant Cell 10.1093/plcell/koaf087
Review: Genomic tools and breeding tools to design salinity-smart food crops
Most food crops are relatively intolerant to soil salinity, yet globally soils are becoming increasingly salinized. This excellent review by Raza et al. pulls together the myriad approaches that are being used to develop salinity-smart crops. It starts with an overview of how soil salinity affects crops plants and some of the mechanisms that facilitate salinity tolerance. The rest of the review describes the ways that genomics-assisted breeding (GAB) tools including genome sequencing, QTL mapping, GWAS, GS, HBB, pan-genomics, single-cell/tissue genomics and phenotyping, epigenomics and transgenomics, are being used to complement conventional approaches to designing salinity-smart crop cultivars. It is a thorough and well-illustrated article that integrates a discussion of today’s powerful tools with a description of how they are being used to address a specific and important food security challenge. This integration of tools with applications makes this an excellent article to share with students. (Summary by Mary Williams @PlantTeaching.bsky.social) Plant Biotechnol. J. 10.1111/pbi.70104
Review: Alternative modes of RLK function: Insights into cleavage-driven plant signaling
Receptor-like kinases (RLKs) constitute a large family of membrane-bound proteins in plants. The Arabidopsis genome encodes over 600 RLKs, while the rice genome contains more than 1,000. RLKs are best known for their role in perceiving environmental stimuli and triggering downstream signaling pathways that promote stress resilience, primarily through protein–protein interactions and phosphorylation cascades. Interestingly, some truncated forms of RLKs appear to function independently of ligand binding, suggesting alternative mechanisms of action. Yu and colleagues review accumulating evidence supporting proteolytic cleavage as a regulatory mechanism for RLK function. They describe two main cleavage modes: (1) ectodomain shedding, where the extracellular domain is released and acts as a signaling molecule to facilitate plant–microbe symbiosis; and (2) intracellular domain shedding, in which the cytoplasmic kinase domain is released and translocates into the nucleus to activate transcriptional programs. Although research in this area remains limited and identifying the responsible proteases is technically challenging, this review highlights an emerging direction in understanding the dynamic and multifaceted roles of RLKs in plant signaling. (Summary by Ching Chan @ntnuchanlab) New Phytol. 10.1111/nph.70174
Viewpoint: A new lens on ectomycorrhizal function: exploring the absorber-miner spectrum
Mycorrhizal symbiosis is widespread in nature, occurring in approximately 90% of terrestrial plant species, and played a crucial role in enabling plant colonization of land over 450 million years ago. The majority (>80%) of these associations are formed by endomycorrhizae, in which fungi from the phylum Glomeromycota penetrate the cortical cells of host plant roots, forming branched hyphal structures that facilitate nutrient exchange. These fungi associate with a wide range of angiosperms, including major crops. In contrast, ectomycorrhizae, which colonize the apoplastic regions of the epidermal and cortical cells, are formed by relatively fewer plant species—primarily trees—but dominate vast areas of the forests. Although mycorrhizal symbiosis is critical to ecosystem function, generalizing their ecological roles, species distributions, and organismal traits remains a challenge. Jörgensen and colleagues propose a stoichiometric model linking nitrogen flux with ectomycorrhizal traits. By conceptualizing fungal lifestyles along a continuum from “absorbers” to “miners,” the model predicts various aspects of ectomycorrhizal ecophysiology—including morphological, physiological, metabolic, and resource acquisition traits—based on their position along this spectrum. Absorbers exhibit high carbon use efficiency (CUE), enabling rapid biomass accumulation and thriving under high nitrogen availability. In contrast, miners have low CUE, leading to slower biomass accumulation but supporting symbiosis in nitrogen-limited environments. Notably, miners also display self-decomposition traits that enhance nutrient recycling under scarcity. This model offers a unified framework for evaluating and understanding the interactions between ectomycorrhizal fungi and their tree hosts. (Summary by Ching Chan @ntnuchanlab) New Phytol. 10.1111/nph.70129
Sweet heat: Organelle-specific carbohydrate metabolism in heat stress
Plant metabolism varies substantially between developmental stages, cell types, and intracellular environments. Similarly, biochemical responses to abiotic stress often deviate between neighboring cell types, but discerning what is changing where becomes more challenging in smaller and more fragile sub-compartments. Seydel et al. investigated how carbohydrate metabolism in Arabidopsis thaliana changed in response to 7 days of elevated temperature. The authors combined serial block-face electron microscopy to quantify the volumes of subcellular compartments and non-aqueous fractionation to quantify metabolites in each organelle. Together, these methods enable an organelle-specific view of carbohydrate metabolism. Although the relative sizes of chloroplasts, the cytosol, and vacuoles, were not affected by the increase in temperature, it reduced total leaf volume and therefore the absolute volumes of each compartment. Before accounting for these absolute volumes, the relative abundance of sucrose and fructose in the cytoplasm showed no change in the elevated temperature, with a small increase in glucose levels. By contrast, the absolute concentrations (accounting for absolute organelle volumes) of cytoplasmic sucrose was lower, with higher fructose and glucose at 34 °C. Under these new conditions, invertase activity is near-completely inhibited in the cytosol. Overall, this study demonstrated a powerful method for understanding metabolism on a sub-cellular level, cautioning that relative versus absolute quantification can tell contrasting stories. (Summary by Ciara O’Brien @ciara-obrien.bsky.social) Plant Physiol. 10.1093/plphys/kiaf117
Stochastic gene expression, an ordinary part of multicellular life
Stochasticity is an important feature of genes, allowing for variability in their abundance and activity prior to ‘fine-tuning’ at later periods of development. Kong et al. describe this feature in auxin responsive genes, attributing their ‘stochastic’- or inherently random expression – as an internal feature of cells, allowing for later canalization (development of robust expression) to inform points of organ outgrowth. Using a coordinate system, they showed that the variability of DR5 (an auxin responsive gene commonly used as a marker for auxin activity) expression was high at early stages, organizing later to form robust regions of signaling points in the flower primordia where the sepals would arise. This high variability at early stages is due to intrinsic molecular noise at a cellular level, across a limited number of cells. The authors found that the development of robust signaling regions where the sepals appear was due to averaging of this stochastic expression across a wider cell area at later stages of development. Other auxin responsive genes, however, were found to act differently, with similar levels of stochasticity but decreased noise in precise locations, indicating self-regulation. Given the differences between auxin responsive genes, this research highlights the opportunity to investigate promoter architecture as a means of precise genetic engineering, whilst also providing insight into how plants manage to balance complex, messy processes with coordinated development of structures. (Summary by Kes Maio) Nature Comms. 10.1038/s41467-025-59943-4
The cell wall controls stem cell fate
Plants are immobile and their cells are contained within cell walls, yet they demonstrate vast post-embryonic developmental plasticity. Evidence shows that the fate of the cell is likely determined by its location within the plant, but the specific mechanisms and pathways involved are currently unknown. Zerin et al. investigated the cell wall signaling pathways that control cell fate in the Arabidopsis shoot apical meristem, showing that the transcription factor WUSCHEL (WUS) modulates levels of pectin methyltransferases (PMEs) in stem cells. They demonstrated that WUS is responsible for stem cell differentiation and associated cell wall modifications. PMEs, controlled by WUS, modify cell wall properties, and low levels are this enzyme are required for aspects of cell differentiation, including auxin patterning and maintenance of stem cell-specific expression profiles. This work directly connects modulation of the cell wall and its properties with cell differentiation in the shoot apical meristem. Whether the processes documented here are more based in biochemical or mechanical interactions is still to be determined, but this evidence has greatly furthered our understanding of cell fate. (Summary by Elise Krespan) bioRxiv https://doi.org/10.1101/2025.05.19
Transgenerational epigenetic cold tolerance in rice
As rice has expanded northwards from its center of origin, it has been exposed to deeper and longer periods of cold. Male fertility is particularly sensitive to cold. Song et al. designed a clever strategy to study mechanisms of cold tolerance. They subjected meiotic-stage cold-sensitive rice varieties to cold and at each generation selected panicles with increased cold tolerance, determined by increased seed set. After three rounds of cold treatment, they carried reciprocal crosses with the same strain that had not been subjected to cold, and all the progeny showed cold tolerance, indicating that it behaved as a dominant trait. Furthermore, this adaptive trait was stable for five generations even in the absence of continued cold treatment. Genomic and epigenomic analysis led the authors to identify the gene responsible for the acquired, heritable cold tolerance, which they named ACT1 (AcquiredColdTolerance1, encoding an arabinogalactan protein). Interestingly, ACT1 contains no sequence variation between cold-tolerant and sensitive varieties, but instead contains a differentially-methylated region. The epiallele in the cold-tolerant varieties is hypomethylated in a promoter region that is bound by a cold-induced transcription factor, Dof1. Furthermore, they found the hypomethylated epiallele is more abundant in landraces from northerly regions. As the authors observe, this study provides a mechanistic explanation for the inheritance of acquired characteristics that was proposed by Lamarck more than 200 years ago. (Summary by Mary Williams @PlantTeaching.bsky.social) Cell 10.1016/j.cell.2025.04.036
Bidirectional root-shoot signaling via CCR1 regulates cluster root and nodule development in legumes
Legume plants are renowned for their ability to form symbiotic relationships with nitrogen-fixing bacteria (rhizobia) in specialized root tissues called nodules. This symbiosis enables the conversion of atmospheric nitrogen into ammonia, a form of nitrogen that plants can readily use for growth. This trait also makes legumes valuable as green manure for sustainable agriculture. However, nodule formation is energetically costly, making excessive nodule production inefficient. To regulate this, legumes have evolved an inhibitory mechanism known as autoregulation of nodulation (AoN), which prevents the overproduction of nodules. AoN involves systemic long-distance signaling: an initial signal originates in the root, is perceived in the shoot, and triggers a second signal from the shoot back to the root to suppress further nodulation. White lupin (Lupinus albus) is a legume with an unusual root adaptation to low phosphorus, in that it produces small, dense lateral roots called cluster roots (CRs) that are specialized for nutrient uptake. In a forward genetic screen in white lupin aimed at identifying regulators of CR formation, Marquès and colleagues discovered four allelic mutants that formed constitutive CRs even under high-phosphate (suppressive) conditions. The affected gene, CONSTITUTIVE CLUSTER ROOT 1 (CCR1), corresponds to homologs known to regulate AoN in other legume species. Interestingly, the EMS-induced ccr1 mutants also exhibited excessive root nodule formation, suggesting that CCR1 functions in both CR and nodule development. Transcriptome analyses further revealed that CCR1 influences genes involved in lateral root development as well as ethylene and cytokinin signaling pathways. The authors thus propose that CCR1-mediated bidirectional long-distance signaling governs a broader root developmental program in legumes, which they term Autoregulation of Cluster Root and Nodule Development (AoDev). (Summary by Ching Chan @ntnuchanlab) PNAS 10.1073/pnas.2418411122
Molecular epidemiology of European wheat powdery mildew
At the height of the Covid pandemic, epidemiologists carried out mass sequencing of the circulating virus populations to track their movements and the emergence of new variants. Such molecular epidemiological studies are rarer for plant pathogens but can be equally effective in learning about their patterns of spread. Powdery mildew is a fungal disease that affects wheat and is caused by Blumeria graminis forma specialis tritici (Bgt), To better understand how it spreads, Jigisha et al. carried out molecular epidemiological studies in 2022 and 2023 on the Bgt population over 90 locations in Europe and the Mediterranean regions, which produce 1/3rd of the global wheat harvest. Whole genome sequencing (WGS) revealed as excess of rare variants in Bgt population indicating a large variance of reproductive success between populations. Furthermore, the Northern Europe regions showed greater homogeneity and evidence that wind dispersal is a key to this stable structure, whereas the Southern Europe regions showed more evidence of smaller isolated populations. Finally, the authors identified evidence of recent selection pressure at several loci, for example at the genomic region containing AvrPm17, an avirulence gene coding for an effector recognized by the wheat resistance gene Pm17. Several sequence variants of AvrPm17 were found, including one, Variant H, that entirely evaded recognition by the plant resistance gene. Thus, this study revealed the fundamental epidemiological dynamics of wheat powdery mildew and contributed to understanding the rapid breakdown of resistance in European wheat population. (Summary by Indrani Kakati @Indranik333 @indranik18.bsky.social) PLOS Bio https://doi.org/10.1371/journal.pbio.3003097 See also the accompanying Primer by @smlatorreo.bsky.social
