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bioRxiv2021

Pectin remodeling belongs to a homeostatic system and triggers transcriptomic and hormonal modulations

O_LIHere, we focused on the biological modifications arisen from a strong and transient variation of the pectin methylesterification status during the seed-to-seedling transition. C_LIO_LIA reverse genetic approach was used to trigger specific reduction of pectin de-methylesterification during the seed maturation stage and the related physiological effects were assessed using a combination of biochemical, transcriptomic and microscopic analyses. C_LIO_LIArabidopsis PME36 is required to implement the characteristic pattern of de-methylesterified pectin in the mature seed. While this pattern is strongly impaired in pme36-1 and pme36-2 mature seed, no phenotypical effect is observed in the knockout mutant during seed germination. By analyzing hormone homeostasis and gene expression regulation, we show a strong and dynamic physiological disorder in the mutant, which reveals the existence of a complex compensatory mechanism overcoming the defect in pectin de-methylesterification. C_LIO_LIOur results reveal that pectin methylesterification status acts as upstream modulator involved in an undescribed homeostatic system in which pectin remodeling, hormone signaling and transcriptomic regulations interact to ensure the maintenance of a normal seed-to-seedling developmental program. C_LI

plant biology↗

bioRxiv2019

Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm and maternal tissues). However, the complexity of the kernel makes it difficult to understand inter compartment interactions without access to spatially accurate information. Here we took advantage of the large size of the maize kernel to characterize genome-wide expression profiles of tissues at embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared to whole seed compartments: The scutellar aleurone layer (SAL), and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 days after pollination and persists for around 11 days, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific (emb) mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated, and to which additional endosperm cells are recruited as the embryo grows.

plant biology↗

bioRxiv2025

Balancing the supply and demand for taxonomy: an analysis of European taxonomic capacity and policy needs.

Taxonomy is a cornerstone of biological science and essential to biodiversity policy, yet it faces persistent structural challenges collectively known as the "taxonomic impediment". These include limited capacity, uneven geographic and taxonomic coverage, and a disconnect between the supply of expertise and its societal demand. In this study, we present a meta-research analysis of taxonomic activity in Europe over the past decade, drawing on publication metadata from OpenAlex, Wikidata, and GBIF. Using an open and reproducible workflow, we identify more than 31,000 authors affiliated with European institutions who have contributed to taxonomic publications, and we assess their taxonomic and institutional distribution. We explore how this supply of expertise compares with the kinds of demands that arise from European biodiversity policy, including legally binding instruments such as the Birds and Habitats Directives and the Marine Strategy Framework Directive, as well as strategic initiatives focused on invasive alien species, crop wild relatives, and species of conservation concern. Our results highlight clear imbalances in capacity across taxonomic groups and regions, with some politically and ecologically significant taxa receiving comparatively little attention. This work illustrates how openly available data can be used to evaluate taxonomic capacity and its alignment with policy needs, and it provides a framework for others to adopt in support of more strategic planning and investment in taxonomy.

plant biology↗

bioRxiv2024

GLARE: DISCOVERING HIDDEN PATTERNS IN SPACEFLIGHT TRANSCRIPTOME USING REPRESENTATION LEARNING

AO_SCPLOWBSTRACTC_SCPLOWSpaceflight studies present novel insights into biological processes through exposure to stressors outside the evolutionary path of terrestrial organisms. Despite limited access to space environments, numerous transcriptomic datasets from spaceflight experiments are now available through NASAs GeneLab data repository, which allows public access to these datasets, encouraging further analysis. While various computational pipelines and methods have been used to process these transcriptomic datasets, learning-model-driven analyses have yet to be applied to a broad array of such spaceflight-related datasets. In this study, we propose an open-source pipeline, GLARE: GeneLAb Representation learning pipelinE, which consists of training different representation learning approaches from manifold learning to self-supervised learning that enhance the performance of downstream analytical tasks. We illustrate the utility of GLARE by applying it to gene-level transcriptional values from the results of the CARA spaceflight experiment, an Arabidopsis root tip transcriptome dataset that spanned light, dark, and microgravity treatments. We show that GLARE not only substantiated the findings of the original study concerning cell wall remodeling but also revealed additional patterns of gene expression affected by the treatments, including evidence of hypoxia. This work suggests there is great potential to supplement the insights drawn from initial studies on spaceflight omics-level data through further machine-learning-enabled analyses.

plant biology↗

bioRxiv2026

Peacock Eye Disease Management (PedMan) System: Validation and Implementation in Addressing Key Biological Questions

Peacock eye disease, caused by Venturia oleaginea, is a major foliar disease of olive (Olea europaea) in Mediterranean regions, resulting in defoliation, reduced tree vigor, and yield losses. Effective disease management relies on precise fungicide timing. In this study, we validated a decision support system (DSS) named PedMan (Peacock eye disease Manager), designed to predict infection events and optimize fungicide application timing in highly susceptible olive cultivars based on rainfall and temperature conditions. The system was validated in seven independent grove experiments conducted during the 2023/24 and 2024/25 growing seasons in commercial olive orchards in Israel. In addition, simulation analyses were performed using weather data from 11 meteorological stations representing diverse climatic regions. Field validation showed that fungicide applications timed according to PedMan significantly reduced leaf abscission by approximately 60% compared with untreated controls. Applications made contrary to system recommendations did not improve disease control, confirming the reliability of both positive and negative predictions. Multi-season analyses indicated cumulative disease suppression, with up to 85% reduction in leaf abscission after three consecutive years of correctly timed applications. The system was implemented by olive growers in 2025/6 with applicable success. Simulation results showed that most infection events occurred in autumn and early winter, with rainfall as the primary driver in autumn and temperature as the main limiting factor in winter and spring. Across all regions and seasons, PedMan recommended 0-3 fungicide applications per season, comparable to or fewer than conventional spray programs. These findings demonstrate that PedMan is a robust, field-validated DSS that improves fungicide timing, enhances disease control efficiency, and supports sustainable management of peacock eye disease without increasing spray frequency under Mediterranean conditions.

plant biology↗

bioRxiv2023

Bait, not reward: CO2-enriched Nepenthes pitchers secrete toxic nectar

Nepenthes pitchers are leaf-evolved biological traps holding high levels of CO2 within them. Extrafloral nectar (EFN) secreted by these pitchers has long been regarded as the major reward to visiting arthropods, but its chemical constituents and their role in prey capture are least explored. Here we demonstrate Nepenthes EFN as a sugar (glucose-fructose-sucrose) mix with high C:N ratio, minimal amino acids, proteins, and vitamin C. Nepenthes khasiana peristome and lid EFNs displayed strong acetylcholinesterase (AChE) inhibition; the naphthoquinone derivative, (+)-isoshinanolone, has been identified as the AChE inhibitor. Plumbagin, the major volatile naphthoquinone in Nepenthes, also showed strong AChE inhibition. Direct EFN- and (+)-isoshinanolone-feeding bioassays demonstrated symptoms of cholinergic toxicity in ants. We testify that Nepenthes EFN is a toxic bait which hinders neuronal activity in visiting arthropods. These unique traps adopt various deceptive strategies for prey capture, and our discovery abolishes the notion that Nepenthes EFN is a reward to visiting ants and other arthropods. Moreover, our findings infer elevated CO2 within their pitchers as the key factor influencing the growth, metabolism, herbivory, and carnivory in Nepenthes. HighlightNepenthes extrafloral nectar has high content of carbohydrates and minimal nitrogenous metabolites. It is laced with (+)-isoshinanolone, an acetylcholinesterase inhibitor, and acts as a toxic bait, aiding prey capture.

plant biology↗

bioRxiv2025

Determinants of fleshiness or dryness for fruits at maturity: fruit shapes and pericarp permeability

[A hypothesis was proposed that fleshiness or dryness of fruits at maturity were determined just by fruit shapes and pericarp permeability influenced by heterogeneous habitats] The ecological origins of diverse fruit types still remain unresolved due to the lack of knowledge about fruit water content variation patterns during fruit development and after fruit maturity. In this study, we explore factors influencing fleshiness or dryness of fruits at maturity through examining the water content variation patterns before and after fruit maturity, and identify biological and environmental mechanisms about fleshiness or not for fruits at maturity, using data from a survey on fruit shapes of 29760 species and one experiment involving water content measure of fruits. Results show that water content in majority of the fleshy (except for drupes and rosehips) and dry fruits increases or decreases, respectively, during fruit development i.e. prior to maturity, and the water variation patterns are determined by fruit shapes and pericarp permeability. After maturation, water loss occurs slowly at room temperature for fleshy fruits, but it is fast for most dry fruits. In general, declining fruit water content due to pericarp lignification occurring and rising pericarp permeability with the development of dry fruits in later stage of fruit development as well as water imbalance between supply and loss induced by open habitats may lead to the formation of dryness for elongated or flaky dry fruits owing to allometric growth between pedicel diameter (or fruit mass) and fruit surface area. Resulted from water balance, the emergence of fleshiness in mature fleshy fruits is attributed to slow water loss through the pericarp influenced by globular shapes (i.e. greater fruit thickness) and pericarp waxification induced by shaded habitats, or by sporoderm lignification occurring (inside the pericarp) induced by open habitats for a subset of fleshy fruits such as drupes and rosehips.

plant biology↗

bioRxiv2023

First report of a successful development of yam hybrids (Dioscorea alata L.) from lyophilized and long-term stored pollens

BackgroundGreater yam, Dioscorea alata L., is a significant food security crop in tropical areas. However, low genetic diversity and various biological constraints, including susceptibility to viruses, ploidy, erratic and low flowering intensity, and asynchronous flowering hinder successful hybrid development and genetic gains in greater yam breeding programs. Therefore, pollen storage has gained much attention to facilitate genetic material exchanges, artificial pollinations and to increase the genetic gains in breeding programs. This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids. Fresh pollens were collected from two D. alata males, then lyophilized (two lyophilization treatments were applied), followed by storage at room temperature (24-25 {degrees}C) for 12 months. Moreover, the lyophilized and stored pollens were tested for viability by crossing with four female varieties. ResultsOur results showed that lyophilization is effective for achieving viable pollens after 12 months of storage. Treatment 1 (48 h drying) showed higher pollen germination and fertility rates than Treatment 2 (72 h drying). Although we observed a reduction in viability of lyophilized pollens after 12 months of storage, we generated hybrid seedlings with success rates from 12 to 21% compared to 21-31% when using fresh pollens. Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings, which grew well in a greenhouse. ConclusionsThe results signify the importance of pollen lyophilization for yam breeding programs.

plant biology↗

bioRxiv2020

Function and regulation of chloroplast peroxiredoxin IIE

Peroxiredoxins (PRX) are thiol peroxidases which are highly conserved throughout all biological kingdoms. Increasing evidence suggests that their high reactivity toward peroxides has a function not only in antioxidant defense but in particular in redox regulation of the cell. Peroxiredoxin IIE is one of three PRX types found in plastids and has previously been linked to pathogen defense and protection from protein nitration. However, its posttranslational regulation and its function in the chloroplast protein network remained to be explored. Using recombinant protein, it was shown that the peroxidatic Cys121 is subjected to multiple posttranslational modifications, namely disulfide formation, S-nitrosation, S-glutathionylation and hyperoxidation. Slightly oxidized glutathione fostered S-glutathionylation and inhibited activity in vitro. Immobilized recombinant PRX-IIE allowed trapping and subsequent identification of interaction partners by mass spectrometry. Interaction with the 14-3-3 {nu} protein was confirmed in vitro and was shown to be stimulated under oxidizing conditions. Interactions did not depend on phosphorylation as revealed by testing phospho-mimicry variants of PRX-IIE. Based on these data it is proposed that 14-3-3{nu} guides PRX-IIE to certain target proteins, possibly for redox regulation. These findings together with the other identified potential interaction partners of type II PRXs localized to plastids, mitochondria and cytosol provide a new perspective on the redox regulatory network of the cell.

plant biology↗

bioRxiv2023

Protocols to enable fluorescence microscopy of microbial interactions on living maize silks (style tissue) that balance the requirements for containment, biological relevance, viability, and experimental accessibility

There is interest in studying microbes that colonize maize silks (style tissue, critical for reproduction) including the fungal pathogen Fusarium graminearum (Fg) and its interactions with the microbiome and biocontrol agents. In planta imaging of these interactions on living silks using confocal fluorescence microscopy would provide key insights. However, newly discovered microbes have unknown effects of on human health, and there are regulatory requirements to prevent the release of fluorescently-tagged microbes into the environment. Therefore, the microbe infection, colonization, and interaction stages on silks prior to microscopy must be contained. At the same time, silk viability must be maintained and experiments conducted that are biologically relevant (e.g. silks should remain attached to the cob), yet the silk tissue must be accessible to the researcher (i.e. not within husk leaves) and allow for multiple replicates. Here we present methods that meet these five contrasting criteria. We tested these methods using Fg and four silk-derived bacterial endophytes. The endophytes were previously known to have anti-Fg activity in vitro, but in planta observations were lacking. In Method 1, a portion of the tip of a cob was dissected, and silks remained attached to the cob in a Petri dish. The cob was placed on a water agar disc to maintain hydration. DsRed-tagged bacteria and GFP-tagged Fg were inoculated onto the silks and incubated, allowing the two microbes to grow towards one another before staining with propidium iodide for confocal microscopy. A variation of the protocol was presented in Method 2, where detached silk segments were placed directly on water agar where they were inoculated with bacteria and Fg to promote dense colonization, and to allow for many replicates and interventions such as silk wounding. The bacterial endophytes were successfully observed colonizing Fg hyphae, silk trichomes, and entering silks via cut ends and wounds. These protocols can be used to study other silk-associated microbes including several globally important fungal pathogens that enter maize grain through silks.

plant biology↗

bioRxiv2024

Efficient mutagenesis of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present a fast-edit approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel- Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The end to end pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

plant biology↗

bioRxiv2025

Developing the Grapevine Hydric Stress Atlas: A Meta-Analysis Resource for Exploring transcriptome Responses to Drought

Climate change poses a significant threat to agriculture, particularly in regions where increased drought periods, abnormal heat, and intensified pest pressure threaten crop productivity. Viticulture, as one of the most economically important crops, is highly vulnerable to these challenges. Understanding the molecular mechanisms underlying drought responses in grapevines is essential for developing innovative molecular breeding strategies aimed at enhancing drought tolerance, improving cultivar resilience, and promoting agricultural sustainability. In this context, transcriptomic meta-analyses have proven valuable for uncovering global regulatory trends, gene co-expression networks and conserved biological responses across diverse conditions. As part of this study, 1107 public transcriptomic datasets from Illumina (631 runs) and ABI SOLID (476 runs) platforms were searched, reclassified and reanalyzed in the latest T2T genome assembly, in order to construct condition, cultivar and tissue-specific gene expression atlases associated with drought stress in grapevine. To facilitate exploration of this data, a web-based application, the Hydric Stress Atlas App (https://plantaeviz.tomsbiolab.com/vitviz/hydric_atlas/), was developed, as part of the Vitis module within the PlantaeViz platform. Together with this tool, we generated a whole-genome co-expression network using the same datasets (https://plantaeviz.tomsbiolab.com/vitviz/networks/non_agg_gcns/T2T/hydric_stress_TI/). This water stress condition-dependent GCN allows to explore and visualize gene co-expression relationships related to stress and identify network hubs holding novel drought stress regulators. We manually curated experimental metadata, and enabled the classification of transcriptomic data by cultivar, tissue, and drought tolerance. Finally, candidate genes associated with drought tolerance were identified via network topology analysis. These genes can be further used as molecular markers, or characterized via gene editing or cisgenesis, providing insights into their molecular roles in drought tolerance. This resource contributes to a deeper understanding of grapevine drought responses, offering a pathway for sustainable viticulture and innovative biotechnological solutions to address climate-related challenges.

plant biology↗

bioRxiv2023

A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present the first Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar "Zhonghuang 13" (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.

plant biology↗

bioRxiv2023

SoyDNGP: A Web-Accessible Deep Learning Framework for Genomic Prediction in Soybean Breeding

Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. Addressing this biological complexity requires innovative and accurate tools for trait prediction. In response to this challenge, we have developed SoyDNGP, a Convolutional Neural Networks (CNN)-based model that offers significant advancements in the field of soybean trait prediction. Compared to existing methods, such as DeepGS and DNNGP, SoyDNGP boasts a distinct advantage due to its lower parameter volume and superior predictive accuracy. Through rigorous performance comparison, including prediction accuracy and model complexity, SoyDNGP consistently outperformed its counterparts. Furthermore, it effectively predicted complex traits with remarkable precision, demonstrating robust performance across different sample sizes and trait complexities. We also tested the versatility of SoyDNGP across multiple crop species, including Cotton, Maize, Rice, and Tomato. Our results showed its consistent and comparable performance, emphasizing SoyDNGPs potential as a versatile tool for genomic prediction across a broad range of crops. To enhance its accessibility to users without extensive programming experience, we have designed a user-friendly web server, available at http://xtlab.hzau.edu.cn/SoyDNGP. The server provides two primary features: Trait Lookup, offering users the ability to access pre-existing trait predictions for over 500 soybean accessions, and Trait Prediction, allowing for the upload of VCF files for trait estimation. By providing a high-performing, accessible tool for trait prediction and genomic analysis, SoyDNGP opens up new possibilities in the quest for efficient and optimized soybean breeding.

plant biology↗

bioRxiv2021

The Evolutionary History of Small RNAs in the Solanaceae

The Solanaceae or "nightshade" family is an economically important group that harbors a remarkable amount of diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the familys small RNA genomic landscape, we downloaded over 255 publicly available small RNA datasets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major small RNA classes: (1) microRNAs (miRNAs), typically 20-22 nt RNAs generated from a hairpin precursor and functioning in gene silencing, and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs (hc-siRNAs) typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs (phasiRNAs) and trans-acting siRNAs (tasiRNAs) generated via miRNA-directed cleavage of a Pol II-derived RNA precursor. Our analyses described thousands of small RNA loci, including poorly-understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these small RNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar small RNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities. ONE-SENTENCE SUMMARYWe use over 255 publicly-available small RNA datasets to characterize the small RNA landscape for the Solanaceae family.

plant biology↗

bioRxiv2026

Gravitropism Shapes the Pareto Front of Root System Architecture

The root systems of wild tomatoes (S. Pimpinellifolium) can be understood as biological networks in which the lateral roots branch from a single main root and together balance two competing objectives: minimizing the material cost of building the network (wiring cost) and minimizing the transport time from the root tips to the shoot (conduction delay). Our prior work showed that S. Pimpinellifolium root architectures cluster near the Pareto-optimal front defined by these two objectives, with morphological diversity resolving into four qualitative topologies ((Chandrasekhar and Julkowska, 2022)). That framework assumed lateral roots grow as straight lines - ignoring gradual onset of lateral root gravitropism, the tendency of roots to curve toward the gravity vector. Because curved trajectories are longer than straight lines, gravitropism directly increases both wiring cost and conduction delay, constraining which architectures are physically realizable and thereby reshaping the Pareto front itself. Here we extend the model to explicitly incorporate lateral root gravitropism, producing predicted architectures that align much more closely with observed S. Pimpinellifolium root systems. We present a computational method to infer gravitropic sensitivity directly from anatomical tracing data - without reorientation assays - and apply it to 2423 arbors across different root topologies, growth conditions, and hormone treatments. Incorporating gravitropism reveals variation invisible to the straight-line model:notably, lateral roots show reduced gravitropic sensitivity under salt stress, mirroring a phenomenon previously described only for main roots and overlooked in lateral roots until now.

plant biology↗

bioRxiv2021

INDEHISCENT regulates explosive seed dispersal

How traits evolve to produce novelty or stasis is an open question in biology. We investigate this question in Cardamine hirsuta, a relative of Arabidopsis thaliana that employs explosive fracture to disperse its seeds. This trait evolved through key morphomechanical innovations that distinguish the otherwise very similar, dehiscent fruit of these two species. Using CRISPR/Cas9, we show that dehiscence zone formation is absolutely required for explosive fracture in C. hirsuta, and is controlled by the bHLH transcription factor INDEHISCENT (IND). Using mutant screens, we identified the MADS-box transcription factor FRUITFULL (FUL) as a negative regulator of IND in C. hirsuta. Although FUL function is conserved in C. hirsuta, the consequences of IND mis-expression differ in ful mutants of C. hirsuta versus A. thaliana. In ful mutants of both species, valve tissue is replaced by dehiscence zone tissue, which comprises two distinct cell types: lignified layer and separation layer cells. While A. thaliana ful mutants develop stunted fruit with ectopic lignified layer cells, C. hirsuta ful mutants have elongated fruit with ectopic separation layer cells. We show that IND dose determines the proportion of these two cell types in ectopic dehiscence zones. We also show that the extent of ectopic lignification caused by IND mis-expression determines fruit length. Our findings indicate developmental system drift in the conserved gene network patterning dehiscent fruit in two related Brassicaceae species.

plant biology↗

bioRxiv2025

Genetic determinants of aerial root traits that support biological nitrogen fixation in maize

Modern agriculture depends on chemically synthesized nitrogen fertilizer, which ensures high yields but also can carry significant environmental and economic costs. Biological nitrogen fixation (BNF) already supplies nitrogen to legume crops and several avenues of research are underway to extend it to non-legume crops. In maize (Zea mays), aerial roots have been shown to contribute to BNF in some varieties, and both having many aerial roots and large aerial roots contributes to the fixation trait. However, much of the genetics controlling aerial root number and size is still unknown. Here we validate and quantify BNF in maize varieties from Southern Mexico under controlled conditions and evaluate a population of double haploids derived from the elite inbred PHZ51 crossed with these varieties. We find that most aerial root traits (root number, nodes with roots, root size) are reasonably heritable (h2 0.5-0.75) and generally uncorrelated with each other. QTL mapping identifies 5 QTL each affecting nodes with aerial roots and aerial root number per node; in both cases all but 1 QTL show an increase from the landrace allele. We also identify 11 QTL for aerial root diameter, with most positive QTL coming from PHZ51. Between the two populations, only a few QTL overlap, indicating a presumably high diversity of genes affecting aerial root morphology in landrace populations. Combining the best QTL into elite material may provide a path toward meaningful levels of BNF for maize, and additional work is needed to determine how viable this approach will be in field settings.

plant biology↗