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<title>bioRxiv Subject Collection: Genetics Plant Biology</title>
<link>https://biorxiv.org</link>
<description>
This feed contains articles for bioRxiv Subject Collection "Genetics Plant Biology"
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.717650v1?rss=1">
<title>
<![CDATA[
Belgian endive-derived biostimulant activity in Arabidopsis, lettuce and sweet pepper at different developmental stages, environmental conditions, and application methods 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.717650v1?rss=1
</link>
<description><![CDATA[
Belgian endive-derived biostimulant (BEE) was previously shown to enhance root and shoot growth of Arabidopsis thaliana and Plectranthus esculentus in in vitro culturing conditions. In this study, we evaluated the eYect of BEE on A. thaliana subjected to abiotic stresses and assessed the translatability of its bioactivity on lettuce (Lactuca sativa) and sweet pepper (Capsicum annuum) cultured in substrate and soil. A first set of experiments tested the impact of BEE on protection during, and restoration after, osmotic or salt (NaCl) stress. BEE treatment had little to no rescuing eYect when plants were exposed to osmotic stress. In contrast, BEE strongly promoted shoot development and leaf health both under standard and NaCl stress conditions. Under mild stress, BEE enhanced photosynthetic eYiciency and chlorophyll content in Arabidopsis, whereas it did not significantly alleviate osmotic stress induced by sorbitol. To evaluate the eYect under ex vitro conditions, BEE was applied via root drenching to substrate-grown A. thaliana, lettuce, and sweet pepper. BEE improved leaf greenness and photosynthesis enhancing Arabidopsis rosette development, but it did not increase lettuce head weight. In sweet pepper, BEE increased fruit yield and promoted fruit maturation. Under drought stress conditions, BEE application did not improve sweet pepper yield.
]]></description>
<dc:creator><![CDATA[ Ogunsanya, H. Y., Petit, C., Audenaert, K., De Zutter, N., Geelen, D. ]]></dc:creator>
<dc:date>2026-04-17</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.717650</dc:identifier>
<dc:title><![CDATA[Belgian endive-derived biostimulant activity in Arabidopsis, lettuce and sweet pepper at different developmental stages, environmental conditions, and application methods]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718773v1?rss=1">
<title>
<![CDATA[
Discovery of the rosalexin pathway expands the modular network of maize diterpenoid chemical defenses. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718773v1?rss=1
</link>
<description><![CDATA[
The evolutionary expansion of specialized metabolism has shaped the ability of plants to adapt to combined pathogen, pest, and other environmental pressures. For instance, the duplication and divergence of ancestral gibberellin pathway genes have given rise to specialized kauralexin and dolabralexin diterpenoids in maize (Zea mays) that serve as core components of disease resistance and stress adaptation. Here, we describe the biosynthesis and elicited production of rosalexins as a previously unrecognized component of the maize chemical defense network. By integrating genomics-enabled gene discovery, combinatorial enzyme assays, and AI-assisted enzyme mechanistic studies we show that maize rosalexin biosynthesis proceeds via a distinct 5-rosanol scaffold formed by the pairwise activity of two diterpene synthases, ZmTPS38/CPS2/AN2 and ZmTPS42/KSL1, recruited from gibberellin metabolism. Further oxygenation by the promiscuous P450 enzyme, ZmCYP71Z18, yields epoxyrosanol that, in turn, can undergo epoxide ring opening to form trihydroxyrosanol. Epoxyrosanol, but not 5-rosanol or trihydroxyrosanol, display strong inhibitory activity on fungal pathogen growth in vitro, highlighting the contribution of the epoxide group to antibiotic efficacy. Large variation in rosalexin presence and abundance exists across maize genotypes due to expansive ZmTPS42/KSL1 gene sequence variation and pseudogenization. Transcriptomics and targeted metabolomics demonstrated the pathogen-elicited accumulation of rosalexins in maize lines featuring functional ZmTPS42/KSL1 genes. However, no dominant pathogen resistance phenotype was observed in association with rosalexin abundance. These collective findings expand our knowledge of how multiple interconnected diterpenoid pathways arose in maize via duplication of hormone-metabolic genes and enable the utilization of a common precursor to form modular chemical defense layers.
]]></description>
<dc:creator><![CDATA[ Cowie, A. E., Wyatt, G., Schumaker, S. S., Khalil, A., Ross, A. S., Bhattacharjee, S., Narayanan, J., Ding, Y., Hurd, D., Peek, J. O., Poretsky, E., Huffaker, A., Tantillo, D. J., Major, D. T., Schmelz, E. A., Zerbe, P. ]]></dc:creator>
<dc:date>2026-04-17</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718773</dc:identifier>
<dc:title><![CDATA[Discovery of the rosalexin pathway expands the modular network of maize diterpenoid chemical defenses.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718704v1?rss=1">
<title>
<![CDATA[
Sustaining smallholder banana production in Banana Bunchy Top Disease endemic landscapes: integrating clean seed, roguing, and farmer training 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718704v1?rss=1
</link>
<description><![CDATA[
Banana bunchy top virus (BBTV) continues to threaten smallholder livelihoods and food security across sub-Saharan Africa. While clean-seed programmes are widely promoted, their long-term effectiveness is often compromised by rapid reinfection in endemic landscapes. We developed an integrated framework combining spatially explicit, stochastic epidemiological modelling with additional cost-benefit analysis and use of socio-behavioural data to evaluate strategies for stabilising production. Our results demonstrate that frequent monthly inspections and accurate symptom detection are essential for disease suppression. Crucially, the economic analysis reveals that prioritizing diagnostic competence as an economic asset is necessary: improving detection efficiency can more than double farmer net revenue under realistic market conditions. Socio-behavioural findings further confirm that a farmer's ability to correctly recognise symptoms is the strongest predictor of roguing adoption, far outweighing demographic characteristics. These results provide quantifiable guidance for disease management and highlight that the sustainability of clean-seed interventions hinges on shifting policy from simple seed replacement to investing in farmer diagnostic capacity. Strengthening this local surveillance capability transforms informal seed systems into resilient, durable tools for safeguarding household nutrition and regional food security.
]]></description>
<dc:creator><![CDATA[ Retkute, R., Omondi, A. B., Zandjanakou-Tachin, M., Agoi, U. R., Staver, C., Kumar, P. L., Thomas, J. E., Gilligan, C. A. ]]></dc:creator>
<dc:date>2026-04-17</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718704</dc:identifier>
<dc:title><![CDATA[Sustaining smallholder banana production in Banana Bunchy Top Disease endemic landscapes: integrating clean seed, roguing, and farmer training]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718787v1?rss=1">
<title>
<![CDATA[
Successful gene editing in tetraploid alfalfa using the open-source, AI-derived OpenCRISPR-1 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718787v1?rss=1
</link>
<description><![CDATA[
While CRISPR/Cas-based gene editing technologies have the potential to greatly advance crop breeding endeavours, intellectual property-related challenges can hinder the ability to move such varieties to the market. Recently, an open-access Cas enzyme derived from large language models (OpenCRISPR-1) was developed and shown to function effectively in human cells. In this study, we demonstrate the successful use of this nuclease in a polyploid plant species (Medicago sativa), with mono- or bi-allelic editing observed in 30% of genotypes bearing OpenCRISPR-1. These findings indicate that OpenCRISPR-1 holds promise to expand the use of gene editing technology in the breeding of polyploid crops.
]]></description>
<dc:creator><![CDATA[ Alam, S., Subedi, U., Burton Hughes, K., Chen, G. G., Da Ros, L., Bilichak, A., Singer, S. ]]></dc:creator>
<dc:date>2026-04-17</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718787</dc:identifier>
<dc:title><![CDATA[Successful gene editing in tetraploid alfalfa using the open-source, AI-derived OpenCRISPR-1]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.717981v1?rss=1">
<title>
<![CDATA[
Circadian Timekeeping in the Tropics: Rhythmic Transcriptome and Diurnal Regulatory Networks in Rubroshorea leprosula 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.717981v1?rss=1
</link>
<description><![CDATA[
Circadian rhythms allow plants to regulate internal processes to align with daily rhythms in the environment. Comparing circadian clocks across environments is essential because latitude-dependent variation in light and temperature imposes distinct selection pressures that shape the evolution and function of circadian timing systems. However, circadian clock studies have largely focused on temperate and subtropical species, leaving transcriptional circadian networks in tropical plants under relatively constant environments poorly understood. We report the first comprehensive circadian transcriptome of the ecologically important dipterocarp species Rubroshorea leprosula, a dominant species in tropical rainforests in Southeast Asia. One sapling was sampled every four hours for 48 hours under constant darkness and used for transcriptomic analyses. Only 283 of 20,748 expressed genes (~1.3%) exhibited significant circadian oscillations, with periods strongly concentrated between 23 and 25 h. Hierarchical clustering revealed four temporal clusters with alternate phases of expression and functional specialisation; morning clusters in processes related to light and chloroplast, midday clusters in hormone and signalling mechanisms, afternoon clusters in mitochondrial and peptide biosynthesis functions, and night clusters in protein quality control and autophagy. Comparative analysis identified clear orthologs for all major Arabidopsis circadian clock components (LHY, CCA1, PRRs, TOC1, ELF4, LUX, GI, ZTL, RVEs), with conserved synteny to Parashorea chinensis, a close relative of R. leprosula. Time-lagged cross-correlation (TLCC) network reconstruction identified a characteristic circadian topological similarity with Arabidopsis, including coupled morning and evening feedback loops and paralog expansion that maintained overall structure. Peak expression timing of these core clock genes in the tropical tree was largely consistent with that observed in Arabidopsis thaliana. In contrast to this conserved phase relationship, Rubroshorea orthologs exhibited reduced amplitudes and lower coefficients of variation in their circadian oscillations, suggesting diminished robustness of rhythmic gene expression. These findings demonstrate a conserved but regulated circadian mechanism in R. leprosula, in preparation for adaptation to tropical rainforest's stable light and temperature regimes. This study lays the molecular foundation for circadian regulation in dipterocarps and offers a system for integrating rhythmic gene expression to ecological function and forest productivity in tropical communities.
]]></description>
<dc:creator><![CDATA[ Singh, S. K., Seki, M., Ito, H., Tani, N., Ikezaki, Y., Ohta, K., Yeoh, S. H., Ching, N. C., Satake, A. ]]></dc:creator>
<dc:date>2026-04-17</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.717981</dc:identifier>
<dc:title><![CDATA[Circadian Timekeeping in the Tropics: Rhythmic Transcriptome and Diurnal Regulatory Networks in Rubroshorea leprosula]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718623v1?rss=1">
<title>
<![CDATA[
Genetic dissection of root-mediated yield heterosis in melon (Cucumis melo) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718623v1?rss=1
</link>
<description><![CDATA[
Heterosis, the superiority of hybrids over their parents, is a major genetic force associated with plant fitness and crop yield enhancement. We previously discovered and characterized root-mediated yield heterosis (RMYH) in melon (Cucumis melo) using a half-diallel population, derived from 20 diverse parents. In the current study we investigated the genetic architecture of RMYH using a segregating population derived from a selected F1 hybrid (HDA019) that consistently induced RMYH under several melon scion varieties and growing conditions. 78 recombinant inbred lines (RILs) and their test-crosses to both parents were analyzed in yield trials as rootstocks under a common commercial scion variety. The population displayed normal root-mediated yield distribution and transgressive segregation relative to the parents but none of the RILs equaled the superior performance of the F1 hybrid. RMYH of HDA019 was dissected to small effect QTLs showing mostly additive or dominant mode-of-inheritance and favorable QTL-alleles were contributed by both parents. Five consistent QTLs were selected and used to demonstrate the potential of root-mediated yield QTL pyramiding, and 20 combinations of QTL pairs and triplets supported the cumulative model for heterosis. Favorable QTLs alleles were introgressed to generate advanced QTL-backcross lines that were used for validation. This study provides first detailed genetic dissection of yield-related rootstock traits in cucurbits, highlighting rootstock breeding as an important underutilized route for improving yield and stress tolerance of crops.
]]></description>
<dc:creator><![CDATA[ Dafna, A., Tzuri, G., Oren, E., Isaacson, T., Halperin, I., Peleg, G., Gur, A. ]]></dc:creator>
<dc:date>2026-04-17</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718623</dc:identifier>
<dc:title><![CDATA[Genetic dissection of root-mediated yield heterosis in melon (Cucumis melo)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718673v1?rss=1">
<title>
<![CDATA[
Catalase 2-dependent regulation of autophagy in response to carbon starvation in Arabidopsis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718673v1?rss=1
</link>
<description><![CDATA[
Reactive oxygen species (ROS) are fundamental regulators of plant development and stress acclimation. However, their roles in carbon starvation tolerance remain largely unresolved. We therefore dissected the dynamics of redox regulation in carbon-starved Arabidopsis leaves. We present data showing the presence of an early ROS wave that activates autophagy, followed by a sustained, accumulation of hydrogen peroxide (H2O2) that leads to programmed cell death. We show that catalase 2 (CAT2) constitutively binds and sequesters the autophagy initiators ATG1a and ATG13a, a process that prevents the activation of autophagy under carbon-replete conditions. The accumulation of H2O2 in response to carbon starvation leads to oxidation of the Cys-370 and Cys-413 residues on the CAT2 protein and dissociation from ATG1a/13a, thereby allowing ATG1-kinase complex assembly and autophagosome formation. The expression of CAT2-C370S or CAT2-C413S variants in the cat2-1 mutant significantly enhanced carbon starvation tolerance, because both variants retain catalase activity but fail to bind ATG1a/13a. We conclude that CAT2 functions as a redox-sensitive regulator of autophagy.
]]></description>
<dc:creator><![CDATA[ Zhang, C., Li, S.-Q., Jing, P., Wu, J.-X., Chen, B.-H., Liao, C.-Y., Yang, H., Lu, K.-K., Song, R.-F., Foyer, C. H., Liu, W.-C. ]]></dc:creator>
<dc:date>2026-04-17</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718673</dc:identifier>
<dc:title><![CDATA[Catalase 2-dependent regulation of autophagy in response to carbon starvation in Arabidopsis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718745v1?rss=1">
<title>
<![CDATA[
Humanized Klotho haplotypes cause widespread transcriptomic changes in mouse brain 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718745v1?rss=1
</link>
<description><![CDATA[
Klotho (KL) is an aging factor that has been associated with Alzheimer's Disease (AD) risk. Two common alleles circulate in human populations: the major allele FC and the minor allele VS, which is defined by two SNPs that cause two amino acid substitutions (F352V and C370S) in KL's second exon. To investigate the possibility that human KL variants influence brain aging and cognition, we developed a novel mouse model with humanized KL alleles. We used RNA-Seq to measure the whole brain transcriptome in four- and 12-month-old male and female C57Bl/6J mice carrying either the FC or the VS KL allele. We found that FC and VS carriers had widespread differences in gene expression in the brain at 12 months old, but not at four months old. The largest differences were in genes annotated to mitochondrial, ribosomal, and synaptic functions. Differential exon usage analysis identified differential splicing of synaptic genes, further supporting a role for KL on neuronal function. A more focused analysis of differential expression identified variation in glutamate receptors and amyloid precursor (APP) processing in particular, thereby linking human KL haplotypes to biological processes integral to AD pathogenesis. These results provide evidence that the human FC and VS KL haplotypes affect the function of the KL protein product in a manner that has widespread effects on gene expression in the brain and supports the hypothesis that these haplotypes may influence AD risk and pathogenesis.
]]></description>
<dc:creator><![CDATA[ Tyler, A. L., Garceau, D., Kotredes, K. P., Haber, A., Spruce, C., Pandey, R. S., Preuss, C., Sasner, M. J., Carter, G. W. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718745</dc:identifier>
<dc:title><![CDATA[Humanized Klotho haplotypes cause widespread transcriptomic changes in mouse brain]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718682v1?rss=1">
<title>
<![CDATA[
Strong inhibition of insulin/IGF-1 signaling in early-mid adulthood compresses morbidity, but in later life accelerates aging 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718682v1?rss=1
</link>
<description><![CDATA[
Reduced insulin/IGF-1 signaling (IIS) can greatly extend lifespan in C. elegans. However, its effects on the duration of healthy life (healthspan) remain unclear, with several reports of either morbidity expansion or scaled effects, though none of morbidity compression. Moreover, life-extension by IIS reduction is particularly inter-individually variable within populations, confounding efforts to understand the intra-individual biology of such interventions. Here, we performed a longitudinal investigation at individual nematode resolution, of IIS reduction on aging-related health and lifespan, through temporally-controlled auxin-induced degradation (AID) of the DAF-2 insulin/IGF-1 receptor. Our results show how inter-individual variation in aging rate within control populations explains the complex demographic effects of age-specific DAF-2 AID on population lifespan. Strikingly, adult-limited IIS reduction causes an inter-individually homogeneous increase in lifespan (reducing Gompertz  rather than {beta}) that is driven by healthspan expansion and compression of morbidity. Unexpectedly, cessation of DAF-2 AID in decrepit elderly individuals rejuvenates locomotory capacity and extends lifespan, showing that higher levels of IIS are optimal for health and survival towards the end of life. We also document a memory effect of transient IIS reduction during early adulthood, that is sufficient to fully extend lifespan (+189% median lifespan). Together, these findings demonstrate that both lifespan and healthspan can be maximized by appropriate temporal and directional modulation of IIS.
]]></description>
<dc:creator><![CDATA[ Zhang, B., Hsiung, K. C., Biju, R., Cameron-Pack, M., Wei, X., Chapman, H., Kelaj, M., Zhang, A., Nguyen Hong, C., Ewald, C. Y., Gems, D. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718682</dc:identifier>
<dc:title><![CDATA[Strong inhibition of insulin/IGF-1 signaling in early-mid adulthood compresses morbidity, but in later life accelerates aging]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718421v1?rss=1">
<title>
<![CDATA[
The Posidonia oceanica Large PSI-LHCII supercomplex reveals the molecular basis of PSI spectral diversification in higher plants 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718421v1?rss=1
</link>
<description><![CDATA[
Land plant Photosystem I (PSI) can capture low-energy photons and convert them into chemical energy through special far-red absorbing chlorophylls, the red-forms. Although the spectral diversity of the red-forms stepped up during land plant evolution, its molecular basis remains largely unknown. The Mediterranean seagrass Posidonia oceanica evolved a large PSI-light-harvesting complex I and II supercomplex (L-PSI-LHCI-LHCII) with blue-shifted absorption and strongly attenuated red-forms. Here, we report the 1.9 A cryo-EM structure of this unique and blue-adapted photosystem, comprising a PSI core with four canonical Lhca proteins (Lhca1-4), a canonically bound LHCII trimer, and an additional Lhca1-Lhca4 dimer anchored through amino-acid residues largely conserved in both marine and land plants. The sub-2 A map revealed several pigment substitutions in the LHC's and further identified amino-acid sites shaping the local red-form environments. Comparison with land plants showed substitution patterns at those sites consistent with the spectral diversification of PSI. These findings suggest a shared structural basis for red-form tuning in higher plants, accounting both seagrass adaptation to seawater light and the broad extent of far-red absorption in land plants.
]]></description>
<dc:creator><![CDATA[ Charras-Ferroussier, Q., Alsenani, T., Al-Amoudi, A., Siponen, M. I., Heilmann, E., Naschberger, A., Jungas, C. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718421</dc:identifier>
<dc:title><![CDATA[The Posidonia oceanica Large PSI-LHCII supercomplex reveals the molecular basis of PSI spectral diversification in higher plants]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718567v1?rss=1">
<title>
<![CDATA[
Rhizo-PET: A Dedicated PET System for 4D Imaging of Carbon Dynamics in the Rhizosphere 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718567v1?rss=1
</link>
<description><![CDATA[
Imaging carbon movements in the rhizosphere is fundamentally limited by high soil heterogeneity, low signal levels, and lack of methodology. We present Rhizo-PET, a dedicated positron emission tomography (PET) imaging and analysis framework designed to characterize the 4D spatiotemporal patterns of tracer distribution in intact plant-soil systems. The system achieved a global energy resolution of 11.93 {+/-} 0.02% FWHM at 511 keV and maintained stable performance over 8 h of continuous acquisition, with a coincidence rate variation of only 0.7%. Spatial resolution reached 1.06 mm near the center of the field of view, establishing a high-fidelity region for root-scale analysis. Dynamic datasets were acquired from live Phaseolus vulgaris plants (N = 3) over 180 min following 11CO2 pulse labeling and reconstructed into 3 min temporal frames. Quantitative analysis across 243 independent regions of interest (ROI) revealed that cumulative tracer accumulation decreases monotonically with radial distance from the root axis, while axial transport delays increase systematically in lower root segments (p < 0.001). Hierarchical variability analysis showed that within-plant spatial organization (CVTTP  = 0.03) is significantly more stable than inter-plant variation (CVTTP  = 0.14), proving that the observed heterogeneity reflects biological spatial organization rather than experimental instability. These results establish Rhizo-PET as a robust, reproducible platform for the non-invasive, time-resolved analysis of carbon dynamics in the rhizosphere under realistic soil conditions.
]]></description>
<dc:creator><![CDATA[ Ullah, M. N., Hastings, D., Lee, S. J., Park, W., Zou, S. J., Anders, D., Park, J. H., Weisenberger, D., Cheng, W., Abbaszadeh, S., Levin, C. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718567</dc:identifier>
<dc:title><![CDATA[Rhizo-PET: A Dedicated PET System for 4D Imaging of Carbon Dynamics in the Rhizosphere]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718228v1?rss=1">
<title>
<![CDATA[
Nitric Oxide Modulates Auxin Signaling through TIR1 S-Nitrosylation During Thermomorphogenesis in Arabidopsis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718228v1?rss=1
</link>
<description><![CDATA[
Auxin, a central hormone coordinating plant growth, integrates both environmental and developmental signals to regulate cell expansion, division, and organ patterning. Among these environmental cues, elevated ambient temperatures trigger a suite of developmental adaptations collectively known as thermomorphogenesis. In this study, we identify nitric oxide (NO) as a key mediator in the temperature-dependent regulation of auxin signaling. Our results show that warm temperatures (28-29 {degrees}C) enhance auxin-induced NO accumulation in Arabidopsis thaliana seedlings. Using pharmacological and genetic approaches, we demonstrate that NO is required for proper thermomorphogenic responses in aerial tissues. This redox signal promotes the stabilization and nuclear localization of the F-box auxin receptor TIR1, a crucial step for the activation of downstream auxin responses. Specifically, tir1-1 seedlings expressing a non-nitrosylatable TIR1 variant mutated at the Cys140 residue exhibit impaired hypocotyl elongation and hyponasty under warm conditions compared to seedlings complemented with wild-type TIR1. These results highlight the functional relevance of the TIR1 Cys140 residue, a known target for S-nitrosylation, in coordinating thermomorphogenic responses. In contrast, the absence of TIR1 S-nitrosylation restricts primary root elongation at 22 {degrees}C but does not affect the growth-promoting effects of warm temperatures. Our findings uncover a novel redox-dependent regulatory layer in auxin signaling, where S-nitrosylation of TIR1 may modulate its stability and subcellular localization in a temperature- and organ-specific manner. This mechanism allows differential growth responses between shoot and root organs and highlights the complexity of hormonal and redox interplay during plant adaptation to elevated temperatures.
]]></description>
<dc:creator><![CDATA[ TEBEZ, N. M., Correa-Aragunde, N., Murcia, M. G., Salvat, S., Casco, A., Fiol, D. F., Casalongue, C. A., Iglesias, M. J., Terrile, M. C. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718228</dc:identifier>
<dc:title><![CDATA[Nitric Oxide Modulates Auxin Signaling through TIR1 S-Nitrosylation During Thermomorphogenesis in Arabidopsis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718293v1?rss=1">
<title>
<![CDATA[
The Euler Characteristic Transform Enables Classification of Complex Plant Shapes and Prediction of Leaf Venation from Blade Geometry 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718293v1?rss=1
</link>
<description><![CDATA[
Rationale: Quantifying and predicting plant morphology is central to understanding development and evolution, yet many plant forms lack homologous features required for traditional morphometrics. We apply the Euler Characteristic Transform (ECT), an injective descriptor from topological data analysis, to encode 2D plant shapes. The ECT converts contours into image-like representations that preserve shape information while enabling deep learning. Methods: We computed ECTs for large datasets of leaf and pavement cell shapes and used convolutional neural networks (CNNs) for classification. We also trained CNNs to approximate the inverse mapping, predicting leaf shape masks from radial ECTs. Key results: ECT-based models achieved high classification accuracy, surpassing previous approaches on millions of herbarium-derived leaves. Notably, grapevine leaf venation was predicted from blade geometry alone, demonstrating that vascular structure is encoded in the outline. Main conclusion: The ECT provides a compact, information-preserving representation of biological shape that integrates naturally with deep learning. It enables both accurate classification and predictive reconstruction, revealing latent morphological information and offering new opportunities to study plant form across scales.
]]></description>
<dc:creator><![CDATA[ Ayub, Y., McGuire-Scullen, S., Percival, S., Weaver, W. N., Karki, N., Yahiaoui, W., Astudillo-Pavon, K., Barrios, A., Check, J. C., Colchado-Lopez, J., Dolgikh, B. A., Espinosa-Martinez, D. V., Fu, Q., Galvan-Lara, K. M., Garcia-Chavez, J. N., Garcia-Rios, S., Grabb, C. N., Guadir-Lara, G. E., Hawkins, J. C., Hendrickson, C. L., Hightower, A. T., Hurtado-Olvera, J. J., Kianian, S., Lennon, J., Li, Z., Li, J., Lieb, B., Lin, J., Lopez-Sanchez, P., Luna-Alvarez, M., Martinez-Martinez, C., Montemayor-Lara, a., Moreno, N. A., Obisesan, I. A., Perez-Flores, O., Pimentel-Ruiz, C., Pineda-Hernandez ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718293</dc:identifier>
<dc:title><![CDATA[The Euler Characteristic Transform Enables Classification of Complex Plant Shapes and Prediction of Leaf Venation from Blade Geometry]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718410v1?rss=1">
<title>
<![CDATA[
Soil-based disease bioassay for the study of rhizogenic Agrobacterium-tomato interactions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718410v1?rss=1
</link>
<description><![CDATA[
Hairy root disease (HRD), caused by rhizogenic Agrobacterium, is an economically important disease affecting hydroponic tomato (Solanum lycopersicum L.) production worldwide. HRD-affected plants show extensive root proliferation, resulting in decreased energy expenditure towards fruit production. Host plant susceptibility to rhizogenic Agrobacterium is typically evaluated through artificial wounding-based infection bioassays. However, under natural infection settings, rhizogenic Agrobacterium can induce disease symptoms without deliberate, artificial wounding. We developed a soil-based, non-wounding bioassay that closely mimics natural rhizosphere interactions and permits quantitative and qualitative assessment of HRD symptoms. The assay measured root dry weight, documented agravitropic root development typical of HRD and confirmed in planta T-DNA gene expression using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). We used this bioassay to evaluate disease symptoms towards rhizogenic Agrobacterium in tomato cv. Moneymaker and the rootstocks Optifort, Maxifort, and Arnold. Optifort and Maxifort exhibited significantly higher root biomass than Arnold and Moneymaker, indicating more pronounced symptom development. The bioassay also differentiated virulence levels amongst various rhizogenic Agrobacterium strains isolated from HRD-affected plants. Together, these results show that our soil-based bioassay provides a robust and ecologically relevant platform for screening tomato genotypes and comparing virulence levels of rhizogenic Agrobacterium strains supporting resistance breeding and disease management efforts.
]]></description>
<dc:creator><![CDATA[ Rodrigues, S. D., Kim, N., Moons, J., Rediers, H., Pauwels, L., De Coninck, B. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718410</dc:identifier>
<dc:title><![CDATA[Soil-based disease bioassay for the study of rhizogenic Agrobacterium-tomato interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718301v1?rss=1">
<title>
<![CDATA[
Genotypic and environmental effects on seed coat patterning and nutritional composition in common bean (Phaseolus vulgaris L.) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718301v1?rss=1
</link>
<description><![CDATA[
Common bean (Phaseolus vulgaris L.) is the leading grain legume consumed directly by humans and a primary source of nutrients in many communities. This study utilized common bean genotypes with diverse seed coat phenotypes to investigate genotypic and environmental effects on pigmented seed coat area and seed macronutrient (protein, starch, fat, ash, moisture), anti-nutrient (phytate), and mineral nutrient (iron, zinc, calcium, phosphorus, magnesium, potassium, sodium) profiles. Recombinant inbred lines (RILs) that comprise six phenotypic classes for seed coat patterning and nine commercial cultivars were field-evaluated for multiple years across inland, coastal, and intermountain environments in California. A custom near-infrared spectroscopy calibration improved macronutrient prediction accuracy relative to a pre-existing calibration. Environmental effects on macronutrients were pronounced; the 2022 coastal growing environment was the most distinct, characterized by significantly higher starch and moisture content and significantly lower protein content in the RILs relative to any other environments. Across growing years in the RILs, greater consistency was observed at the inland site, where only protein was significantly different; all macronutrient traits significantly differed within the intermountain site. Certain commercial cultivars largely maintained their relative rank for protein content across environments, indicating consistency of genotypic performance, and Black Nightfall ranked among the highest for iron, zinc, phosphorus, and magnesium. Percent pigmented seed coat area was significantly negatively correlated with both calcium and magnesium concentrations. These results underscore the importance of genotype-by-environment field trials for seed coat patterning, seed nutritional composition, and their interplay, to support breeding of common bean among other grain legumes.
]]></description>
<dc:creator><![CDATA[ Bolt, T. M., Cole, A., Bains, R., Tian, L., Parker, T. A., Gepts, P., Palkovic, A., Bornhorst, G., Diepenbrock, C. H. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718301</dc:identifier>
<dc:title><![CDATA[Genotypic and environmental effects on seed coat patterning and nutritional composition in common bean (Phaseolus vulgaris L.)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718129v1?rss=1">
<title>
<![CDATA[
Expanding the repertoire of suicidal germination stimulants for control of parasitic weeds 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718129v1?rss=1
</link>
<description><![CDATA[
Witchweeds (Striga spp.) are parasitic plants that severely constrain cereal production across sub-Saharan Africa, threatening food security for millions of people (Runo and Kuria, 2018). Striga infection begins when dormant seeds germinate in response to host-derived biomolecules, primarily strigolactones which plants emit to regulate shoot branching and to communicate with beneficial microbes. This obligate dependence on host signals can be exploited for Striga control through suicidal germination, whereby strigolactone-like compounds induce parasite germination in the absence of a host. Although this strategy proved highly effective during Striga eradication efforts in the United States using ethylene gas as a Striga germination inducer (Eplee, 1975; Iverson et al., 2011), its deployment in Africa has been limited by capacity to synthesize cost-effective strigolactone-like Striga germination inducers. Here, we show that structure-guided in silico screening of chemical libraries using AlphaFold2-modeled receptor-ligand interactions improve the efficiency and likelihood of identifying previously unknown strigolactone analogs. Using this approach, we identify a structurally simple synthetic lactone scaffold that induces Striga germination at nanomolar concentrations. These results present new avenues for the development of strigolactone analogs and support revisiting suicidal germination as a practical Striga control strategy in Africa.
]]></description>
<dc:creator><![CDATA[ Mave, G. D., Musyoka, T. M., Mutinda, S., Mutindi, F., Kibet, W., Toili, M. E. M., Muiruri, S., Onguso, J., Tripathi, J., Tripathi, L., Runo, S. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718129</dc:identifier>
<dc:title><![CDATA[Expanding the repertoire of suicidal germination stimulants for control of parasitic weeds]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718140v1?rss=1">
<title>
<![CDATA[
A NOVEL MITOCHONDRIAL PEPTIDE ESSENTIAL FOR RESPIRATORY CAPACITY PROMOTES GROWTH, YIELD AND ABIOTIC STRESS TOLERANCE IN PLANTS 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718140v1?rss=1
</link>
<description><![CDATA[
SUMMARY Efforts to boost crop productivity have focused on improving photosynthesis. However, plant respiration consumes over 90% of fixed carbon, fueling growth, stress responses, and resource acquisition. Despite its metabolic centrality, respiratory regulation remains underexplored as a yield target. Here, we identify AtMLSP1 (At4g17085), a 57-amino-acid mitochondrial inner membrane peptide in Arabidopsis thaliana. Loss-of-function atmlsp1 mutants show impaired growth, while AtMLSP1 overexpression boosts biomass, seed yield, and high light tolerance. No induction of alternative oxidase protein abundance or activity was observed in atmlsp1 plants, a response normally triggered by respiratory perturbation. Mitochondria isolated from atmlsp1 lines had an approximately 90% reduction in the amount of the intermembrane space protein Cytochrome c and a 30% reduction in all subunits of complex III, while other respiratory complexes remain unaffected. As expected, loss-of-function plants atmlsp1 reveal a significant decrease in total respiratory capacity and membrane potential, but mitochondrial integrity, and abundance of complex I, II and complex IV were unchanged. Overexpression of the orthologues of this gene in Oryza sativa (rice) and Glycine max (soybean) results in a significant increases in yield (seed number and size) under field conditions across different locations.
]]></description>
<dc:creator><![CDATA[ Gan, L., Zhu, Y., Wang, X., Whelan, J., Shou, H. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718140</dc:identifier>
<dc:title><![CDATA[A NOVEL MITOCHONDRIAL PEPTIDE ESSENTIAL FOR RESPIRATORY CAPACITY PROMOTES GROWTH, YIELD AND ABIOTIC STRESS TOLERANCE IN PLANTS]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718703v1?rss=1">
<title>
<![CDATA[
Independent Trafficking and Diverse Stability of XyG-Synthesizing Glycosyltransferases in Distinct Golgi cisternae 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718703v1?rss=1
</link>
<description><![CDATA[
XyG-synthesizing glycosyltransferases (GTs) are localized in Golgi, and their protein-protein interactions suggest the formation of multiprotein complexes; however, the mechanisms underlying protein complex assembly and transportation, protein stability and degradation remain unknown. We have uncovered that protein-protein interactions among XyG-synthesizing GTs are not prerequisites for Golgi localization and different GTs are first delivered to Golgi as independent proteins. By employing the transient expression of YFP-fused GTs along with a cis-Golgi marker and generating fluorescence intensity profiles, we demonstrated the differential distribution of GTs in Golgi apparatus. We treated Arabidopsis seedlings expressing GTs with cycloheximide (CHX) to estimate half-lives, The GTs exhibit distinct half-lives, and based on their turnover rates, divided into two groups. Our findings revealed that cellulose synthase-like C4 (CSLC4), galactosyltransferase (MUR3), and fucosyltransferase (FUT1) exhibit longer stability. In contrast, XyG xylosyltransferases XXT1, XXT2, XXT5, and galactosyltransferase XLT2 are significantly shorter-living proteins. XyG-synthesizing proteins traffic independently to Golgi, exhibiting distinct sub-Golgi localization that shapes multiprotein complex assembly in specific cisternae. This spatial organization governs partner GT access and residence time for functional efficiency, while GT half-life variations regulate stability and interaction dynamics. Collectively, these factors provide a critical framework for independent operation and coordinated organization of Golgi-resident XyG-synthesizing proteins.
]]></description>
<dc:creator><![CDATA[ Zhang, N., Uthe, K., Zabotina, O. A. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718703</dc:identifier>
<dc:title><![CDATA[Independent Trafficking and Diverse Stability of XyG-Synthesizing Glycosyltransferases in Distinct Golgi cisternae]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718249v1?rss=1">
<title>
<![CDATA[
Genome-wide CRISPR screens identify DNA repair and R-loop suppression as regulators of the cellular sensitivity to environmentally relevant Bisphenol A exposure 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718249v1?rss=1
</link>
<description><![CDATA[
Bisphenol A (BPA) is a prevalent chemical used in the production of plastics. While adverse effects on the reproductive system have been documented, more recent studies also associated BPA exposure with carcinogenesis as well as genomic instability. However, these studies were generally performed using BPA concentrations much higher than those observed in the serum or urine of the general population, making their relevance unclear. To address this, we report here an unbiased genetic study to identify mechanisms responding to environmentally relevant BPA exposure. We performed genome-wide CRISPR knockout screens in HeLa and RPE1 cells upon continuous exposure to 0.5uM BPA, a concentration similar to the mean BPA concentration found in the urine of plastics manufacturing workers, for 19 days. We found genome stability genes among the top common hits between the two cell lines, suggesting that BPA causes DNA damage at this environmentally relevant exposure dose. We validated the DNA repair gene RAD51C and the RNA helicase DDX21 as genes required for BPA resistance. Moreover, we show that BPA exposure increases the formation of R-loops which are resolved by DDX21. Our study suggests that BPA exposure at environmentally relevant doses can cause DNA damage, highlighting the relevance of BPA for carcinogenesis.
]]></description>
<dc:creator><![CDATA[ Hale, A., Nusawardhana, A., Straka, J., Nicolae, C. M., Moldovan, G.-L. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718249</dc:identifier>
<dc:title><![CDATA[Genome-wide CRISPR screens identify DNA repair and R-loop suppression as regulators of the cellular sensitivity to environmentally relevant Bisphenol A exposure]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718201v1?rss=1">
<title>
<![CDATA[
Loss of Propionyl-CoA Carboxylase Reprograms Hepatic Metabolism by Suppressing Mitochondrial Pyruvate Carboxylation and Fatty Acid Oxidation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718201v1?rss=1
</link>
<description><![CDATA[
Propionic acidemia (PA) is an inborn error of metabolism caused by propionyl-CoA carboxylase (PCC) deficiency due to mutations in either PCCA or PCCB. Without proper management, the disease is associated with high mortality. Even with dietary restriction, patients often develop complications later in life, and the underlying pathological mechanisms remain poorly understood. The liver is the primary organ responsible for propionyl-CoA metabolism, yet the metabolic alterations induced by PCC deficiency in the liver have not been systematically investigated. In this study, we used a hepatocyte model of PA-- PCCAnull-HepG2 cells--to comprehensively examine metabolic alterations using stable isotope-based metabolic flux analysis. The PCCA knockout recapitulated key metabolic features of PA in HepG2 cells. Furthermore, PCCA deficiency reduced mitochondrial fatty acid oxidation while increasing glucose oxidation through pyruvate dehydrogenase. In contrast, pyruvate anaplerosis via pyruvate carboxylase was markedly reduced in PCCA knockout cells. This reduction in anaplerotic flux impaired the capacity for gluconeogenesis and lipid synthesis, consistent with observations from in vivo studies in Pcca-/- (A138T) mice. Additionally, branched-chain keto acid catabolism was reduced in PCCA knockout HepG2 cells. Threonine showed minimal metabolic contribution in this model, further supporting the role of propionate as a major source of propionyl-CoA production. Collectively, these findings highlight the metabolic vulnerabilities associated with PCC deficiency and underscore the increased risk of prolonged fasting in patients with PA, particularly those with severe disease.
]]></description>
<dc:creator><![CDATA[ Lu, F., Paiboonrungruang, C., He, W., Xiong, Z., Tang, P., Kasumov, T., Chen, X., Zhang, G. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718201</dc:identifier>
<dc:title><![CDATA[Loss of Propionyl-CoA Carboxylase Reprograms Hepatic Metabolism by Suppressing Mitochondrial Pyruvate Carboxylation and Fatty Acid Oxidation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718132v1?rss=1">
<title>
<![CDATA[
Plant LETM1 homologs are required for fungus-induced antibiotic resistance and biostimulation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718132v1?rss=1
</link>
<description><![CDATA[
Our findings confirm that CIRA15A / LEUCINE ZIPPER-EF-HAND CONTAINING TRANSMEMBRANE PROTEIN1 (LETM1) is critical for Trichoderma-induced growth biostimulation in sugar beet and the Cellulase-Induced Resistance to Alamethicin (CIRA) response in Arabidopsis. Notably, this plant homolog of a gene associated with human disease plays a vital role in both defense against Trichoderma antimicrobial peptides and the biostimulation of plant growth. We identified AtCIRA15A/LETM1 and AtCIRA15B/LETM2 as key genetic determinants of CIRA through Arabidopsis analysis and comparative studies of sugar beet inbred lines. BvLETM1 allelic variations correlated with differential biostimulation responses, and complementation confirmed functional LETM1 alleles restore CIRA in Arabidopsis mutants. These findings highlight LETM1 as a crucial factor in Trichoderma-plant interactions, with potential applications in breeding for enhanced microbial-induced plant biostimulation and agricultural productivity.
]]></description>
<dc:creator><![CDATA[ Dotson, B. R., Panthapulakkal Narayanan, S., Behnamian, S., Kailasam, S., Shah, M., Kraft, T., Schmidt, J., Ekblad, T., Veeckman, E., Fredlund, K., Grenville-Briggs, L. J., Rasmusson, A. G. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718132</dc:identifier>
<dc:title><![CDATA[Plant LETM1 homologs are required for fungus-induced antibiotic resistance and biostimulation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718066v1?rss=1">
<title>
<![CDATA[
Managed Bee Pollination Enhances Yield and Seed Quality in Brassica napus through Flowering Duration and Agronomic Trait Modulation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718066v1?rss=1
</link>
<description><![CDATA[
Managed bees are widely recognized as beneficial for agricultural production. However, their impacts vary across plant varieties, and the underlying mechanisms for this variation remain poorly understood. In the present study, the effects of bee pollination were investigated in nine Brassica napus varieties were investigated for flowering duration, fruiting duration, agronomic traits, fruit yield, and seed quality. These effects were then compared with those of non-bee pollination treatments. Bee pollination shortened the flowering duration by an average of 7.3 days and extended the fruiting duration by 2.3 days for all varieties. It also induced changes in agronomic traits in a subset of varieties, including reduced plant height and fewer primary and secondary branches. Correlation analysis indicated that a shortened flowering duration was conducive to enhancing both yield and quality. Increased fruiting duration and the total flowering and fruiting duration contributed to increased grain size-related parameters, including 1000-seed weight and number of seeds per silique. Reduced plant height increased yield by increasing the number of siliques (despite a concurrent decrease in 1000-seed weight), whereas significant reductions in branch number led to lower oleic acid and higher erucic acid content. These findings suggest that bee pollination may substantially improve fruit yield and seed quality, potentially by affecting plant nutrient allocation strategies. Notably, the contribution of a shortened flowering duration appears to be more universally applicable. For practical applications, pollination should be implemented before flowering, and varieties exhibiting favorable agronomic trait changes after bee pollination should be prioritized for promotion and cultivation.
]]></description>
<dc:creator><![CDATA[ Daoyin, C., yihuan, l., Jinhu, S., Dongxu, Z., Zhichu, H., Fuliang, H., Bin, Y., Xiaoling, S. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718066</dc:identifier>
<dc:title><![CDATA[Managed Bee Pollination Enhances Yield and Seed Quality in Brassica napus through Flowering Duration and Agronomic Trait Modulation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718433v1?rss=1">
<title>
<![CDATA[
A C. elegans model for functional analysis of ADPKD variants in cilia, extracellular vesicles, and sensory signaling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718433v1?rss=1
</link>
<description><![CDATA[
Interpreting the pathogenic significance of missense variants in human disease gene candidates remains a major challenge in precision medicine. Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic cause of kidney failure and caused by mutations in the PKD1 or PKD2 genes that encode polycystin-1 and polycystin-2. Here, we establish C. elegans as a platform for the functional classification of PC2 variants by characterizing PKD-2C180S, the C. elegans ortholog of the likely pathogenic human variant PC2C331S. Using CRISPR/Cas9 endogenous genome editing combined with dual-color fluorescent reporters and super-resolution imaging, we show that PKD-2C180S severely reduces protein stability, abolishes ciliary and extracellular vesicle (EV) localization, and eliminates sensory function comparable to a pkd-2 null allele. In heterozygous animals, PKD-2C180S is recessive and exerts no dominant-negative effect on wild-type PKD-2 trafficking, protein levels, or function, establishing that PKD-2 is haplosufficient in this model. PKD-2C180S also abolishes ciliary and EV localization of the PC1 homolog LOV-1 and reduces LOV-1 cell body levels comparable to pkd-2 null animals, consistent with PC2 functioning as a molecular chaperone for PC1 stability and trafficking. Genetic epistasis experiments show that PKD-2C180S protein levels are unaffected in lov-1 mutants, indicating that the PKD-2C180S mutation acts prior to complex assembly. Quantitative analysis reveals that LOV-1*PKD-2 complexes are more stable at the ciliary membrane and more efficiently packaged into EVs than PKD-2 lacking LOV-1. Together, this work demonstrates that PC2C331S may act recessively via loss of polycystin complex function and establishes a C. elegans pipeline for the mechanistic classification of ADPKD-associated variants.
]]></description>
<dc:creator><![CDATA[ Wang, J., Nava Cruz, C., Walsh, J. D., desRanleau, E., Nikonorova, I. A., Barr, M. M. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718433</dc:identifier>
<dc:title><![CDATA[A C. elegans model for functional analysis of ADPKD variants in cilia, extracellular vesicles, and sensory signaling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718181v1?rss=1">
<title>
<![CDATA[
High-efficiency, site-specific integration of kilobase-scale DNA into plant genomic safe harbors via PrimeStack editors 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718181v1?rss=1
</link>
<description><![CDATA[
Precise, site-specific integration of large DNA sequences into plant genomes is a cornerstone of crop biotechnology and synthetic biology, yet remains constrained by random insertion, inefficient homologous recombination, and gene targeting. Here, we present PrimeStack, a DSB-independent platform that integrates prime editing with the unidirectional large serine integrase Bxb1, leveraging evolved variants for enhanced activity, to achieve the programmable insertion of multigene, multikilobase cargos at predefined genomic safe harbors in rice. Optimized prime editors first install attP landing sites with high fidelity and heritability followed by Bxb1-mediated recombination that generates irreversible integration of genetic information. PrimeStack achieves integration frequencies of approximately 43-46% (as detected by junction-specific PCR in rice calli), with phenotypic neutrality in regenerated plants, comparing favorably with bidirectional Cre-lox systems. We validate its utility by achieving targeted insertion of a carotenoid cassette at an experimentally confirmed genomic safe harbor. PrimeStack delivers a modular, site-specific gene-stacking platform that enables predictable, multigene trait pyramiding and pathway construction at genomic safe harbors, thereby accelerating the development of improved and resilient crop varieties, as well as scalable plant-based biomanufacturing and a powerful chassis for synthetic biology.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/718181v1_ufig1.gif" ALT="Figure 1">
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]]></description>
<dc:creator><![CDATA[ Sanchez, E., Sedeek, K., Butt, H., Mahfouz, M. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718181</dc:identifier>
<dc:title><![CDATA[High-efficiency, site-specific integration of kilobase-scale DNA into plant genomic safe harbors via PrimeStack editors]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718284v1?rss=1">
<title>
<![CDATA[
Genetic analysis of bone morphometry and ivory vertebrae in threespine stickleback 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718284v1?rss=1
</link>
<description><![CDATA[
Previous genetic studies of skeletal variation in threespine stickleback fish (Gasterosteus aculeatus) have focused primarily on striking morphological differences. Here, we examine the largely unexplored genetic architecture of internal bone microstructural variation between marine and freshwater stickleback. {micro}CT X-ray analysis revealed differences in the porosity, bone thickness, and bone volume fraction within armor plates and vertebrae from a marine and freshwater stickleback. Quantitative trait locus mapping in F2 progeny from a marine x freshwater stickleback cross identified a significant locus on chromosome 4 influencing multiple aspects of armor plate internal microstructure. This locus overlaps the well-characterized Eda region previously known to control armor plate number and size. Co-mapping of bone microstructure could be due to pleiotropic effects of Eda on multiple aspects of plate development or to changes in closely linked genes including Itm2a, which also plays a role in bone formation. Most bone microstructure traits in vertebrae showed weak or no genetic signal, consistent with a polygenic architecture. However, we identified a highly significant locus on chromosome 17 that is strongly associated with abnormally thickened "ivory vertebrae" that occurred in 8.4% of F2 offspring. This phenotype resembles Pagets disease in humans, and the major locus region contains Tnfrsf1b, the stickleback ortholog of a human Pagets disease susceptibility gene TNFRSF11A. Together, our findings identify genetic loci underlying natural variation in bone microstructure in wild fish and reveal a candidate gene associated with a disease-like skeletal phenotype, highlighting stickleback as a model for studying both evolutionary and pathological bone biology.
]]></description>
<dc:creator><![CDATA[ Behrens, V. C., Lee, D., Wucherpfennig, J. I., Kingsley, D. M. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718284</dc:identifier>
<dc:title><![CDATA[Genetic analysis of bone morphometry and ivory vertebrae in threespine stickleback]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717730v1?rss=1">
<title>
<![CDATA[
Resolution of the D4Z4 repeat responsible for facioscapulohumeral muscular dystrophy with HiFi sequencing 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717730v1?rss=1
</link>
<description><![CDATA[
The D4Z4 macrosatellite repeat encompasses some of the most difficult-to-resolve disease-related variations in the human genome. D4Z4 has a repeat unit of 3.3 kb (encoding the DUX4 gene) that is present in up to 100 copies on two chromosomes (4 and 10), while DUX4 can only be expressed in somatic cells from the permissive A haplotype that usually occurs on chromosome 4. Facioscapulohumeral muscular dystrophy (FSHD) is caused by chromatin relaxation and ectopic expression of DUX4 in skeletal muscle, mediated by contraction of D4Z4 to 1-10 copies (FSHD1, 95% of FSHD cases) or mutations in chromatin factor genes such as SMCHD1 (FSHD2, 5% of FSHD cases). Due to its large size, disease specific haplotypes and sequence homology between chromosomes, D4Z4 is challenging to resolve by current sequencing technologies. We report a computational tool, Kivvi, to genotype D4Z4 using PacBio whole-genome long-read sequence data. Kivvi detects all D4Z4 alleles in a sample, reporting the repeat size, chromosome (4 vs. 10), distal haplotype (A vs. non-permissive haplotypes) and the methylation level of each allele. We validated Kivvi against gold standard assays for FSHD diagnostics, detecting 100% of contracted alleles and correctly classifying 90% of noncontracted alleles. We showed differential methylation signals between FSHD1 and candidate FSHD2 samples. We profiled D4Z4 across 601 individuals from five ancestral populations, revealing extensive genetic diversity. We identified common haplotypes of D4Z4 alleles and characterized hybrid repeat units, hybrid repeat arrays, and translocation alleles. Combined with HiFi long reads, Kivvi enables the consolidation of multiple FSHD assays into a single workflow and facilitates the discovery of novel genetic modifiers of FSHD through population-scale studies.
]]></description>
<dc:creator><![CDATA[ Chen, X., Lemmers, R. J. L. F., Kronenberg, Z., Devaney, J. M., Noya, J., Berlyoung, A. S., Yusuff, S., Lynch, S., Nykamp, K., Lyndy, A. S., Dolzhenko, E., van der Maarel, S. M., Eberle, M. A. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717730</dc:identifier>
<dc:title><![CDATA[Resolution of the D4Z4 repeat responsible for facioscapulohumeral muscular dystrophy with HiFi sequencing]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.717636v1?rss=1">
<title>
<![CDATA[
Structural Evolution of LEAFY Reveals DNA-Mediated Cooperativity and Dimerization Shifts at the Water-to-Land Transition 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.717636v1?rss=1
</link>
<description><![CDATA[
The evolution of transcription factor (TF) DNA-binding specificity is a major driver of gene regulatory innovation. Unlike most TFs, which diversify through gene duplication and neofunctionalization, the plant-specific LEAFY (LFY) TF evolved novel binding specificities without extensive duplication. Here, we combine experimental structural determination and biochemical assays to reveal how LFYs dimerization and DNA-binding preferences shifted during the water-to-land transition. We present crystal structures of the LFY DNA-binding domain (DBD) from the hornwort Nothoceros aenigmaticus and the alga Interfilum paradoxum bound to DNA, demonstrating two distinct dimerization mechanisms: one mediated by direct protein-protein interactions and another driven by DNA-mediated cooperativity. In the ancestral state, LFY likely bound DNA as a dimer through DNA-mediated cooperativity, with protein-protein dimerization emerging later, enforcing new DNA-binding preferences. Our findings support a revised evolutionary scenario for LFY, highlighting the dynamic interplay between protein-DNA and protein-protein interactions as key drivers of TF binding specificity. This work deepens our understanding of how structural adaptations in TFs underpin evolutionary transitions in gene regulation.
]]></description>
<dc:creator><![CDATA[ Verhage, L., Thevenon, E., Chahtane, H., Grandvuillemin, L., Nanao, M. H., Dumas, R., Zubieta, C., PARCY, F. ]]></dc:creator>
<dc:date>2026-04-13</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.717636</dc:identifier>
<dc:title><![CDATA[Structural Evolution of LEAFY Reveals DNA-Mediated Cooperativity and Dimerization Shifts at the Water-to-Land Transition]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717696v1?rss=1">
<title>
<![CDATA[
Genotype frequency dynamics in finite-sized, partially clonal population with mutation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717696v1?rss=1
</link>
<description><![CDATA[
Most eukaryotes reproduce using partial clonality, for which appropriate population genetic models remain limited. This gap constrains our ability to accurately reconstruct past population dynamics, predict future trajectories, and infer the evolutionary processes involved.

We present a Wright-Fisher-like model tailored for tracking the mean and the variance of genotype frequencies over generations at one locus with multiple alleles in a same finite-sized population with mutation.

Different initial conditions and rates of clonality generate unique mean trajectories of genotype frequencies. Partially clonal populations converge to the same unique stable equilibrium as exclusively sexual populations, that only depends on the reciprocal mutation rates between alleles. The dynamics unfold in two phases: First, genotype frequencies move towards Hardy-Weinberg proportions; Then iterate along the Hardy-Weinberg proportions until reaching the stable equilibrium. Mean allele frequencies and gene diversity remain unchanged by different rates of clonality along the trajectories. Instead, clonality influences the speed at which populations return to Hardy-Weinberg proportions and thus shapes the temporal sequence of genotype frequency distributions over generations. Variance around each mean trajectory depends only on parental genotype frequency distributions and population size, not on clonality. Taken together, these explain why both negative and positive Fis values are expected in partially clonal populations, and why variance of Fis across loci is a reliable proxy for inferring clonal rates.

Our model will enable the analysis and prediction of changes in genotype frequencies within monitored populations, and will support future inference methods relying on time-series genotyping data from a target population.

HighlightsO_LIOut of equilibrium, sexual and clonal populations share the same two-step dynamics.
C_LIO_LIFirst, return to Hardy-Weinberg parabola impacted by rates of clonality; Then, iteration along this parabola until reaching equilibrium that only depends on mutation rates
C_LIO_LIIncreasing clonality change the speed and direction of mean dynamics out of Hardy-Weinberg parabola without affecting mean allele frequencies
C_LIO_LIVariance around mean dynamics depends on parental genotype frequencies and population size but not affected by clonality
C_LI

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/717696v1_ufig1.gif" ALT="Figure 1">
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]]></description>
<dc:creator><![CDATA[ Stoeckel, S., Masson, J.-P. ]]></dc:creator>
<dc:date>2026-04-13</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717696</dc:identifier>
<dc:title><![CDATA[Genotype frequency dynamics in finite-sized, partially clonal population with mutation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717708v1?rss=1">
<title>
<![CDATA[
Evolutionary-scale protein language models uncover beneficial variants in a Sorghum bicolor diversity panel 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717708v1?rss=1
</link>
<description><![CDATA[
Quantitative genetic approaches such as genome-wide association studies and genomic prediction are widely used to identify favourable genetic variation, but they have limited resolution due to linkage disequilibrium. Comparative genomics approaches, especially Protein Language Models (PLMs), have emerged as powerful alternatives, by detecting phylogenetic residue conservation (PRC) across evolutionary time scales. However, the extent to which these tools can guide the detection of impactful variants for field agronomic traits is still unclear.

In this study, we used the pre-trained PLM ESM2 to predict PRC scores of nonsynonymous mutations segregating within a diverse panel of 387 accessions in sorghum (SAP). The distribution of fitness effects (DFE) of the same set of nonsynonymous mutations was inferred using unfolded site frequency spectra to assess whether the DFE distribution covaried with PRC scores. Furthermore, we estimated the load of putatively nonneutral mutations of SAP accessions and evaluated associations between this mutation load and phenotypic performance across multiple agronomic traits. Our results show that ESM2 can detect mutations associated with fitness-enhancing effects in SAP, as indicated by enrichments in positive selection signatures among the variants with positive PRC scores. Significant associations were also detected between phenotypic performance and mutation load for several agronomic traits, indicating that PLMs can identify functionally important genetic variation. However, these signals were not consistent across all traits in the SAP population. Altogether, our findings suggest that large language models may support breeding efforts, as PLM predictions covaried with fitness effects and captured agronomic performance for some traits in plant populations.
]]></description>
<dc:creator><![CDATA[ Johansen, N. H., Sendowski, J. S.-O., Nikolaidou, E., Chatzivasileiou, S., Wang, S., Song, B., Olson, A., Bataillon, T., Ramstein, G. P. ]]></dc:creator>
<dc:date>2026-04-13</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717708</dc:identifier>
<dc:title><![CDATA[Evolutionary-scale protein language models uncover beneficial variants in a Sorghum bicolor diversity panel]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.09.717374v1?rss=1">
<title>
<![CDATA[
Inoculation of Malus baccata 'Jackii'-derived offspring and QTL analysis reveal a polygenic inheritance pattern of apple blotch resistance 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.09.717374v1?rss=1
</link>
<description><![CDATA[
Apple blotch, caused by Diplocarpon coronariae, is an increasingly important fungal disease that leads to premature leaf fall and significant yield losses in apple orchards. Breeding resistant cultivars offers a sustainable strategy to reduce disease impact, as all commercial apple cultivars are susceptible to this pathogen. This study aimed to investigate the disease resistance of Malus baccata  Jackii-derived offspring to D. coronariae through artificial inoculation and to identify loci associated with resistance. Simple interval mapping was performed using phenotypic and genotypic data from 122 individuals of an F1 population (Idared x M. baccata  Jackii), together with analyses of M. baccata  Jackii-derived open-pollinated populations. Our results indicate that resistance to apple blotch is a complex, polygenic trait, with four important QTLs identified on linkage groups 1, 2, 12 and 13. Disease severity was strongly affected by inoculum, phenotyping method and environmental factors. These findings have direct implications for apple breeding programmes aimed at developing apple blotch-resistant cultivars.
]]></description>
<dc:creator><![CDATA[ Pfeifer, M., Peil, A., Flachowsky, H., Emeriewen, O. F., Woehner, T. W. ]]></dc:creator>
<dc:date>2026-04-13</dc:date>
<dc:identifier>doi:10.64898/2026.04.09.717374</dc:identifier>
<dc:title><![CDATA[Inoculation of Malus baccata 'Jackii'-derived offspring and QTL analysis reveal a polygenic inheritance pattern of apple blotch resistance]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-13</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
