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PLANTS, PEOPLE, PLANET

Wiley

Preprints posted in the last 30 days, ranked by how well they match PLANTS, PEOPLE, PLANET's content profile, based on 27 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.

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From mountaintops to metacollections: using genomics to evaluate ex situ conservation collections. A case study from tropical montane cloud forest plants

Cascini, M.; Simpson, L.; Worboys, S.; Worboys, W.; Guja, L.; Knapp, Z.; Bredell, P.; Percival, J.; Rossetto, M.; Crayn, D.

2026-07-03 genomics 10.64898/2026.06.27.734930 medRxiv
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A core aim of ex situ conservation is to represent wild genetic diversity in managed living collections. For the climate-threatened tropical montane cloud forest (TMCF) flora of northeast Australia, an ex situ metacollection of plants and seeds has been established by the Tropical Mountain Plant Science (TroMPS) project. In this study we used reduced-representation sequencing (DArTseq) of wild, herbarium, and ex situ material alongside provenance information for ten species, to pursue two central aims: to characterise landscape-scale genetic structure across species' ranges, and to evaluate how well the assembled metacollections represent that wild diversity. Analyses revealed consistent patterns of genetic differentiation among mountain top populations across multiple species, reflecting the isolating influence of lowland gaps between upland habitats, with the degree of differentiation varying among species. These results provide the first genetic baseline for Australian TMCF flora and reinforce the importance of treating individual mountain top populations as distinct units for conservation management. Additionally, the project provided valuable insights into the logistical challenges of coordinated multi-institutional collecting, informing strategies for metacollection design more broadly. Evaluation of the metacollection revealed both strengths and gaps in representation across species, providing an evidence base to refine the current holdings and guide future targeted collecting to strengthen their long-term conservation value.

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Small representative samples can capture global vascular plant diversity patterns

Baldaszti, L.; Moonlight, P.; Brummitt, N.; Pironon, S.; Sarkinen, T.

2026-07-10 plant biology 10.64898/2026.07.08.737287 medRxiv
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Incomplete information on distributions for a high proportion of the world's plant species together with biases in global biodiversity data mean that current estimates of plant diversity patterns are skewed. A key issue is that current predictions rely on a subset of species that is not representative of all plant species. Here we tested the feasibility of a representative sampling approach for mapping global vascular plant diversity at the finest scale where comprehensive data is available. Using the World Checklist of Vascular Plants as a reference, we generate random samples of species with increasing sample sizes from the global species pool. We compare the diversity patterns retrieved from the samples against the patterns of the reference dataset using spatially weighted correlation coefficients and four different diversity metrics. We find that at the botanical country scale, representative global maps of species and phylogenetic diversity can be created with small numbers of species (~1% [0.2% and 0.4%, respectively]) at the botanical country scale. For effective growth form and family diversity sample sizes encompassing ~20% [19.2% and 19.5%, respectively] of all species are needed. Random samples require markedly fewer species to reach high correlations than when restricting the pool of species to single plant families or genera. We show that when representative samples are used robust inferences of plant diversity patterns can be made from only a small proportion of species.

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Seasonal climatic impacts on orchid productivity in an urban ecosystem

Brundrett, M.

2026-06-30 Plant Biology 10.64898/2026.06.29.735162 medRxiv
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ContextThe global diversity hotspot in Southwest Australia has >480 orchids facing increasing threats from climate extremes, fire and habitat decline. AimsTo develop effective and consistent tools for measuring climate impacts on productivity in a diverse urban orchid community. MethodsAnnual variations in flower and seed production for 17 orchids were determined using thousands of records over a decade with extreme climate variability. Key resultsRainfall deficits and temperatures in autumn, winter and spring increased substantially over 125 years. Seasonal climate anomalies reduced flowering and seed production for orchids, but this varied between species and seasons. These effects were summarised by climate response (CRI) and sensitivity (CSI) indexes. Early or late flowering species were most vulnerable to seasonal drought, and visually deceptive pollination preferred warm dry conditions. CRIs were strongly correlated with orchid pollination syndromes and flowering times. Effects on mycorrhizal fungi and pollinators were also observed. Extrapolating climate trends to 2100 predicted further impacts on orchid productivity (-5-40%). ConclusionsOrchid climate responses were diverse and deeply integrated with pollination, phenology, fire sensitivity and other key traits. ImplicationsResearch in an urban climate observatory produced a climate analysis framework that is likely relevant to many orchids and other biota.

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Diversity Assessment with SNP, SSR, AFLP, and RAPD Markers in Plants: A Systematic Review and Meta-Analysis

Olagunju, Y. O.; Olawuyi, O. J.

2026-07-07 plant biology 10.64898/2026.07.03.736291 medRxiv
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Background. DNA-based molecular markers underpin plant genetic diversity assessment, germplasm characterisation, and conservation prioritisation. Four marker systems dominate the field: Amplified Fragment Length polymorphisms (AFLPs), simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and random amplified polymorphic DNA (RAPDs). No quantitative meta-analysis had pooled their performance on the canonical diversity metrics: polymorphism information content (PIC), expected heterozygosity (He), and resolution power, across plants. Existing reviews are narrative, marker-restricted, or qualitatively conclusive of infeasibility. Methods. A PRISMA 2020-compliant systematic review (registered at the Open Science Framework) was executed. Eligible studies were within-study paired comparisons genotyping the same accession panel with at least two of {SNP, SSR, AFLP, RAPD} and reporting at least one diversity metric. Effect sizes were paired standardised mean differences (Hedges' g) computed under the Bernoulli-variance approximation. Random-effects REML meta-analysis used metafor 5.0.1 with Knapp-Hartung adjustment, leave-one-out, and r-sensitivity. Results. Fifteen within-study paired contrasts were eligible, distributed across three pools. Pool 2 (SSR vs SNP, He, k = 5) yielded a pooled Hedges' g of 0.494 (95% CI: -0.078 to 1.066, p = 0.075; I-squared = 90.2%; 95% PI [-0.82, 1.81]). SSRs exceeded SNPs on He in 4 of 5 studies; leave-one-out removal of the panel-size-asymmetric outlier raised the estimate to g = 0.644 (p = 0.025). Pool 3a (dominant-marker stratum, k = 6) yielded g = 0.419 (95% CI: -0.121 to 0.960, p = 0.103; I-squared = 56.5%); five of six contrasts showed SSR or AFLP exceeding RAPD on per-locus PIC. Pool 1 (PIC, k = 3, exploratory) gave a consistent direction (g = 0.453). All three pools point in the same direction: codominant or AFLP markers carry more per-locus information than the alternative being compared. Conclusions. SSR markers reported higher per-locus diversity than SNP and RAPD markers in plant within-study paired comparisons, mechanistically grounded in the SNP biallelic ceiling and the multi-allelic richness of SSRs. The effect attenuated or reversed in selfing/low-diversity panels and at the per-panel level when SNP panels exceeded approximately 1000 loci. RAPDs show the lowest per-locus information content of the four classes.

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Dissecting antibiosis resistance to Phthorimaea absoluta in wild and cultivated tomato accessions

Amegan, K. E.; Magot, F.; Desneux, N.; Del-Valle, S.; Salgon, S.; Kergunteuil, A.; Caromel, B.; Larbat, R.; Lavoir, A.-V.

2026-07-13 plant biology 10.64898/2026.07.11.737942 medRxiv
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AbstractTomato production faces a persistent challenge from the tomato leaf miner, Phthorimaea absoluta, a pest that severely limits yields while effective resistance in cultivated varieties remains scarce. To address this gap, wild tomato relatives represent a promising reservoir of resistance traits. In this study, 24 tomato accessions, including both cultivated types and wild species, were evaluated under greenhouse (no-choice) and tunnel (choice) conditions. Resistance mechanisms were characterized through measures of antibiosis such as leaflet lesion type, proportion of attacked leaflets, and mine density. The results revealed substantial variation between and within species, allowing classification of accessions into resistant, intermediate, and susceptible groups through multivariate analysis. Notably, the wild accession Solanum habrochaites PI248707 exhibited strong resistance, in contrast to susceptible cultivated varieties such as Rose de Berne. Under choice conditions, PI248707 sustained limited damage and disrupted larval development, with early instar larvae present but few reaching advanced stages, indicating an inhibitory defense response. Untargeted metabolomic profiling further highlighted pronounced constitutive differences between wild and cultivated accessions, with S. pennellii and S. habrochaites displaying higher metabolic diversity. By integrating phenotypic and metabolic data, specific metabolite classes associated with resistance were identified. These findings underscore the potential of wild tomato germplasm in breeding programs, with PI248707 standing out as a strong candidate for resistance introgression.

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Restoration of tropical dry evergreen forest in southern India: balancing carbon sequestration with biodiversity conservation

Shanmugam, M.; Pulla, S.; Epinal, L. N.

2026-07-10 ecology 10.64898/2026.07.08.737378 medRxiv
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Tropical dry evergreen forests (TDEFs) are a unique and highly threatened forest type of the dry tropics. Their restoration could be strengthened if native species demonstrate carbon sequestration comparable to widely used non-native trees. We assessed biodiversity and carbon sequestration in a restored TDEF in India, developed over 50 years from a largely barren landscape. The site now supports high woody-plant diversity, with 91 native species across 34 families. Aboveground biomass (AGB) averaged 66.91 +/- 41.2 Mg/ha comparable to seasonally dry tropical forests globally. Although native species were planted more recently and are shorter than non-natives, they contributed 23.86 +/- 23.4 Mg/ha to AGB and show potential for future increases in basal area. Given their comparable wood densities and capacity to attain similar heights, native species are predicted to sequester carbon at levels similar to non-natives in the long term. AGB was unrelated to species diversity. Overall, native TDEF species can achieve carbon storage while maintaining ecological integrity.

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A Highly Contiguous Reference Genome for Scalesia gordilloi (Asteraceae), a Critically Endangered Plant Endemic to the Galapagos Islands

Pozo, G.; Rivas-Torres, G.; Velez-Darquea, E.; Barragan-Orbe, D.; Torres, M. d. L.

2026-06-29 genomics 10.64898/2026.06.25.734018 medRxiv
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Scalesia gordilloi is a critically endangered species endemic to San Cristobal Island in the Galapagos archipelago and represents one of the most unique and vulnerable lineages within the adaptive radiation of the genus Scalesia. Despite its evolutionary distinctiveness and conservation importance, no genomic resources have been available for this species. Here, we present the first high-quality reference genome of S. gordilloi, generated using Oxford Nanopore long-read sequencing. Across three PromethION R10.4.1 flow cells, we obtained 80.5 Gb of long reads (~25X coverage), which enabled a highly contiguous 3.61 Gb assembly composed of only 549 contigs and an N50 of 106.6 Mb. BUSCO completeness reached 98.6%, with assembly metrics comparable to other high-quality Asteraceae genomes. Repeat annotation revealed that 76.2% of the genome is composed of interspersed elements, dominated by LTR retrotransposons. Structural annotation resulted in 47,913 high-confidence protein-coding genes, consistent with expectations for large, repetitive Asteraceae genomes. This genome provides a critical foundation for conservation genomics, enabling assessments of genetic diversity, inbreeding, and adaptive potential in the species. It further establishes a framework for comparative genomics across the Scalesia radiation and supports future efforts to protect and restore one of the most threatened plant lineages of the Galapagos Islands.

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Multi-trait evaluation of a tomato MAGIC population identifies promising lines with improved nitrogen use efficiency (NUE)

Baraja-Fonseca, V.; Gil-Villar, D.; Bancic, J.; Renau-Morata, B.; Salud Justamante, M.; Plazas, M.; Gramazio, P.; Vilanova, S.; Perez-Perez, J. M.; Granell, A.; Molina, R. V.; Nebauer, S. G.; Prohens, J.; Arrones, A.

2026-07-15 plant biology 10.64898/2026.07.14.738388 medRxiv
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Nitrogen-use efficiency (NUE) is a pivotal breeding target in tomato (Solanum lycopersicum L.) to sustain production under reduced N inputs. Here, we leveraged a recently developed tomato multi-parent advanced generation inter-cross (ToMAGIC) population to identify lines with superior performance under reduced N availability. The eight founders and a core subset of 118 ToMAGIC lines were characterized with 10,684 SNP markers and evaluated under optimal (opN, 15 mM) and suboptimal (subN, 8 mM) N supply in an experiment totalling 1,576 plants, generating 48,068 data points across 61 phenotypic variables. Under both N treatments, ToMAGIC lines exhibited transgressive segregation for most traits, confirming the value of this population as a reservoir of untapped variation. Notably, under subN conditions, harvest index (Hi) increased by 29-44%, suggesting adaptive resource redistribution toward reproductive sinks. Variance partitioning revealed that agronomic and NUE-related traits were largely under genetic control, with heritability estimates frequently above 0.80 and broadly conserved across N treatments. Multivariate trait analysis identified fruit yield N concentration (NUE component, CN,y), shoot biomass N content (NAb), and shoot growth-related traits as the main drivers of treatment differentiation. Finally, proxy traits were prioritized by integrating response magnitude, heritability, trait correlations, and treatment-discriminatory power into multi-trait selection indices. This strategy generated favorable predicted genetic gains, reaching 158% for high-performance lines and 170% for subN-adapted lines, and consistently identified lines 402, 428, 518, 800, and 816 as promising pre-breeding materials. Overall, this study supports ToMAGIC as a powerful resource for developing N-efficient cultivars suited for sustainable agriculture.

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A Taxonomic Revision of the Monocaul Phanerophyte Ardisia (Primulaceae) of Gabon

Cheek, M.;Murdoch, H.

2026-06-27 Plant Biology 10.64898/2026.06.26.734757 medRxiv
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Monocaul Ardisia (Primulaceae) have a single, vertical, woody stem and spiral phyllotaxy. They range from 30 cm to 100 cm tall. Three species of this architectural group, Ardisia mayumbensis, A. hallei and A. bracteata, have been recorded from Gabon hitherto. In this taxonomic revision we show that A. mayumbensis does not occur in Gabon, and we describe three new species. Two of these, Ardisia doudou sp. nov.and A. mica sp.nov., are endemic to Gabon and one, A. litterbin sp.nov, is found in both Gabon and Republic of the Congo. Ardisia hallei and A. bracteata are redescribed. All five species have a litter-gathering habit with a terminal funnel of leaves, and two of these species, Ardisia doudou and Ardisia litterbin, also possess adventitious roots in the distal part of the stem, a well-established strategy found in litter-gathering forest species of other plant families in tropical Africa. We provisionally assess the conservation status of all five taxa using the 2012 IUCN standard, finding that all monocaul Ardisia in Gabon fall within threatened categories. Two of the species, Ardisia bracteata and A. mica, are known from single collections and have not been seen for 164 and 63 years respectively and are conceivably extinct although further surveys are needed to establish this. We employ new characters in delineating and describing African Ardisia using leaf thickness and oil gland data.

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Making the most out of it: shallow genome-skimming possibilities for the systematics of prickly lineages of Solanum (Solanaceae)

Alves, R. T. d. L.; Gouvea, Y. F.; Dalapicolla, J.; Poczai, P.; Giacomin, L. L.

2026-07-09 plant biology 10.64898/2026.07.08.737304 medRxiv
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Premise: Genome skimming (GS) is a cost-effective approach for plant phylogenomics, but its ability to recover informative datasets from different genomic compartments, particularly genome-wide SNPs, remains poorly explored in Solanum. Methods: We evaluated shallow GS for phylogenetic inference in South American prickly Solanum lineages by recovering plastid, mitochondrial, and nuclear datasets, including coding regions and genome-wide SNPs. Phylogenies were inferred using maximum-likelihood and coalescent approaches under different SNP filtering strategies. Results: GS successfully recovered complete plastomes, organellar coding regions, and large SNP datasets, but failed to consistently assemble mitochondrial genomes or recover low-copy nuclear genes. SNP-based analyses, especially from the nuclear genome, produced stable, well-supported phylogenies that were largely congruent across inference methods. In contrast, coding-region datasets, particularly from the mitochondrial genome, showed greater topological discordance, revealing cytonuclear conflict. Discussion: Our results demonstrate that shallow GS is an effective strategy for generating informative SNP datasets for phylogenetic inference in Solanum, despite limitations in recovering complete mitochondrial genomes and low-copy nuclear loci. SNP-based analyses substantially expand the phylogenetic potential of GS, providing a practical and cost-effective alternative for systematic studies.

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Far-red timing uncovers cultivar-dependent yield and bolting responses in vertical-farm spinach (Spinacia oleracea L.)

McGovern, C.; Adrio, M.; Aliki, H.; Vichos, R.; Powell, W.; Sharma, R.

2026-07-13 plant biology 10.64898/2026.07.10.737849 medRxiv
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Far-red light (FR; 700-750 nm) is increasingly incorporated into controlled-environment lighting because it can improve photosynthetic efficiency when combined with comparatively shorter wavelengths. In long-day leafy crops such as spinach, however, FR may also promote the transition from vegetative to reproductive growth and thereby reduce marketable yield. Most studies have evaluated FR fraction, intensity or end-of-day exposure, whereas the developmental timing of FR has rarely been tested, particularly in spinach. Here, we evaluated six commercial spinach cultivars (Amador, Harp, Renegade, Responder, Rubino and Santa Cruz) in an indoor vertical farm under a common red-green-blue background (PPFD 260-264 {micro}mol m-{superscript 2} s-{superscript 1}, 12 h photoperiod, 24 {degrees}C) and four FR timing treatments: no FR (Control), FR throughout production (FullFR), FR during early development only (EarlyFR), and FR during late development only (LateFR). LateFR increased marketable fresh weight relative to Control (244 vs 224 g) and reduced flowering incidence, whereas far-red supplied during early development reduced fresh weight (158 g) and increased flowering. The magnitude of the timing response differed among cultivars: switching from EarlyFR to LateFR recovered 0 % fresh weight in Amador but 107 % in Renegade and Rubino, with the largest penalties occurring in otherwise bolt-resistant cultivars. EarlyFR also increased total chlorophyll and reduced the chlorophyll a:b ratio. These results show that FR response in spinach is strongly conditioned by developmental stage and cultivar. Although LateFR received more total far-red than EarlyFR, it behaved like the Control, indicating that the penalty was set by far-red timing rather than dose. Treatment differences in bolting and yield tracked an estimated phytochrome photostationary-state deficit during early development: a phytochrome-deficit model markedly outperformed a cumulative-dose model ({Delta}AIC = 441), and the deficit x cultivar interaction was strong (p < 0.001), with bolt-resistant cultivars losing most yield when far-red coincided with the early developmental window. We therefore propose that FR should be treated as a genotype-dependent management variable rather than as a fixed spectral input, with late application and bolt-resistant cultivars offering the most favourable combination for vertical-farm spinach production. Framed within the breeders equation, the close match between the trial and production environment and the scope for shorter breeding cycles indoors suggest that genotype and far-red timing can be optimised jointly to accelerate genetic gain.

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A first pangenomic framework for globe artichoke supports SNP-based varietal fingerprinting

Portis, E.;Vergnano, E.;Gaccione, L.;Acquadro, A.;Comino, C.;Carli, C.;Barchi, L.;Martina, M.

2026-06-26 Plant Biology 10.64898/2026.06.25.734495 medRxiv
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Globe artichoke (Cynara cardunculus var. scolymus L.) comprises a broad range of local ecotypes and varietal groups whose genetic diversity has been investigated through different molecular markers. However, recent advances in next-generation sequencing and pangenomics approaches provide new opportunities to capture genome-wide variation at higher resolution and to develop practical tools for varietal discrimination, traceability, and germplasm conservation. In this study, we developed the first pangenomic framework for cultivated artichoke and evaluated pangenome-informed SNP markers for varietal fingerprinting. Whole-genome resequencing data from the Italian local ecotype Asti Sori were integrated with publicly available genomic data from representative globe artichoke and cultivated cardoon accessions to construct and annotate a pangenome. Genome-wide SNP and presence/absence variation (PAV) analyses were combined with pangenome-anchored genotyping-by-sequencing (GBS) data from 45 accessions representing the main cultivated varietal groups. The pangenome revealed a largely conserved core gene repertoire alongside a smaller accessory component, with gene accumulation curves suggesting a tendency toward saturation within the sampled cultivated germplasm. SNP- and PAV-based analyses provided complementary views of accession relationships and consistently resolved the principal cultivated groups. Across the broader germplasm panel, pangenome-anchored GBS-derived SNPs identified well-supported phylogenetic clusters corresponding to recognized varietal types. A reduced panel of 50 SNPs, selected through iterative random subsampling, retained at least 90% of the genetic diversity captured by the full dataset and reproduced its main population structure. This compact pangenome-anchored marker set provides a practical foundation for varietal fingerprinting, DUS-oriented applications, traceability, and conservation of traditional globe artichoke germplasm. Validation across independent collections will be required before routine deployment.

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A Practical Roadmap For Sampling Floral Nectar From Communities of Many Plant Species

Kirschke, G. E.; Bain, J. A.; Ogilvie, J. E.; CaraDonna, P. J.

2026-06-23 ecology 10.64898/2025.12.19.695174 medRxiv
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O_LIFloral nectar plays a critical role in shaping the ecology and evolution of plant-pollinator interactions. Effective and efficient methods that allow for broad-scale sampling of nectar volume and sugar concentration across a diversity of taxa are needed to improve our understanding of many dimensions of mutualistic plant-pollinator interactions--including their basic ecology and evolution, their responses to environmental change, and their conservation and restoration. C_LIO_LIDespite the key importance of nectar for mediating plant-pollinator interactions, quantifying floral nectar in the field from many different plant species is challenging because there is often no one-size-fits-all sampling method that is effective across a diversity of floral structures and nectar traits. Different methods require different preparation, and sampling from many species involves a variety of logistical challenges. C_LIO_LIHere we provide a methodological roadmap for sampling floral nectar in the field from many different plant species. We describe our nectar collection methods in detail, including necessary equipment, calculations, and approaches appropriate for different floral morphologies. We also provide a troubleshooting guide for common problems encountered while collecting nectar in the field. To demonstrate the utility and effectiveness of our methods for collecting nectar from many different species, we present results on nectar trait variation from 53 species in an ecosystem. C_LIO_LIOur method illustrates that nectar traits vary considerably within and among plant species, indicating that large-scale nectar sampling projects are an important consideration for many basic and applied questions in pollination ecology and evolution. We hope that across many plant communities and ecosystems, our paper provides a practical roadmap for how to navigate the complexities of quantifying floral nectar traits. C_LI

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Small scale habitat components as key drivers of biodiversity in urban park design

Trigos-Peral, G.; Reyes Lopez, J. L.

2026-07-01 ecology 10.64898/2026.06.30.735471 medRxiv
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Urban green spaces are increasingly recognised as important refuges for biodiversity, yet their ecological value depends strongly on design and management. Here, we investigate how fine-scale structural and microhabitat components shape urban ant assemblages, using ants as indicators of broader arthropod responses to urbanisation. Ant communities were sampled in twelve urban green spaces in Cordoba (southern Spain) over a ten-year period (2004 to 2013) using pitfall traps, alongside detailed characterisation of vegetation structure and ground-layer microhabitats. In total, 38 species and 25,578 individuals were recorded. Microhabitat variables explained 58% of the variation in species occurrence. Community differences among microhabitats were driven primarily by nestedness, with dense herbaceous cover acting as a core habitat and edge-related components contributing disproportionately to beta diversity. Tree abundance showed a unimodal relationship with species richness, with maximum diversity at intermediate densities, while shrub and lawn cover had weak or inconsistent effects. Fine-scale elements such as leaf litter, stones, woody debris, and small bare-ground patches strongly influenced species occurrence by providing thermal refugia, nesting substrates, and foraging opportunities. The invasive Argentine ant (Linepithema humile) exhibited strong but spatially restricted dominance and species-specific negative effects on native ants, emphasising the role of habitat context in mediating invasion impacts. Our results demonstrate that urban biodiversity is maximised by enhancing fine-scale habitat heterogeneity rather than increasing green cover alone. We highlight practical design principles for urban green infrastructure that prioritise structural diversity and ground-layer complexity to support resilient arthropod communities.

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The Viability Gambit: An Optimized Sterilisation Protocol for Industrial Hemp ( Cannabis sativa L.) Seeds

Gowlikar, R.;Pender, G.;Kacprzyk, J.;Destailleur, A.;Nayak, A.;Melzer, R.;Schilling, S.

2026-06-26 Plant Biology 10.64898/2026.06.25.732887 medRxiv
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Hemp (Cannabis sativa L.) is an increasingly important crop with applications spanning fibre, seed oil and bioactive cannabinoid production, yet the development of reliable tissue culture systems for this species remains a significant challenge. The establishment of axenic seedling cultures is a prerequisite for hypocotyl-based regeneration and future genetic transformation pipelines, but hemp seeds harbour diverse endophytic microbial communities that frequently overwhelm standard surface sterilisation protocols. Here, we present a systematic comparative evaluation of seed sterilisation strategies across seven industrial hemp accessions, examining the effects of sterilisation chemistry, seed provenance and accession identity on both contamination outcome and the subsequent morphogenic competence of hypocotyl explants. Across all treatments and accessions, in-house glasshouse-harvested seeds achieved higher sterility rates than commercially sourced material regardless of protocol applied. This provenance effect, combined with considerable batch-to-batch variation within seed sources, indicates that contamination load is a primary determinant of successful hemp seed sterilisation. Among the sterilisation treatments evaluated, a baseline of 75% ethanol combined with sequential 1% hydrogen peroxide incubation performed consistently well for low-load seed batches, while supplementation with Plant Preservative Mixture (PPMTM) might be necessary to achieve acceptable rates of non-contaminated seedlings from high contamination load batches. Beyond their effect on contamination, sterilisation treatments influenced the morphogenic fate of hypocotyl explants independently of sterility outcomes. Notably, seedling treatment with the Prochloraz-based fungicide Octave promoted shoot and root co-regeneration in the absence of exogenous plant growth regulators in some cases. Hormone-free organogenesis from hypocotyl explants was achievable across multiple hemp accessions, demonstrating that this developmental capacity is broadly distributed within hemp, though its frequency and consistency varied with accession identity and protocol conditions. Together, these findings provide a practical framework for axenic hemp seed culture that can be used as starting point requiring local adaptation based on seed source, batch history and the intended downstream application.

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A multiregional image-text dataset and benchmark for vision-language modeling of plant diseases

Nguyen, T. V.; Quoc, K. N.; Harwath, D.; Quach, L.-D.; Dao, P. D.

2026-07-09 plant biology 10.64898/2026.07.01.735881 medRxiv
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Plant diseases remain a major challenge to global food production, and timely, accurate, and scalable detection of plant stress is critical to reducing these losses. Recent advances in digital imaging and artificial intelligence offer unprecedented opportunities for precision crop disease detection and management. Yet, existing plant disease datasets remain often fragmented across crop and disease systems, and are largely dominated by controlled-environment imagery. The lack of standardized, interoperable, and representative datasets limits reproducibility, transferability, and scalability of AI systems, thereby constraining their deployment in operational agricultural applications. Here we present LeafMD, an integrated multimodal plant disease dataset and benchmark resource that includes LeafNet 2.0, a large-scale multimodal digital image dataset comprising 255,855 image-text pairs across 37 crop species, 197 crop-disease classes, and 9 geographic regions spanning tropical, subtropical, and temperate agricultural systems. Unlike conventional datasets, LeafNet 2.0 integrates biologically grounded symptom descriptions with image-level annotations of early and late disease stages, enabling symptom-aware analysis of disease progression under realistic field conditions. We further introduce LeafBench 2.0 as part of LeafMD, a visual-question answering benchmark covering nine fine-grained plant pathology tasks, including pathogen classification, lesion characterization, symptom interpretation, and disease severity assessment. Evaluation across 16 vision-language models revealed substantial performance gaps between coarse disease recognition and fine-grained pathological reasoning, while agriculture-adapted models consistently outperformed several larger general-domain architectures on symptom-oriented tasks. Together, LeafNet 2.0 and LeafBench 2.0 establish LeafMD as a multimodal resource for developing disease-aware agricultural foundation models and studying fine-grained pathological reasoning in real-world environments.

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Beyond climatic drought indices : an hydraulic approach to quantifying forest water stress

Cochard, H.

2026-07-15 plant biology 10.64898/2026.07.13.738371 medRxiv
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The article introduces a new Forest Stress Index (ISF) based on a plant hydraulic modelling approach rather than classical climatic drought indices. Unlike other index like scPDSI or SPEI, ISF is grounded in xylem embolism dynamics simulated with the mechanistic SurEau model. The goal is to better link climatic anomalies to tree physiological functioning and mortality risk. ISF is defined using a locally adapted ideotype characterized by an optimal P50 value under a reference hydraulic functioning threshold. Simulations are performed across Europe and France using multiple climate datasets. The index is robust to model parameterization choices and assumptions about plant functional traits. Results show strong spatial and temporal consistency and significant correlations with SPEI and scPDSI. However, ISF more strongly highlights extreme drought years and exhibits a more skewed distribution. Future projections under SSP5-8.5 indicate a widespread increase in hydraulic stress with strong regional contrasts. Overall, ISF provides a mechanistic and complementary drought indicator more directly linked to forest mortality processes.

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Introducing PHJ Media: A Unique Machine Learning -Driven Basal Formulation to Overcome Recalcitrance for Multi-Genotype Micropropagation of Cannabis sativa L.

Pepe, M.; Hesami, M.; Jones, M.

2026-07-15 plant biology 10.64898/2026.07.14.738465 medRxiv
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Applications of tissue culture are critical for Cannabis sativa L. (cannabis), supporting clonal propagation, germplasm preservation, pathogen elimination, among other biotechnological applications. However, extensive genetic diversity associated with cannabis results in highly variable responses to in vitro conditioning, and no consensus basal media formulation exists to support reproducible micropropagation across genotypes. To address these limitations, a hybridized ensemble-NSGA-II approach was employed for concurrent optimization of individual media components to create a species specific, cultivar inclusive basal salt formulation for cannabis micropropagation. The resulting PHJ media represents a unique formulation that overcomes recalcitrance across a wide array of cannabis cultivars, facilitating improved growth and uniformity for the nine cultivars used in its development and validation. These results remain consistent from explant initiation through multiple rounds of subculture. The ability of PHJ to overcome genotypic recalcitrance is telling of its potential applicability with an array of plant species beyond cannabis. Additionally, robust performance both with and without plant growth regulators underscores the plausible use of PHJ for diverse applications beyond standard micropropagation. Ultimately, this cultivar-inclusive basal medium demonstrates utility for both scientific research and industrial-scale operations.

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Climatic and non-climatic drivers of rangeland vegetation change in Nepal

Shrestha, U. B.; Joshi, S.

2026-07-10 ecology 10.64898/2026.07.09.737421 medRxiv
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Nepal's rangelands provide multiple benefits, including support for pastoral livelihoods and alpine biodiversity, regulation of water and soil nutrients, and sequestering carbon. Climate change and anthropogenic pressures are altering these rangelands, leading to vegetation and biodiversity change. However, national-scale assessments of rangeland change are limited in Nepal. This study quantified rangeland changes at multiple spatial scales and assessed the climatic and non-climatic drivers of rangeland change. About 80.7% of Nepal's high-altitude rangeland (> 2,000m) outside protected areas showed no significant change. Among areas exhibiting significant annual maximum NDVI trends, 383,281 ha (18.6%) showed positive and 14,702 ha (0.7%) showed negative trends, corresponding the ratio of increase in vegetation greenness and decline in vegetation greenness to 26:1. Climate predicted positive trends covered 627,184 ha (30.5%), whereas residual trends caused by non-climatic drivers covered 94,656 ha (4.6%). Climate induced negative trends covered 47,609 ha (2.3%) while residual trends were observed in 6,260 ha (0.3%). Negative trend pixels were concentrated mainly within the 3,000 to 5,000 m elevation band, with Karnali Province recording the highest proportional climate predicted decline in vegetation greenness (3.4%). At the municipality scale, rangeland change showed no significant relationship with grazing pressure derived from gridded livestock data, suggesting that grazing pressure alone did not explain the non-climatic vegetation signal. These spatially explicit, nationally consistent results identify where rangeland change is occurring and help distinguish climatic and non-climatic drivers of rangeland vegetation change, providing evidence to support targeted rangeland management under Nepal's federal governance structure.

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When suitable habitat is not enough: climate change, habitat loss, and dispersal limitation increase the vulnerability of bald-headed uakaris (Cacajao sp.) in the Amazon Rainforest

Ennes Silva, F.; Mourthe, I.; Plaza Pinto, M.; Rabelo, R. M.; dos Santos Junior, M. A.; Borges, L. H. M.; Diogenes, L. C. R.; Marsh, L. K.; Alvares Oliveira, M.; Ribas, C. C.; Boubli, J. P.

2026-07-03 ecology 10.64898/2026.07.02.736086 medRxiv
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Aims: Species' distributions are determined by the interplay between ecological niche and dispersal ability, constrained by biogeographical barriers. Bald-headed uakaris (Cacajao spp.) are highly specialized primates often associated with seasonally flooded forests. In this study, we used ecological niche models to assess changes in habitat suitability and geographic distribution of uakari species under future scenarios. Location: Western Amazonia. Methods: We integrated ecological niche models, current deforestation data, and dispersal ability to estimate habitat suitability under two Shared Socioeconomic Pathway (SSP) scenarios: intermediate (SSP2-4.5) and very high (SSP5-8.5) greenhouse gas (GHG) emissions. Results: Our models project shifts in suitable conditions for all species. Three of the five species are projected to experience substantial reductions ([&ge;]62%) in suitable habitat conditions within their current ranges by 2050 under both future scenarios. Across the western Amazonia, up to 219,189 km2 and 211,276 km2 of land are projected to be unsuitable within the uakari ranges under the intermediate and very high emissions scenarios, respectively. This is particularly relevant for C. calvus, C. rubicundus, and C. ucayalii. At the species level, the uakaris may lose between 343 km2 and 84,531 km2 of their ranges in the intermediate scenario and 858 km2 and 76,216 km2 in the very high scenario. Shifts in suitability due to climate change are expected to vary from 6 to 191 km in the intermediate scenario and from 5 to 168 km in the very high scenario. Furthermore, the uakaris may lose between 0.5% and 8% of their current ranges due to deforestation in all scenarios. Main conclusions: Our findings reveal a high sensitivity of the uakaris to climate change impacts. It is projected that all species may experience contractions in the suitable areas and spatial suitability within their ranges by 2050, underscoring climate change as a relevant threat to these taxa.