New Phytologist

BackgroundMost land plants depend on the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these non-mycorrhizal plants meet their nutritional requirements without this crucial partnership. ResultsComparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90-122 million years ago. Field surveys of 42 wild populations across seven sites revealed that while non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors, lower shoot P levels can be observed in low P soils. To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57-69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders. Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions. ConclusionsOur findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities.

Background and AimsHybrid seed failure (HSF) is a common reproductive barrier in flowering plants, but how divergence in so-called effective ploidy translates into genome-wide allelic imbalance in hybrid endosperm remains unresolved. Using wild tomatoes (Solanum sect. Lycopersicon) as our model system, we test whether parent-of-origin expression shifts in hybrids are consistent with simple dosage effects or instead reflect lineage-specific trans regulation. MethodsUsing reciprocal interspecific crosses, we quantified parent-of-origin (allele-specific) expression in developing endosperm and analyzed patterns of differential parent-of-origin expression (DPE) across cross contexts. Guided by strong patterns in parental expression, we further classified DPE genes into four functional classes defined by their relationship to Solanum peruvianum (Per). This exercise captured distinct modes of trans-allelic regulation and guided functional interpretation. Key ResultsParental expression proportions are strongly asymmetric in hybrids, with the most pronounced and repeatable shifts occurring in crosses involving Per. These shifts recur across reciprocal contexts and include elevated maternal proportions even in crosses phenotypically classified as paternal-excess-like, arguing against a dosage-only model. Instead, we observed cross-consistent, coordinated DPE patterns corresponding to trans-acting dominance associated with Per. Functional enrichment of Per-associated DPE highlights chromatin regulation, including DNA methylation/RdDM- and chromatin remodeling-related factors, and Polycomb-linked regulators, implicating disruption of chromatin-based repression in hybrid endosperm. Concurrently, Per-associated activation of auxin- and cell-cycle regulatory pathways in non-Per alleles suggests mis-timed hormone-dependent developmental transitions that can destabilize proliferation-cellularization programs. ConclusionsOur findings support a model of trans-allelic epigenetic dominance in which Per-associated regulatory inputs reshape allelic expression landscapes in hybrid endosperm largely independent of parental origin. This provides a mechanistic link between effective ploidy divergence, genome-wide transcriptional imbalance, and HSF, and motivates reciprocal hybrid studies that integrate expression with chromatin-state and accessibility profiling.

O_LIIn fluctuating environments, the kinetics of stomatal opening and closing influence the balance between carbon gain and water loss. Smaller guard cells may respond faster to fluctuating environmental conditions because of their greater surface area for osmolyte flux relative to cell volume. A related hypothesis is that operational stomatal conductance (gop) is often well below its theoretical maximum (gmax) because at this stomatal aperture, guard cell volume is poised to change rapidly with small changes in turgor pressure. C_LIO_LIWe analyzed 2,124 estimates of stomatal closure kinetics in response to an abrupt increase in vapor pressure deficit (VPD) among 29 diverse wild tomato populations in the genus Solanum. C_LIO_LILeaves with small guard cells and a lower gop to gmax ratio (fgmax) closed faster, but explained variation in kinetic parameters at different levels of biological organization. Guard cell size had high phylogenetic heritability and varied relatively little within populations, whereas fgmax varied mostly among individuals and between light intensity treatments. C_LIO_LISmaller stomata can be speedier, but only if stomata are held at an aperture where they are responsive to changing turgor pressure. Selection on stomatal speed may influence not only anatomical traits like guard cell size, but also physiological controls on gop. C_LI

O_LIPlant functional traits vary across leaf ontogeny and phenology, yet most trait data are snapshots from narrow time windows that miss this temporal dimension. Leaf spectra are increasingly used with empirical models to predict traits, but whether such models accurately capture phenological variation remains unclear. C_LIO_LIWe monitored leaf traits and spectra weekly across a full growing season, generating 7,515 spectra from seven temperate species. Using partial least squares regression, we built three models --all-season and week-as-covariate models (both trained on full-phenology data), and a peak-season model -- and evaluated them alongside a widely used model against directly measured traits. C_LIO_LIFull-phenology models predicted LMA and equivalent water thickness (EWT) with high accuracy (R{superscript 2} > 0.85) and nitrogen with intermediate accuracy (R{superscript 2} = 0.64); carbon accuracy was low across all models (R{superscript 2} < 0.26), likely due to a small sample size. Peak-season trained models performed poorly when evaluated across the full season, often producing biologically unrealistic predictions. Traits and spectra varied significantly across phenological stages both within and among species. C_LIO_LIIgnoring phenological variation systematically biases trait estimates and ecological inference. Coupled with phenologically representative training data, spectra can capture the temporal dynamics of plant function, enabling novel research in ecology and evolution. C_LI

Polyploidy is often thought to cause immediate reproductive isolation due to sterility and inviability of inter-ploidy offspring. However, recent research demonstrated genome-wide introgression in natural populations of diploids and tetraploids. Yet, it still remains unknown whether introgression varies in strength along the genome and what are the forces underlying such variation. Here we analyzed whole-genome resequencing data from natural populations of the Alder tree, Alnus glutinosa agg., which includes a widespread diploid lineage found across large parts of Europe and two autotetraploid lineages with more limited ranges on the Balkan and Iberian Peninsulas. Our sampling involved mixed-ploidy populations, where diploids, triploids and tetraploids co-occur as well as ploidy pure populations. We identified genomic regions of increased admixture, which coincide with putative locations of centromeres. We hypothesize that this pattern of shared variation at pericentromeric regions involves centromere drive, which happens when centromeres increase the likelihood of being included in the oocyte during female meiosis and which has been studied in only a few plant species. While it was previously suggested that centromere drive could cause reproductive isolation and speciation, here we propose that driving centromeres could be able to lift reproductive barriers caused by ploidy differences.

BackgroundDuckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fastest-growing angiosperms, they exhibit extreme morphological reduction yet retain remarkable genomic plasticity through recurrent interspecific hybridisation, chromosomal rearrangements, and selective gene-family remodelling. The genomic mechanisms that distinguish this secondarily aquatic lifestyle from terrestrial ancestors, and whether these changes are convergent with other aquatic lineages such as seagrasses, have remained incompletely resolved. ResultsHere we report chromosome-scale genome assemblies for four duckweed species, Spirodela polyrhiza, Lemna minuta, Lemna japonica, and Lemna aequinoctialis, generated with PacBio HiFi long reads and Omni-C chromatin conformation capture. These assemblies include the first genomic characterisation of an unresolved hybrid lineage (L. aequinoctialis x) that harbours a previously uncharacterised 3.5 Mb reciprocal translocation between subgenomes, as well as confirmation of the allodiploid origin of L. japonica. Comparative phylogenomics with land plants and the seagrass Zostera marina reveals a coherent, non-random programme of gene loss: effector-triggered immunity (ETI) components (EDS1 and PAD4) and the high-affinity nitrate transporter NRT2 are convergently absent across duckweeds and Zostera marina, consistent with relaxed pathogen pressure and abundant dissolved nutrients in aquatic habitats. In contrast, secondary-metabolite biosynthesis pathways for flavonoids, anthocyanins, flavones and flavonols are retained or expanded despite overall genome compaction. ConclusionThese findings illustrate how the return to aquatic environments following terrestrialisation shaped duckweed genome evolution through convergent gene loss and selective pathway retention, and provide high-quality genomic resources to support future research in plant evolutionary biology and biotechnology.

Background and AimsUnderstanding how reproductive barriers combine to restrict gene flow remains a central challenge in speciation research. Although reproductive isolation is inherently a composite process, most empirical studies have focused on individual barriers in isolation, limiting our ability to capture their joint effects particularly in systems undergoing evolutionary transitions such as shifts in mating system. MethodsHere, we provide a comprehensive, life-cycle-wide quantification of reproductive isolation between two closely related species of the Erysimum incanum complex that differ strikingly in mating system: the predominantly selfing E. incanum and the outcrossing E. wilczekianum. Key ResultsBy integrating ecological, phenological, behavioural, and post-pollination components, we show that total reproductive isolation is nearly complete (T{approx}0.999), but overwhelmingly driven by pre-pollination barriers. Ecogeographical differentiation and, most prominently, pollinator-mediated isolation dominate, with pollinators exhibiting a strong bias toward E. wilczekianum. Floral traits linked to mating system divergence, particularly flower size, emerge as key drivers of assortative mating, supporting their role as "magic traits" coupling ecological divergence with reproductive isolation. In contrast, post-pollination barriers are weaker but strongly asymmetric. Hybrid seed formation is largely prevented when E. wilczekianum acts as the maternal parent, consistent with expectations from mating system differences, whereas reciprocal crosses are relatively successful. Despite reduced germination, hybrids display enhanced growth and no evidence of hybrid breakdown, suggesting that intrinsic incompatibilities remain incomplete. ConclusionsThese findings reveal that mating system divergence restructures the entire architecture of reproductive isolation rather than acting as a single barrier. More broadly, our results highlight that early-stage speciation can be driven by coordinated shifts in ecological and reproductive traits, emphasizing the need for integrative approaches to fully understand how barriers interact to generate species boundaries.

Renowned for its aromatic fruits and economic importance, the genus Vanilla poses longstanding taxonomic and phylogenetic challenges. Despite recent molecular studies, a comprehensive species tree is lacking, and the evolutionary processes and historical patterns shaping the genus remain poorly understood. We present a new, comprehensive phylogenomic framework for Vanilla, based on 349 low-copy nuclear genes and 76 plastid loci from the Angiosperms353 probe set, which we used to infer evolutionary relationships, assess cyto-nuclear and gene-species tree discordance, and thoroughly investigate its historical distribution and diversification. Sampling 43% of the genus, our framework resolves phylogenetic uncertainties, clarifies major clades, confirms prior hypotheses, and reveals novel placements, including V. planifolia and Vanilla subg. Gondwana. Discordances are primarily driven by incomplete lineage sorting, particularly in the vanillin-producing clade, with evidence of both ancient and recent hybridization, including a natural hybrid from the Yucatan Peninsula. Biogeographic analyses indicate a Guiana Shield origin ([~]30 Mya), Amazonia as a major diversification source, the Andes as a permeable barrier, and Central America as the main diversification sink. This study provides a robust evolutionary framework for Vanilla, supporting taxonomic revisions, comparative trait analyses, and a deeper understanding of the processes shaping this economically and biologically important orchid genus.

Understanding evolutionary relationships in hyperdiverse plant groups remains a major challenge in systematics. The orchid genus Bulbophyllum, the second largest genus of flowering plants, represents an exceptional example of phylogenetic and morphological complexity. Relationships, particularly within the species-rich Asian clade, have remained poorly resolved due to extensive morphological variation and limited resolution in previous phylogenetic studies. Here, we reconstructed phylogenetic relationships using 63 plastid genes from 355 specimens representing 322 species and 65 of the 97 recognised sections of Bulbophyllum. Our analyses confirmed that the genus comprises five major evolutionary lineages comprised of species predominantly from Australasia, Madagascar, Continental Africa, Neotropics, and Asia. We provide the first robust phylogenetic evidence for a dichotomous split within the Asian clade into two well-supported lineages: the Asian-Malesian clade and the Malesian-Papuasian clade, with the latter containing a strongly supported Papuasian subclade. Additionally, this study supports the monophyly of several currently recognised sections while clarifying relationships in previously problematic groups. This study provides the most comprehensive plastid-based phylogenomic framework for Bulbophyllum to date and establishes a foundation for future taxonomic revision and integrative analyses of diversification and trait evolution within this hyperdiverse genus.

Background and AimsComplex genomic histories driven by hybridization and polyploidy can shape key plant traits such as defense, stress tolerance, and toxicity, particularly in Amaran-thaceae, which includes crops such as quinoa and spinach. Within this family, white goosefoot (Chenopodium album) is both a widespread agricultural weed and a traditional food resource. However, its evolutionary history is complicated by discordant signals among genomic markers within the C. album complex, comprising diploid, tetraploid, and hexaploid taxa. Here, we tested whether reticulate evolution underlies this genome-wide discordance. MethodsUsing genome-scale phylogenomic data, we analysed 2,298 conserved nuclear loci (BUSCO genes) across 27 Amaranthaceae genomes. Both single- and multicopy gene families were included to capture signals of gene duplication, incomplete lineage sorting, and hybridization. Complementary phylogenomic approaches were used to evaluate whether the evolutionary history is best supported by strictly bifurcating relationships or by reticulate evolution. Key ResultsA consistent C. album lineage was recovered, comprising tetraploid and hexaploid C. album cytotypes together with C. suecicum, C. strictum, C. formosanum, C. acuminatum, and C. opulifolium. Phylogenetic discordance was concentrated within Chenopodium, particularly around the C. album and C. quinoa lineages. Models incorporating hybridization fit better than strictly bifurcating relationships, supporting at least two reticulation events. Hybridization signals were detected in 271 loci in tetraploid and 270 in hexaploid C. album, of which 232 were shared, indicating a shared hybrid origin rather than independent lineages. ConclusionsThe evolutionary history of the C. album lineage is best explained by reticulate processes involving hybridization and polyploidy. Conserved nuclear loci retain persistent signatures of these events, helping to resolve complex evolutionary histories in polyploid plant systems.

Polyploidization is widely recognised as a major driver of plant diversification, with many species persisting as mixed-ploidy systems where multiple cytotypes co-exist. Polyploids are disproportionately represented among invasive species, yet their role in facilitating biological invasions remains poorly understood. Lantana camara, one of the worlds most successful invasive plants, exhibits remarkable cytotype diversity, but the distribution and evolutionary relationships of these cytotypes in its native and invasive ranges have remained unclear. Here, we characterise ploidy variation and assess genetic differentiation among cytotypes in invasive L. camara populations across India. Flow cytometry of more than a thousand individuals reveals that tetraploids overwhelmingly dominate the invasive range, accounting for more than 95% of individuals, while triploids and hexaploids occur at much lower frequencies. Using genome-wide ddRAD-derived SNP markers from diploids, triploids, tetraploids, and hexaploids, we find no genetic differentiation among cytotypes. Instead, individuals of different ploidy levels cluster together across multiple genetic clusters, consistent with recurrent and potentially independent origins of polyploids. These patterns further suggest that L. camara polyploids likely arise via autopolyploid formation. Together, our results establish tetraploidy as the predominant cytotype in Indias invasive populations and reveal a lack of cytotype-specific genetic structure. These findings highlight the need to investigate the ecological advantages of tetraploids and the mechanisms that generate cytotype diversity, key steps toward understanding how polyploidy contributes to the invasive success of this globally important species.

The remarkable diversity of life on Earth results from evolutionary processes functioning across different spatial and temporal scales. Species diversification occurs through various mechanisms and at widely varying rates, but identifying the conditions that trigger bursts of diversification over short timescales remains a central challenge in evolutionary biology. This difficulty is more pronounced when incomplete lineage sorting (ILS), hybridization, and ongoing gene flow obscure evolutionary relationships and complicate species delimitation. In this study, we investigated the evolutionary history and species boundaries within a group of recently diverged Petunia lineages shaped by pervasive gene flow. We integrated phylogenomic, population genetic, and species delimitation approaches to reconstruct lineage relationships and assess whether these lineages represent distinct species or stages along a speciation continuum. By applying methods that account for both ILS and gene flow, we revealed that most lineages are not fully independent evolutionary units but rather occupy intermediate positions along this continuum. Gene flow played a crucial role during diversification, blurring species boundaries and generating reticulate evolutionary patterns. Our findings demonstrate that traditional phylogenetic trees may oversimplify relationships in such systems, while phylogenetic networks offer a more accurate representation of evolutionary history. Comprehensive and integrative analyses, such as those employed here, are essential for capturing these complex dynamics. Ultimately, only four lineages could be confidently recognized as distinct species, whereas the remaining represent cases of ongoing divergence. These results emphasize the need to refine species delimitation frameworks for systems characterized by recent divergence and extensive reticulation.

Desiccation tolerance (DT) serves as a cornerstone for seed survival and for long-term persistence in the natural environment. DT is acquired during seed development, as seeds undergo a drastic change in internal water content during maturation drying. Although the physiological effects of drying on the acquisition of DT and other seed traits have been described, the molecular mechanisms underlying these effects have not yet been fully understood. Here, we addressed this gap by submitting maturing seeds of Arabidopsis thaliana L. to three different drying regimes - fast drying (FD), slow drying (SD), and a combination of both (SDFD) and studying physiological, transcriptional, and post-transcriptional responses. We found that SD not only accelerated DT acquisition but also seed maturation. Each drying regime showed a distinct transcriptional signature, with SD and SDFD showing greater global gene downregulation compared to FD. This downregulation appeared to be crucial for establishing DT in developing seeds. Interestingly, FD triggered a specific defense-related transcriptional response that was detrimental to seed longevity. Using an abscisic acid deficient mutant, we found that most of the drying-mediated transcriptional changes were largely independent of the wild-type ABA levels. On a post-transcriptional level, SD led to a major turnover of mRNA populations undergoing co-translational mRNA decay (CTRD) and promoted CTRD of stress-related genes. Overall, our study provides fundamental insights into the mechanisms by which seeds perceive and respond to drying, advancing our basic understanding of the molecular regulation of DT and seed maturation. Significance StatementSeed maturation is a critical phase of the plant life cycle when seeds acquire desiccation tolerance (DT) required for long-term storage. Drying rate, together with abscisic acid (ABA), has been implicated in this process, but whether seed development actively responds to different drying rates and how such responses are regulated has remained unclear. Here, we show that maturing seeds sense and respond to different drying regimes through distinct molecular programs, with slow drying triggering coordinated transcriptional and post-transcriptional reprogramming associated with enhanced DT. This response occurs partly independent of wild-type ABA levels, revealing drying rate as a developmental signal acting alongside hormonal regulation to direct seed maturation. These findings provide a framework for improving drying strategies and identifying molecular markers of seed quality.

Phenotypic plasticity allows plants to rapidly respond to changing environments without the need for evolutionary change or migration. While selection can create variation in plasticity across natural populations, these responses are not adaptive in all environments. To predict whether plasticity will be adaptive requires evaluation of its fitness effects across a range of environments, including novel ones. Here, we test how traits and their plasticity vary for genotypes collected across a natural hybrid zone between two tree species with contrasting climatic niches. Fast-growing Populus trichocarpa inhabits maritime environments with relatively warm and stable temperatures, while P. balsamifera inhabits continental environments with cold winters and large temperature variance throughout the year. We planted 44 clonally replicated genotypes into thirteen common gardens and measured vegetative phenology, leaf morphology, stomata morphology and conductance, and photochemistry. Overall, genotypes from colder, more continental environments exhibited higher plasticity. P. balsamifera ancestry was associated with increased plasticity in timing of fall phenology, stomatal conductance, and leaf mass per unit area. We assessed the effects of trait plasticity on fitness estimated as yearly growth across common gardens and found that the plasticity-fitness relationship was often garden-specific, indicating that the planting environment did not consistently mediate plasticity-fitness relationships. When the effects of trait plasticity on growth varied by garden temperature, higher plasticity generally had neutral or negative associations with growth in warmer environments. These results suggest that elevated plasticity evolved in a P. balsamifera genomic background as part of a climate generalist strategy to seasonal temperature variability, but that there is a trade-off between plasticity and growth in warmer environments. Consequently, less-plastic but warm-adapted P. trichocarpa genotypes are likely to have a fitness advantage under warming climates. These results demonstrate that plasticity may sometimes be maladaptive and will not be universally beneficial in a warming world.

Background and AimsNon-native species are now ubiquitous members of regional floras. The factors that lead to establishment and dominance of non-native species are continuously debated. Fundamental hypotheses about drivers of invasion success include the role of phylogeny, polyploidy, genome size, and rapid niche evolution. These hypotheses have been tested in the seed plants, but ferns, the second largest group of vascular plants, have rarely been considered in these analyses, despite making up a non-trivial portion of non-native floras. MethodsWe compiled a dataset of global non-native ferns and categorized them along the invasion spectrum using descriptions from the literature and natural history collections. Using this dataset, we assessed I) the taxonomic diversity and phylogenetic clustering of non-native ferns, II) the geographic distribution of fern introductions, testing for shifts in climatic niches, and III) test for the association of invader traits across the invasion continuum, including smaller genome sizes and higher ploidal levels. Key ResultsWe generated a dataset that includes 83 taxa; of these, we classified 18 as casual, 35 as naturalized (but not invasive), and 30 as invasive. Using this dataset, we found I) weak or no phylogenetic clustering of non-native ferns, II) some regions are overrepresented as sources and recipients of introductions, III) climatic niches are often conserved between native and introduced ranges, but can differ between introductions, IV) naturalized ferns have smaller genomes, and V) invaders have higher ploidal levels. ConclusionsWe integrated regional floras, occurrence and climate data, phylogeny, and cytology to test fundamental hypotheses regarding the colonization success of ferns. This study provides insights into the ecological, genomic, and phylogenetic features associated with the colonization of new habitats by non-native ferns, a largely overlooked portion of non-native plant taxa.

Iron (Fe) deficiency is a widespread disorder limiting global soybean (Glycine max (L.) Merr.) production. Although root exudation is a key adaptive mechanism for Fe scarcity in species like Arabidopsis, a detailed chemical characterization of soybean exudates is lacking. Here, we examined the accumulation and secretion of phenolic compounds in soybean roots and their correlation with intraspecific tolerance to Fe-deficiency chlorosis. Seven soybean genotypes with contrasting tolerance, derived from U.S. breeding programs, were analyzed. Root exudates from Fe-deficient soybean plants solubilized ferric oxide. We identified and quantified 28 coumarin-type phenolics, with catechol methylsideretin as the predominant component. Although the qualitative coumarin profile was consistent across all genotypes, Fe-efficient lines secreted these compounds at higher levels or earlier during Fe deficiency than Fe-inefficient lines. The efficient genotype A7 showed coordinated upregulation of coumarin biosynthesis and secretion, whereas this response was weaker in the Fe-inefficient genotype IsoClark. Catechol methylsideretin concentrations strongly correlated with the ability of root exudates to mobilize Fe from ferric oxide. The conserved phenolic profile, together with divergence from those reported in non-legume species, suggests lineage-specific adaptations and ecological roles beyond Fe mobilization. These results highlight genotype-dependent exudation as a determinant of soybean Fe-deficiency tolerance, with implications for breeding. HIGHLIGHTIron deficiency induces soybean root exudates containing predominantly catechol methylsideretin which mobilize iron; genotypes differing in Fe efficiency show conserved qualitative but contrasting quantitative coumarin profiles.

Climate change is reshaping the adaptive landscape of forest ecosystems, demanding more efficient strategies to identify and deploy resilient tree genotypes. Genomic prediction offers a powerful framework to accelerate selection for complex physiological traits underlying climate adaptability in long-lived species such as sessile oak (Quercus petraea (Matt.) Liebl.). Here, we conducted genomic prediction for three key physiological traits carbon isotope composition, nitrogen isotope composition, and the carbon-to-nitrogen content ratio (C/N ratio) measured in 746 trees genotyped with dense genome-wide markers ([~]580,000 SNPs). High genomic heritabilities were estimated across traits, with within-year prediction accuracies (Pearsons r between genomic estimated values and observed phenotypes) reaching 0.77. Notably, across-year and across-provenance predictions remained substantial (0.41 < r < 0.82), with predictability declining with increasing genetic distance (FST) between training and test provenances for nitrogen isotope composition and C/N ratio. In addition, GWAS-guided SNP preselection increased heritability capture by [~]15% relative to random SNP subsets. And, the pronounced provenance-by-environment interactions observed indicated substantial phenotypic plasticity in these traits. These results demonstrate the strong potential of applying genomic prediction to foliar physiological traits as polygenic predictors for climate adaptation in plants, support provenance-aware breeding to improve forest establishment, and provide practical strategies for deploying genomic prediction in long-lived species.

How plants allocate carbon determines their productivity, responses to stress, and interactions with other organisms. A substantial amount of plant carbon is stored as non-structural carbohydrates (NSC), which sustain turgor via osmoregulation and fuel metabolism when carbon is limited. NSC also support root-colonizing mycorrhizal fungi, thus we hypothesized that under carbon-limiting conditions such as drought, a trade-off between feeding mycorrhizal fungi and maintaining turgor may arise. We reduced carbon allocation to ectomycorrhizal (EcM) networks by girdling Pinus ponderosa trees exposed to drought or ambient conditions and manipulated putative fungal connections between trees by trenching. We show that, in droughted plots, trees putatively connected to girdled trees by EcM networks had 33 % less needle NSC and >10% less turgor than those connected to ungirdled trees. Trees disconnected from the mycorrhizal network by trenching had increased NSC likely from the increased water availability with girdling, but these gains were offset in the presence of networks. Our results demonstrate that the increased carbon demand by EcM fungi in response to reduced carbon inputs from some trees can deplete NSC in neighboring trees via shared mycorrhizal networks. At least in the short term, allocation trade-offs under carbon-limiting conditions may expose networked trees to carbon deficits. This may increase vulnerability to drought, which may be particularly acute given shifts in climate.

O_LIBackground and Aims: Chemodiversity is a fitness-relevant trait shaped by genetics, environment, and their interaction. Populus trichocarpa naturally inhabits broad climatic gradients and shows extensive variation in specialised metabolism. We investigated whether provenance and climate of origin imprint leaf chemodiversity and class-level relationships under common-garden conditions, and how these patterns relate to gene expression. C_LIO_LIMethods: Leaves from 87 P. trichocarpa genotypes representing 22 provenances from the west coast of North America growing in a common garden were profiled by untargeted FT-ICR-MS (1030 features) and targeted LC-MS/MS. A subset of 41 genotypes was subject to RNA-seq analyses. We tested whether provenance influenced multivariate patterns and whether metabolomic differences were related to geographic and climatic distance, where chemodiversity was quantified as Functional Hill Diversity. C_LIO_LIKey Results: P. trichocarpa metabolomes differed among origins despite shared growth conditions and showed distance-decay with both geography and climate. North-south extremes were well separated, and within-drainage samples shared high similarity. Flavonoid and isoprenoid pools strongly co-varied across individuals, whereas isoprene synthase activity did not predict total isoprenoids. Transcriptomes showed within-pathway coherence but limited overall provenance separation. C_LIO_LIConclusions: Leaf chemistry in P. trichocarpa retains signatures of geographic origin even under common-garden conditions. Coordinated investment in flavonoids and isoprenoids, together with among-origin differences in functional chemodiversity, reveals provenance-linked chemical fingerprints that complement genomic and metabolic trait data for climate-informed deployment. C_LI

Crop improvement can enhance food security, but side effects, such as trade-offs between valuable agronomic traits, are common. Likewise, fertilisation helps ensure high yields, but can devalue mutualisms with soil microbes that would otherwise be essential for nutrient acquisition. If the need for nutritional mutualisms is reduced in crops, mutualisms could be disrupted by selection relaxation or allocation trade-offs. Thus, crops could achieve high yields in spite of, or because of, disruption of nutritional mutualisms. Alternatively, the highest-yielding plants might flourish because they maximise nutrient acquisition from both symbionts and the soil. Here, enhanced mutualism could evolve over the course of agricultural crop improvement. To investigate whether high yields in cultivars and wild accessions are negatively or positively genetically correlated with outcomes in the legume-rhizobia mutualism, we measured whether yield and symbiosis traits trade-off or are positively genetically correlated among cultivars and wild accessions. We also tested whether this relationship differs between accessions released before or after 1950. We measured genetic correlations between yield and mutualism traits in 87 domesticated pea (Pisum sativum) accessions in a common garden agricultural field across three years. Seed yield and N2 fixation (%Ndfa) were positively genetically correlated. While N fixation was more strongly predictive of yield in the pre-1950 accessions than the post-1950 accessions, the underlying positive genetic correlation between the traits did not differ between the groups. The positive genetic correlation between yield and N2 fixation indicates that selection to increase yields has maintained or increased the benefits of the rhizobial mutualism in pea. Our findings predict that breeding to increase yield may continue to produce pea cultivars that get a greater proportion of their N from rhizobia, enhancing symbiotic mutualism and reducing the proportion of N supplied by fertilisation.