American Journal of Botany

PremiseHerbarium specimens are increasingly used to extract morphological traits for ecological and evolutionary studies, yet the effects of tissue desiccation on trait measurements remain poorly understood. Here, we tested whether higher tissue water content leads to greater measurement changes after herborization (H1) and whether fresh trait values can be reliably predicted from herbarium measurements (H2). MethodsWe evaluated the reliability of herbarium-based measurements by comparing fresh and dried traits of leaves, flowers, fleshy fruits, and seeds across 262 individuals representing 133 Neotropical Myrtaceae species. Phylogenetic least square models and machine-learning regressions were used to test H1 and H2. ResultsLeaves and flowers generally shrank after herborization, fruits size metrics tended to increase, and seeds were largely unaffected. Water content was significantly associated with the magnitude of herborization effects in flowers and some leaf and seed traits. Fresh trait values were accurately predicted from herbarium measurements. Prediction errors were lowest for leaf traits, followed by fruits, flowers, and seeds. DiscussionThese results partially support H1 and support H2, indicating that herbarium specimens can be reliably used for trait analyses when organ-specific responses are considered, providing a practical framework to account for potential desiccation bias in functional trait research.

The temperate rainforests of the Pacific Northwest of North America harbor many endemic taxa whose evolutionary histories have been shaped by major climatic and geologic events. The enigmatic taildropper slugs (genus Prophysaon) are one example, notable for their ability to autonomize their tails to escape predators. Despite extensive work uncovering the evolutionary history of individual lineages, relationships among the nine recognized species of Prophysaon remain poorly understood due to insufficient molecular data. To address this, we collected transcriptomes for six of the nine currently accepted species of Prophysaon. Using these data, we were able to resolve species relationships, calling into question the existing subgeneric classification based on morphology. We also detected undescribed phenotypic diversity within the P. andersonii--P. foliolatum species complex, with molecular data supporting the distinctness of two phenotypically distinct populations from Washington. Finally, our transcriptomic data suggest a moderate role of introgression in shaping the evolutionary history of Prophysaon. Here, we synonymize the subgenus Mimetarion with nominotypical Prophysaon. Future work should further investigate whether the undescribed diversity detected here represents species level differentiation.

Premise of studyUnder increasingly frequent pollinator-limited environments, plants need to rely on modes of reproductive assurance such as selfing and cloning. However, few studies investigate the interplay between selfing and cloning in plants that can do both. Here, we explore mechanisms determining the relative expression of selfing and cloning throughout the European distribution of the wild woodland strawberry (Fragaria vesca) under a pollinator-free environment. MethodsWe established an outdoor common garden with 121 woodland strawberry genotypes from across Europe and excluded them from pollinators. For each genotype, we recorded reproductive traits and performed hand-pollination treatments. Key ResultsWe found a weak trade-off between cloning and selfing, driven by increased seed and fruit provisioning rather than flower production. The capacity to autonomously self-fertilize was determined by the lateral proximity of the anthers to the pistils (lateral herkogamy), but not by early inbreeding depression. Genotypes sampled at lower latitudes and altitudes were better at self-fertilizing and had smaller petals. The propensity to clone increased towards the east, where genotypes also had smaller petals, particularly at higher latitudes. ConclusionAt the species level, we detected a trade-off between the propensity for clonal reproduction and the capacity for self-fertilization. At a continental scale, the capacity to self-fertilize varied along a north-south gradient, whereas clonal propensity varied along an east-west gradient. Our results suggest that these two modes of reproductive assurance may compensate for reduced pollinator attractiveness (smaller petals) in regions where each mode is most strongly expressed.

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.

BackgroundPlants are exposed to various environmental challenges. With ongoing climate change, droughts and insect outbreaks are expected to become more frequent. Thus, a better understanding is needed of how different plant species respond to such single and combined challenges. This study investigated common versus species-specific responses to environmental challenges in three perennial plant species of different growth forms and whether responses differ intraspecifically among accessions. Clones of different accessions of the herbaceous species Tanacetum vulgare, the woody vine Solanum dulcamara, and the tree Populus nigra were subjected to similar control, herbivory, drought, and combined (drought and herbivory) treatments for the same periods. After the exposure, concentrations of foliar phytohormones and various morphological traits were measured. ResultsAcross all species, several foliar phytohormones and one of ten morphological traits responded consistently to the environmental challenges. Jasmonoyl-isoleucine was induced by herbivory and the combined treatment, abscisic acid (ABA) by drought and the combined treatment, and indole acetic acid by the combined treatment in all species. Root mass remained unchanged in all species. However, structural equation models (SEMs) revealed a shared regulatory pathway across species in which ABA connected treatment and root mass, indicating a common hormonal response potentially linking challenges to growth responses. Despite these common patterns, species-specific responses were pronounced. In P. nigra, a unique induction of salicylic acid was found under the combined treatment, while aboveground mass and root-shoot ratio remained unaffected by any treatment, in contrast to the other two species. Species-specific SEMs further indicated distinct phytohormone-mediated pathways underlying morphological variation. Phenotypic plasticity reflected these species-specific patterns, with none of the phytohormones or morphological traits exhibiting uniform plasticity across species. Intraspecific variation further shaped responses, as phytohormone and morphological trait plasticity depended on accession, indicating substantial accession-specific plant responses. ConclusionsOur results indicate that some responses to comparable challenges may be conserved across species, while others are species-specific. The combined treatment elicited the most pronounced responses, and such complex responses may become more frequent under current global change. Our study highlights that comprehensive understanding of plant responses requires systematic comparisons at both interspecific and intraspecific scales.

Timing of flowering is shifting with climate change. Although climate-driven shifts in phenology sometimes affect seed production, whether changing phenology will scale up to affect population dynamics of long-lived plants remains largely unknown, particularly under changing precipitation. Understanding how phenology affects persistence and extinction risk is a pressing need given contemporary biodiversity loss. We combined nearly a decade of demographic censuses and a four-year phenological survey in a rainfall manipulation experiment to examine the effects of experimental drought and irrigation on flowering phenology, vital rates (e.g., survival and individual growth), and population growth in the perennial herb Lomatium utriculatum. We found that drought advanced flowering by 3.3 days on average, and that earlier-flowering plants produced more seeds regardless of treatment. However, both rainfall treatments reduced seed production compared to controls. We quantified the phenology-mediated and direct, non-phenological effects of rainfall manipulation on population growth rates using integral projection models and a life table response experiment. Drought and irrigation increased {lambda} through increased individual growth, but these effects were partially negated by treatment-driven declines in seed output. In contrast, changes to seed production resulting from shifting flowering times had negligible effects on population growth. Our results suggest that climate-driven phenological shifts may only marginally impact population dynamics in perennial plants and highlight that assessing phenologys consequences for persistence under climate change must also account for direct demographic effects of the climate driver(s) themselves. SignificanceWill changing flowering times under climate change increase extinction risk in plant populations? Despite well-documented earlier flowering and its influence on the number of offspring produced, how changing flowering times will affect population growth or decline is still mostly unknown. We study this in a perennial wildflower subject to changes in rainfall. While we found that drought meant earlier flowering and that, all else equal, early flowering meant more seeds, these effects only marginally affected population growth. Instead, population growth was influenced mostly by rainfall-driven changes to individual plant growth. While shifting flowering times remain an important indicator of climate change, assessing extirpation in plants requires considering flowering times as only one of many life cycle processes changing with climate.

Text AbstractIn this study, we characterized the genetic structure and reconstructed the demographic history of cactus wrens (Campylorhynchus brunneicapillus), an endemic species of desert regions of North America, that shows a clear phenotypic and genotypic variation. We evaluated the effects of historical climate change on the structure and population dynamics of desert species using genomic data through genotyping by sequencing (GBS) and applied a population structure analysis (FST and ADMIXTURE), revealing two genetically differentiated groups: one continental and another peninsular in Baja California. Subsequently, we implemented the MSMC2 coalescent model on data divided into autosomal regions and the Z sex chromosome to estimate changes in effective population size (Ne) through evolutionary time. Additionally, we developed ecological niche models (ENMs) projected to the Last Glacial Maximum (LGM), Last Interglacial (LIG), Present times, and Future (2060 - 2080). Results indicate that both populations maintained moderated Nes before the LGM, experienced severe bottlenecks (Ne [~] 102-103), followed by a sustained expansion. However, recovery was limited to the Z chromosome of the peninsular population. These findings reveal how glaciations and interglacials shaped the evolutionary history of desert species and provide genomic evidence of the splitting of C. affinis from C. brunneicapillus. Article summaryThis research examines how climate changes shaped genetic diversity of cactus wrens across North American warm deserts. Using coalescent methods, researchers tracked effective population size changes over 100,000 years, using ecological niche modeling they predicted habitat suitability across climate periods. Results showed that continental and peninsular populations experienced bottlenecks during the Last Glacial Maximum, followed by demographic recovery on warm periods. However, the sex chromosome (Z) revealed male-biased demographic patterns in peninsular populations. Future projections indicated habitat suitability reductions for peninsular populations, highlighting conservation concerns. These findings demonstrate that past climate shaped genetic diversity of cactus wrens.

The ecological and evolutionary processes determining species range limits remain poorly understood. Ultimately, range limits depend on the species abilities to persist under heterogeneous conditions, by adaptive differentiation and phenotypic plasticity, including transgenerational effects. To investigate ecological differentiation and transgenerational effects in the clonal invasive knotweed, Reynoutria japonica, in Europe, we conducted a two-phase transplant experiment: plants sampled along the entire latitudinal gradient were planted in three sites located at the northern range margin, mid-range and near the southern range margin, and then re-transplanted among all three sites after two years. Biomass production and allocation were generally not associated with latitude of origin and previous growth at the same site did not promote performance. We therefore find no evidence that adaptive differentiation or transgenerational effects contribute to the wide distribution of R. japonica in Europe. However, at the northern site, with a 25% shorter season, knotweed plants invested much less biomass below-ground, and the pattern was further strengthened in plants that had grown in the northern site in the previous generation. Overwintering below-ground rhizomes are essential for survival and spread. We further explored limiting climate conditions in a species distribution model for the European range and found that mean annual temperature and temperature annual range are the main predictors of the European distribution of R. japonica. Taken together, our study suggests that low temperatures and associated short seasons may pose a limit to the broad environmental tolerance of R. japonica and restrict its northward spread by reducing below-ground biomass accumulation.

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.

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.

Restoration and management of natural populations often assume that local genotypes are best suited for transplantation to their local environment. Prioritizing a single local genotype, however, contrasts with the framework of maximizing intraspecific diversity to increase population resilience to environmental change. Local populations may also become maladapted to a rapidly changing environment, motivating alternative frameworks that instead minimize environmental distance between source and transplantation sites. Here, we tested the predictive power of the local is best, maximize intraspecific diversity, and minimize environmental distance frameworks on the survival and growth of Eastern oyster (Crassostrea virginica) genotypes in field common gardens that differed in salinity and disease pressure. Although a genome scan revealed patterns of adaptation to disease, heat stress, and salinity among source populations, we did not find strong support for the local is best framework: geographically distant southern genotypes performed comparably to local selection lines and a local wild population. Higher genetic diversity within monocultures was associated with higher survival, yet highly diverse polycultures survived at lower rates than the best-performing monocultures, providing mixed support for the maximize intraspecific diversity framework. Temperature and salinity of the environments-of-origin of parents predicted the survival of their offspring in common gardens, but the relationship between survival and environmental distance was context-dependent, leading to mixed support for the minimize environmental distance framework. Together, these results demonstrate that no single framework reliably predicted transplantation success, suggesting that effective management strategies may need to integrate genomic and environmental lines of evidence to guide genotype selection.

Spinach (Spinacia oleraceae) is a principal vegetable crop commercially grown in Controlled Environment Agriculture (CEA). Recent research suggests that root morphological and architectural differences among crop species influence yield, resource use efficiency, and environmental stress tolerance. These root traits may be exploited to increase yield, promote efficient nutrient use, and mitigate environmental stressors. This study measured differences between various spinach cultivars in CEA systems to reveal morphological and anatomical variation. We grew three spinach cultivars with different reported growing rates ( Income, Darkside, and El-Majestic) under NFT hydroponic and substrate-based systems in a controlled greenhouse environment over 45 days with destructive harvests at days 15, 30, and 45. Supplemental light (250 {micro}mol/m2/s) with 12-hour photoperiod and periodic fertigation was used. Harvests included the collection of leaf and root biomass, and scanning of root systems in WinRhizo software, measuring ten variables. On day 45, root cross-sections from orders 1-5 were embedded in JB-4 resin, sectioned, stained, and analyzed for diameter, vasculature, and rhizodermis characteristics. Results indicate that in spinach, differences in root system morphology are linked to cultivation systems over cultivar identity. Vascular and root anatomical alterations are minor compared to morphological differences in response to the cultivation system. Hydroponic-style growth systems are associated with the proliferation of fine-root ideotypes compared with substrate-based conditions. Such findings affirm previous studies, which suggest plastic root morphology in response to growth systems, and may be used to help create more resilient, resource-efficient cultivars. HighlightsO_LIIn spinach, root system morphology differences are linked to cultivation systems. C_LIO_LIRoot vascular and anatomical alterations are minor in response to cultivation system. C_LIO_LIHydroponic growth systems are linked to fine-root ideotype proliferation in spinach. C_LIO_LIFine-root ideotype proliferation may be a breeding target for CEA spinach. C_LI

CoverCress is a new winter annual oilseed crop developed from field pennycress within the past 20 years. Field pennycress is commonly considered to be self-pollinated but little basic research has been published and there is some misalignment of conclusions. Our experience working with pennycress plant growth in greenhouse and field conditions over the past 13 years suggests that outcrossing is uncommon. We conducted lab, greenhouse, and field experiments to strengthen the body of work. Pollen viability kinetics analysis showed that longevity of pollen viability is negatively impacted by increasing temperatures and by direct exposure to light. Samples treated at 4C declined to 50% viability in 12 hours while it took just 2.5 hrs at 37C, and 1.6 hrs in full sunlight on a cool early April day. Cross-pollination was absent among greenhouse-grown plants flowering inside an agitated plastic pollen-containment covering. Across greenhouse tests, high rates of cross-pollination occurred only in an emasculation treatment that rendered flowers male sterile and opened the pistil to cross-fertilization. Field trials designed to measure pollen flow distance using a trackable fae1 knockout reporter gene failed to show detectable movement of pollen under field conditions in two locations. This data strongly suggests that domesticated field pennycress may be considered a self-pollinated crop and managed as such.

Successful establishment of a species in a new range is a useful way to understand the impact of demography and selection on the evolution of globally distributed species. In particular, introductions influence genetic diversity and population structure in the introduced range in unpredictable ways. Additionally, introgressive hybridization is often associated with successful establishment in new ranges. In this study, we explore the impact of introgressive hybridization on the polyploid Capsella bursa-pastoris in the New York City metropolitan area. We find Capsella bursa-pastoris in the New York City metropolitan area likely originated from multiple introductions from northern Eurasia, and that populations across the New York City metropolitan area are generally panmictic. As with Capsella bursa-pastoris in Eurasia, we discover evidence of introgression from the diploid Capsella rubella in this population. By evaluating ancestry in regions across the genome, we find introgressed regions are rich in gene content and contribute to genetic diversity in this population. These results suggest that introgressive hybridization before introductions may buffer species from the negative effects of population bottlenecks and allow for successful establishment.

IntroductionHuman land-use intensification and the resulting habitat loss are primary drivers of insect pollinator declines. Habitat restoration offers a promising approach to counteract these declines, yet landscape-level evaluations of bee responses to restoration and management remain limited. We conducted a two-year, landscape-scale study in Wisconsin, USA, to assess how different intensities of tallgrass prairie restoration and management affect bumble bees (Bombus spp.). ObjectivesThis study aimed to determine whether (1) bumble bee abundance and diversity increase with assisted restoration, and (2) outcomes differ between low-(seeded only) and moderate-intensity (seeded and managed with prescribed fire) interventions. MethodsUsing catch-and-release surveys, we measured bumble bee abundance and diversity at 32 sites representing a gradient in restoration intervention: no intervention (unassisted recovery), low intervention, and moderate intervention. ResultsBumble bee abundance and diversity were higher at assisted restoration sites (low and moderate intervention) than at unassisted sites. Although both tended to be greater at moderate than low intervention intensities, these differences were not statistically significant. Bumble bee community composition also differed across intervention intensity, driven by shifts in dominant species (e.g., B. impatiens and B. griseocollis). Rarer taxa, including endangered and vulnerable species, occurred only at assisted restoration sites, with the largest populations at moderate intervention sites. Across all sites, bumble bee responses were strongly and positively associated with floral abundance, but not with semi-natural habitat in the surrounding landscape. ConclusionOur findings demonstrate that assisted grassland restoration can effectively increase bumble bee abundance and diversity, supporting its value as a conservation practice for pollinators. Implications for Practice: (1) Grassland restorations targeting plant communities can successfully support nontarget pollinators across a range of management intensities and landscape contexts. Adding seeds of pollinator-preferred plants could improve restorations with low floral abundance and diversity. (2) Management of existing restorations is important to maintain abundant floral resources and diverse pollinator communities. Because sites varied widely in prescribed fire use, our findings likely represent a conservative estimate of its benefits, and higher intervention intensity (e.g., repeated seeding, regular fire, mechanical or chemical shrub and invasive plants control) may further enhance outcomes for bumble bees.

Although genetic diversity is a fundamental component of biodiversity, we lack data for a majority of species, particularly in biodiversity hotspots such as tropical forests. We present a comparative genetic dataset of 19 tropical tree species (including one palm) from the Caribbean island of Puerto Rico and neighboring islands (Hispanola and the US Virgin Islands). Using a reduced-representation sequencing technique (SLAF-seq), we identified species-specific single-nucleotide polymorphism (SNP) datasets with 24,413 to 433,637 high-quality SNPs per species. The focal species represent a range of life-history and climate associations, which may be relevant to their genetic structure. Therefore, we also include complementary information on species functional traits (wood density, leaf thickness, specific leaf area, maximum height, and seed dry mass), as well as geographic distributions and climatic associations from species distribution models.

Microbial communities can shift under drought in ways that enhance plant performance during drought ("microbe-mediated acclimation"). However, it is also possible for microbial communities to shift in ways that worsen the effects of drought ("mal-acclimation"). It is unclear how and where microbe-mediated acclimation vs. mal-acclimation occurs, or if there are types of soils or microbial communities that are more likely to harbor microbes that enhance plant acclimation and limit mal-acclimation. We tested for microbe-mediated plant acclimation/mal-acclimation to drought in soils from 21 maize farms in the midwestern United States, spanning a range of climate, soil types, and management practices. We first conditioned soil microbial communities to drought vs. well-watered conditions in a greenhouse and then tested for microbe-mediated acclimation by growing maize in soils inoculated with the conditioned microbial communities under drought and well-watered conditions. Drought-conditioned soils did not enhance plant performance under drought. In fact, one third of the farms exhibited mal-acclimation, especially under well-watered conditions where wet-conditioned soils reduced plant performance in well-watered contemporary conditions. Farm management practices, climate, soil texture, and microbial diversity generally did not predict when this microbe-mediated mal-acclimation occurred. Overall, these results suggest that in agricultural soils, microbes may frequently impede-rather than facilitate-plant acclimation to soil moisture levels. Open research statementThe plant and soil data used in this study are available via the Environmental Data Initiative repository at https://doi.org/10.6073/pasta/f4a0db3a076cf6d8cef908947f82736e. The bacterial and fungal amplicon sequence data are available via the European Nucleotide Archive under accessions PRJEB110071 and PRJEB109827, respectively.

Improving photosynthesis is a promising approach to enhance sugar beet productivity. However, genetic variation in leaf photosynthesis and its relationship with disease resistance remain underexplored. We evaluated 98 sugar beet genotypes representing different breeding categories, including commercial F1 hybrids, seed-parent lines, and pollinator lines, in Hokkaido, northern Japan. Leaf gas exchange was measured during early growth under field conditions around the infection period of Cercospora leaf spot (CLS). To account for fluctuating irradiance during large-scale phenotyping, we applied a multilevel mixed-effects light-response model to estimate genotype-specific photosynthetic characteristics. Substantial genotypic variations in photosynthetic characteristics were detected. F1 hybrids exhibited higher photosynthetic capacity than breeding lines, whereas differences among breeding categories were unclear due to large within-category variation. Some breeding lines exhibited photosynthetic rates higher than those of hybrids, indicating exploitable genetic resources within the present genetic panel. We did not detect statistically significant trade-off between leaf photosynthesis and CLS resistance among 98 genotypes; in a subset of 19 genotypes analysed in detail, the relationship was even synergistic. Our results highlight the genetic diversity of leaf photosynthesis and its category-dependent structure, and suggest that selection for enhanced photosynthesis can proceed without substantial trade-off with CLS resistance. HighlightLeaf photosynthesis of 98 sugar beet genotypes showed significant genetic variation and dependence on breeding category. Active photosynthesis incurred minimal trade-off with Cercospora leaf spot resistance.

Belowground, plants are exposed to a wide range of biotic stresses that vary in severity and nature, including tissue damage, disruption of vascular connectivity, and depletion of assimilates. How plants adapt their root systems to cope with different types of belowground biotic stresses is not well known. In this paper we compare above- and belowground plant adaptations to three nematode species with distinct tissue migration and feeding behaviours to study mechanisms underlying tolerance to different types of biotic stresses. We monitored both green canopy growth and changes in root system architecture of Arabidopsis inoculated with Pratylenchus penetrans, Heterodera schachtii, and Meloidogyne incognita. This revealed three distinct phases in aboveground plant responses: (i) initial growth inhibition associated with host invasion and tissue damage, (ii) persistent growth reduction associated with nematode sedentarism, and (iii) late growth stimulus in more advanced stages of infection. Specific adaptations in the root systems further revealed fundamentally different stress coping strategies. Tissue damage and intermittent feeding by P. penetrans in the root cortex did not induce significant changes in root system architecture. Tissue damage to the root cortex and prolonged feeding on host vascular cells by H. schachtii induced secondary root formation compensating for primary root growth inhibition. Prolonged feeding on host vascular cell by M. incognita alone did not induce secondary root formation, but was accompanied by typical local tissue swelling instead. Our data suggest that local secondary root formation and tissue swelling are two distinct compensatory mechanisms underlying tolerance to sedentarism by root-feeding nematodes. HighlightHow plants utilize root system plasticity to cope with different types of biotic stresses by root feeding nematodes remains largely unknown. Here, we report on specific adaptive growth responses in Arabidopsis roots to three nematode species, Pratylenchus penetrans, Heterodera schachtii, and Meloidogyne incognita, with fundamentally different strategies for host invasion, subsequent migration through host tissue, and feeding on host cells.

Grapevine cluster architecture is a key selection target in breeding programs because it influences disease susceptibility, yield stability and juice quality. High-throughput phenotyping offers a rapid and non-destructive approach to capture biochemical and structural variation in these traits, yet the influence of plant organ reflectance and data partitioning strategies on trait prediction remains poorly understood. In this study, we evaluated how hyperspectral reflectance from different grapevine organs contributes to the prediction of cluster architecture and juice quality traits in two clonal populations of Riesling and Pinot. Using partial least squares regression (PLSR), we assessed the prediction accuracy of eight cluster architecture and six juice quality traits under two data partitioning strategies. Models based on cluster reflectance outperformed those using dry leaf reflectance for most traits, except for pH. Partitioning the dataset by cluster type increased trait variance and improved predictions for number of berries (R{superscript 2} = 0.53), berry diameter (R{superscript 2} = 0.79), and total acidity (R{superscript 2} = 0.48). Visible, red-edge and NIR spectra were most informative regions to predict the traits studied. Together, our results highlight the importance of organ-specific data and appropriate calibration strategies to improve phenomic models for the development of scalable proxies for grapevine improvement. HighlightSpectral phenomics reveals that prediction accuracy in grapevine depends on organ spectral signatures and traits, with cluster reflectance outperforming leaves, informing new phenotyping strategies for breeding improvement.