Polar auxin transport is implicated in vessel differentiation and spatial patterning during secondary growth in Populus

A systems genetic analysis identifies putative mechanisms and candidate genes regulating vessel traits in poplar wood

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.

A Solanum lycopersicum polyamine oxidase contributes to the control of plant growth, xylem differentiation, and drought stress tolerance

Polyamines are involved in several plant physiological processes. In Arabidopsis thaliana, five FAD-dependent polyamine oxidases (AtPAO1 to AtPAO5) contribute to polyamine homeostasis. AtPAO5 catalyzes the back-conversion of thermospermine (T-Spm) to spermidine and plays a role in plant development, xylem differentiation, and abiotic stress tolerance. In the present study, to verify whether T-Spm metabolism can be exploited as a new route to improve stress tolerance in crops and to investigate the underlying mechanisms, tomato (Solanum lycopersicum) AtPAO5 homologs were identified (SlPAO2, SlPAO3, and SlPAO4) and CRISPR/Cas9-mediated loss-of-function slpao3 mutants were obtained. Morphological, molecular, and physiological analyses showed that slpao3 mutants display increased T-Spm levels and exhibit changes in growth parameters, number and size of xylem elements, and expression levels of auxin- and gibberellin-related genes compared to wild-type plants. The slpao3 mutants are also characterized by improved tolerance to drought stress, which can be attributed to a diminished xylem hydraulic conductivity that limits water loss, as well as to a reduced vulnerability to embolism. Altogether, this study evidences conservation, though with some significant variations, of the T-Spm-mediated regulatory mechanisms controlling plant growth and differentiation across different plant species and highlights the T-Spm role in improving stress tolerance while not constraining growth.

Temperature and Turgor "Limitation" and Environmental "Control" in Xylem Biology and Dendrochronology

Trees and other woody plants are immensely ecologically important, making it essential to understand the causes of relationships between tree structure and function. To help these efforts, we highlight persistent traditions in plant biology of appealing to environmental factors "limiting" or "controlling" woody plant features. Examples include the idea that inevitable drops in cell turgor with plant height limit cell expansion and thus leaf size and tree height; that low temperatures prohibit lignification of cells and thus the growth of woody plants at high elevation; and notions from dendrochronology and related fields that climate factors such as rainfall and temperature "control" growth ring features. We show that notions of "control," "limitation," and the like imply that selection would favor a given trait value, but that these would-be favored values are developmentally impossible to produce. Such "limitation" scenarios predict trait frequency distributions that are very narrow and are abruptly curtailed at the upper limit of developmental possibility (the right-hand side of the distribution). Such distributions have, to our knowledge, never been observed, so we see little empirical support for "limitation" hypotheses. We suggest that, as a more productive starting point, plant biologists should examine adaptation hypotheses, in which developmental possibility is wide (congruent with the wide ranges of trait variation that really are observed), but only some of the possible variants are favored. We suggest that (1) the traditional the proximate/ultimate causation distinction, (2) purging scenarios of teleology/anthropomorphism, and (3) stating hypotheses in terms of developmental potential and natural selection are three simple ways of making "limitation" hypotheses clearer with regard to biological process and thus empirically testable.

PtrVCS2 Regulates Drought Resistance by Changing Vessel Morphology and Stomatal Closure in Populus trichocarpa

Drought has severe effects on plant growth, forest productivity, and survival throughout the world. Understanding the molecular regulation of drought resistance in forest trees can enable effective strategic engineering of novel drought-resistant genotypes of tree species. In this study, we identified a gene, PtrVCS2, encoding a zinc finger (ZF) protein of the ZF-homeodomain transcription factor in Populus trichocarpa (Black Cottonwood) Torr. & A. Gray. ex Hook. Overexpression of PtrVCS2 (OE-PtrVCS2) in P. trichocarpa resulted in reduced growth, a higher proportion of smaller stem vessels, and strong drought-resistance phenotypes. Stomatal movement experiments revealed that the OE-PtrVCS2 transgenics showed lower stomata apertures than wild-type plants under drought conditions. RNA-seq analysis of the OE-PtrVCS2 transgenics showed that PtrVCS2 regulates the expression of multiple genes involved in regulation of stomatal opening and closing, particularly the PtrSULTR3;1-1 gene, and several genes related to cell wall biosynthesis, such as PtrFLA11-12 and PtrPR3-3. Moreover, we found that the water use efficiency of the OE-PtrVCS2 transgenic plants was consistently higher than that of wild type plants when subjected to chronic drought stress. Taken together, our results suggest that PtrVCS2 plays a positive role in improving drought adaptability and resistance in P. trichocarpa.

Leaf out time correlates with wood anatomy across large geographic scales and within local communities

There is a long-standing idea that the timing of leaf production in seasonally cold climates is linked to xylem anatomy, specifically vessel diameter because of the hydraulic requirements of expanding leaves. We tested for a relationship between the timing of leaf out and vessel diameter in 220 plants in three common gardens accounting for species' phylogenetic relationships. We investigated how vessel diameter related to wood porosity, plant height and leaf length. We also used dye perfusion tests to determine whether plants relied on xylem produced during the previous growing season at the time of leaf out. In all three gardens, there was later leaf out in species with wider vessels. Ring-porous species had the widest vessels, exhibited latest leaf out and relied less on xylem made during the previous growing season than diffuse-porous species. Wood anatomy and leaf phenology did not exhibit a phylogenetic signal. The timing of leaf out is correlated with wood anatomy across species regardless of species' geographic origin and phylogenetic relationships. This correlation could be a result of developmental and physiological links between leaves and wood or tied to a larger safety efficiency trade-off.

A poplar option: the 'within-individual approach' for elucidating xylem structure-function relationships

This article comments on:

Baer AB, Fickle JC, Medina J, Robles C, Pratt RB, Jacobsen AL. 2021. Xylem biomechanics, water storage, and density within roots and shoots of an angiosperm tree species. Journal of Experimental Botany 72, 7984–7997.

The role of ontogeny in wood diversity and evolution

Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony-the change in rate and timing of developmental events, (2) homeosis-the ontogenetic replacement of features, (3) heterometry-the change in quantity of a feature, (4) exaptation-the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty-the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.

Tip-to-base xylem conduit widening as an adaptation: causes, consequences, and empirical priorities

In the stems of terrestrial vascular plants studied to date, the diameter of xylem water-conducting conduits D widens predictably with distance from the stem tip L approximating D ∝ L^b , with b ≈ 0.2. Because conduit diameter is central for conductance, it is essential to understand the cause of this remarkably pervasive pattern. We give reason to suspect that tip-to-base conduit widening is an adaptation, favored by natural selection because widening helps minimize the increase in hydraulic resistance that would otherwise occur as an individual stem grows longer and conductive path length increases. Evidence consistent with adaptation includes optimality models that predict the 0.2 exponent. The fact that this prediction can be made with a simple model of a single capillary, omitting much biological detail, itself makes numerous important predictions, e.g. that pit resistance must scale isometrically with conduit resistance. The idea that tip-to-base conduit widening has a nonadaptive cause, with temperature, drought, or turgor limiting the conduit diameters that plants are able to produce, is less consistent with the data than an adaptive explanation. We identify empirical priorities for testing the cause of tip-to-base conduit widening and underscore the need to study plant hydraulic systems leaf to root as integrated wholes.

Auxin-Induced SaARF4 Downregulates SaACO4 to Inhibit Lateral Root Formation in Sedum alfredii Hance

Lateral root (LR) formation promotes plant resistance, whereas high-level ethylene induced by abiotic stress will inhibit LR emergence. Considering that local auxin accumulation is a precondition for LR generation, auxin-induced genes inhibiting ethylene synthesis may thus be important for LR development. Here, we found that auxin response factor 4 (SaARF4) in Sedum alfredii Hance could be induced by auxin. The overexpression of SaARF4 decreased the LR number and reduced the vessel diameters. Meanwhile, the auxin distribution mode was altered in the root tips and PIN expression was also decreased in the overexpressed lines compared with the wild-type (WT) plants. The overexpression of SaARF4 could reduce ethylene synthesis, and thus, the repression of ethylene production decreased the LR number of WT and reduced PIN expression in the roots. Furthermore, the quantitative real-time PCR, chromatin immunoprecipitation sequencing, yeast one-hybrid, and dual-luciferase assay results showed that SaARF4 could bind the promoter of 1-aminocyclopropane-1-carboxylate oxidase 4 (SaACO4), associated with ethylene biosynthesis, and could downregulate its expression. Therefore, we concluded that SaARF4 induced by auxin can inhibit ethylene biosynthesis by repressing SaACO4 expression, and this process may affect auxin transport to delay LR development.

The comparative method is not macroevolution: across-species evidence for within-species process

It is common for studies that employ the comparative method for the study of adaptation, i.e. documentation of potentially adaptive across-species patterns of trait-environment or trait-trait correlation, to be designated as "macroevolutionary." Authors are justified in using "macroevolution" in this way by appeal to definitions such as "evolution above the species level." I argue that regarding the comparative method as "macroevolutionary" is harmful because it hides in serious ways the true causal content of hypotheses tested with the comparative method. The comparative method is a means of testing hypotheses of adaptation and their alternatives. Adaptation is a population level phenomenon, involving heritable interindividual variation that is associated with fitness differences. For example, given heritable intrapopulational variation, more streamlined individuals in populations of fast-moving aquatic animals have higher locomotory efficiency and thus better survivorship and more resources directed to reproduction than less streamlined ones. Direct evidence consistent with this population-level scenario includes the observation that many unrelated species of fast-moving aquatic animals have similar streamlined shapes, an example of the comparative method. Crucial to note in this example is that although the data are observed across species, the comparative method for studying adaptation tests hypotheses regarding standard population-level natural selection with no content that can be construed as "macro." Even less "macro," individual-level developmental dynamics can limit or bias the range of variants available for selection. Calling any of these studies "macroevolutionary" implies that some additional process is at work, shrouding the need to test adaptation hypotheses and study the range of variants that can be produced in development.

Genome-wide identification of polar auxin transporter gene families reveals a possible new polar auxin flow in inverted cuttings of Populus yunnanensis

Inverted cuttings of Populus yunnanensis are characterized by enlarged stems and dwarfed new shoots, and phytohormones play a crucial role in the response to inversion. The polar auxin transport (PAT) system is distinct from the transport systems of other hormones and is controlled by three major transporter gene families: pin-formed (PIN), auxin-resistant/like aux (AUX/LAX) and ATP-binding cassette transporters of the B class (ABCB). Here, we identified these three families in P. trichocarpa, P. euphratica and P. yunnanensis through a genome-wide analysis. The Populus PIN, AUX/LAX and ABCB gene families comprised 15, 8 and 31 members, respectively. Most PAT genes in Populus and Arabidopsis were identified as clear sister pairs, and some had unique motifs. Transcriptome profiling revealed that the expression of most PAT genes was unrelated to cutting inversion and that only several genes showed altered expression when cuttings were inverted. The auxin content difference at positions was opposite in upright and inverted cutting bodies during rooting, which obeyed the original plant polarity. However, during plant growth, the two direction types exhibited similar auxin movements in the cutting bodies, and the opposite auxin changes were observed in new shoots. Four PAT genes with a positive response to cutting inversion, PyuPIN10, PyuPIN11, PyuLAX6 and PyuABCB27, showed diverse expression patterns between upright and inverted cuttings during rooting and plant growth. Furthermore, PAT gene expression retained its polarity, which differs from the results found for auxin flow during plant growth. The inconformity indicated that a new downward auxin flow in addition to the old upward flow might be established during the growth of inverted cuttings. Some highly polar PAT genes were involved in the maintenance of original auxin polarity, which might cause the enlarged stems of inverted cuttings. This work lays a foundation for understanding the roles of auxin transport in plant responses to inversion.

Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees

Wood formation was present in early angiosperms, but has been highly modified through evolution to generate the anatomical diversity seen in extant angiosperm lineages. In this project, we modeled changes in gene coexpression relationships associated with the evolution of wood formation in a phylogenetic survey of 13 angiosperm tree species. Gravitropic stimulation was used as an experimental treatment to alter wood formation and also perturb gene expression. Gene transcript abundances were determined using RNA sequencing of developing wood tissues from upright trees, and from the top (tension wood) and bottom (opposite wood) tissues of gravistimulated trees. A network-based approach was employed to align gene coexpression networks across species based on orthologous relationships. A large-scale, multilayer network was modeled that identified both lineage-specific gene coexpression modules and modules conserved across multiple species. Functional annotation and analysis of modules identified specific regulatory processes associated with conserved modules, including regulation of hormones, protein phosphorylation, meristem development and epigenetic processes. Our results provide novel insights into the evolution and development of wood formation, and demonstrate the ability to identify biological processes and genes important for the evolution of a foundational trait in nonmodel, undomesticated forest trees.

Expression Analysis of Key Auxin Biosynthesis, Transport, and Metabolism Genes of Betula pendula with Special Emphasis on Figured Wood Formation in Karelian Birch

Auxin status in woody plants is believed to be a critical factor for the quantity and quality of the wood formed. It has been previously demonstrated that figured wood formation in Karelian birch (Betula pendula Roth var. carelica (Merckl.) Hämet-Ahti) is associated with a reduced auxin level and elevated sugar content in the differentiating xylem, but the molecular mechanisms of the abnormal xylogenesis remained largely unclear. We have identified genes involved in auxin biosynthesis (Yucca), polar auxin transport (PIN) and the conjugation of auxin with amino acids (GH3) and UDP-glucose (UGT84B1) in the B. pendula genome, and analysed their expression in trunk tissues of trees differing in wood structure. Almost all the investigated genes were overexpressed in Karelian birch trunks. Although Yucca genes were overexpressed, trunk tissues in areas developing figured grain had traits of an auxin-deficient phenotype. Overexpression of GH3s and UGT84B1 appears to have a greater effect on figured wood formation. Analysis of promoters of the differentially expressed genes revealed a large number of binding sites with various transcription factors associated with auxin and sugar signalling. These data agree with the hypothesis that anomalous figured wood formation in Karelian birch may be associated with the sugar induction of auxin conjugation.

From Carlquist's ecological wood anatomy to Carlquist's Law: why comparative anatomy is crucial for functional xylem biology

All students of xylem structure-function relations need to be familiar with the work of Sherwin Carlquist. He studies xylem through the lens of the comparative method, which uses the appearance of similar anatomical features under similar conditions of natural selection to infer function. "Function" in biology implies adaptation; maximally supported adaptation inferences require experimental and comparative xylem scientists to work with one another. Engaging with comparative inferences of xylem function will, more likely sooner rather than later, bring one to the work of Sherwin Carlquist. To mark his 90th birthday, I highlight just a few examples of his extraordinarily perceptive and general comparative insights. One is "Carlquist's Law", the pervasive tendency for vessels to be solitary when background cells are conductive. I cover his pioneering of "ecological" wood anatomy, viewing xylem variation as reflecting the effects of selection across climate and habit variation. Another is the embolism vulnerability-conduit diameter relationship, one of the most widely invoked structure-function relationships in xylem biology. I discuss the inferential richness within the notion of Carlquistian paedomorphosis, including detailed functional inferences regarding ray cell orientation. My final example comes from his very recent work offering the first satisfactory hypothesis accounting for the geographical and histological distribution of scalariform perforation plates as an adaptation, including "Carlquist's Ratchet", why scalariform plates are adaptive but do not re-evolve once lost. This extraordinarily rich production over six decades is filled with comparative inferences that should keep students of xylem function busy testing for decades to come.

Early-stage sugar beet taproot development is characterized by three distinct physiological phases

Despite the agronomic importance of sugar beet (Beta vulgaris L.), the early-stage development of its taproot has only been poorly investigated. Thus, the mechanisms that determine growth and sugar accumulation in sugar beet are largely unknown. In the presented study, a physiological characterization of early-stage sugar beet taproot development was conducted. Activities were analyzed for fourteen key enzymes of carbohydrate metabolism in developing taproots over the first 80 days after sowing. In addition, we performed in situ localizations of selected carbohydrate-metabolic enzyme activities, anatomical investigations, and quantifications of soluble carbohydrates, hexose phosphates, and phytohormones. Based on the accumulation dynamics of biomass and sucrose, as well as on anatomical parameters, the early phase of taproot development could be subdivided into three stages-prestorage, transition, secondary growth and sucrose accumulation stage-each of which was characterized by distinct metabolic and phytohormonal signatures. The enzyme activity signatures corresponding to these stages were also shown to be robustly reproducible in experiments conducted in two additional locations. The results from this physiological phenotyping approach contribute to the identification of the key regulators of sugar beet taproot development and open up new perspectives for sugar beet crop improvement concerning both physiological marker-based breeding and biotechnological approaches.

Stem length, not climate, controls vessel diameter in two trees species across a sharp precipitation gradient

Variation in xylem conduit diameter traditionally has been explained by climate, whereas other evidence suggests that tree height is the main driver of conduit diameter. The effect of climate versus stem length on vessel diameter was tested in two tree species (Embothrium coccineum, Nothofagus antarctica) that both span an exceptionally wide precipitation gradient (2300-500 mm). To see whether, when taking stem length into account, plants in wetter areas had wider vessels, not only the scaling of vessel diameter at the stem base across individuals of different heights, but also the tip-to-base scaling along individuals of similar heights across sites were examined. Within each species, plants of similar heights had similar mean vessel diameters and similar tip-to-base widening of vessel diameter, regardless of climate, with the slopes and intercepts of the vessel diameter-stem length relationship remaining invariant within species across climates. This study focusing on within-species variation--thus, avoiding noise associated with the great morphological variation across species--showed unequivocally that plant size, not climate, is the main driver of variation in vessel diameter. Therefore, to the extent that climate selects for differing vessel diameters, it will inevitably also affect plant height.

Exogenous Application of Phytohormones Promotes Growth and Regulates Expression of Wood Formation-Related Genes in Populus simonii × P. nigra

Although phytohormones are known to be important signal molecules involved in wood formation, their roles are still largely unclear. Here, Populus simonii × P. nigra seedlings were treated with different concentrations of exogenous phytohormones, indole-3-acetic acid (IAA), gibberellin (GA₃), and brassinosteroid (BR), and the effects of phytohormones on growth were investigated. Next, 27 genes with known roles in wood formation were selected for qPCR analysis to determine tissue-specificity and timing of responses to phytohormone treatments. Compared to the control, most IAA, GA₃, and BR concentrations significantly increased seedling height. Meanwhile, IAA induced significant seedling stem diameter and cellulose content increases that peaked at 3 and 30 mg·L⁻¹, respectively. Significant increase in cellulose content was also observed in seedlings treated with 100 mg·L⁻¹ GA₃. Neither stem diameter nor cellulose content of seedlings were affected by BR treatment significantly, although slight effects were observed. Anatomical measurements demonstrated improved xylem, but not phloem, development in IAA- and BR-treated seedlings. Most gene expression patterns induced by IAA, GA₃, and BR differed among tissues. Many IAA response genes were also regulated by GA₃, while BR-induced transcription was weaker and slower in Populus than for IAA and GA₃. These results reveal the roles played by phytohormones in plant growth and lay the foundation for exploring molecular regulatory mechanisms of wood formation in Populus.

Plant Vascular Tissues-Connecting Tissue Comes in All Shapes

For centuries, humans have grown and used structures based on vascular tissues in plants. One could imagine that life would have developed differently without wood as a resource for building material, paper, heating energy, or fuel and without edible tubers as a food source. In this review, we will summarise the status of research on Arabidopsis thaliana vascular development and subsequently focus on how this knowledge has been applied and expanded in research on the wood of trees and storage organs of crop plants. We will conclude with an outlook on interesting open questions and exciting new research opportunities in this growing and important field.