Small but thick enough--the Arabidopsis hypocotyl as a model to study secondary growth

Physiological Analysis and Genetic Mapping of Short Hypocotyl Trait in Brassica napus L

Hypocotyl length is a botanical trait that affects the cold tolerance of Brassica napus L. (B. napus). In this study, we constructed an F2 segregating population using the cold-resistant short hypocotyl variety '16VHNTS158' and the cold-sensitive long hypocotyl variety 'Tianyou 2288' as the parents, and BSA-seq was employed to identify candidate genes for hypocotyl length in B. napus. The results of parental differences showed that the average hypocotyl lengths of '16VHNTS158' and 'Tianyou 2288' were 0.41 cm and 0.77 cm at the 5~6 leaf stage, respectively, after different low-temperature treatments, and '16VHNTS158' exhibited lower relative ion leakage rates compared to 'Tianyou 2288'. The contents of indole acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) in hypocotyls of '16VHNTS158' and 'Tianyou 2288' increased with decreasing temperatures, but the IAA and GA contents were significantly higher than those of 'Tianyou 2288', and the BR content was lower than that of 'Tianyou 2288'. The genetic analysis results indicate that the genetic model for hypocotyl length follows the 2MG-A model. By using SSR molecular markers, a QTL locus associated with hypocotyl length was identified on chromosome C04. The additive effect value of this locus was 0.025, and it accounted for 2.5% of the phenotypic variation. BSA-Seq further localized the major effect QTL locus on chromosome C04, associating it with 41 genomic regions. The total length of this region was 1.06 Mb. Within this region, a total of 20 non-synonymous mutation genes were identified between the parents, and 26 non-synonymous mutation genes were found within the pooled samples. In the reference genome of B. napus, this region was annotated with 24 candidate genes. These annotated genes are predominantly enriched in four pathways: DNA replication, nucleotide excision repair, plant hormone signal transduction, and mismatch repair. The findings of this study provide a theoretical basis for cloning genes related to hypocotyl length in winter rapeseed and their utilization in breeding.

The Course of Mechanical Stress: Types, Perception, and Plant Response

Mechanical stimuli, together with the corresponding plant perception mechanisms and the finely tuned thigmomorphogenetic response, has been of scientific and practical interest since the mid-17th century. As an emerging field, there are many challenges in the research of mechanical stress. Indeed, studies on different plant species (annual/perennial) and plant organs (stem/root) using different approaches (field, wet lab, and in silico/computational) have delivered insufficient findings that frequently impede the practical application of the acquired knowledge. Accordingly, the current work distils existing mechanical stress knowledge by bringing in side-by-side the research conducted on both stem and roots. First, the various types of mechanical stress encountered by plants are defined. Second, plant perception mechanisms are outlined. Finally, the different strategies employed by the plant stem and roots to counteract the perceived mechanical stresses are summarized, depicting the corresponding morphological, phytohormonal, and molecular characteristics. The comprehensive literature on both perennial (woody) and annual plants was reviewed, considering the potential benefits and drawbacks of the two plant types, which allowed us to highlight current gaps in knowledge as areas of interest for future research.

Influence of Switchgrass TDIF-like Genes on Arabidopsis Vascular Development

As a member of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) family, the dodecapeptide tracheary element differentiation inhibitory factor (TDIF) has a major impact on vascular development in plants. However, the influence of polymorphisms in the TDIF peptide motif on activity remains poorly understood. The model plant, Arabidopsis provides a fast and effective tool for assaying the activity of TDIF homologs. Five TDIF homologs from a group of 93 CLE genes in switchgrass (Panicum virgatum), a perennial biomass crop, named PvTDIF-like (PvTDIFL) genes were studied. The expression levels of PvTDIFL1, PvTDIFL3 ^MR3, and PvTDIFL3 ^MR2 were relatively high and all of them were expressed at the highest levels in the rachis of switchgrass. The precursor proteins for PvTDIFL1, PvTDIFL3^MR3, and PvTDIFL3^MR2 contained one, three, and two TDIFL motifs, respectively. Treatments with exogenous PvTDIFL peptides increased the number of stele cells in the hypocotyls of Arabidopsis seedlings, with the exception of PvTDIFL_4p. Heterologous expression of PvTDIFL1 in Arabidopsis strongly inhibited plant growth, increased cell division in the vascular tissue of the hypocotyl, and disrupted the cellular organization of the hypocotyl. Although heterologous expression of PvTDIFL3 ^MR3 and PvTDIFL3 ^MR2 also affected plant growth and vascular development, PvTDIFL activity was not enhanced by the multiple TDIFL motifs encoded by PvTDIFL3 ^MR3 and PvTDIFL3 ^MR2. These data indicate that in general, PvTDIFLs are functionally similar to Arabidopsis TDIF but that the processing and activities of the PvTDIFL peptides are more complex.

Auxin and gibberellin signaling cross-talk promotes hypocotyl xylem expansion and cambium homeostasis

During secondary growth, the thickening of plant organs, wood (xylem) and bast (phloem) is continuously produced by the vascular cambium. In Arabidopsis hypocotyl and root, we can distinguish two phases of secondary growth based on cell morphology and production rate. The first phase, in which xylem and phloem are equally produced, precedes the xylem expansion phase in which xylem formation is enhanced and xylem fibers differentiate. It is known that gibberellins (GA) trigger this developmental transition via degradation of DELLA proteins and that the cambium master regulator BREVIPEDICELLUS/KNAT1 (BP/KNAT1) and receptor like kinases ERECTA and ERL1 regulate this process downstream of GA. However, our understanding of the regulatory network underlying GA-mediated secondary growth is still limited. Here, we demonstrate that DELLA-mediated xylem expansion in Arabidopsis hypocotyl is mainly achieved through DELLA family members RGA and GAI, which promote cambium senescence. We further show that AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8, which physically interact with DELLAs, specifically repress phloem proliferation and induce cambium senescence during the xylem expansion phase. Moreover, the inactivation of BP in arf6 arf8 background revealed an essential role for ARF6 and ARF8 in cambium establishment and maintenance. Overall, our results shed light on a pivotal hormone cross-talk between GA and auxin in the context of plant secondary growth.

Gene Regulatory Network Guided Investigations and Engineering of Storage Root Development in Root Crops

The plasticity of plant development relies on its ability to balance growth and stress resistance. To do this, plants have established highly coordinated gene regulatory networks (GRNs) of the transcription factors and signaling components involved in developmental processes and stress responses. In root crops, yields of storage roots are mainly determined by secondary growth driven by the vascular cambium. In relation to this, a dynamic yet intricate GRN should operate in the vascular cambium, in coordination with environmental changes. Despite the significance of root crops as food sources, GRNs wired to mediate secondary growth in the storage root have just begun to emerge, specifically with the study of the radish. Gene expression data available with regard to other important root crops are not detailed enough for us directly to infer underlying molecular mechanisms. Thus, in this review, we provide a general overview of the regulatory programs governing the development and functions of the vascular cambium in model systems, and the role of the vascular cambium on the growth and yield potential of the storage roots in root crops. We then undertake a reanalysis of recent gene expression data generated for major root crops and discuss common GRNs involved in the vascular cambium-driven secondary growth in storage roots using the wealth of information available in Arabidopsis. Finally, we propose future engineering schemes for improving root crop yields by modifying potential key nodes in GRNs.

Over-expression of transcription factor ARK1 gene leads to down-regulation of lignin synthesis related genes in hybrid poplar '717'

Improving wood growth rate and wood quality are worthy goals in forest genetics and breeding research. The ARK1 gene is one member of the ARBORKNOX family in all plants, which play an essential role in the process of plant growth and development, but the mechanism associated with its gene network regulation is poorly investigated. In order to generate over-expression transgenic hybrid poplar, the agrobacterium-mediated transformation was used to obtain transgenic hybrid poplar ‘717’ plants to provide insight into the function of the ARK1 gene in poplar. Moreover, the morphology of transgenic plants was observed, and transcriptome analysis was performed to explore the ARK1 gene function. The results showed that there were significant differences in pitch, stem diameter, petiole length, leaf width, leaf length and seedling height between ARK1 transgenic seedlings and non-transgenic seedlings. The transgenic seedlings usually had multiple branches and slender leaves, with some leaves not being fully developed. The results of transcriptome analysis showed that the differentially expressed genes were involved in the growth of poplars, including proteins, transcription factors and protein kinases. Genes related to the positive regulation in plant hormone signal transduction pathways were up-regulated, and the genes related to lignin synthesis were down-regulated. The RT-qPCR analysis confirmed the expression levels of the genes involved in the plant hormone signal transduction pathways and phenylpropanoid pathway. In conclusion, the ARK1 gene had a positive regulatory effect on plant growth, and the gene’s coding enzymes related to lignin synthesis were down-regulated.

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.

Jasmonic acid to boost secondary growth in hemp hypocotyl

The application of jasmonic acid results in an increased secondary growth, as well as additional secondary phloem fibres and higher lignin content in the hypocotyl of textile hemp (Cannabis sativa L.). Secondary growth provides most of the wood in lignocellulosic biomass. Textile hemp (Cannabis sativa L.) is cultivated for its phloem fibres, whose secondary cell wall is rich in crystalline cellulose with a limited amount of lignin. Mature hemp stems and older hypocotyls are characterised by large blocks of secondary phloem fibres which originate from the cambium. This study aims at investigating the role of exogenously applied jasmonic acid on the differentiation of secondary phloem fibres. We show indeed that the exogenous application of this plant growth regulator on young hemp plantlets promotes secondary growth, differentiation of secondary phloem fibres, expression of lignin-related genes, and lignification of the hypocotyl. This work paves the way to future investigations focusing on the molecular network underlying phloem fibre development.

Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot

The homeobox gene family, a large family represented by transcription factors, has been implicated in secondary growth, early embryo patterning, and hormone response pathways in plants. However, reports about the information and evolutionary history of the homeobox gene family in carrot are limited. In the present study, a total of 130 homeobox family genes were identified in the carrot genome. Specific codomain and phylogenetic analyses revealed that the genes were classified into 14 subgroups. Whole genome and proximal duplication participated in the homeobox gene family expansion in carrot. Purifying selection also contributed to the evolution of carrot homeobox genes. In Gene Ontology (GO) analysis, most members of the HD-ZIP III and IV subfamilies were found to have a lipid binding (GO:0008289) term. Most HD-ZIP III and IV genes also harbored a steroidogenic acute regulatory protein-related lipid transfer (START) domain. These results suggested that the HD-ZIP III and IV subfamilies might be related to lipid transfer. Transcriptome and quantitative real-time PCR (RT-qPCR) data indicated that members of the WOX and KNOX subfamilies were likely implicated in carrot root development. Our study provided a useful basis for further studies on the complexity and function of the homeobox gene family in carrot.

Transcription factors PRE3 and WOX11 are involved in the formation of new lateral roots from secondary growth taproot in A. thaliana

The spatial deployment of lateral roots determines the ability of a plant to interact with the surrounding environment for nutrition and anchorage. This paper shows that besides the pericycle, the vascular cambium becomes active in Arabidopsis thaliana taproot at a later stage of development and is also able to form new lateral roots. To demonstrate the above, we implemented a two-step approach in which the first step leads to development of a secondary structure in A. thaliana taproot, and the second applies a mechanical stress on the vascular cambium to initiate formation of a new lateral root primordium. GUS staining showed PRE3, DR5 and WOX11 signals in the cambial zone of the root during new lateral root formation. An advanced level of wood formation, characterized by the presence of medullar rays, was achieved. Preliminary investigations suggest the involvement of auxin and two transcription factors (PRE3/ATBS1/bHLH135/TMO7 and WOX11) in the transition of some vascular cambium initials from a role as producers of xylem/phloem mother cells to founder cells of a new lateral root primordium.

Repression of BLADE-ON-PETIOLE genes by KNOX homeodomain protein BREVIPEDICELLUS is essential for differentiation of secondary xylem in Arabidopsis root

Repression of boundary genes by KNOTTED1-like homeodomain transcription factor BREVIPEDICELLUS promotes the differentiation of phase II secondary xylem in Arabidopsis roots. Plant growth and development relies on the activity of meristems. Boundaries are domains of restricted growth that separate forming organs and the meristem. Class I KNOX homeodomain transcription factors are important regulators of meristem maintenance. Members of this class including BREVIDICELLUS also called KNOTTED-LIKE FROM ARABIDOPSIS THALIANA1 (BP/KNAT1) fulfill this function in part by spatially regulating boundary genes. The vascular cambium is a lateral meristem that allows for radial expansion of organs during secondary growth. We show here that BP/KNAT1 repression of boundary genes plays a crucial role in root secondary growth. In particular, exclusion of BLADE-ON-PETIOLE1/2 (BOP1/2) and other members of this module from xylem is required for the differentiation of lignified fibers and vessels during the xylem expansion phase of root thickening. These data reveal a previously undiscovered role for boundary genes in the root and shed light on mechanisms controlling wood development in trees.

Modeling hormonal control of cambium proliferation

Rise of atmospheric CO₂ is one of the main causes of global warming. Catastrophic climate change can be avoided by reducing emissions and increasing sequestration of CO₂. Trees are known to sequester CO₂ during photosynthesis, and then store it as wood biomass. Thus, breeding of trees with higher wood yield would mitigate global warming as well as augment production of renewable construction materials, energy, and industrial feedstock. Wood is made of cellulose-rich xylem cells produced through proliferation of a specialized stem cell niche called cambium. Importance of cambium in xylem cells production makes it an ideal target for the tree breeding programs; however our knowledge about control of cambium proliferation remains limited. The morphology and regulation of cambium are different from those of stem cell niches that control axial growth. For this reason, translating the knowledge about axial growth to radial growth has limited use. Furthermore, genetic approaches cannot be easily applied because overlaying tissues conceal cambium from direct observation and complicate identification of mutants. To overcome the paucity of experimental tools in cambium biology, we constructed a Boolean network CARENET (CAmbium REgulation gene NETwork) for modelling cambium activity, which includes the key transcription factors WOX4 and HD-ZIP III as well as their potential regulators. Our simulations predict that: (1) auxin, cytokinin, gibberellin, and brassinosteroids act cooperatively in promoting transcription of WOX4 and HD-ZIP III; (2) auxin and cytokinin pathways negatively regulate each other; (3) hormonal pathways act redundantly in sustaining cambium activity; (4) individual cambium cells can have diverse molecular identities. CARENET can be extended to include components of other signalling pathways and be integrated with models of xylem and phloem differentiation. Such extended models would facilitate breeding trees with higher wood yield.

Beyond flexibility: controlling stem cells in an ever changing environment

Developmental plasticity is a defining feature of plants allowing them to colonize a wide range of different ecosystems by promoting environmental adaptation. Their postembryonic development requires life-long maintenance of stem cells, which are embedded into specialized tissues, called meristems. The shoot apical meristem gives rise to all above ground tissues and is a complex and dynamic three-dimensional structure harboring cells of different clonal origins and fates. Functionally divergent subdomains are stably maintained despite permanent cell division, however their relative sizes are modified in response to developmental and environmental signals. In this review, we briefly describe the core regulatory program of the shoot apical meristem and discuss progress in the fields of mechanical and environmental control of its activity.

Vascular Morphodynamics During Secondary Growth

Quantification of vascular morphodynamics during secondary growth has been hampered by the scale of the process. Even in the tiny model plant Arabidopsis thaliana, the xylem can include more than 2000 cells in a single cross section, rendering manual counting impractical. Moreover, due to its deep location, xylem is an inaccessible tissue, limiting live imaging. A novel method to visualize and measure secondary growth progression has been proposed: "the Quantitative Histology" approach. This method is based on a detailed anatomical atlas, and image segmentation coupled with machine learning to automatically extract cell shapes and identify cell type. Here we present a new version of this approach, with a user-friendly interface implemented in the open source software LithoGraphX.

Novel tools for quantifying secondary growth

Secondary growth occurs in dicotyledons and gymnosperms, and results in an increased girth of plant organs. It is driven primarily by the vascular cambium, which produces thousands of cells throughout the life of several plant species. For instance, even in the small herbaceous model plant Arabidopsis, manual quantification of this massive process is impractical. Here, we provide a comprehensive overview of current methods used to measure radial growth. We discuss the issues and problematics related to its quantification. We highlight recent advances and tools developed for automated cellular phenotyping and its future applications.

Studying Secondary Growth and Bast Fiber Development: The Hemp Hypocotyl Peeks behind the Wall

Cannabis sativa L. is an annual herbaceous crop grown for the production of long extraxylary fibers, the bast fibers, rich in cellulose and used both in the textile and biocomposite sectors. Despite being herbaceous, hemp undergoes secondary growth and this is well exemplified by the hypocotyl. The hypocotyl was already shown to be a suitable model to study secondary growth in other herbaceous species, namely Arabidopsis thaliana and it shows an important practical advantage, i.e., elongation and radial thickening are temporally separated. This study focuses on the mechanisms marking the transition from primary to secondary growth in the hemp hypocotyl by analysing the suite of events accompanying vascular tissue and bast fiber development. Transcriptomics, imaging and quantification of phytohormones were carried out on four representative developmental stages (i.e., 6-9-15-20 days after sowing) to provide a comprehensive overview of the events associated with primary and secondary growth in hemp. This multidisciplinary approach provides cell wall-related snapshots of the growing hemp hypocotyl and identifies marker genes associated with the young (expansins, β-galactosidases, and transcription factors involved in light-related processes) and the older hypocotyl (secondary cell wall biosynthetic genes and transcription factors).

Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis

Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis.

Secondary growth of the Arabidopsis hypocotyl-vascular development in dimensions

The secondary thickening of plant organs in extant dicotyledons is a massive growth process that constitutes the major carbon sink in perennial, woody plants. Yet, our understanding of its molecular genetic control has been mostly obtained by its analysis in an herbaceous annual model, Arabidopsis. Recent years have seen increased interest in this somewhat under-researched topic, and various (non-)cell autonomous factors that guide the extent and vascular patterning of secondary growth have been identified. Concomitantly, a more detailed understanding of vascular differentiation processes has been obtained through analyses of primary growth, mostly in the root meristem. A future challenge will be the integration of these patterning and differentiation modules together with cambial activity into the 4-dimensional frame of secondary thickening.

Xylem development - from the cradle to the grave

The development and growth of plants, as well as their successful adaptation to a variety of environments, is highly dependent on the conduction of water, nutrients and other important molecules throughout the plant body. Xylem is a specialized vascular tissue that serves as a conduit of water and minerals and provides mechanical support for upright growth. Wood, also known as secondary xylem, constitutes the major part of mature woody stems and roots. In the past two decades, a number of key factors including hormones, signal transducers and (post)transcriptional regulators have been shown to control xylem formation. We outline the main mechanisms shown to be essential for xylem development in various plant species, with an emphasis on Arabidopsis thaliana, as well as several tree species where xylem has a long history of investigation. We also summarize the processes which have been shown to be instrumental during xylem maturation. This includes mechanisms of cell wall formation and cell death which collectively complete xylem cell fate.

Proteomic analysis of soybean hypocotyl during recovery after flooding stress

Soybean is a nutritionally important crop, but exhibits reduced growth and yields under flooding stress. To investigate soybean responses during post-flooding recovery, a gel-free proteomic technique was used to examine the protein profile in the hypocotyl. Two-day-old soybeans were flooded for 2 days and hypocotyl was collected under flooding and during the post-flooding recovery period. A total of 498 and 70 proteins were significantly changed in control and post-flooding recovering soybeans, respectively. Based on proteomic and clustering analyses, three proteins were selected for mRNA expression and enzyme activity assays. Pyruvate kinase was increased under flooding, but gradually decreased during post-flooding recovery period at protein abundance, mRNA, and enzyme activity levels. Nucleotidylyl transferase was decreased under flooding and increased during post-flooding recovery at both mRNA expression and enzyme activity levels. Beta-ketoacyl reductase 1 was increased under flooding and decreased during recovery at protein abundance and mRNA expression levels, but its enzyme activity gradually increased during the post-flooding recovery period. These results suggest that pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase play key roles in post-flooding recovery in soybean hypocotyl by promoting glycolysis for the generation of ATP and regulation of secondary metabolic pathways.

BIOLOGICAL SIGNIFICANCE

This study analyzed post-flooding recovery response mechanisms in soybean hypocotyl, which is a model organ for studying secondary growth, using a gel-free proteomic technique. Mass spectrometry analysis of proteins extracted from soybean hypocotyls identified 20 common proteins between control and flooding-stressed soybeans that changed significantly in abundance over time. The hypocotyl proteins that changed during post-flooding recovery were assigned to protein, development, secondary metabolism, and glycolysis categories. The analysis revealed that three proteins, pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase, were increased in hypocotyl under flooding conditions and during post-flooding recovery. The proteins are involved in glycolysis, nucleotide synthesis and amino acid activation, and complex fatty acid biosynthesis.

Vascular Cambium Development

Secondary phloem and xylem tissues are produced through the activity of vascular cambium, the cylindrical secondary meristem which arises among the primary plant tissues. Most dicotyledonous species undergo secondary development, among them Arabidopsis. Despite its small size and herbaceous nature, Arabidopsis displays prominent secondary growth in several organs, including the root, hypocotyl and shoot. Together with the vast genetic resources and molecular research methods available for it, this has made Arabidopsis a versatile and accessible model organism for studying cambial development and wood formation. In this review, we discuss and compare the development and function of the vascular cambium in the Arabidopsis root, hypocotyl, and shoot. We describe the current understanding of the molecular regulation of vascular cambium and compare it to the function of primary meristems. We conclude with a look at the future prospects of cambium research, including opportunities provided by phenotyping and modelling approaches, complemented by studies of natural variation and comparative genetic studies in perennial and woody plant species.