Expression Profile of PIN-Formed Auxin Efflux Carrier Genes during IBA-Induced In Vitro Adventitious Rooting in Olea europaea L

Reactive oxygen species and NADPH oxidase-encoding genes underly the plant growth and developmental responses to Trichoderma

The modulation of plant growth and development through reactive oxygen species (ROS) is a hallmark during the interactions with microorganisms, but how fungi and their molecules influence endogenous ROS production in the root remains unknown. In this report, we correlated the biostimulant effect of Trichoderma atroviride with Arabidopsis root development via ROS signaling. T. atroviride enhanced ROS accumulation in primary root tips, lateral root primordia, and emerged lateral roots as revealed by total ROS imaging through the fluorescent probe H2DCF-DA and NBT detection. Acidification of the substrate and emission of the volatile organic compound 6-pentyl-2H-pyran-2-one appear to be major factors by which the fungus triggers ROS accumulation. Besides, the disruption of plant NADPH oxidases, also known as respiratory burst oxidase homologs (RBOHs) including ROBHA, RBOHD, but mainly RBOHE, impaired root and shoot fresh weight and the root branching enhanced by the fungus in vitro. RbohE mutant plants displayed poor lateral root proliferation and lower superoxide levels than wild-type seedlings in both primary and lateral roots, indicating a role for this enzyme for T. atroviride-induced root branching. These data shed light on the roles of ROS as messengers for plant growth and root architectural changes during the plant-Trichoderma interaction.

Expression of CsSCL1 and Rooting Response in Chestnut Leaves Are Dependent on the Auxin Polar Transport and the Ontogenetic Origin of the Tissues

The mechanisms underlying the de novo regeneration of adventitious roots are still poorly understood, particularly in trees. We developed a system for studying adventitious rooting (AR) at physiological and molecular levels using leaves excised from chestnut microshoots of the same genotype but with two distinct ontogenetic origins that differ in rooting competence. Leaves were treated with auxin and N-1-naphthyl-phthalamic acid (NPA), an inhibitor of auxin polar transport (PAT). The physiological effects were investigated by recording rooting rates and the number and quality of the roots. Molecular responses were examined by localizing and monitoring the changes in the expression of CsSCL1, an auxin-inducible gene in juvenile and mature shoots during AR. The rooting response of leaves was ontogenetic-stage dependent and similar to that of the donor microshoots. Initiation of root primordia and root development were inhibited by application of NPA, although its effect depended on the timing of application. CsSCL1 was upregulated by auxin only in rooting-competent leaves during the novo root organogenesis, and the expression was reduced by NPA. The inhibitory effect on gene expression was detected during the reprograming of rooting competent cells towards root initials in response to auxin, indicating that PAT-mediated upregulation of CsSCL1 is required in the initial steps of AR in chestnut leaves. The localized expression of CsSCL1 in the quiescent center (QC) also suggests a role for this gene in the maintenance of meristematic competence and root radial patterning.

Transcriptome Dynamics of Rooting Zone and Leaves during In Vitro Adventitious Root Formation in Eucalyptus nitens

Wood properties and agronomic traits associated with fast growth and frost tolerance make Eucalyptus nitens a valuable forest alternative. However, the rapid age-related decline in the adventitious root (AR) formation (herein, meaning induction, initiation, and expression stages) limits its propagation. We analyzed transcriptomic profile variation in leaves and stem bases during AR induction of microcuttings to elucidate the molecular mechanisms involved in AR formation. In addition, we quantified expressions of candidate genes associated with recalcitrance. We delimited the ontogenic phases of root formation using histological techniques and Scarecrow and Short-Root expression quantification for RNA sequencing sample collection. We quantified the gene expressions associated with root meristem formation, auxin biosynthesis, perception, signaling, conjugation, and cytokinin signaling in shoots harvested from 2- to 36-month-old plants. After IBA treatment, 702 transcripts changed their expressions. Several were involved in hormone homeostasis and the signaling pathways that determine cell dedifferentiation, leading to root meristem formation. In part, the age-related decline in the rooting capacity is attributable to the increase in the ARR1 gene expression, which negatively affects auxin homeostasis. The analysis of the transcriptomic variation in the leaves and rooting zones provided profuse information: (1) To elucidate the auxin metabolism; (2) to understand the hormonal and signaling processes involved; (3) to collect data associated with their recalcitrance.

Mutation of OsPIN1b by CRISPR/Cas9 Reveals a Role for Auxin Transport in Modulating Rice Architecture and Root Gravitropism

The distribution and content of auxin within plant tissues affect a variety of important growth and developmental processes. Polar auxin transport (PAT), mainly mediated by auxin influx and efflux transporters, plays a vital role in determining auxin maxima and gradients in plants. The auxin efflux carrier PIN-FORMED (PIN) family is one of the major protein families involved in PAT. Rice (Oryza sativa L.) genome possesses 12 OsPIN genes. However, the detailed functions of OsPIN genes involved in regulating the rice architecture and gravity response are less well understood. In the present study, OsPIN1b was disrupted by CRISPR/Cas9 technology, and its roles in modulating rice architecture and root gravitropism were investigated. Tissue-specific analysis showed that OsPIN1b was mainly expressed in roots, stems and sheaths at the seedling stage, and the transcript abundance was progressively decreased during the seedling stages. Expression of OsPIN1b could be quickly and greatly induced by NAA, indicating that OsPIN1b played a vital role in PAT. IAA homeostasis was disturbed in ospin1b mutants, as evidenced by the changed sensitivity of shoot and root to NAA and NPA treatment, respectively. Mutation of OsPIN1b resulted in pleiotropic phenotypes, including decreased growth of shoots and primary roots, reduced adventitious root number in rice seedlings, as well as shorter and narrower leaves, increased leaf angle, more tiller number and decreased plant height and panicle length at the late developmental stage. Moreover, ospin1b mutants displayed a curly root phenotype cultured with tap water regardless of lighting conditions, while nutrient solution culture could partially rescue the curly root phenotype in light and almost completely abolish this phenotype in darkness, indicating the involvement of the integration of light and nutrient signals in root gravitropism regulation. Additionally, amyloplast sedimentation was impaired in the peripheral tiers of the ospin1b root cap columella cell, while it was not the main contributor to the abnormal root gravitropism. These data suggest that OsPIN1b not only plays a vital role in regulating rice architecture but also functions in regulating root gravitropism by the integration of light and nutrient signals.

Understanding the Role of PIN Auxin Carrier Genes under Biotic and Abiotic Stresses in Olea europaea L

The PIN-FORMED (PIN) proteins represent the most important polar auxin transporters in plants. Here, we characterized the PIN gene family in two olive genotypes, the Olea europaea subsp. europaea var. sylvestris and the var. europaea (cv. ‘Farga’). Twelve and 17 PIN genes were identified for vars. sylvestris and europaea, respectively, being distributed across 6 subfamilies. Genes encoding canonical OePINs consist of six exons, while genes encoding non-canonical OePINs are composed of five exons, with implications at protein specificities and functionality. A copia-LTR retrotransposon located in intron 4 of OePIN2b of var. europaea and the exaptation of partial sequences of that element as exons of the OePIN2b of var. sylvestris reveals such kind of event as a driving force in the olive PIN evolution. RNA-seq data showed that members from the subfamilies 1, 2, and 3 responded to abiotic and biotic stress factors. Co-expression of OePINs with genes involved in stress signaling and oxidative stress homeostasis were identified. This study highlights the importance of PIN genes on stress responses, contributing for a holistic understanding of the role of auxins in plants.

Auxin and its role in plant development: structure, signalling, regulation and response mechanisms

Auxins are plant hormones that play a central role in controlling plant growth and development across different environmental conditions. Even at low concentrations, auxins can regulate gene expression through specific transcription factors and proteins that are modulated to environmental responses in the signalling cascade. Auxins are synthesized in tissues with high cell division activity and distributed by specific transmembrane proteins that regulate efflux and influx. This review presents recent advances in understanding the biosynthetic pathways, both dependent and independent of tryptophan, highlighting the intermediate indole compounds (indole-3-acetamide, indole-3-acetaldoxime, indole-3-pyruvic acid and tryptamine) and the key enzymes for auxin biosynthesis, such as YUCs and TAAs. In relation to the signalling cascade, it has been shown that auxins influence gene expression regulation by the connection between synthesis and distribution. Moreover, the molecular action of the auxin response factors and auxin/indole-3-acetic acid transcription factors with the F-box TIR1/AFB auxin receptors regulates gene expression. In addition, the importance of microRNAs in the auxin signalling pathway and their influence on plant plasticity to environmental fluctuations is also demonstrated. Finally, this review describes the chemical and biological processes involving auxins in plants.

Laser Microdissection of Specific Stem-Base Tissue Types from Olive Microcuttings for Isolation of High-Quality RNA

Simple Summary

Only a small portion of the stem cells participate in the process of adventitious root formation and the cells/tissues types involved in this process is species-dependent. In olive, it is still unclear which type of cells acquire competence for rooting. Regardless, the entire stem nodal segment (containing a mixture of distinct cell types) continues to be used in studies related to the molecular mechanisms underlying this process. Laser microdissection (LM) technology has been applied to isolate specific tissue and cell types. However, it is difficult to find a standard LM protocol suitable for all plant species and cell types and, thus, LM procedures must be developed and optimized for each particular tissue. In this study, we aimed to evaluate the efficiency of a LM protocol in olive microcuttings stem-base samples. This work presents a simple, rapid and efficient LM procedure for harvesting specific tissue types used for further high-quality RNA isolation. This will encourage future cell type-specific transcriptomic studies, contributing at deciphering rooting-competent cells in olive stems and to better understand the molecular mechanisms underlying the process of adventitious root formation.

Abstract

Higher plants are composed of different tissue and cell types. Distinct cells host different biochemical and physiological processes which is reflected in differences in gene expression profiles, protein and metabolite levels. When omics are to be carried out, the information provided by a specific cell type can be diluted and/or masked when using a mixture of distinct cells. Thus, studies performed at the cell- and tissue-type level are gaining increasing interest. Laser microdissection (LM) technology has been used to isolate specific tissue and cell types. However, this technology faces some challenges depending on the plant species and tissue type under analysis. Here, we show for the first time a LM protocol that proved to be efficient for harvesting specific tissue types (phloem, cortex and epidermis) from olive stem nodal segments and obtaining RNA of high quality. This is important for future transcriptomic studies to identify rooting-competent cells. Here, nodal segments were flash-frozen in liquid nitrogen-cooled isopentane and cryosectioned. Albeit the lack of any fixatives used to preserve samples’ anatomy, cryosectioned sections showed tissues with high morphological integrity which was comparable with that obtained with the paraffin-embedding method. Cells from the phloem, cortex and epidermis could be easily distinguished and efficiently harvested by LM. Total RNA isolated from these tissues exhibited high quality with RNA Quality Numbers (determined by a Fragment Analyzer System) ranging between 8.1 and 9.9. This work presents a simple, rapid and efficient LM procedure for harvesting specific tissue types of olive stems and obtaining high-quality RNA.

High efficient de novo root-to-shoot organogenesis in Citrus jambhiri Lush.: Gene expression, genetic stability and virus indexing

A protocol for high-frequency direct organogenesis from root explants of Kachai lemon (Citrus jambhiri Lush.) was developed. Full-length roots (~3 cm) were isolated from the in vitro grown seedlings and cultured on Murashige and Skoog basal medium supplemented with Nitsch vitamin (MSN) with different concentrations of cytokinin [6-benzylaminopurine, (BAP)] and gibberellic acid (GA₃). The frequency of multiple shoot proliferation was very high, with an average of 34.3 shoots per root explant when inoculated on the MSN medium supplemented with BAP (1.0 mg L^–1) and GA₃ (1.0 mg L^–1). Optimal rooting was induced in the plantlets under half strength MSN medium supplemented with indole-3-acetic acid (IAA, 0.5–1.0 mg L^–1). IAA induced better root structure than 1-naphthaleneacetic acid (NAA), which was evident from the scanning electron microscopy (SEM). The expressions of growth regulating factor genes (GRF1 and GRF5) and GA₃ signaling genes (GA2OX1 and KO1) were elevated in the regenerants obtained from MSN+BAP (1.0 mg L^-1)+GA₃ (1.0 mg L^-1). The expressions of auxin regulating genes were high in roots obtained in ½ MSN+IAA 1.0 mg L^-1. Furthermore, indexing of the regenerants confirmed that there was no amplicons detected for Huanglongbing bacterium and Citrus tristeza virus. Random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers detected no polymorphic bands amongst the regenerated plants. This is the first report that describes direct organogenesis from the root explant of Citrus jambhiri Lush. The high-frequency direct regeneration protocol in the present study provides an enormous significance in Citrus organogenesis, its commercial cultivation and genetic conservation.

Expression Levels of Genes Encoding Proteins Involved in the Cell Wall-Plasma Membrane-Cytoskeleton Continuum Are Associated With the Maturation-Related Adventitious Rooting Competence of Pine Stem Cuttings

Stem cutting recalcitrance to adventitious root formation is a major limitation for the clonal propagation or micropropagation of elite genotypes of many forest tree species, especially at the adult stage of development. The interaction between the cell wall-plasma membrane and cytoskeleton may be involved in the maturation-related decline of adventitious root formation. Here, pine homologs of several genes encoding proteins involved in the cell wall-plasma membrane-cytoskeleton continuum were identified, and the expression levels of 70 selected genes belonging to the aforementioned group and four genes encoding auxin carrier proteins were analyzed during adventitious root formation in rooting-competent and non-competent cuttings of Pinus radiata. Variations in the expression levels of specific genes encoding cell wall components and cytoskeleton-related proteins were detected in rooting-competent and non-competent cuttings in response to wounding and auxin treatments. However, the major correlation of gene expression with competence for adventitious root formation was detected in a family of genes encoding proteins involved in sensing the cell wall and membrane disturbances, such as specific receptor-like kinases (RLKs) belonging to the lectin-type RLKs, wall-associated kinases, Catharanthus roseus RLK1-like kinases and leucine-rich repeat RLKs, as well as downstream regulators of the small guanosine triphosphate (GTP)-binding protein family. The expression of these genes was more affected by organ and age than by auxin and time of induction.

Identifying Molecular Chechkpoints for Adventitious Root Induction: Are We Ready to Fill the Gaps?

The molecular mechanisms underlying de novo root organogenesis have been under intense study for the last decades. As new tools and resources became available, a comprehensive model connecting the processes and factors involved was developed. Separate phases that allow for specific analyses of individual checkpoints were well defined. Physiological approaches provided information on the importance of metabolic processes and long-distance signaling to balance leaf and stem status and activation of stem cell niches to form new root meristems. The study of plant hormones revealed a series of sequential roles for cytokinin and auxin, dynamically interconnected and modulated by jasmonic acid and ethylene. The identification of genes specifying cell identity uncovered a network of sequentially acting transcriptional regulators that link hormonal control to cell fate respecification. Combined results from herbaceous model plants and the study of recalcitrant woody species underscored the need to understand the limiting factors that determine adventitious rooting competence. The relevance of epigenetic control was emphasized by the identification of microRNAs and chromatin remodeling agents involved in the process. As the different players are set in place and missing pieces become apparent, findings in related processes can be used to identify new candidates to complete the picture. Molecular knobs connecting the balance cell proliferation/differentiation to hormone signaling pathways, transcriptional control of cell fate or metabolic modulation of developmental programs can offer clues to unveil new elements in the dynamics of adventitious rooting regulatory networks. Mechanisms for cell non-autonomous signaling that are well characterized in other developmental processes requiring establishment and maintenance of meristems, control of cell proliferation and cell fate specification can be further explored. Here, we discuss possible candidates and approaches to address or elude the limitations that hinder propagation programs requiring adventitious rooting.

Molecular Bases for the Regulation of Adventitious Root Generation in Plants

The formation of adventitious roots (ARs) is an ecologically and economically important developmental process in plants. The evolution of AR systems is an important way for plants to cope with various environmental stresses. This review focuses on identified genes that have known to regulate the induction and initiation of ARs and offers an analysis of this process at the molecular level. The critical genes involved in adventitious rooting are the auxin signaling-responsive genes, including the AUXIN RESPONSE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES-DOMAIN (LOB) gene families, and genes associated with auxin transport and homeostasis, the quiescent center (QC) maintenance, and the root apical meristem (RAM) initiation. Several genes involved in cell wall modulation are also known to be involved in the regulation of adventitious rooting. Furthermore, the molecular processes that play roles in the ethylene, cytokinin, and jasmonic acid signaling pathways and their crosstalk modulate the generation of ARs. The crosstalk and interaction among many molecular processes generates complex networks that regulate AR generation.

Somatic Embryogenesis from Mature Embryos of Olea europaea L. cv. 'Galega Vulgar' and Long-Term Management of Calli Morphogenic Capacity

Several olive cultivars, characterized by high-quality olive oil show agronomical issues such as excessive vigor, high susceptibility to biotic and abiotic stresses, and low propagation ability. They are strong candidates for breeding based on new technologies to improve their performance in a short period of time. For this reason, the first step is developing efficient somatic embryogenesis (SE) protocols. Somatic embryogenesis in olive is highly genotype-dependent for both adult tissues and mature embryos as initial explants, requiring the development of specific protocols for each genotype. Trials using cotyledons and radicles as initial explants, isolated from ripe seeds from the Portuguese olive cv. ‘Galega vulgar’, gave more than 95% calli development. Radicles proved to be the most responsive tissue for SE induction, with an average of 2 embryos per callus after callus transfer to expression medium, and 14 embryos per callus after subculture on the olive cyclic embryogenesis medium (ECO). Embryogenic competence could be recovered after several subcultures on ECO medium that maintained cyclic embryogenesis for an indeterminate period of time. Embryo conversion and plant acclimatization were also attained with high success rates. Media management for cyclic embryogenesis maintenance is of general importance for SE protocols in any olive genotype. Somatic embryogenesis was thus attained for the first time in embryo-derived explants of cv. ‘Galega vulgar’.