Type-B ARABIDOPSIS RESPONSE REGULATORs Specify the Shoot Stem Cell Niche by Dual Regulation of WUSCHEL

Integration of genome wide association studies and co-expression networks reveal roles of PtoWRKY 42-PtoUGT76C1-1 in trans-zeatin metabolism and cytokinin sensitivity in poplar

Cytokinins are important for in vitro shoot regeneration in plants. Cytokinin N-glucosides are produced via an irreversible glycosylation pathway, which regulates the endogenous cytokinin content. Although cytokinin N-glucoside pathways have been uncovered in higher plants, no regulator has been identified to date. We performed a metabolome genome-wide association study (mGWAS), weighted gene co-expression network analysis (WGCNA), and expression quantitative trait nucleotide (eQTN) mappings to build a core triple genetic network (mGWAS-gene expression-phenotype) for the trans-zeatin N-glucoside (ZNG) metabolite using data from 435 unrelated Populus tomentosa individuals. Variation of the ZNG level in poplar is attributed to the differential transcription of PtoWRKY42, a member of WRKY multigene family group IIb. Functional analysis revealed that PtoWRKY42 negatively regulated ZNG accumulation by binding directly to the W-box of the UDP-glycosyltransferase 76C 1-1 (PtoUGT761-1) promoter. Also, PtoWRKY42 was strongly induced by leaf senescence, 6-BA, wounding, and salt stress, resulting in a reduced ZNG level. We identified PtoWRKY42, a negative regulator of cytokinin N-glucosides, which contributes to the natural variation in ZNG level and mediates ZNG accumulation by directly modulating the key glycosyltransferase gene PtoUGT76C1-1.

Meeting at the DNA: Specifying Cytokinin Responses through Transcription Factor Complex Formation

Cytokinin is a plant hormone regulating numerous biological processes. Its diverse functions are realized through the expression control of specific target genes. The transcription of the immediate early cytokinin target genes is regulated by type-B response regulator proteins (RRBs), which are transcription factors (TFs) of the Myb family. RRB activity is controlled by phosphorylation and protein degradation. Here, we focus on another step of regulation, the interaction of RRBs among each other or with other TFs to form active or repressive TF complexes. Several examples in Arabidopsis thaliana illustrate that RRBs form homodimers or complexes with other TFs to specify the cytokinin response. This increases the variability of the output response and provides opportunities of crosstalk between the cytokinin signaling pathway and other cellular signaling pathways. We propose that a targeted approach is required to uncover the full extent and impact of RRB interaction with other TFs.

Synthesis and regulation of auxin and abscisic acid in maize

Indole-3-acetic acid (IAA), the primary auxin in higher plants, and abscisic acid (ABA) play crucial roles in the ability of maize (Zea mays L.) to acclimatize to various environments by mediating growth, development, defense and nutrient allocation. Although understanding the biochemical reactions for IAA and ABA biosynthesis and signal transduction has progressed, the mechanisms by which auxin and ABA are synthesized and transduced in maize have not been fully elucidated to date. The synthesis and signal transduction pathway of IAA and ABA in maize can be analyzed using an existing model. This article focuses on the research progress toward understanding the synthesis and signaling pathways of IAA and ABA, as well as IAA and ABA regulation of maize growth, providing insight for future development and the significance of IAA and ABA for maize improvement.

Seedling-derived leaf and root tip as alternative explants for callus induction and plant regeneration in maize

While being one of the world's most important crops, maize (Zea mays L.) is still relatively difficult to regenerate in tissue culture, which severely limits its improvement by genetic engineering. Currently, immature zygotic embryos provide the predominant material for transformation and regeneration. However, the procedures involved are often laborious and season-dependent. Therefore, new explants to replace or complement immature embryos are desirable. Here, we exploited root tips and young leaves isolated from 3-day-old dark-grown seedlings as alternative explant sources for establishing plant regeneration. As novel explants, the root tips could generate embryogenic calli similar to that from the young leaves. The rate of primary callus induction from root tips reached 97.2% and almost as high as 98.8% from immature embryos. The difference in callus induction rates among these explants may be closely related to the differences in expression level of stem cell-related genes in callus tissue. Moreover, the alternative explants are easy to obtain in large quantities. These combined results indicate that explants from seedling-derived root tips and leaf tissue have the potential to replace immature embryos for plant regeneration and transformation.

Molecular mechanism of MdWUS2-MdTCP12 interaction in mediating cytokinin signaling to control axillary bud outgrowth

Shoot branching is an important factor that influences the architecture of apple trees and cytokinin is known to promote axillary bud outgrowth. The cultivar 'Fuji', which is grown on ~75% of the apple-producing area in China, exhibits poor natural branching. The TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family genes BRANCHED1/2 (BRC1/2) are involved in integrating diverse factors that function locally to inhibit shoot branching; however, the molecular mechanism underlying the cytokinin-mediated promotion of branching that involves the repression of BRC1/2 remains unclear. In this study, we found that apple WUSCHEL2 (MdWUS2), which interacts with the co-repressor TOPLESS-RELATED9 (MdTPR9), is activated by cytokinin and regulates branching by inhibiting the activity of MdTCP12 (a BRC2 homolog). Overexpressing MdWUS2 in Arabidopsis or Nicotiana benthamiana resulted in enhanced branching. Overexpression of MdTCP12 inhibited axillary bud outgrowth in Arabidopsis, indicating that it contributes to the regulation of branching. In addition, we found that MdWUS2 interacted with MdTCP12 in vivo and in vitro and suppressed the ability of MdTCP12 to activate the transcription of its target gene, HOMEOBOX PROTEIN 53b (MdHB53b). Our results therefore suggest that MdWUS2 is involved in the cytokinin-mediated inhibition of MdTCP12 that controls bud outgrowth, and hence provide new insights into the regulation of shoot branching by cytokinin.

Osmotic stress-induced somatic embryo maturation of coffee Coffea arabica L., shoot and root apical meristems development and robustness

Somatic embryogenesis (SE) is the most important plant biotechnology process for plant regeneration, propagation, genetic transformation and genome editing of coffee, Coffea arabica L. Somatic embryo (SEs) conversion to plantlets is the principal bottleneck for basic and applied use of this process. In this study we focus on the maturation of SEs of C. arabica var. Typica. SEs conversion to plantlet up to 95.9% was achieved under osmotic stress, using 9 g/L gelrite, as compared with only 39.34% in non-osmotic stress. Mature SEs induced in osmotic stress developed shoot and root apical meristems, while untreated SEs were unable to do it. C. arabica regenerated plants from osmotic stress were robust, with higher leaf and root area and internode length. To understand a possible regulatory mechanism, gene expression of key genes of C. arabica, homologous to sequences in the Arabidopsis thaliana genome, were analyzed. A set of two component system and cytokinin signaling-related coding genes (AHK1, AHK3, AHP4 and ARR1) which interact with WUSCHEL and WOX5 homedomains and morphogenic genes, BABY-BOOM, LEC1, FUS3 and AGL15, underwent significant changes during maturation of SEs of C. arabica var. Typica. This protocol is currently being applied in genetic transformation with high rate of success.

Auxin and cytokinin mediated regulation involved in vitro organogenesis of papaya

In vitro organogenesis is a multistep process which is largely controlled by the balance between auxin and cytokinin. Previous studies revealed a complex network regulating in vitro organogenesis in Arabidopsis thaliana; however, our knowledge of the molecular mechanisms underlying de novo shoot formation in papaya (Carica papaya) remains limited. Here, we optimized multiple factors to achieve an efficient and reproducible protocol for the induction of papaya callus formation and shoot regeneration. Subsequently, we analyzed the dynamic transcriptome profiles of samples undergoing this process, identified 5381, 642, 4047, and 2386 differentially expressed genes (DEGs), including 447, 66, 350, and 263 encoding transcription factors (TFs), in four stage comparisons. The DEGs were mainly involved in phytohormone modulation and transduction processes, particularly for auxin and cytokinin. Of these, 21 and 7 candidate genes involved in the auxin and cytokinin pathways, respectively, had distinct expression patterns throughout in vitro organogenesis. Furthermore, we found two genes encoding key TFs, CpLBD19 and CpESR1, were sharply induced on callus induction medium and shoot induction medium, indicating these two TFs may serve as proxies for callus induction and shoot formation in papaya. We therefore report a regulatory network of auxin and cytokinin signaling in papaya according to the one previously modeled for Arabidopsis. Our comprehensive analyses provide insight into the early molecular regulation of callus initiation and shoot formation in papaya, and are useful for the further identification of the regulators governing in vitro organogenesis.

Cytokinin signaling localized in phloem noncell-autonomously regulates cambial activity during secondary growth of Populus stems

The regulation of cytokinin on secondary vascular development has been uncovered by modulating cytokinin content. However, it remains unclear how cytokinin enriched in developing secondary phloem regulates cambium activity in poplar. Here, we visualized the gradient distribution of cytokinin with a peak in the secondary phloem of poplar stem via immunohistochemical imaging, and determined the role of phloem-located cytokinin signaling during wood formation. We generated transgenic poplar harboring cytokinin oxidase/dehydrogenase (CKX)2, a gene encoding a cytokinin degrading enzyme, driven by the phloem-specific CLE41b promoter, indicating that the disruption of the cytokinin gradient pattern restricts the cambial activity. The RNA interference-based knockdown of the histidine kinase (HK) genes encoding cytokinin receptors specifically in secondary phloem significantly compromised the division activity of cambial cells, whereas the phloem-specific expression of a type-B response regulator (RR) transcription factor stimulated cambial proliferation, providing evidence for the noncell-autonomous regulation of local cytokinin signaling on the cambial activity. Moreover, the cambium-specific knockdown of HKs also led to restricted cambial activity, and the defects were aggravated by the reduced cytokinin accumulation. Our results showed that local cytokinin signaling in secondary phloem regulates cambial activity noncell-autonomously, and coordinately with its local signaling in cambium.

Gene Expression Analysis of Microtubers of Potato Solanum tuberosum L. Induced in Cytokinin Containing Medium and Osmotic Stress

Potato microtuber productions through in vitro techniques are ideal propagules for producing high quality seed potatoes. Microtuber development is influenced by several factors, i.e., high content sucrose and cytokinins are among them. To understand a molecular mechanism of microtuberization using osmotic stress and cytokinin signaling will help us to elucidate this process. We demonstrate in this work a rapid and efficient protocol for microtuber development and gene expression analysis. Medium with high content of sucrose and gelrite supplemented with 2iP as cytokinin under darkness condition produced the higher quantity and quality of microtubers. Gene expression analysis of genes involved in the two-component signaling system (StHK1), cytokinin signaling, (StHK3, StHP4, StRR1) homeodomains (WUSCHEL, POTH1, BEL5), auxin signaling, ARF5, carbon metabolism (TPI, TIM), protein synthesis, NAC5 and a morphogenetic regulator of tuberization (POTH15) was performed by qPCR real time. Differential gene expression was observed during microtuber development. Gene regulation of two component and cytokinin signaling is taking place during this developmental process, yielding more microtubers. Further analysis of each component is required to elucidate it.

Structural variation at the maize WUSCHEL1 locus alters stem cell organization in inflorescences

Structural variation in plant genomes is a significant driver of phenotypic variability in traits important for the domestication and productivity of crop species. Among these are traits that depend on functional meristems, populations of stem cells maintained by the CLAVATA-WUSCHEL (CLV-WUS) negative feedback-loop that controls the expression of the WUS homeobox transcription factor. WUS function and impact on maize development and yield remain largely unexplored. Here we show that the maize dominant Barren inflorescence3 (Bif3) mutant harbors a tandem duplicated copy of the ZmWUS1 gene, ZmWUS1-B, whose novel promoter enhances transcription in a ring-like pattern. Overexpression of ZmWUS1-B is due to multimerized binding sites for type-B RESPONSE REGULATORs (RRs), key transcription factors in cytokinin signaling. Hypersensitivity to cytokinin causes stem cell overproliferation and major rearrangements of Bif3 inflorescence meristems, leading to the formation of ball-shaped ears and severely affecting productivity. These findings establish ZmWUS1 as an essential meristem size regulator in maize and highlight the striking effect of cis-regulatory variation on a key developmental program.

The WUSCHEL transcription factor promotes plant stem cell proliferation. Here the authors show that the maize Bif3 mutant contains a duplication of the ZmWUS1 locus leading to cytokinin hypersensitivity and overproliferation at the shoot meristem demonstrating the role of WUSCHEL in maize and how structural variation can impact plant morphology.

Interpreting Cytokinin Action as Anterograde Signaling and Beyond

Among the major phytohormones, the cytokinin exhibits unique features for its ability to positively affect the developmental status of plastids. Even early on in its research, cytokinins were known to promote plastid differentiation and to reduce the loss of chlorophyll in detached leaves. Since the discovery of the components of cytokinin perception and primary signaling, the genes involved in photosynthesis and plastid differentiation have been identified as those directly targeted by type-B response regulators. Furthermore, cytokinins are known to modulate versatile cellular processes such as promoting the division and differentiation of cells and, in concert with auxin, initiating the de novo formation of shoot apical meristem (SAM) in tissue cultures. Yet how cytokinins precisely participate in such diverse cellular phenomena, and how the associated cellular processes are coordinated as a whole, remains unclear. A plausible presumption that would account for the coordinated gene expression is the tight and reciprocal communication between the nucleus and plastid. The fact that cytokinins affect plastid developmental status via gene expression in both the nucleus and plastid is interpreted here to suggest that cytokinin functions as an initiator of anterograde (nucleus-to-plastid) signaling. Based on this viewpoint, we first summarize the physiological relevance of cytokinins to the coordination of plastid differentiation with de novo shoot organogenesis in tissue culture systems. Next, the role of endogenous cytokinins in influencing plastid differentiation within the SAM of intact plants is discussed. Finally, a presumed plastid-derived signal in response to cytokinins for coupled nuclear gene expression is proposed.

Model systems for regeneration: Arabidopsis

Plants encompass unparalleled multi-scale regenerative potential. Despite lacking specialized cells that are recruited to injured sites, and despite their cells being encased in rigid cell walls, plants exhibit a variety of regenerative responses ranging from the regeneration of specific cell types, tissues and organs, to the rebuilding of an entire organism. Over the years, extensive studies on embryo, shoot and root development in the model plant species Arabidopsis thaliana have provided insights into the mechanisms underlying plant regeneration. These studies highlight how Arabidopsis, with its wide array of refined molecular, genetic and cell biological tools, provides a perfect model to interrogate the cellular and molecular mechanisms of reprogramming during regeneration.

Cytokinin Type-B Response Regulators Promote Bulbil Initiation in Lilium lancifolium

The bulbil is an important vegetative reproductive organ in triploid Lilium lancifolium whose development is promoted by cytokinins. Type-B response regulators (RRs) are critical regulators that mediate primary cytokinin responses and promote cytokinin-induced gene expression. However, the function of cytokinin type-B Arabidopsis RRs (ARRs) in regulating bulbil formation is unclear. In this study, we identified five type-B LlRRs, LlRR1, LlRR2, LlRR10, LlRR11 and LlRR12, in L. lancifolium for the first time. The five LlRRs encode proteins of 715, 675, 573, 582 and 647 amino acids. All of the regulators belong to the B-I subfamily, whose members typically contain a conserved CheY-homologous receiver (REC) domain and an Myb DNA-binding (MYB) domain at the N-terminus. As transcription factors, all five type-B LlRRs localize at the nucleus and are widely expressed in plant tissues, especially during axillary meristem (AM) formation. Functional analysis showed that type-B LlRRs are involved in bulbil formation in a functionally redundant manner and can activate LlRR9 expression. In summary, our study elucidates the process by which cytokinins regulate bulbil initiation in L. lancifolium through type-B LlRRs and lays a foundation for research on the molecular mechanism of bulbil formation in the lily.

In Vitro Plant Regeneration in Conifers: The Role of WOX and KNOX Gene Families

Conifers are a group of woody plants with an enormous economic and ecological importance. Breeding programs are necessary to select superior varieties for planting, but they have many limitations due to the biological characteristics of conifers. Somatic embryogenesis (SE) and de novo organogenesis (DNO) from in vitro cultured tissues are two ways of plant mass propagation that help to overcome this problem. Although both processes are difficult to achieve in conifers, they offer advantages like a great efficiency, the possibilities to cryopreserve the embryogenic lines, and the ability of multiplying adult trees (the main bottleneck in conifer cloning) through DNO. Moreover, SE and DNO represent appropriate experimental systems to study the molecular bases of developmental processes in conifers such as embryogenesis and shoot apical meristem (SAM) establishment. Some of the key genes regulating these processes belong to the WOX and KNOX homeobox gene families, whose function has been widely described in Arabidopsis thaliana. The sequences and roles of these genes in conifers are similar to those found in angiosperms, but some particularities exist, like the presence of WOXX, a gene that putatively participates in the establishment of SAM in somatic embryos and plantlets of Pinus pinaster.

Improving architectural traits of maize inflorescences

The domestication and improvement of maize resulted in radical changes in shoot architecture relative to its wild progenitor teosinte. In particular, critical modifications involved a reduction of branching and an increase in inflorescence size to meet the needs for human consumption and modern agricultural practices. Maize is a major contributor to global agricultural production by providing large and inexpensive quantities of food, animal feed, and ethanol. Maize is also a classic system for studying the genetic regulation of inflorescence formation and its enlarged female inflorescences directly influence seed production and yield. Studies on the molecular and genetic networks regulating meristem proliferation and maintenance, including receptor-ligand interactions, transcription factor regulation, and hormonal control, provide important insights into maize inflorescence development and reveal potential avenues for the targeted modification of specific architectural traits. In this review, we summarize recent findings on the molecular mechanisms controlling inflorescence formation and discuss how this knowledge can be applied to improve maize productivity in the face of present and future environmental challenges.

Auxin Metabolism in Plants

The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism-which comprises biosynthesis, conjugation, and degradation-modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.

The WOX family transcriptional regulator SlLAM1 controls compound leaf and floral organ development in Solanum lycopersicum

Plant-specific WOX family transcription factors play important roles ranging from embryogenesis to lateral organ development. The WOX1 transcription factors, which belong to the modern clade of the WOX family, are known to regulate outgrowth of the leaf blade specifically in the mediolateral axis; however, the role of WOX1 in compound leaf development remains unknown. Phylogenetic analysis of the whole WOX family in tomato (Solanum lycopersicum) indicates that there are 10 members that represent the modern, intermediate, and ancient clades. Using phylogenetic analysis and a reverse genetic approach, in this study we identified SlLAM1 in the modern clade and examined its function and tissue-specific expression pattern. We found that knocking out SlLAM1 via CRISPR/Cas9-mediated genome editing led to narrow leaves and a reduced number of secondary leaflets. Overexpression of tomato SlLAM1 could rescue the defects of the tobacco lam1 mutant. Anatomical and transcriptomic analyses demonstrated that floral organ development, fruit size, secondary leaflet initiation, and leaf complexity were altered due to loss-of-function of SlLAM1. These findings demonstrate that tomato SlLAM1 plays an important role in the regulation of secondary leaflet initiation, in addition to its conserved function in blade expansion.

Function of histone H2B monoubiquitination in transcriptional regulation of auxin biosynthesis in Arabidopsis

The auxin IAA is a vital plant hormone in controlling growth and development, but our knowledge about its complicated biosynthetic pathways and molecular regulation are still limited and fragmentary. cytokinin induced root waving 2 (ckrw2) was isolated as one of the auxin-deficient mutants in a large-scale forward genetic screen aiming to find more genes functioning in auxin homeostasis and/or its regulation. Here we show that CKRW2 is identical to Histone Monoubiquitination 1 (HUB1), a gene encoding an E3 ligase required for histone H2B monoubiquitination (H2Bub1) in Arabidopsis. In addition to pleiotropic defects in growth and development, loss of CKRW2/HUB1 function also led to typical auxin-deficient phenotypes in roots, which was associated with significantly lower expression levels of several functional auxin synthetic genes, namely TRP2/TSB1, WEI7/ASB1, YUC7 and AMI1. Corresponding defects in H2Bub1 were detected in the coding regions of these genes by chromatin immunoprecipitation (ChIP) analysis, indicating the involvement of H2Bub1 in regulating auxin biosynthesis. Importantly, application of exogenous cytokinin (CK) could stimulate CKRW2/HUB1 expression, providing an epigenetic avenue for CK to regulate the auxin homeostasis. Our results reveal a previously unknown mechanism for regulating auxin biosynthesis via HUB1/2-mediated H2Bub1 at the chromatin level.

Cytokinin Signaling and De Novo Shoot Organogenesis

The ability to restore or replace injured tissues can be undoubtedly named among the most spectacular achievements of plant organisms. One of such regeneration pathways is organogenesis, the formation of individual organs from nonmeristematic tissue sections. The process can be triggered in vitro by incubation on medium supplemented with phytohormones. Cytokinins are a class of phytohormones demonstrating pleiotropic effects and a powerful network of molecular interactions. The present study reviews existing knowledge on the possible sequence of molecular and genetic events behind de novo shoot organogenesis initiated by cytokinins. Overall, the review aims to collect reactions encompassed by cytokinin primary responses, starting from phytohormone perception by the dedicated receptors, to transcriptional reprogramming of cell fate by the last module of multistep-phosphorelays. It also includes a brief reminder of other control mechanisms, such as epigenetic reprogramming.

WOX9 functions antagonistic to STF and LAM1 to regulate leaf blade expansion in Medicago truncatula and Nicotiana sylvestris

WOX family transcription factors regulate multiple developmental programs. The intermediate clade transcriptional activator WOX9 functions together with the modern clade transcriptional repressor WOX genes in embryogenesis and meristems maintenance, but the mechanism of this interaction is unclear. STF and LAM1 are WOX1 orthologs required for leaf blade outgrowth in Medicago truncatula and Nicotiana sylvestris, respectively. Using biochemical methods and genome editing technology, here we show that WOX9 is an abaxial factor and functions antagonistically to STF and LAM1 to regulate leaf blade development. While NsWOX9 ectopic expression enhances the lam1 mutant phenotype, and antisense expression partially rescues the lam1 mutant, both overexpression and knockout of NsWOX9 in N. sylvestris resulted in a range of severe leaf blade distortions, indicating important role in blade development. Our results indicate that direct repression of WOX9 by WUS clade repressor STF/LAM1 is required for correct blade architecture and patterning in M. truncatula and N. sylvestris. These findings suggest that controlling transcriptional activation and repression mechanisms by direct interaction of activator and repressor WOX genes may be required for cell proliferation and differentiation homeostasis, and could be an evolutionarily conserved mechanism for the development of complex and diverse morphology in flowering plants.

ARF4 regulates shoot regeneration through coordination with ARF5 and IAA12

ARF4-regulated shoot regeneration through competing with ARF5 for the interaction with IAA12. Plant possess the ability to regenerate shoot meristem and subsequent the whole individual. This process is the foundation for in vitro propagation and genetic engineering and provides a system for studying fundamental biological questions, such as hormonal signaling. Auxin response factor (ARF) family transcription factors are critical components of auxin signaling pathway that regulate the transcription of target genes. To date, the mechanisms underlying the functions of class-B ARFs which act as transcription repressors remains unclear. In this study, we found that ARF4, the transcriptional repressor, was involved in regulating shoot regeneration. ARF4 interacted with auxin/Indole-3-Acetic-Acid12 (IAA12). The expression signals of ARF4 displayed a dynamic pattern similar with those of ARF5 and IAA12 during shoot meristem formation. Enhanced expression of IAA12 compromised the shoot regeneration capacity. Induced expression of ARF4 complemented the regeneration phenotype of IAA12-overexpression but did not rescued the defects in the arf5 mutant, mp-S319. Further analysis revealed that ARF4 competed with ARF5 for the interaction with IAA12. The results indicate that ARF4-regulated shoot regeneration through cooperating with ARF5 and IAA12. Our findings provided new information for deciphering the function of class-B ARFs.

Cytokinins as central regulators during plant growth and stress response

Cytokinins are a class of phytohormone that participate in the regulation of the plant growth, development, and stress response. In this review, the potential regulating mechanism during plant growth and stress response are discussed. Cytokinins are a class of phytohormone that participate in the regulation of plant growth, physiological activities, and yield. Cytokinins also play a key role in response to abiotic stresses, such as drought, salt and high or low temperature. Through the signal transduction pathway, cytokinins interact with various transcription factors via a series of phosphorylation cascades to regulate cytokinin-target gene expression. In this review, we systematically summarize the biosynthesis and metabolism of cytokinins, cytokinin signaling, and associated gene regulation, and highlight the function of cytokinins during plant development and resistance to abiotic stress. We also focus on the importance of crosstalk between cytokinins and other classes of phytohormones, including auxin, ethylene, strigolactone, and gibberellin. Our aim is to provide a comprehensive overview of recent findings on the mechanisms by which cytokinins act as central regulators of plant development and stress reactions, and highlight topics for future research.

Pars Pro Toto: Every Single Cell Matters

Compared to other species, plants stand out by their unparalleled self-repair capacities. Being the loss of a single cell or an entire tissue, most plant species are able to efficiently repair the inflicted damage. Although this self-repair process is commonly referred to as "regeneration," depending on the type of damage and organ being affected, subtle to dramatic differences in the modus operandi can be observed. Recent publications have focused on these different types of tissue damage and their associated response in initiating the regeneration process. Here, we review the regeneration response following loss of a single cell to a complete organ, emphasizing key molecular players and hormonal cues involved in the model species Arabidopsis thaliana. In addition, we highlight the agricultural applications and techniques that make use of these regenerative responses in different crop and tree species.

Cytokinin regulates the activity of the inflorescence meristem and components of seed yield in oilseed rape

The number of flowers and seed-bearing structures formed by the inflorescence meristem and the formation of ovules in the female reproductive part of the flowers are important yield-related traits of crop plants. It has been shown that cytokinin is a pivotal factor regulating these traits. Here, we explore the impact of mutation of CYTOKININ OXIDASE/DEHYDROGENASE (CKX) genes encoding cytokinin-degrading enzymes on these yield-related traits in oilseed rape (Brassica napus L.). We describe the identification of four BnCKX3 and two BnCKX5 genes as regulators of reproductive development in the allotetraploid B. napus. RNA-seq analysis and in situ hybridization showed expression of these genes in reproductive organs. Loss-of-function mutants for each of these CKX gene copies were identified by targeting induced local lesions in genomes (TILLING) and combined by crossing. Sextuple ckx3 ckx5 mutants showed an increased cytokinin concentration and larger and more active inflorescence meristems. They also produced up to 72% more flowers with gynoecia containing 32% more ovules and up to 54% more pods on the main stem. The weight of seeds harvested from the main stem of plants grown in the greenhouse or in the field was increased by 20-32%. Our results show that cytokinin regulates inflorescence meristem and placenta activity in oilseed rape. The work demonstrates the potential to achieve yield enhancement in a dicot crop plant by modulating the cytokinin status through mutagenesis of specific CKX genes.

Trichostatin A and sodium butyrate promotes plant regeneration in common wheat

Histone acetylation modification plays a vital role in plant cell division and differentiation. However, the function on wheat mature embryo culture has not been reported. Here, we used the mature embryo of wheat genotypes including CB037, Fielder, and Chinese Spring (CS) as materials to analyze the effects of different concentrations of trichostatin A (TSA) and sodium butyrate (SB) on plant regeneration efficiency. The results showed that, compared with the control group, the induction rates of embryogenic callus and green shoot were significantly increased with the addition of 0.5 µM TSA, while they were reduced under treatment of 2.5 µM TSA on wheat mature embryo. With the respective addition of 200 µM and 1000 µM SB, regeneration frequency of three genotypes was enhanced, especially in Fielder, which reached significant difference compared with the control group. Unfortunately, 0.5 µM TSA and 200 µM SB combination had no apparent effect on wheat regeneration frequency. The results indicated that TSA and SB increase plant regeneration in common wheat. In addition, TSA had a common effect and SB had different effect among genotypes on wheat regeneration frequency. The mechanism of action needs further investigation.

The Effect of Sodium Butyrate on Adventitious Shoot Formation Varies among the Plant Species and the Explant Types

Histone acetylation plays an important role in plant growth and development. Here, we investigated the effect of sodium butyrate (NaB), a histone deacetylase inhibitor, on adventitious shoot formation from protoplast-derived calli and cotyledon explants of tobacco (Nicotiana benthamiana) and tomato (Solanum lycopersicum). The frequency of adventitious shoot formation from protoplast-derived calli was higher in shoot induction medium (SIM) containing NaB than in the control. However, the frequency of adventitious shoot formation from cotyledon explants of tobacco under the 0.1 mM NaB treatment was similar to that in the control, but it decreased with increasing NaB concentration. Unlike in tobacco, NaB decreased adventitious shoot formation in tomato explants in a concentration-dependent manner, but it did not have any effect on adventitious shoot formation in calli. NaB inhibited or delayed the expression of D-type cyclin (CYCD3-1) and shoot-regeneration regulatory gene WUSCHEL (WUS) in cotyledon explants of tobacco and tomato. However, compared to that in control SIM, the expression of WUS was promoted more rapidly in tobacco calli cultured in NaB-containing SIM, but the expression of CYCD3-1 was inhibited. In conclusion, the effect of NaB on adventitious shoot formation and expression of CYCD3-1 and WUS genes depended on the plant species and whether the effects were tested on explants or protoplast-derived calli.

Altering Plant Architecture to Improve Performance and Resistance

High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change.

The HK5 and HK6 cytokinin receptors mediate diverse developmental pathways in rice

The phytohormone cytokinin regulates diverse aspects of plant growth and development. Our understanding of the metabolism and perception of cytokinin has made great strides in recent years, mostly from studies of the model dicot Arabidopsis Here, we employed a CRISPR/Cas9-based approach to disrupt a subset of cytokinin histidine kinase (HK) receptors in rice (Oryza sativa) in order to explore the role of cytokinin in a monocot species. In hk5 and hk6 single mutants, the root growth, leaf width, inflorescence architecture and/or floral development were affected. The double hk5 hk6 mutant showed more substantial defects, including severely reduced root and shoot growth, a smaller shoot apical meristem, and an enlarged root cap. Flowering was delayed in the hk5 hk6 mutant and the panicle was significantly reduced in size and infertile due to multiple defects in floral development. The hk5 hk6 mutant also exhibited a severely reduced cytokinin response, consistent with the developmental phenotypes arising from a defect in cytokinin signaling. These results indicate that HK5 and HK6 act as cytokinin receptors, with overlapping functions to regulate diverse aspects of rice growth and development.

Early Low-Fluence Red Light or Darkness Modulates the Shoot Regeneration Capacity of Excised Arabidopsis Roots

In plants, light is an important environmental signal that induces meristem development and interacts with endogenous signals, including hormones. We found that treatment with 24 h of low-fluence red light (24 h R) or 24 h of darkness (24 h D) following root excision greatly increased the frequency of shoot generation, while continuous low-fluence red light in callus and shoot induction stages blocked the explants' ability to generate shoots. Shoot generation ability was closely associated with WUS expression and distribution pattern. 1-N-naphthylphtalamic acid (NPA) disrupted the dynamic distribution of the WUS signal induced by early 24 h R treatment, and NPA plus 24 R treatment increased the average shoot number compared with early 24 h R alone. Transcriptome analysis revealed that differentially expressed genes involved in meristem development and hormone signal pathways were significantly enriched during 24 R or 24 D induced shoot regeneration, where early 24 h R or 24 h D treatment upregulated expression of WOX5, LBD16, LBD18 and PLT3 to promote callus initiation and formation of root primordia, and also activated WUS, STM, CUC1 and CUC2 expression, leading to initiation of the shoot apical meristem (SAM). This finding demonstrates that early exposure of explants to transient low-fluence red light or darkness modulates the expression of marker genes related with callus development and shoot regeneration, and dynamic distribution of WUS, leading to an increased ability to generate shoots.

The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors

Clonal propagation and genetic engineering of plants requires regeneration, but many species are recalcitrant and there is large variability in explant responses. Here, we perform a genome-wide association study using 190 natural Arabidopsis accessions to dissect the genetics of shoot regeneration from root explants and several related in vitro traits. Strong variation is found in the recorded phenotypes and association mapping pinpoints a myriad of quantitative trait genes, including prior candidates and potential novel regeneration determinants. As most of these genes are trait- and protocol-specific, we propose a model wherein shoot regeneration is governed by many conditional fine-tuning factors and a few universal master regulators such as WUSCHEL, whose transcript levels correlate with natural variation in regenerated shoot numbers. Potentially novel genes in this last category are AT3G09925, SUP, EDA40 and DOF4.4. We urge future research in the field to consider multiple conditions and genetic backgrounds.

Identification of Players Controlling Meristem Arrest Downstream of the FRUITFULL-APETALA2 Pathway

The end of the reproductive phase in monocarpic plants is determined by a coordinated arrest of all active meristems, a process known as global proliferative arrest (GPA). GPA is linked to the correlative control exerted by developing seeds and, possibly, the establishment of strong source-sink relationships. It has been proposed that the meristems that undergo arrest at the end of the reproductive phase behave at the transcriptomic level as dormant meristems, with low mitotic activity and high expression of abscisic acid response genes. Meristem arrest is also controlled genetically. In Arabidopsis (Arabidopsis thaliana), the MADS-box transcription factor FRUITFULL induces GPA by directly repressing genes of the APETALA2 (AP2) clade. The AP2 genes maintain shoot apical meristem (SAM) activity in part by keeping WUSCHEL expression active, but the mechanisms downstream of this pathway remain elusive. To identify target genes, we performed a transcriptomic analysis, inducing AP2 activity in meristems close to arrest. Our results suggest that AP2 controls meristem arrest by repressing genes related to axillary bud dormancy in the SAM and negative regulators of cytokinin signaling. In addition, our analysis indicates that genes involved in the response to environmental signals also respond to AP2, suggesting that it could modulate the end of flowering by controlling responses to both endogenous and exogenous signals. Our results support the previous observation that at the end of the reproductive phase the arrested SAM behaves as a dormant meristem, and they strongly support AP2 as a master regulator of this process.

Natural Variation in Plant Pluripotency and Regeneration

Plant regeneration is essential for survival upon wounding and is, hence, considered to be a strong natural selective trait. The capacity of plant tissues to regenerate in vitro, however, varies substantially between and within species and depends on the applied incubation conditions. Insight into the genetic factors underlying this variation may help to improve numerous biotechnological applications that exploit in vitro regeneration. Here, we review the state of the art on the molecular framework of de novo shoot organogenesis from root explants in Arabidopsis, which is a complex process controlled by multiple quantitative trait loci of various effect sizes. Two types of factors are distinguished that contribute to natural regenerative variation: master regulators that are conserved in all experimental systems (e.g., WUSCHEL and related homeobox genes) and conditional regulators whose relative role depends on the explant and the incubation settings. We further elaborate on epigenetic variation and protocol variables that likely contribute to differential explant responsivity within species and conclude that in vitro shoot organogenesis occurs at the intersection between (epi) genetics, endogenous hormone levels, and environmental influences.

De Novo Shoot Regeneration Controlled by HEN1 and TCP3/4 in Arabidopsis

Plants have the ability to regenerate whole plant body parts, including shoots and roots, in vitro from callus derived from a variety of tissues. However, the underlying mechanisms for this de novo organogenesis, which is based on the totipotency of callus cells, are poorly understood. Here, we report that a microRNA (miRNA)-mediated posttranscriptional regulation plays an important role in de novo shoot regeneration. We found that mutations in HUA ENHANCER 1 (HEN1), a gene encoding a small RNA methyltransferase, cause cytokinin-related defects in de novo shoot regeneration. A hen1 mutation caused a large reduction in the miRNA319 (miR319) level and a subsequent increase in its known target (TCP3 and TCP4) transcript levels. TCP transcription factors redundantly inhibited shoot regeneration and directly activated the expression of a negative regulator of cytokinin response ARABIDOPSIS THALIANA RESPONSE REGULATOR 16 (ARR16). A tcp4 mutation at least partly rescued the shoot-regeneration defect and derepression of ARR16 in hen1. These findings demonstrate that the miR319-TCP3/4-ARR16 axis controls de novo shoot regeneration by modulating cytokinin responses.

The SUMO E3 Ligase SIZ1 Negatively Regulates Shoot Regeneration

Plants form calluses and regenerate new organs when incubated on phytohormone-containing media. While accumulating evidence suggests that these regenerative processes are governed by transcriptional networks orchestrating wound response and developmental transitions, it remains unknown if posttranslational regulatory mechanisms are involved in this process. In this study, we demonstrate that SAP AND MIZ1 DOMAIN- CONTAINING LIGASE1 (SIZ1), an E3 ligase-catalyzing attachment of the SMALL UBIQUITIN-LIKE MODIFIER (SUMO) to proteins, regulates wound-induced signal transduction and organ regeneration in Arabidopsis (Arabidopsis thaliana). We show that loss-of-function mutants for SIZ1 exhibit overproduction of shoot meristems under in vitro tissue culture conditions, while this defect is rescued in a complementation line expressing pSIZ1::SIZ1 RNA sequencing analysis revealed that siz1-2 mutants exhibit enhanced transcriptional responses to wound stress, resulting in the hyper-induction of over 400 genes immediately after wounding. Among them, we show that elevated levels of WOUND INDUCED DEDIFFERENTIATION1 (WIND1) and WIND2 contribute to the enhanced shoot regeneration observed in siz1 mutants, as expression of the dominant-negative chimeric protein WIND1-SRDX (SUPERMAN repression domain) in siz1-3 mutants partly rescues this phenotype. Although compromised SIZ1 function does not modify the transcription of genes implicated in auxin-induced callus formation and/or pluripotency acquisition, it does lead to enhanced induction of cytokinin-induced shoot meristem regulators such as WUSCHEL, promoting the formation of WUSCHEL-expressing foci in explants. This study thus suggests that SIZ1 negatively regulates shoot regeneration in part by repressing wound-induced developmental reprogramming.

Integration of pluripotency pathways regulates stem cell maintenance in the Arabidopsis shoot meristem

Pluripotent stem cells are critical in both animal and plant development. Unlike higher animals, plants have unique postembryonic development, which continuously produce organs depending on shoot and root meristems. In the shoot meristem, division of the stem cells in the outermost layers provides the cells for all shoot structures. How those meristem cells are tightly controlled attracted intense studies. Genetic and molecular analyses in Arabidopsis have identified the key transcription factors WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM) as the major regulators of pluripotency in the shoot meristem. Here, the results provide solid evidence showing how those two pluripotency factors WUS and STM coordinate to control shoot meristem cells strictly in plants.

In the shoot meristem, both WUSCHEL (WUS) and SHOOT MERISTEMLESS (STM), two transcription factors with overlapping spatiotemporal expression patterns, are essential for maintaining stem cells in an undifferentiated state. Despite their importance, it remains unclear how these two pathways are integrated to coordinate stem cell development. Here, we show that the WUS and STM pathways in Arabidopsis thaliana converge through direct interaction between the WUS and STM proteins. STM binds to the promoter of CLAVATA3 (CLV3) and enhances the binding of WUS to the same promoter through the WUS–STM interaction. Both the heterodimerization and simultaneous binding of WUS and STM at two sites on the CLV3 promoter are required to regulate CLV3 expression, which in turn maintains a constant number of stem cells. Furthermore, the expression of STM depends on WUS, and this WUS-activated STM expression enhances the WUS-mediated stem cell activity. Our data provide a framework for understanding how spatial expression patterns within the shoot meristem are translated into regulatory units of stem cell homeostasis.

Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Saccharum spp. Interspecific Hybrids) Microshoots

Adventitious root (AR) formation was enhanced following the treatment of sugarcane microshoots with indole-3-butyric acid (IBA) and 1-naphthalene acetic acid (NAA) combined, suggesting that auxin is a positive regulator of sugarcane microshoot AR formation. The transcriptome profile identified 1737 and 1268 differentially expressed genes (DEGs) in the basal tissues (5 mm) of sugarcane microshoots treated with IBA+NAA compared to nontreated control on the 3rd and 7th days post-auxin or water treatment (days post-treatment—dpt), respectively. To understand the molecular changes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. This analysis showed that DEGs associated with the pathways were associated with plant hormone signaling, flavonoid and phenylpropanoid biosyntheses, cell cycle, and cell wall modification, and transcription factors could be involved in sugarcane microshoot AR formation. Furthermore, qRT–PCR analysis was used to validate the expression patterns of nine genes associated with root formation and growth, and the results were consistent with the RNA-seq results. Finally, a hypothetical hormonal regulatory working model of sugarcane microshoot AR formation is proposed. Our results provide valuable insights into the molecular processes associated with auxin-induced AR formation in sugarcane.

Mechanism of exogenous cytokinins inducing bulbil formation in Lilium lancifolium in vitro

The cytokinin pathway promotes the initiation of bulbil formation, and iPA may an important type of cytokinin during bulbil formation in Lilium lancifolium. Bulbils are important vegetative reproductive organs in triploid Lilium lancifolium. We previously showed that cytokinins are involved in bulbil formation, but how cytokinins participate in bulbil formation is not clear. In this study, bulbil formation was divided into three stages on the basis of anatomical and histological observations: the bulbil initiation stage, bulbil primordium-formation stage and bulbil structure-formation stage. The results indicated that iPA was the most critical cytokinin during the bulbil initiation. qRT-PCR revealed that increased iPA content during bulbil initiation was mainly due to increased expression of cytokinin synthesis genes (IPT1/5) and cytokinin activation genes (LOG1/3/5/7) and significantly decreased expression of the cytokinin degradation gene CKX4. Exogenous 6-BA and lovastatin affected the cytokinin pathway and promoted or inhibited bulbil initiation by increasing or decreasing the content of endogenous iPA, respectively. In summary, we demonstrate that cytokinins positively regulate bulbil formation and provide preliminary insight into the regulatory mechanisms by which the cytokinin pathway promotes bulbil initiation.

Initiation and maintenance of plant stem cells in root and shoot apical meristems

Plant stem cells are a small group of cells with a self-renewal capacity and serve as a steady supply of precursor cells to form new differentiated tissues and organs in plants. Root stem cells and shoot stem cells, which are located in the root apical meristem and in the shoot apical meristem, respectively, play a critical role in plant longitudinal growth. These stem cells in shoot and root apical meristems remain as pluripotent state throughout the lifespan of the plant and control the growth and development of plants. The molecular mechanisms of initiation and maintenance of plant stem cells have been extensively investigated. In this review, we mainly discuss how the plant phytohormones, such as auxin and cytokinin, coordinate with the key transcription factors to regulate plant stem cell initiation and maintenance in root and shoot apical meristems. In addition, we highlight the common regulatory mechanisms of both root and shoot apical meristems.

The Type-B Cytokinin Response Regulator ARR1 Inhibits Shoot Regeneration in an ARR12-Dependent Manner in Arabidopsis

Exogenous cytokinin is critical for in vitro shoot regeneration. Proteins involved in the cytokinin signal transduction pathway, including type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs), participate in shoot regeneration in Arabidopsis (Arabidopsis thaliana). Some type-B ARRs (e.g., ARR1 and ARR12) promote shoot regeneration by directly activating WUSCHEL (WUS) expression; however, it is unclear how type-B ARRs inhibit shoot regeneration. Here, we show that ARR12 is a central enhancer of callus formation and shoot regeneration, whereas ARR1 is a strong inhibitor of this process that counteracts the positive effect of ARR12. ARR1 indirectly represses CLAVATA3 (CLV3) expression in an ARR12-dependent manner via competing with ARR12 for binding to the CLV3 promoter, which contributes to its ARR12-dependent inhibitory effect on callus formation and shoot regeneration. In parallel, ARR1 inhibits shoot regeneration through transcriptional activation of INDOLE-3-ACETIC ACID INDUCIBLE17, an auxin response repressor gene, and the consequent indirect repression of WUS expression. Thus, type-B ARRs have diverse effects on callus formation and shoot regeneration. Our study reveals novel molecular pathways linking cytokinin signaling, the CLV3 regulator, and auxin signaling, and sheds light on the mechanism underlying cytokinin-regulated shoot regeneration.

Control of cell fate during axillary meristem initiation

Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.

Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response

Epigenetic regulation of gene expression is important for plant adaptation to environmental changes. Previous results showed that Arabidopsis RPD3-like histone deacetylase HDA9 is known to function in repressing plant response to stress in Arabidopsis. However, how HDA9 targets to specific chromatin loci and controls gene expression networks involved in plant response to stress remains largely unclear. Here, we show that HDA9 represses stress tolerance response by interacting with and regulating the DNA binding and transcriptional activity of WRKY53, which functions as a high-hierarchy positive regulator of stress response. We found that WRKY53 is post-translationally modified by lysine acetylation at multiple sites, some of which are removed by HDA9, resulting in inhibition of WRKY53 transcription activity. Conversely, WRKY53 negatively regulates HDA9 histone deacetylase activity. Collectively, our results indicate that HDA9 and WRK53 are reciprocal negative regulators of each other's activities, illustrating how the functional interplay between a chromatin regulator and a transcription factor regulates stress tolerance in plants.

Gibberellin repression of axillary bud formation in Arabidopsis by modulation of DELLA-SPL9 complex activity

The formation of lateral branches has an important and fundamental contribution to the remarkable developmental plasticity of plants, which allows plants to alter their architecture to adapt to the challenging environment conditions. The Gibberellin (GA) phytohormones have been known to regulate the outgrowth of axillary meristems (AMs), but the specific molecular mechanisms remain unclear. Here we show that DELLA proteins regulate axillary bud formation by interacting and regulating the DNA-binding ability of SQUAMOSA-PROMOTER BINDING PROTEIN LIKE 9 (SPL9), a microRNA156-targeted squamosa promoter binding protein-like transcription factor. SPL9 participates in the initial regulation of axillary buds by repressing the expression of LATERAL SUPPRESSOR (LAS), a key regulator in the initiation of AMs, and LAS contributes to the specific expression pattern of the GA deactivation enzyme GA2ox4, which is specifically expressed in the axils of leaves to form a low-GA cell niche in this anatomical region. Nevertheless, increasing GA levels in leaf axils by ectopically expressing the GA-biosynthesis enzyme GA20ox2 significantly impaired axillary meristem initiation. Our study demonstrates that DELLA-SPL9-LAS-GA2ox4 defines a core feedback regulatory module that spatially pattern GA content in the leaf axil and precisely control the axillary bud formation in different spatial and temporal.

MYB94 and MYB96 additively inhibit callus formation via directly repressing LBD29 expression in Arabidopsis thaliana

Plant somatic cells can be reprogrammed during in vitro culture. Callus induction is the initial step of a typical plant regeneration system. Recent studies showed that auxin-induced callus formation in multiple organs occurs from the pericycle or pericycle-like cells via a root developmental pathway. However, the molecular control of callus formation is largely unknown. Here, two MYB transcription factors, MYB94 and MYB96, were shown to play negative roles in auxin-induced callus formation in Arabidopsis. MYB94 and MYB96 were expressed in the newly formed callus. myb96, myb94, and myb94 myb96 generated more calli than the WT, with myb94 myb96 producing the most. MYB94 and MYB96 repressed expression of LATERAL ORGAN BOUNDARIES-DOMAIN 29 (LBD29) via directly binding to the gene's promoter. The loss of function of LBD29 partly rescued the callus formation defect of myb94 myb96. Our findings found MYB94 and MYB96 to be important repressors of callus formation and MYB94/96-LBD29 as a new regulatory pathway acting in parallel with ARF7/19-LBDs' pathway to modulate in vitro callus formation.

Hormonal and gene dynamics in de novo shoot meristem formation during adventitious caulogenesis in cotyledons of Pinus pinea

KEY MESSAGE

Several members of WOX and KNOX gene families and several plant growth regulators, basically cytokinins and auxins, play a key role during adventitious caulogenesis in the conifer Pinus pinea. Similar to Arabidopsis thaliana, Pinus pinea shoot organogenesis is a multistep process. However, there are key differences between both species, which may alter the underlying physiological and genetic programs. It is unknown if the genic expression models during angiosperm development may be applicable to conifers. In this work, an analysis of the endogenous content of different plant growth regulators and the expression of genes putatively involved in adventitious caulogenesis in P. pinea cotyledons was conducted. A multivariate analysis of both datasets was also realized through partial least squares regression and principal component analysis to obtain an integral vision of the mechanisms involved in caulogenesis in P. pinea. Analyses show that cotyledons cultured in the presence of benzyladenine during long times (2-6 days) cluster separately from the rest of the samples, suggesting that the benzyladenine increase observed during the first hours of culture is sufficient to trigger the caulogenic response through the activation of specific developmental programs. In particular, the most relevant factors involved in this process are the cytokinins trans-zeatin, dihydrozeatin, trans-zeatin riboside and isopentenyl adenosine; the auxin indoleacetic acid; and the genes PpWUS, PpWOX5, PpKN2, PpKN3 and PipiRR1. WUS is functional in pines and has an important role in caulogenesis. Interestingly, WOX5 also seems to participate in the process, although its specific role has not been determined.

The BIG gene controls size of shoot apical meristems in Arabidopsis thaliana

BIG regulates the shoot stem cell population. The shoot apical meristem (SAM) contains a population of self-renewing cells, and provides daughter cells for initiation and development of aerial parts of plants. However, the underlying mechanisms of SAM size regulation remain largely unclear. Here, we identified a mutant that displayed a large SAM, designated big-shoot meristem (big-m), in Arabidopsis thaliana. The phenotype of big-m is caused by a new T-DNA insertion allele of BIG, causing a loss of function. The big-m mutant had more stem cells in the SAM than in the wild type. Expression of WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM) was promoted in big-m compared with the wild type, showing that BIG functions upstream of WUS and STM. Therefore, BIG is an important regulator of the stem cell population in the SAM. Furthermore, genetic analysis indicated that BIG acts synergistically with PIN-FORMED1 (PIN1) in controlling SAM size. Our results suggest that BIG plays an important role in controlling Arabidopsis thaliana SAM growth via PIN1-mediated auxin homeostasis.

WUSCHEL: a master regulator in plant growth signaling

This review summarizes recent knowledge on functions of WUS and WUS-related homeobox (WOX) transcription factors in diverse signaling pathways governing shoot meristem biology and several other aspects of plant dynamics. Transcription factors (TFs) are master regulators involved in controlling different cellular and biological functions as well as diverse signaling pathways in plant growth and development. WUSCHEL (WUS) is a homeodomain transcription factor necessary for the maintenance of the stem cell niche in the shoot apical meristem, the differentiation of lateral primordia, plant cell totipotency and other diverse cellular processes. Recent research about WUS has uncovered several unique features including the complex signaling pathways that further improve the understanding of vital network for meristem biology and crop productivity. In addition, several reports bridge the gap between WUS expression and plant signaling pathway by identifying different WUS and WUS-related homeobox (WOX) genes during the formation of shoot (apical and axillary) meristems, vegetative-to-embryo transition, genetic transformation, and other aspects of plant growth and development. In this respect, the WOX family of TFs comprises multiple members involved in diverse signaling pathways, but how these pathways are regulated remains to be elucidated. Here, we review the current status and recent discoveries on the functions of WUS and newly identified WOX family members in the regulatory network of various aspects of plant dynamics.

Endogenous auxin determines the pattern of adventitious shoot formation on internodal segments of ipecac

Endogenous auxin determines the pattern of adventitious shoot formation. Auxin produced in the dominant shoot is transported to the internodal segment and suppresses growth of other shoots. Adventitious shoot formation is required for the propagation of economically important crops and for the regeneration of transgenic plants. In most plant species, phytohormones are added to culture medium to induce adventitious shoots. In ipecac (Carapichea ipecacuanha (Brot.) L. Andersson), however, adventitious shoots can be formed without phytohormone treatment. Thus, ipecac culture allows us to investigate the effects of endogenous phytohormones during adventitious shoot formation. In phytohormone-free culture, adventitious shoots were formed on the apical region of the internodal segments, and a high concentration of IAA was detected in the basal region. To explore the relationship between endogenous auxin and adventitious shoot formation, we evaluated the effects of auxin transport inhibitors, auxin antagonists, and auxin biosynthesis inhibitors on adventitious shoot formation in ipecac. Auxin antagonists and biosynthesis inhibitors strongly suppressed adventitious shoot formation, which was restored by exogenously applied auxin. Auxin biosynthesis and transport inhibitors significantly decreased the IAA level in the basal region and shifted the positions of adventitious shoot formation from the apical region to the middle region of the segments. These data indicate that auxin determines the positions of the shoots formed on internodal segments of ipecac. Only one of the shoots formed grew vigorously; this phenomenon is similar to apical dominance. When the largest shoot was cut off, other shoots started to grow. Naphthalene-1-acetic acid treatment of the cut surface suppressed shoot growth, indicating that auxin produced in the dominant shoot is transported to the internodal segment and suppresses growth of other shoots.

Transcriptional circuits in control of shoot stem cell homeostasis

Plant shoot apical meristems (SAMs) play essential roles in plant growth and development. Located at the growing tip of a plant stem, these dome-like structures contain stem cells, which serve to perpetuate themselves in an undifferentiated state while continually adding new cells that differentiate and eventually form all above-ground tissues. In a SAM, the pool of stem cells is dynamically maintained through a balance between cell division (self-renewal) and differentiation (loss of stem-cell identity). In the model plant Arabidopsis thaliana, a negative feedback loop between WUSCHEL (WUS) and the CLAVATA3 (CLV3) plays important roles in maintaining the stem cell population. In this review, we highlight recent findings mainly from studies in Arabidopsis, and summarize the research progress on understanding how multiple transcriptional circuits integrate and function at different cell layers to control the WUS-CLV3 loop and stem cell homeostasis.