TCP1 Modulates DWF4 Expression via Directly Interacting with the GGNCCC Motifs in the Promoter Region of DWF4 in Arabidopsis thaliana

Different viral effectors hijack TCP17, a key transcription factor for host Auxin synthesis, to promote viral infection

Auxin is an important class of plant hormones that play an important role in plant growth development, biotic stress response, and viruses often suppress host plant auxin levels to promote infection. However, previous research on auxin-mediated disease resistance has focused mainly on signaling pathway, and the molecular mechanisms of how pathogenic proteins manipulate the biosynthetic pathway of auxin remain poorly understood. TCP is a class of plant-specific transcription factors, of which TCP17 is a member that binds to the promoter of YUCCAs, a key rate-limiting enzyme for auxin synthesis, and promotes the expression of YUCCAs, which is involved in auxin synthesis in plants. In this study, we reported that Tomato spotted wilt virus (TSWV) infection suppressed the expression of YUCCAs through its interaction with TCP17. Further studies revealed that the NSs protein encoded by TSWV disrupts the dimerization of TCP17, thereby inhibit its transcriptional activation ability and reducing the auxin content in plants. Consequently, this interference inhibits the auxin response signal and promotes the TSWV infection. Transgenic plants overexpressing TCP17 exhibit resistance against TSWV infection, whereas plants knocking out TCP17 were more susceptible to TSWV infection. Additionally, proteins encoded by other RNA viruses (BSMV, RSV and TBSV) can also interact with TCP17 and interfere with its dimerization. Notably, overexpression of TCP17 enhanced resistance against BSMV. This suggests that TCP17 plays a crucial role in plant defense against different types of plant viruses that use viral proteins to target this key component of auxin synthesis and promote infection.

Development and evolution of the Asteraceae capitulum

Asteraceae represent one of the largest and most diverse families of plants. The evolutionary success of this family has largely been contributed to their unique inflorescences, capitula that mimic solitary flowers but are typically aggregates of multiple florets. Here, we summarize the recent molecular and genetic level studies that have promoted our understanding of the development and evolution of capitula. We focus on new results on patterning of the enlarged meristem resulting in the iconic phyllotactic arrangement of florets in Fibonacci numbers of spirals. We also summarize the current understanding of the genetic networks regulating the characteristic reproductive traits in the family such as floral dimorphism and differentiation of highly specialized floral organs. So far, developmental studies in Asteraceae are still limited to a very narrow selection of model species. Along with the recent advancements in genomics and phylogenomics, Asteraceae and its relatives provide an outstanding model clade for extended evo-devo studies to exploit the morphological diversity and the underlying molecular networks and to translate this knowledge to the breeding of the key crops in the family.

Arabidopsis BBX14 negatively regulates nitrogen starvation- and dark-induced leaf senescence

Senescence is a highly regulated process driven by developmental age and environmental factors. Although leaf senescence is accelerated by nitrogen (N) deficiency, the underlying physiological and molecular mechanisms are largely unknown. Here, we reveal that BBX14, a previously uncharacterized BBX-type transcription factor in Arabidopsis, is crucial for N starvation-induced leaf senescence. We find that inhibiting BBX14 by artificial miRNA (amiRNA) accelerates senescence during N starvation and in darkness, while BBX14 overexpression (BBX14-OX) delays it, identifying BBX14 as a negative regulator of N starvation- and dark-induced senescence. During N starvation, nitrate and amino acids like glutamic acid, glutamine, aspartic acid, and asparagine were highly retained in BBX14-OX leaves compared to the wild type. Transcriptome analysis showed a large number of senescence-associated genes (SAGs) to be differentially expressed between BBX14-OX and wild-type plants, including ETHYLENE INSENSITIVE3 (EIN3) which regulates N signaling and leaf senescence. Chromatin immunoprecipitation (ChIP) showed that BBX14 directly regulates EIN3 transcription. Furthermore, we revealed the upstream transcriptional cascade of BBX14. By yeast one-hybrid screen and ChIP, we found that MYB44, a stress-responsive MYB transcription factor, directly binds to the promoter of BBX14 and activates its expression. In addition, Phytochrome Interacting Factor 4 (PIF4) binds to the promoter of BBX14 to repress BBX14 transcription. Thus, BBX14 functions as a negative regulator of N starvation-induced senescence through EIN3 and is directly regulated by PIF4 and MYB44.

Genome-wide identification and expression pattern analysis of the TCP transcription factor family in Ginkgo biloba

Plant-specific TCP transcription factors play an essential role in plant growth and development. They can regulate leaf curvature, flower symmetry and the synthesis of secondary metabolites. The flavonoids in Ginkgo biloba leaf are one of the main medicinally bioactivate compounds, which have pharmacological and beneficial health effects for humans. In this study, a total of 13 TCP genes were identified in G. biloba, and 5 of them belonged to PCF subclades (GbTCP03, GbTCP07, GbTCP05, GbTCP13, GbTCP02) while others belonged to CIN (GbTCP01, GbTCP04, GbTCP06, GbTCP08, GbTCP09, GbTCP10, GbTCP11, GbTCP12) subclades according to phylogenetic analysis. Numerous cis-acting elements related to various biotic and abiotic signals were predicted on the promoters by cis-element analysis, suggesting that the expression of GbTCPs might be co-regulated by multiple signals. Transcript abundance analysis exhibited that most of GbTCPs responded to multiple phytohormones. Among them, the relative expression levels of GbTCP06, GbTCP11, and GbTCP13 were found to be significantly influenced by exogenous ABA, SA and MeJA application. In addition, a total of 126 miRNAs were predicted to target 9 TCPs (including GbTCP01, GbTCP02, GbTCP04, GbTCP05, GbTCP06, GbTCP08, GbTCP11, GbTCP12, GbTCP13). The correlation analysis between the expression level of GbTCPs and the flavonoid contents showed that GbTCP03, GbTCP04, GbTCP07 might involve in flavonoid biosynthesis in G. biloba. In short, this study mainly provided a theoretical foundation for better understanding the potential function of TCPs in G. biloba.

Integrating GWAS, linkage mapping and gene expression analyses reveal the genetic control of first branch height in Brassica napus L

Rapeseed (Brassica napus L.) is a crucial oil crop cultivated worldwide. First branch height, an essential component of rapeseed plant architecture, has an important effect on yield and mechanized harvesting; however, the underlying genetic mechanism remains unclear. In this study, based on the 60K single nucleotide polymorphism array and a recombinant inbred lines population derived from M083 and 888-5, a total of 19 QTLs were detected in five environments, distributed on linkage groups A02, A09, A10, C06, and C07, which explained phenotypic variation ranging from 4.87 to 29.87%. Furthermore, 26 significant SNPs were discovered on Chr.A02 by genome-wide association study in a diversity panel of 324 re-sequencing accessions. The major QTL of the first branch height trait was co-located on Chr.A02 by integrating linkage mapping and association mapping. Eleven candidate genes were screened via allelic variation analysis, inter-subgenomic synteny analysis, and differential expression of genes in parental shoot apical meristem tissues. Among these genes, BnaA02g13010D, which encodes a TCP transcription factor, was confirmed as the target gene according to gene function annotation, haplotype analysis, and full-length gene sequencing, which revealed that TATA insertion/deletion in the promoter region was closely linked to significantly phenotypic differences BnaA02.TCP1 ^M083 overexpression resulted in decreased branch height and increased branch number in Arabidopsis. These results provide a genetic basis for first branch height and the ideal architecture of B. napus.

A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales

BACKGROUND

An outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype-Lamiales flower monosymmetry-defined by a developmental program that relies on regulatory interaction among CYCLOIDEA, RADIALIS, DIVARICATA, and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program.

RESULTS

We found that RADIALIS, DIVARICATA, and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. In addition, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog.

CONCLUSION

Our results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.

Unraveling the impact on agronomic traits of the genetic architecture underlying plant-density responses in canola

Plant density defines vegetative architecture and the competition for light between individuals. Brassica napus (canola, rapeseed) presents a radically different plant architecture compared to traditional crops commonly cultivated at high density, and can act as a model system of indeterminate growth. Using a panel of 152 spring-type accessions and a double-haploid population of 99 lines from a cross between the cultivars Lynx and Monty, we performed genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping for 12 growth and yield traits at two contrasting plant densities of 15 and 60 plants m-2. The most significant associations were found for time to flowering, biomass at harvest, plant height, silique and seed numbers, and seed yield. These were generally independent of plant density, but some density-dependent associations were found in low-density populations. RNA-seq transcriptomic analysis revealed distinctive latent gene-regulatory responses to simulated shade between Lynx and Monty. Having identified candidate genes within the canola QTLs, we further examined their influence on density responses in Arabidopsis lines mutated in certain homologous genes. The results suggested that TCP1 might promote growth independently of plant density, while HY5 could increase biomass and seed yield specifically at high plant density. For flowering time, the results suggested that PIN genes might accelerate flowering in plant a density-dependent manner whilst FT, HY5, and TCP1 might accelerate it in a density-independent. This work highlights the advantages of using agronomic field experiments together with genetic and transcriptomic approaches to decipher quantitative complex traits that potentially mediate improved crop productivity.

Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome

Genetic diversity becomes structured among populations over time due to genetic drift and divergent selection. Although population structure is often treated as a uniform underlying factor, recent resequencing studies of wild populations have demonstrated that diversity in many regions of the genome may be structured quite dissimilar to the genome-wide pattern. Here, we explored the adaptive and nonadaptive causes of such genomic heterogeneity using population-level, whole genome resequencing data obtained from annual Mimulus guttatus individuals collected across a rugged environment landscape. We found substantial variation in how genetic differentiation is structured both within and between chromosomes, although, in contrast to other studies, known inversion polymorphisms appear to serve only minor roles in this heterogeneity. In addition, much of the genome can be clustered into eight among-population genetic differentiation patterns, but only two of these clusters are particularly consistent with patterns of isolation by distance. By performing genotype-environment association analysis, we also identified genomic intervals where local adaptation to specific climate factors has accentuated genetic differentiation among populations, and candidate genes in these windows indicate climate adaptation may proceed through changes affecting specialized metabolism, drought resistance, and development. Finally, by integrating our findings with previous studies, we show that multiple aspects of plant reproductive biology may be common targets of balancing selection and that variants historically involved in climate adaptation among populations have probably also fuelled rapid adaptation to microgeographic environmental variation within sites.

GrTCP11, a Cotton TCP Transcription Factor, Inhibits Root Hair Elongation by Down-Regulating Jasmonic Acid Pathway in Arabidopsis thaliana

TCP transcription factors play important roles in diverse aspects of plant development as transcriptional activators or repressors. However, the functional mechanisms of TCPs are not well understood, especially in cotton fibers. Here, we identified a total of 37 non-redundant TCP proteins from the diploid cotton (Gossypium raimondii), which showed great diversity in the expression profile. GrTCP11, an ortholog of AtTCP11, was preferentially expressed in cotton anthers and during fiber initiation and secondary cell wall synthesis stages. Overexpression of GrTCP11 in Arabidopsis thaliana reduced root hair length and delayed flowering. It was found that GrTCP11 negatively regulated genes involved in jasmonic acid (JA) biosynthesis and response, such as AtLOX4, AtAOS, AtAOC1, AtAOC3, AtJAZ1, AtJAZ2, AtMYC2, and AtERF1, which resulted in a decrease in JA concentration in the overexpressed transgenic lines. As with the JA-deficient mutant dde2-2, the transgenic line 4-1 was insensitive to 50 μM methyl jasmonate, compared with the wild-type plants. The results suggest that GrTCP11 may be an important transcription factor for cotton fiber development, by negatively regulating JA biosynthesis and response.

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.

Genome-Wide Identification and Characterization of the TCP Gene Family in Cucumber (Cucumis sativus L.) and Their Transcriptional Responses to Different Treatments

TCP proteins are plant-specific transcription factors widely implicated in leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, the relationship between the transcription pattern of TCPs and organ development in cucumber has not been systematically studied. In this study, we performed a genome-wide identification of putative TCP genes and analyzed their chromosomal location, gene structure, conserved motif, and transcript expression. A total of 27 putative TCP genes were identified and characterized in cucumber. All 27 putative CsTCP genes were classified into class I and class II. Class I comprised 12 CsTCPs and Class II contained 15 CsTCPs. The 27 putative CsTCP genes were randomly distributed in five of seven chromosomes in cucumber. Four putative CsTCP genes were found to contain putative miR319 target sites. Quantitative RT-PCR revealed that 27 putative CsTCP genes exhibited different expression patterns in cucumber tissues and floral organ development. Transcript expression and phenotype analysis showed that the putative CsTCP genes responded to temperature and photoperiod and were induced by gibberellin (GA)and ethylene treatment, which suggested that CsTCP genes may regulate the lateral branching by involving in multiple signal pathways. These results lay the foundation for studying the function of cucumber TCP genes in the future.

Genome-Wide Identification of the TCP Gene Family in Broussonetia papyrifera and Functional Analysis of BpTCP8, 14 and 19 in Shoot Branching

The plant-specific TCP family proteins play an important role in the processes of plant growth and development. Broussonetia papyrifera is a versatile perennial deciduous tree, and its genome data have been published. However, no comprehensive analysis of the TCP gene family in B. papyrifera has been undertaken. In this study, 20 BpTCP genes (BpTCPs) were identified in the B. papyrifera genome. Phylogenetic analysis divided BpTCPs into three subclades, the PCF subclade, the CIN subclade and the CYC/TB1 subclade. Gene structure analysis displayed that all BpTCPs except BpTCP19 contained one coding region. Conserved motif analysis showed that BpTCP proteins in the same subclade possessed similar motif structures. Segmental duplication was the primary driving force for the expansion of BpTCPs. Expression patterns showed that BpTCPs may play diverse biological functions in organ or tissue development. Transcriptional activation activity analysis of BpTCP8, BpTCP14 and BpTCP19 showed that they possessed transcriptional activation ability. The ectopic expression analysis in Arabidopsis wild-type and AtBRC1 ortholog mutant showed that BpTCP8, BpTCP14 and BpTCP19 could prevent rosette branch outgrowth. Collectively, our study not only established the first genome-wide analysis of the B. papyrifera TCP gene family, but also provided valuable information for understanding the function of BpTCPs in shoot branching.

Molecular Mechanisms of Brassinosteroid-Mediated Responses to Changing Environments in Arabidopsis

Plant adaptations to changing environments rely on integrating external stimuli into internal responses. Brassinosteroids (BRs), a group of growth-promoting phytohormones, have been reported to act as signal molecules mediating these processes. BRs are perceived by cell surface receptor complex including receptor BRI1 and coreceptor BAK1, which subsequently triggers a signaling cascade that leads to inhibition of BIN2 and activation of BES1/BZR1 transcription factors. BES1/BZR1 can directly regulate the expression of thousands of downstream responsive genes. Recent studies in the model plant Arabidopsis demonstrated that BR biosynthesis and signal transduction, especially the regulatory components BIN2 and BES1/BZR1, are finely tuned by various environmental cues. Here, we summarize these research updates and give a comprehensive review of how BR biosynthesis and signaling are modulated by changing environments and how these changes regulate plant adaptive growth or stress tolerance.

Designed Manipulation of the Brassinosteroid Signal to Enhance Crop Yield

Brassinosteroid (BR), a plant steroid hormone, plays crucial role in modulating plant growth and development, which affect crop architecture and yield. However, BR application cannot highly benefit to agricultural production as expectation, because it regulates multiple processes in different tissues and leads to side effect. In addition, accurately modifying BR signal at transcriptional level is difficult. Effective manipulation of the BR signal and avoidance of side effects are required to enhance yield in different crops. Application of BR by spraying at specific developmental stages can enhance crop yield, but this method is impractical for use on a large scale. The accurate molecular design of crops would be much more helpful to manipulate the BR signal in specific organs and/or at particular developmental stages to enhance crop yield. This minireview summarizes the BR regulation of yield in different crops, especially horticultural crops, and the strategies used to regulate the BR signal to enhance crop yield. One popular strategy is to directly modulate the BR signal through modifying the functions of important components in the BR signal transduction pathway. Another strategy is to identify and modulate regulators downstream of, or in crosstalk with, the BR signal to manipulate its role in specific processes and increase crop yield. Efforts to accurately design a BR manipulation strategy will ultimately lead to effective control of the BR signal to avoid side effects and enhance crop yield.

Regulation of Brassinosteroid Homeostasis in Higher Plants

Brassinosteroids (BRs) are known as one of the major classes of phytohormones essential for various processes during normal plant growth, development, and adaptations to biotic and abiotic stresses. Significant progress has been achieved on revealing mechanisms regulating BR biosynthesis, catabolism, and signaling in many crops and in model plant Arabidopsis. It is known that BRs control plant growth and development in a dosage-dependent manner. Maintenance of BR homeostasis is therefore critical for optimal functions of BRs. In this review, updated discoveries on mechanisms controlling BR homeostasis in higher plants in response to internal and external cues are discussed.

Evolutionary Conservation of the Orchid MYB Transcription Factors DIV, RAD, and DRIF

The MYB transcription factors DIVARICATA (DIV), DIV-and-RAD-Interacting-Factor (DRIF), and the small interfering peptide RADIALIS (RAD) can interact, forming a regulatory module that controls different plant developmental processes. In the snapdragon Antirrhinum majus, this module, together with the TCP transcription factor CYCLOIDEA (CYC), is responsible for the establishment of floral dorsoventral asymmetry. The spatial gene expression pattern of the OitDIV, OitDRIF, and OitRAD homologs of Orchis italica, an orchid with zygomorphic flowers, has suggested a possible conserved role of these genes in bilateral symmetry of the orchid flower. Here, we have identified four DRIF genes of orchids and have reconstructed their genomic organization and evolution. In addition, we found snapdragon transcriptional cis-regulatory elements of DIV and RAD loci generally conserved within the corresponding orchid orthologues. We have tested the biochemical interactions among OitDIV, OitDRIF1, and OitRAD of O. italica, showing that OitDRIF1 can interact both with OitDIV and OitRAD, whereas OitDIV and OitRAD do not directly interact, as in A. majus. The analysis of the quantitative expression profile of these MYB genes revealed that in zygomorphic orchid flowers, the DIV, DRIF1, and RAD transcripts are present at higher levels in the lip than in lateral inner tepals, whereas in peloric orchid flowers they show similar expression levels. These results indicate that MYB transcription factors could have a role in shaping zygomorphy of the orchid flower, potentially enriching the underlying orchid developmental code.

Identification, Characterization, and Expression Patterns of TCP Genes and microRNA319 in Cotton

The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) gene family is a group of plant-specific transcription factors that have versatile functions in developmental processes and stress responses. In this study, a total of 73 TCP genes in upland cotton were identified and characterizated. Phylogenetic analysis classified them into three subgroups: 50 belonged to PCF, 16 to CIN, and 7 to CYC/TB1. GhTCP genes are randomly distributed in 22 of the 26 chromosomes in cotton. Expression patterns of GhTCPs were analyzed in 10 tissues, including different developmental stages of ovule and fiber, as well as under heat, salt, and drought stresses. Transcriptome analysis showed that 44 GhTCP genes exhibited varied transcript accumulation patterns in the tested tissues and 41 GhTCP genes were differentially expressed in response to heat, salt, and drought stresses. Furthermore, three GhTCP genes of the CIN clade were found to contain miR319-binding sites. An anti-correlation expression of GhTCP21 and GhTCP54 was analyzed with miR319 under salt and drought stress. Our results lay the foundation for understanding the complex mechanisms of GhTCP-mediated developmental processes and abiotic stress-signaling transduction pathways in cotton.

Soybean TCP transcription factors: Evolution, classification, protein interaction and stress and hormone responsiveness

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors, a family of plant-specific proteins, play crucial roles in plant growth and development and stress response. However, systematical information is unknown regarding the TCP gene family in soybean. In the present study, a total of 54 GmTCPs were identified in soybean, which were grouped into 11 groups with the typical TCP conserved domains. Phylogenetic relationship, protein motif and gene structure analyses distinguished the GmTCPs into two homology classes: Class I and Class II. Class II was then differentiated into two subclasses: CIN and CYC/TB1. Unique cis-element number and composition existed in the promoter regions which might be involved in the gene transcriptional regulation of different GmTCPs. Tissue expression analysis demonstrated the diverse spatiotemporal expression profiles of GmTCPs. Furthermore, the interaction protein of one previously functionally unknown TCP protein-GmTCP8 was investigated. Yeast two-hybrid assay showed the interaction between GmTCP8 and an abscisic acid receptor (GmPYL10). QRT-PCR assays indicated the distinct expression profiles of GmTCPs in response to abiotic stresses (heat, drought and salt) and stress-related signals (abscisic acid, brassinolide, salicylicacid and methyl jasmonate). These results will facilitate to uncover the possible roles of GmTCPs under abiotic stress and hormone signal responses in soybean.

Novel Traits, Flower Symmetry, and Transcriptional Autoregulation: New Hypotheses From Bioinformatic and Experimental Data

A common feature in developmental networks is the autoregulation of transcription factors which, in turn, positively or negatively regulate additional genes critical for developmental patterning. When a transcription factor regulates its own expression by binding to cis-regulatory sites in its gene, the regulation is direct transcriptional autoregulation (DTA). Indirect transcriptional autoregulation (ITA) involves regulation by proteins expressed downstream of the target transcription factor. We review evidence for a hypothesized role of DTA in the evolution and development of novel flowering plant phenotypes. We additionally provide new bioinformatic and experimental analyses that support a role for transcriptional autoregulation in the evolution of flower symmetry. We find that 5' upstream non-coding regions are significantly enriched for predicted autoregulatory sites in Lamiales CYCLOIDEA genes-an upstream regulator of flower monosymmetry. This suggests a possible correlation between autoregulation of CYCLOIDEA and the origin of monosymmetric flowers near the base of Lamiales, a pattern that may be correlated with independently derived monosymmetry across eudicot lineages. We find additional evidence for transcriptional autoregulation in the flower symmetry program, and report that Antirrhinum DRIF2 may undergo ITA. In light of existing data and new data presented here, we hypothesize how cis-acting autoregulatory sites originate, and find evidence that such sites (and DTA) can arise subsequent to the evolution of a novel phenotype.

TCP factors: new kids on the signaling block

The TCP transcription factors govern key plant developmental processes and have profound effects on the growth patterns of meristems and organs, partly explained by direct transcriptional control of cell cycle genes. This view is nevertheless incomplete, as accumulated evidence indicates that TCPs also act through other mechanisms, such as the regulation of hormone activity. Several TCP factors not only act as mediators of hormone-induced changes in cell proliferation, but also as modulators, or even key players, of hormone synthesis, transport and signal transduction. This adds another layer of complexity to the role of TCPs in plant development.

Interaction between hormonal and mitochondrial signalling during growth, development and in plant defence responses

Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key metabolic reactions such as the TCA cycle. The energy and building blocks produced by mitochondria are essential to drive plant growth and development as well as to provide fuel for responses to abiotic and biotic stresses. The majority of mitochondrial proteins are encoded in the nuclear genome and have to be imported into the organelle. For the regulation of the corresponding genes intricate signalling pathways exist to adjust their expression. Signals directly regulate nuclear gene expression (anterograde signalling) to adjust the protein composition of the mitochondria to the needs of the cell. In parallel, mitochondria communicate back their functional status to the nucleus (retrograde signalling) to prompt transcriptional regulation of responsive genes via largely unknown signalling mechanisms. Plant hormones are the major signalling components regulating all layers of plant development and cellular functions. Increasing evidence is now becoming available that plant hormones are also part of signalling networks controlling mitochondrial function and their biogenesis. This review summarizes recent advances in understanding the interaction of mitochondrial and hormonal signalling pathways.

Brassinosteroids Regulate Root Growth, Development, and Symbiosis

Brassinosteroids (BRs) are natural plant hormones critical for growth and development. BR deficient or signaling mutants show significantly shortened root phenotypes. However, for a long time, it was thought that these phenotypes were solely caused by reduced cell elongation in the mutant roots. Functions of BRs in regulating root development have been largely neglected. Nonetheless, recent detailed analyses, revealed that BRs are not only involved in root cell elongation but are also involved in many aspects of root development, such as maintenance of meristem size, root hair formation, lateral root initiation, gravitropic response, mycorrhiza formation, and nodulation in legume species. In this review, current findings on the functions of BRs in mediating root growth, development, and symbiosis are discussed.

Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa

Populus tomentosa (Chinese white poplar) is well adapted to various extreme environments, and is considered an important species to study the effects of salinity stress on poplar trees. To decipher the mechanism of poplar's rapid response to short-term salinity stress, we firstly detected the changes in H2O2 and hormone, and then profiled the gene expression pattern of 10-week-old seedling roots treated with 200 mM NaCl for 0, 6, 12, and 24 h (h) by RNA-seq on the Illumina-Solexa platform. Physiological determination showed that the significant increase in H2O2 began at 6 h, while that in hormone ABA was at 24 h, under salt stress. Compared with controls (0 h), 3991, 4603, and 4903 genes were up regulated, and 1408, 2206, and 3461 genes were down regulated (adjusted P ≤ 0.05 and |log2Ratio|≥1) at 6, 12, and 24 h time points, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in hormone- and reactive oxygen species-related biological processes, including "response to oxidative stress or abiotic stimulus," "peroxidase activity," "regulation of transcription," "hormone synthetic and metabolic process," "hormone signal transduction," "antioxidant activity," and "transcription factor activity." Moreover, K-means clustering demonstrated that DEGs (total RPKM value>12 from four time points) could be categorized into four kinds of expression trends: quick up/down over 6 or 12 h, and slow up/down over 24 h. Of these, DEGs involved in H2O2- and hormone- producing and signal-related genes were further enriched in this analysis, which indicated that the two kinds of small molecules, hormones and H2O2, play pivotal roles in the short-term salt stress response in poplar. This study provides a basis for future studies of the molecular adaptation of poplar and other tree species to salinity stress.