TCP Transcription Factors at the Interface between Environmental Challenges and the Plant's Growth Responses

Multi-kernel feature extraction with dynamic fusion and downsampled residual feature embedding for predicting rice RNA N6-methyladenine sites

RNA N$^{6}$-methyladenosine (m$^{6}$A) is a critical epigenetic modification closely related to rice growth, development, and stress response. m$^{6}$A accurate identification, directly related to precision rice breeding and improvement, is fundamental to revealing phenotype regulatory and molecular mechanisms. Faced on rice m$^{6}$A variable-length sequence, to input into the model, the maximum length padding and label encoding usually adapt to obtain the max-length padded sequence for prediction. Although this can retain complete sequence information, resulting in sparse information and invalid padding, reducing feature extraction accuracy. Simultaneously, existing rice-specific m$^{6}$A prediction methods are still at an early stage. To address these issues, we develop a new end-to-end deep learning framework, MFDm$^{6}$ARice, for predicting rice m$^{6}$A sites. In particular, to alleviate sparseness, we construct a multi-kernel feature fusion module to mine essential information in max-length padded sequences by multi-kernel feature extraction function and effectively transfer information through global-local dynamic fusion function. Concurrently, considering the complexity and computational efficiency of high-dimensional features caused by invalid padding, we design a downsampling residual feature embedding module to optimize feature space compression and achieve accurate feature expression and efficient computational performance. Experiments show that MFDm$^{6}$ARice outperforms comparison methods in cross-validation, same- and cross-species independent test sets, demonstrating good robustness and generalization. The application on maize m$^{6}$A indicates the MFDm$^{6}$ARice's scalability. Further investigations have shown that combining different kernel features, focusing on global channel-local spatial, and employing reasonable downsampling and residual connections can improve feature representation and extraction, ensure effective information transfer, and significantly enhance model performance.

Identification and Expression Analysis of TCP Transcription Factors Under Abiotic Stress in Phoebe bournei

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes-PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15-under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family's functional characteristics and stress resistance regulation in P. bournei.

Antioxidant activity and comparative RNA-seq analysis support mitigating effects of an algae-based biostimulant on drought stress in tomato plants

Drought is a significant global environmental stress. Biostimulants offer a sustainable solution to enhance crop tolerance and mitigate productivity losses. This study assessed the impact of foliar application of ERANTHIS®, a biostimulant derived from the algae Ascophyllum nodosum and Laminaria digitata and yeast extracts, on tomato plants under mild water stress. Evaluations were conducted at 5 and 24 hours after the third treatment. Under optimal water conditions, the biostimulant showed a priming effect, with an early increase of stress markers and a timing-specific modulation of ROS non enzymatic and enzymatic ROS scavenging activities. Under drought stress, the biostimulant later decreased stress markers, by aligning the majority of analyzed ROS scavengers closer to levels in well-irrigated plants. Transcriptome analysis using RNA-seq data revealed differentially expressed genes (DEGs) and multivariate data highlighted groups of co-regulated genes (k-means clustering). Genes involved in water channel activity, transcription regulator activity, and oxidoreductase activity were significantly modulated. Cluster analysis identified distinct gene clusters influenced by the biostimulant under optimal conditions, including early responses (cell wall modification, hormone signaling) and late responses (RNA modification, nutrient uptake process). Under water stress, early responses involved actin filament organization and MAPK signaling, while late responses were related to plasma membrane components and cell wall organization. This study, integrating biochemical and transcriptomic data, provides a comprehensive understanding of how a biostimulant primes plants under optimal conditions and mitigates water stress effects, offering valuable insights for sustainable agriculture.

Interaction between plant-specific transcription factors TCP and YABBY expressed in the tendrils of the melon Cucumis melo

Plant tendrils are specialized organs that can twine around other structures to facilitate climbing. They occur in a variety of plant families and have diverse ontogenic origins. In cucurbits, tendrils originate from lateral shoots. Fine mapping verified that the tendril-less ctl mutation of the melon Cucumis melo corresponds to a frameshift mutation in the CmTCP1 gene, which encodes a TCP transcription factor. A yeast two-hybrid screen for CmTCP1/CTL-interacting proteins identified a member of the plant-specific YABBY transcription factor family, which was named CmYAB1. Each of the N- and C-terminal regions of CmTCP1 interacted with CmYAB1. The ctl mutation impaired the interaction between CmTCP1 and CmYAB1. Both proteins interacted in vitro and were localized to the nucleus in plant cells. In situ expression analysis revealed the coexistence of the CmTCP1 and CmYAB1 mRNAs in the abaxial domains of developing tendrils. An RNA-seq analysis of the seven YABBY genes in the melon genome revealed relatively high expression ratios of CmYAB1 in tendrils compared with those in leaves. These results suggest a novel function of the YABBY protein through its interaction with a TCP protein in the development of cucurbit tendrils.

A viral small interfering RNA-host plant mRNA pathway modulates virus-induced drought tolerance by enhancing autophagy

Virus-induced drought tolerance presents a fascinating facet of biotic-abiotic interaction in plants, yet its molecular intricacies remain unclear. Our study shows that cowpea mild mottle virus (CPMMV) infection enhances drought tolerance in common bean (Phaseolus vulgaris) plants through a virus-derived small interfering RNA (vsiRNA)-activated autophagy pathway. Specifically, a 21 nt vsiRNA originating from the CPMMV Triple Gene Block1 (TGB1) gene targeted the 5' untranslated region (UTR) of the host Teosinte branched 1, Cycloidea, Proliferating Cell Factor (TCP) transcription factor gene PvTCP2, independent of the known role of TGB1 as an RNA silencing suppressor. This targeting attenuated the expression of PvTCP2, which encodes a transcriptional repressor, and in turn upregulated the core autophagy-related gene (ATG) PvATG8c, leading to activated autophagy activity surpassing the level induced by drought or CPMMV infection alone. The downstream EARLY RESPONSIVE TO DEHYDRATION (ERD) effector PvERD15 is a homologue of Arabidopsis thaliana AtERD15, which positively regulates stomatal aperture. PvERD15 was degraded in PvATG8c-mediated autophagy. Therefore, we establish a TGB1-PvTCP2-PvATG8c-PvERD15 module as a trans-kingdom fine-tuning mechanism that contributes to virus-induced drought tolerance in plant-drought-virus interactions.

Genome-Wide Identification of a Maize Chitinase Gene Family and the Induction of Its Expression by Fusarium verticillioides (Sacc.) Nirenberg (1976) Infection

Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins remain unknown. The economic importance of maize (Zea mays L.) makes it relevant for studying the function of plant chitinases and their biological roles. This work aims to identify chitinase genes in the maize genome to study their gene structure, family/class classification, cis-related elements, and gene expression under biotic stress, such as Fusarium verticillioides infection. Thirty-nine chitinase genes were identified and found to be distributed in three glycosyl hydrolase (GH) families (18, 19 and 20). Likewise, the conserved domains and motifs were identified in each GH family member. The identified cis-regulatory elements are involved in plant development, hormone response, defense, and abiotic stress response. Chitinase protein-interaction network analysis predicted that they interact mainly with cell wall proteins. qRT-PCR analysis confirmed in silico data showing that ten different maize chitinase genes are induced in the presence of F. verticillioides, and that they could have several roles in pathogen infection depending on chitinase structure and cell wall localization.

Salicylic acid-mediated alleviation of salt stress: Insights from physiological and transcriptomic analysis in Asarum sieboldii Miq

As global agriculture faces the pressing threat of salt stress, innovative solutions are imperative for sustainable agriculture. The remarkable potential of salicylic acid (SA) in enhancing plant resilience against environmental stressors has recently gained attention. However, the specific molecular mechanisms by which SA mitigates salt stress in Asarum sieboldii Miq., a valuable medicinal plant, remain poorly understood. Here, we evaluated the physiological and transcriptomic regulatory responses of A. sieboldii under salt stress (100 mM NaCl), both in the presence (1 mM SA) and absence of exogenous SA. The results highlighted that SA significantly alleviates salt stress, primarily through enhancing antioxidant activities as evidenced by increased superoxide dismutase, and peroxidase activities. Additionally, we observed an increment in chlorophyll (a and b), proline, total soluble sugar, and plant fresh weight, along with a decrease in malondialdehyde contents. Transcriptome analysis suggested consistency in the regulation of many differentially expressed genes and transcription factors (TFs); however, genes targets (GSTs, TIR1, and NPR1), and TFs (MYB, WRKY, TCP, and bHLH) possessed expressional uniqueness, and majority had significantly up-regulated trends in SA-coupled salt stress treatments. Further, bioinformatics and KEGG enrichment analysis indicated several SA-induced significantly enriched biological pathways. Specifically, plant hormone signal transduction was identified as being populated with key genes distinctive to auxin, cytokinin, ethylene, and salicylic acid signaling, suggesting their important role in salt stress alleviation. Inclusively, this report presents a comprehensive analysis encompassing gene targets, TFs, and biological pathways, and these insights may offer a valuable contribution to our knowledge of SA-mediated regulation and its crucial role in enhancing plant defense against diverse abiotic stressors.

Class I TCP in fruit development: much more than growth

Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue.

Mediator kinase subunit CDK8 phosphorylates transcription factor TCP15 during tomato pollen development

Pollen development in flowering plants has strong implications for reproductive success. Pollen DNA can be targeted to improve plant traits for yield and stress tolerance. In this study, we demonstrated that the Mediator subunit CYCLIN-DEPENDENT KINASE 8 (CDK8) is a key modulator of pollen development in tomato (Solanum lycopersicum). SlCDK8 knockout led to significant decreases in pollen viability, fruit yield, and fruit seed number. We also found that SlCDK8 directly interacts with transcription factor TEOSINTE BRANCHED1-CYCLOIDEA-PCF15 (SlTCP15) using yeast two-hybrid screens. We subsequently showed that SlCDK8 phosphorylates Ser 187 of SlTCP15 to promote SlTCP15 stability. Phosphorylated TCP15 directly bound to the TGGGCY sequence in the promoters of DYSFUNCTIONAL TAPETUM 1 (SlDYT1) and MYB DOMAIN PROTEIN 103 (SlMYB103), which are responsible for pollen development. Consistently, disruption of SlTCP15 resembled slcdk8 tomato mutants. In sum, our work identified a new substrate of Mediator CDK8 and revealed an important regulatory role of SlCDK8 in pollen development via cooperation with SlTCP15.

Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses

Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including stress-responsive mechanisms. However, their role in common bean and their response to stressful conditions remain poorly understood. Here, we identified 35 MADS-box gene family members in common bean, with conserved MADS-box domains and other functional domains. Gene duplication events were observed, suggesting the significance of duplication in the evolutionary development of gene families. The analysis of promoter regions revealed diverse elements, including stress-responsive elements, indicating their potential involvement in stress responses. Notably, PvMADS31, a member of the PvMADS-box gene family, demonstrated rapid upregulation under various abiotic stress conditions, including NaCl, polyethylene glycol, drought, and abscisic acid (ABA) treatments. Transgenic plants overexpressing PvMADS31 displayed enhanced lateral root development, root elongation, and seed germination under stress conditions. Furthermore, PvMADS31 overexpression in Arabidopsis resulted in improved drought tolerance, likely attributed to the enhanced scavenging of ROS and increased proline accumulation. These findings suggest that PvMADS31 might play a crucial role in modulating seed germination, root development, and stress responses, potentially through its involvement in auxin and ABA signaling pathways. Overall, this study provides valuable insights into the potential roles of PvMADS-box genes in abiotic stress responses in common bean, offering prospects for crop improvement strategies to enhance resilience under changing environmental conditions.

Transcriptome-Wide Identification of TCP Transcription Factor Family Members in Pinus massoniana and Their Expression in Regulation of Development and in Response to Stress

Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and development processes. At present, TCP TFs have been widely studied in multiple plant species, but research in P. massoniana has not been carried out. In this study, 13 PmTCP TFs were identified from the transcriptomes of P. massoniana. The phylogenetic results revealed that these PmTCP members were divided into two categories: Class I and Class II. Each PmTCP TF contained a conserved TCP domain, and the conserved motif types and numbers were similar in the same subgroup. According to the transcriptional profiling analysis under drought stress conditions, it was found that seven PmTCP genes responded to drought treatment to varying degrees. The qRT-PCR results showed that the majority of PmTCP genes were significantly expressed in the needles and may play a role in the developmental stage. Meanwhile, the PmTCPs could respond to several stresses and hormone treatments at different levels, which may be important for stress resistance. In addition, PmTCP7 and PmTCP12 were nuclear localization proteins, and PmTCP7 was a transcriptional suppressor. These results will help to explore the regulatory factors related to the growth and development of P. massoniana, enhance its stress resistance, and lay the foundation for further exploration of the physiological effects on PmTCPs.

Calceolariaceae809: A bait set for targeted sequencing of nuclear loci

Premise

The genus Calceolaria (Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless and many offer floral oils as a pollination reward collected by specialist bees. Despite their evolutionary and ecological significance, obtaining a resolved phylogeny for the group has proved difficult. To address this challenge, we present a new bait set for targeted sequencing of nuclear loci in Calceolariaceae and close relatives.

Methods

We developed a bioinformatic workflow to use incomplete, low-coverage genomes of 10 Calceolaria species to identify single-copy loci suitable for phylogenetic studies and design baits for targeted sequencing.

Results

Our approach resulted in the identification of 809 single-copy loci (733 noncoding and 76 coding regions) and the development of 39,937 baits, which we validated in silico (10 specimens) and in vitro (29 Calceolariaceae and six outgroups). In both cases, the data allowed us to recover robust phylogenetic estimates.

Discussion

Our results demonstrate the appropriateness of the bait set for sequencing recent and historic specimens of Calceolariaceae and close relatives, and open new doors for further investigation of the evolutionary history of this hyperdiverse genus.

Pseudanthia in angiosperms: a review

BACKGROUND

Pseudanthia or 'false flowers' are multiflowered units that resemble solitary flowers in form and function. Over the last century the term 'pseudanthium' has been applied to a wide array of morphologically divergent blossoms, ranging from those with easily noticeable florets to derived, reduced units in which individual flowers become almost indistinguishable. Although initially admired mostly by botanists, the diversity and widespread distribution of pseudanthia across angiosperms has already made them a fascinating topic for evolutionary and developmental comparative studies.

SCOPE

This review synthesizes historical and current concepts on the biology of pseudanthia. Our first aim is to establish a clear, operational definition of pseudanthium and disentangle common terminological misconceptions surrounding that term. Our second aim is to summarize knowledge of the morphological and developmental diversity of pseudanthia and embed it within a modern phylogenetic framework. Lastly, we want to provide a comprehensive overview on the evolution and ecological importance of pseudanthia and outline perspectives for future studies.

CONCLUSIONS

The understanding of pseudanthia has changed multiple times and reflects three different interpretations of their 'flower-like' qualities: developmental (similarity in structure), figural (similarity in form and function) and phylogenetic (homology between angiosperm flowers and monoecious reproductive shoots in gymnosperms). Here, we propose to narrow the term pseudanthium to multiflowered blossoms resembling zoophilous flowers in form, i.e. in being structurally subdivided in a showy periphery and a reproductive centre. According to this definition, pseudanthia sensu stricto evolved independently in at least 41 angiosperm families. The recurrent acquisition of pseudanthia sensu stricto in all major lineages of flowering plants indicates repeated interactions between developmental constraints (smallness of flowers, meristematic conditions) and selective pressures, such as demands of pollinators and/or environmental conditions.

Genome-Wide Identification and Expression Analysis of the TCP Gene Family Related to Developmental and Abiotic Stress in Ginger

Ginger (Zingiber officinale Roscoe), a widely consumed edible and medicinal plant, possesses significant nutritional and economic value. Abiotic stresses such as drought and low temperatures can impact the growth and development of ginger. The plant-specific transcription factor Teosinte branched1/cycloidea/proliferating cell factor (TCP) has progressively been identified in various plants for its role in regulating plant growth and development as well as conferring resistance to abiotic stresses. However, limited information on the TCP family is available in ginger. In this study, we identified 20 TCP members in the ginger genome, which were randomly distributed across 9 chromosomes. Based on phylogenetic analysis, these ginger TCP were classified into two subfamilies: Class I (PCF) and Class II (CIN, CYC/TB). The classification of the identified ginger TCPs was supported by a multi-species phylogenetic tree and motif structure analysis, suggesting that the amplification of the ginger TCP gene family occurred prior to the differentiation of angiosperms. The promoter region of ginger TCP genes was found to contain numerous cis-acting elements associated with plant growth, development, and abiotic stress response. Among these elements, the stress response element, anaerobic induction, and MYB binding site play a dominant role in drought responsiveness. Additionally, expression pattern analysis revealed variations in the expression of ginger TCP gene among different tissues and in response to diverse abiotic stresses (drought, low temperature, heat, and salt). Our research offers a thorough examination of TCP members within the ginger plant. This analysis greatly contributes to the understanding of how TCP genes regulate tissue development and response to stress, opening up new avenues for further exploration in this field.

Phenotypic plasticity in the monoclonal marbled crayfish is associated with very low genetic diversity but pronounced epigenetic diversity

Clonal organisms are particularly useful to investigate the contribution of epigenetics to phenotypic plasticity, because confounding effects of genetic variation are negligible. In the last decade, the apomictic parthenogenetic marbled crayfish, Procambarus virginalis, has been developed as a model to investigate the relationships between phenotypic plasticity and genetic and epigenetic diversity in detail. This crayfish originated about 30 years ago by autotriploidy from a single slough crayfish Procambarus fallax. As the result of human releases and active spreading, marbled crayfish has established numerous populations in very diverse habitats in 22 countries from the tropics to cold temperate regions. Studies in the laboratory and field revealed considerable plasticity in coloration, spination, morphometric parameters, growth, food preference, population structure, trophic position, and niche width. Illumina and PacBio whole-genome sequencing of marbled crayfish from representatives of 19 populations in Europe and Madagascar demonstrated extremely low genetic diversity within and among populations, indicating that the observed phenotypic diversity and ability to live in strikingly different environments are not due to adaptation by selection on genetic variation. In contrast, considerable differences were found between populations in the DNA methylation patterns of hundreds of genes, suggesting that the environmentally induced phenotypic plasticity is mediated by epigenetic mechanisms and corresponding changes in gene expression. Specific DNA methylation fingerprints persisted in local populations over successive years indicating the existence of epigenetic ecotypes, but there is presently no information as to whether these epigenetic signatures are transgenerationally inherited or established anew in each generation and whether the recorded phenotypic plasticity is adaptive or nonadaptive.

Overexpression of TCP9-like gene enhances salt tolerance in transgenic soybean

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors are a plant-specific family and play roles in plant growth, development, and responses to biotic and abiotic stresses. However, little is known about the functions of the TCP transcription factors in the soybean cultivars with tolerance to salt stress. In this study, TCP9-like, a TCP transcription factor, was identified in the soybean cultivars exposed to salt stress. The expression of TCP9-like gene in the roots of salt-tolerant soybean cultivars was higher than that in salt-sensitive cultivars treated with NaCl. The overexpression of TCP9-like enhanced the salt tolerance of the salt-sensitive soybean cultivar 'DN50'. In T2 generation, the plants with TCP9-like overexpression had significantly lower Na+ accumulation and higher K+ accumulation than the WT plants exposed to 200 or 250 mmol/L NaCl. The K+/Na+ ratio in the plants overexpressing TCP9-like was significantly higher than that in WT plants treated with 200 mmol/L NaCl. Meanwhile, the overexpression of TCP9-like up-regulated the expression levels of GmNHX1, GmNHX3, GmSOS1, GmSOS2-like, and GmHKT1, which were involved in the K+/Na+ homeostasis pathway. The findings indicated that TCP9-like mediated the regulation of both Na+ and K+ accumulation to improve the tolerance of soybean to salt stress.

In-frame mutation in rice TEOSINTE BRANCHED1 (OsTB1) improves productivity under phosphorus deficiency

Tillering is an important trait in rice productivity. We introduced mutations into the coding region of rice TEOSINTE BRANCHED1 (OsTB1), which is a negative regulator of tillering, using CRISPR/Cas9. The frameshift mutants exhibited substantially enhanced tillering and produced 3.5 times more panicles than the non-mutated plants at maturity. This enhanced tillering resulted in increased spikelet number; however, grain yields did not increase due to substantially reduced filled grain rate and 1,000-grain weight. In contrast, in-frame mutations in OsTB1 had the effect of slightly increasing tiller numbers, and the in-frame mutants had 40% more panicles than non-mutated plants. The grain yield of in-frame mutants also did not increase on nutrient-rich soil; however, under phosphorus-deficient conditions, where tillering is constrained, the in-frame mutants gave a significantly higher grain yield than non-mutated plants due to higher spikelet number and maintained filled grain rate. Rice grassy tiller1 (OsGT1)/OsHox12, which is directly regulated by OsTB1 to suppress tillering, was moderately down-regulated in in-frame mutants, suggesting that OsTB1 with the in-frame mutation shows partial function of intact OsTB1 in regulating OsGT1/OsHox12. We propose that mildly enhanced tillering by in-frame mutation of OsTB1 can improve grain yield under low phosphorus conditions.

Reciprocal inhibition of expression between RAV1 and BES1 modulates plant growth and development in Arabidopsis

RAV1 (Related to ABI3/VP1) is a plant-specific B3 and AP2 domain-containing transcription factor that acts as a negative regulator of growth in many plant species. The expression of RAV1 is downregulated by brassinosteroids (BRs); large-scale transcriptome analyses have shown that the expression of RAV1 was previously targeted by BRI1-EMS-SUPPRESOR1 (BES1) and BRASSINAZOLE-RESISTANT1 (BZR1), which are critical transcription factors for the BR-signaling process. Using RAV1-overexpressing transgenic plants, we showed that RAV1 overexpression reduced the BR signaling capacity, resulting in the downregulation of BR biosynthetic genes and BES1 expression. Furthermore, we demonstrated that BES1, not BZR1, is directly bound to the RAV1 promoter and repressed RAV1 expression, and vice versa; RAV1 is also bound to the BES1 promoter and repressed BES1 expression. This mutual inhibition was specific to RAV1 and BES1 because RAV1 exhibited binding activity to the BZR1 promoter but did not repress BZR1 expression. We observed that constitutively activated BR signaling phenotypes in bes1-D were attenuated by the repression of endogenous BES1 expression in transgenic bes1-D plants overexpressing RAV1. RNA-sequencing analysis of RAV1-overexpressing transgenic plants and bes1-D mutant plants revealed differentially expressed genes by RAV1 and BES1 and genes that were oppositely co-regulated by RAV1 and BES1. RAV1 and BES1 regulated different transcriptomes but co-regulated a specific set of genes responsible for the balance between growth and defense. These results suggested that the mutual inhibitory transcriptional activities of RAV1 and BES1 provide fine regulatory mechanisms for plant growth and development.

TCP Transcription Factors in Plant Reproductive Development: Juggling Multiple Roles

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors (TFs) are plant-specific transcriptional regulators exerting multiple functions in plant growth and development. Ever since one of the founding members of the family was described, encoded by the CYCLOIDEA (CYC) gene from Antirrhinum majus and involved in the regulation of floral symmetry, the role of these TFs in reproductive development was established. Subsequent studies indicated that members of the CYC clade of TCP TFs were important for the evolutionary diversification of flower form in a multitude of species. In addition, more detailed studies of the function of TCPs from other clades revealed roles in different processes related to plant reproductive development, such as the regulation of flowering time, the growth of the inflorescence stem, and the correct growth and development of flower organs. In this review, we summarize the different roles of members of the TCP family during plant reproductive development as well as the molecular networks involved in their action.

GmTCP and GmNLP Underlying Nodulation Character in Soybean Depending on Nitrogen

Soybean is a cereal crop with high protein and oil content which serves as the main source of plant-based protein and oil for human consumption. The symbiotic relationship between legumes and rhizobia contributes significantly to soybean yield and quality, but the underlying molecular mechanisms remain poorly understood, hindering efforts to improve soybean productivity. In this study, we conducted a transcriptome analysis and identified 22 differentially expressed genes (DEGs) from nodule-related quantitative trait loci (QTL) located in chromosomes 12 and 19. Subsequently, we performed functional characterisation and haplotype analysis to identify key candidate genes among the 22 DEGs that are responsive to nitrate. Our findings identified GmTCP (TEOSINTE-BRANCHED1/CYCLOIDEA/PCF) and GmNLP (NIN-LIKE PROTEIN) as the key candidate genes that regulate the soybean nodule phenotype in response to nitrogen concentration. We conducted homologous gene mutant analysis in Arabidopsis thaliana, which revealed that the homologous genes of GmTCP and GmNLP play a vital role in regulating root development in response to nitrogen concentration. We further performed overexpression and gene knockout of GmTCP and GmNLP through hairy root transformation in soybeans and analysed the effects of GmTCP and GmNLP on nodulation under different nitrogen concentrations using transgenic lines. Overexpressing GmTCP and GmNLP resulted in significant differences in soybean hairy root nodulation phenotypes, such as nodule number (NN) and nodule dry weight (NDW), under varying nitrate conditions. Our results demonstrate that GmTCP and GmNLP are involved in regulating soybean nodulation in response to nitrogen concentration, providing new insights into the mechanism of soybean symbiosis establishment underlying different nitrogen concentrations.

Genome-Wide Identification, Characterization, and Expression of TCP Genes Family in Orchardgrass

Plant-specific TCP transcription factors regulate several plant growth and development processes. Nevertheless, little information is available about the TCP family in orchardgrass (Dactylis glomerata L.). This study identified 22 DgTCP transcription factors in orchardgrass and determined their structure, phylogeny, and expression in different tissues and developmental stages. The phylogenetic tree classified the DgTCP gene family into two main subfamilies, including class I and II supported by the exon-intron structure and conserved motifs. The DgTCP promoter regions contained various cis-elements associated with hormones, growth and development, and stress responses, including MBS (drought inducibility), circadian (circadian rhythms), and TCA-element (salicylic acid responsiveness). Moreover, DgTCP9 possibly regulates tillering and flowering time. Additionally, several stress treatments upregulated DgTCP1, DgTCP2, DgTCP6, DgTCP12, and DgTCP17, indicting their potential effects regarding regulating responses to the respective stress. This research offers a valuable basis for further studies of the TCP gene family in other Gramineae and reveals new ideas for increasing gene utilization.

SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants

SPINDLY (SPY) is a novel nucleocytoplasmic protein O-fucosyltransferase that regulates target protein activity or stability via O-fucosylation of specific Ser/Thr residues. Previous genetic studies indicate that AtSPY regulates plant development during vegetative and reproductive growth by modulating gibberellin and cytokinin responses. AtSPY also regulates the circadian clock and plant responses to biotic and abiotic stresses. The pleiotropic phenotypes of spy mutants point to the likely role of AtSPY in regulating key proteins functioning in diverse cellular pathways. However, very few AtSPY targets are known. Here, we identified 88 SPY targets from Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana via the purification of O-fucosylated peptides using Aleuria aurantia lectin followed by electron transfer dissociation-MS/MS analysis. Most AtSPY targets were nuclear proteins that function in DNA repair, transcription, RNA splicing, and nucleocytoplasmic transport. Cytoplasmic AtSPY targets were involved in microtubule-mediated cell division/growth and protein folding. A comparison with the published O-linked-N-acetylglucosamine (O-GlcNAc) proteome revealed that 30% of AtSPY targets were also O-GlcNAcylated, indicating that these distinct glycosylations could co-regulate many protein functions. This study unveiled the roles of O-fucosylation in modulating many key nuclear and cytoplasmic proteins and provided a valuable resource for elucidating the regulatory mechanisms involved.

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and the modulation of different hormonal pathways. They are divided into two main classes, I and II. This review focuses on the function and regulation of class I TCP proteins (TCPs). We describe the role of class I TCPs in cell growth and proliferation and summarize recent progresses in understanding the function of class I TCPs in diverse developmental processes, defense, and abiotic stress responses. In addition, their function in redox signaling and the interplay between class I TCPs and proteins involved in immunity and transcriptional and posttranslational regulation is discussed.

Genome-wise association study identified genomic regions associated with drought tolerance in mungbean (Vigna radiata (L.) R. Wilczek)

A total of 282 mungbean accessions were resequenced to identify genome-wide variants and construct a highly precise variant map, and drought tolerance-related loci and superior alleles were identified by GWAS. Mungbean (Vigna radiata (L.) R. Wilczek) is an important food legume crop that is highly adapted to drought environments, but severe drought significantly curtails mungbean production. Here, we resequenced 282 mungbean accessions to identify genome-wide variants and constructed a highly precise map of mungbean variants. A genome-wide association study was performed to identify genomic regions for 14 drought tolerance-related traits in plants grown under stress and well-watered conditions over three years. One hundred forty-six SNPs associated with drought tolerance were detected, and 26 candidate loci associated with more than two traits were subsequently selected. Two hundred fifteen candidate genes were identified at these loci, including eleven transcription factor genes, seven protein kinase genes and other protein coding genes that may respond to drought stress. Furthermore, we identified superior alleles that were associated with drought tolerance and positively selected during the breeding process. These results provide valuable genomic resources for molecular breeding and will accelerate future efforts aimed at mungbean improvement.

Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms

As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.

The N-terminal region located upstream of the TCP domain is responsible for the antagonistic action of the Arabidopsis thaliana TCP8 and TCP23 transcription factors on flowering time

TCP proteins (TCPs) are plant-exclusive transcription factors that exert effects on multiple aspects of plant development, from germination to flower and fruit formation. TCPs are divided into two main classes, I and II. In this study, we found that the Arabidopsis thaliana class I TCP transcription factor TCP8 is a positive regulator of flowering time. TCP8 mutation and constitutive expression delayed and accelerated flowering, respectively. Accordingly, TCP8 mutant plants showed a delay in the maximum expression of FT and reduced SOC1 transcript levels, while plants overexpressing TCP8 presented increased transcript levels of both genes. Notably, the related class I protein TCP23 showed the opposite behavior, since TCP23 mutation and overexpression accelerated and retarded flowering, respectively. To elucidate the molecular basis of these differences, we analyzed TCP8 and TCP23 comparatively. We found that both proteins are able to physically interact and bind class I TCP motifs, but only TCP8 shows transcriptional activation activity when expressed in plants, which is negatively affected by TCP23. From the analysis of plants expressing different chimeras between the TCPs, we found that the N-terminal region located upstream of the TCP domain is responsible for the opposite effect that TCP8 and TCP23 exert over flowering time and regulation of FT and SOC1 expression. These results suggest that structural features outside the TCP domain modulate the specificity of action of class I TCPs.

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.

Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics

Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".

A spatiotemporal transcriptomic network dynamically modulates stalk development in maize

Maize (Zea mays) is an important cereal crop with suitable stalk formation which is beneficial for acquiring an ideal agronomic trait to resist lodging and higher planting density. The elongation pattern of stalks arises from the variable growth of individual internodes driven by cell division and cell expansion comprising the maize stalk. However, the spatiotemporal dynamics and regulatory network of the maize stalk development and differentiation process remain unclear. Here, we report spatiotemporally resolved transcriptomes using all internodes of the whole stalks from developing maize at the elongation and maturation stages. We identified four distinct groups corresponding to four developmental zones and nine specific clusters with diverse spatiotemporal expression patterns among individual internodes of the stalk. Through weighted gene coexpression network analysis, we constructed transcriptional regulatory networks at a fine spatiotemporal resolution and uncovered key modules and candidate genes involved in internode maintenance, elongation, and division that determine stalk length and thickness in maize. Further CRISPR/Cas9-mediated knockout validated the function of a cytochrome P450 gene, ZmD1, in the regulation of stalk length and thickness as predicted by the WGCN. Collectively, these results provide insights into the high genetic complexity of stalk development and the potentially valuable resources with ideal stalk lengths and widths for genetic improvements in maize.

Modulating Expression Levels of TCP Transcription Factors by Mentha x piperita Volatiles-An Allelopathic Tool to Influence Leaf Growth?

Peppermint (Mentha x piperita) is a species with inhibitory allelopathic properties due to its high amounts of terpenes. Recent studies have disclosed dosage dependent growth promotion or defense reactions in plants when facing appropriate amounts of Mentha bouquet terpenes. These positive effects could be of interest for agricultural applications. To obtain more insights into leaf growth modulations, the expression of Arabidopsis and Brassica rapa TCP transcription factors were studied after fumigation with M. x piperita bouquets (Arabidopsis), with M. x piperita essential oil or with limonene (Arabidopsis and Chinese cabbage). According to qPCR studies, expression of TCP3, TCP24, and TCP20 were downregulated by all treatments in Arabidopsis, leading to altered leaf growth. Expressions of B. rapa TCPs after fumigation with the essential oil or limonene were less affected. Extensive greenhouse and polytunnel trials with white cabbage and Mentha plants showed that the developmental stage of the leaves, the dosage, and the fumigation time are of crucial importance for changed fresh and dry weights. Although further research is needed, the study may contribute to a more intensive utilization of ecologically friendly and species diversity conservation and positive allelopathic interactions in future agricultural systems.

Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations

Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.

Comparative genomic investigation of TCP gene family in eggplant (Solanum melongena L.) and expression analysis under divergent treatments

The putative TCP genes and their responses to abiotic stress in eggplant were comprehensively characterized, and SmTCP genes (Smechr0202855.1 and Smechr0602431.1) may be involved in anthocyanin synthesis. The Teosinte branched1/Cycloidea/Proliferating cell factors (TCPs), a family of plant-specific transcription factors, plays paramount roles in a plethora of developmental and physiological processes. We here systematically characterized putative TCP genes and their response to abiotic stress in eggplant. In total, 30 SmTCP genes were categorized into two subfamilies based on the classical TCP conserved domains. Chromosomal location analysis illustrated the random distribution of putative SmTCP genes along 12 eggplant chromosomes. Cis-acting elements and miRNA target prediction suggested that versatile and complicated regulatory mechanisms that control SmTCPs gene expression, and 3 miRNAs (miR319a, miR319b, and miR319c-3p) might act as major regulators targeting SmTCPs. Tissue expression profiles indicated divergent spatiotemporal expression patterns of SmTCPs. qRT-PCR assays demonstrated different expression profiles of SmTCP under 4 °C, drought and ABA treatment conditions, suggesting the possible participation of SmTCP genes in multiple signaling pathways. Furthermore, RNA-seq data of eggplant anthocyanin synthesis coupled with yeast one-hybrid and dual-luciferase assays suggested the involvement of SmTCP genes (Smechr0202855.1 and Smechr0602431.1) in the mediation of anthocyanin synthesis. Our study will facilitate further investigation on the putative functional characterization of eggplant TCP genes and lay a solid foundation for the in-depth study of the involvement of SmTCP genes in the regulation of anthocyanin synthesis.

miR319-Regulated TCP3 Modulates Silique Development Associated with Seed Shattering in Brassicaceae

Seed shattering is an undesirable trait that leads to crop yield loss. Improving silique resistance to shattering is critical for grain and oil crops. In this study, we found that miR319-targeted TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR (TCPs) inhibited the process of post-fertilized fruits (silique) elongation and dehiscence via regulation of FRUITFULL (FUL) expression in Arabidopsis thaliana and Brassica napus. AtMIR319a activation resulted in a longer silique with thickened and lignified replum, whereas overexpression of an miR319a-resistant version of AtTCP3 (mTCP3) led to a short silique with narrow and less lignified replum. Further genetic and expressional analysis suggested that FUL acted downstream of TCP3 to negatively regulate silique development. Moreover, hyper-activation of BnTCP3.A8, a B. napus homolog of AtTCP3, in rapeseed resulted in an enhanced silique resistance to shattering due to attenuated replum development. Taken together, our findings advance our knowledge of TCP-regulated silique development and provide a potential target for genetic manipulation to reduce silique shattering in Brassica crops.

The TCP transcription factor HvTB2 heterodimerizes with VRS5 and controls spike architecture in barley

Understanding the molecular network, including protein-protein interactions, of VRS5 provide new routes towards the identification of other key regulators of plant architecture in barley. The TCP transcriptional regulator TEOSINTE BRANCHED 1 (TB1) is a key regulator of plant architecture. In barley, an important cereal crop, HvTB1 (also referred to as VULGARE SIX-ROWED spike (VRS) 5), inhibits the outgrowth of side shoots, or tillers, and grains. Despite its key role in barley development, there is limited knowledge on the molecular network that is utilized by VRS5. In this work, we performed protein-protein interaction studies of VRS5. Our analysis shows that VRS5 potentially interacts with a diverse set of proteins, including other class II TCP's, NF-Y TF, but also chromatin remodelers. Zooming in on the interaction capacity of VRS5 with other TCP TFs shows that VRS5 preferably interacts with other class II TCP TFs in the TB1 clade. Induced mutagenesis through CRISPR-Cas of one of the putative VRS5 interactors, HvTB2 (also referred to as COMPOSITUM 1 and BRANCHED AND INDETERMINATE SPIKELET 1), resulted in plants that have lost their characteristic unbranched spike architecture. More specifically, hvtb2 mutants exhibited branches arising at the main spike, suggesting that HvTB2 acts as inhibitor of branching. Our protein-protein interaction studies of VRS5 resulted in the identification of HvTB2 as putative interactor of VRS5, another key regulator of spike architecture in barley. The study presented here provides a first step to underpin the protein-protein interactome of VRS5 and to identify other, yet unknown, key regulators of barley plant architecture.

Complex developmental and transcriptional dynamics underlie pollinator-driven evolutionary transitions in nectar spur morphology in Aquilegia (columbine)

PREMISE

Determining the developmental programs underlying morphological variation is key to elucidating the evolutionary processes that generated the stunning biodiversity of the angiosperms. Here, we characterized the developmental and transcriptional dynamics of the elaborate petal nectar spur of Aquilegia (columbine) in species with contrasting pollination syndromes and spur morphologies.

METHODS

We collected petal epidermal cell number and length data across four Aquilegia species, two with short, curved nectar spurs of the bee-pollination syndrome and two with long, straight spurs of the hummingbird-pollination syndrome. We also performed RNA-seq on A. brevistyla (bee) and A. canadensis (hummingbird) distal and proximal spur compartments at multiple developmental stages. Finally, we intersected these data sets with a previous QTL mapping study on spur length and shape to identify new candidate loci.

RESULTS

The differential growth between the proximal and distal surfaces of curved spurs is primarily driven by differential cell division. However, independent transitions to straight spurs in the hummingbird syndrome have evolved by increasing differential cell elongation between spur surfaces. The RNA-seq data reveal these tissues to be transcriptionally distinct and point to auxin signaling as being involved with the differential cell elongation responsible for the evolution of straight spurs. We identify several promising candidate genes for future study.

CONCLUSIONS

Our study, taken together with previous work in Aquilegia, reveals the complexity of the developmental mechanisms underlying trait variation in this system. The framework we established here will lead to exciting future work examining candidate genes and processes involved in the rapid radiation of the genus.

In-Silico Study of Brassinosteroid Signaling Genes in Rice Provides Insight Into Mechanisms Which Regulate Their Expression

Brassinosteroids (BRs) regulate a diverse spectrum of processes during plant growth and development and modulate plant physiology in response to environmental fluctuations and stress factors. Thus, the BR signaling regulators have the potential to be targeted for gene editing to optimize the architecture of plants and make them more resilient to environmental stress. Our understanding of the BR signaling mechanism in monocot crop species is limited compared to our knowledge of this process accumulated in the model dicot species - Arabidopsis thaliana. A deeper understanding of the BR signaling and response during plant growth and adaptation to continually changing environmental conditions will provide insight into mechanisms that govern the coordinated expression of the BR signaling genes in rice (Oryza sativa) which is a model for cereal crops. Therefore, in this study a comprehensive and detailed in silico analysis of promoter sequences of rice BR signaling genes was performed. Moreover, expression profiles of these genes during various developmental stages and reactions to several stress conditions were analyzed. Additionally, a model of interactions between the encoded proteins was also established. The obtained results revealed that promoters of the 39 BR signaling genes are involved in various regulatory mechanisms and interdependent processes that influence growth, development, and stress response in rice. Different transcription factor-binding sites and cis-regulatory elements in the gene promoters were identified which are involved in regulation of the genes’ expression during plant development and reactions to stress conditions. The in-silico analysis of BR signaling genes in O. sativa provides information about mechanisms which regulate the coordinated expression of these genes during rice development and in response to other phytohormones and environmental factors. Since rice is both an important crop and the model species for other cereals, this information may be important for understanding the regulatory mechanisms that modulate the BR signaling in monocot species. It can also provide new ways for the plant genetic engineering technology by providing novel potential targets, either cis-elements or transcriptional factors, to create elite genotypes with desirable traits.

OsbHLHq11, the Basic Helix-Loop-Helix Transcription Factor, Involved in Regulation of Chlorophyll Content in Rice

Photosynthesis is an important factor in determining the yield of rice. In particular, the size and efficiency of the photosynthetic system after the heading has a great impact on the yield. Research related to high-efficiency photosynthesis is essential to meet the growing demands of crops for the growing population. Chlorophyll is a key molecule in photosynthesis, a pigment that acts as an antenna to absorb light energy. Improvement of chlorophyll content characteristics has been emphasized in rice breeding for several decades. It is expected that an increase in chlorophyll content may increase photosynthetic efficiency, and understanding the genetic basis involved is important. In this study, we measured leaf color (CIELAB), chlorophyll content (SPAD), and chlorophyll fluorescence, and quantitative trait loci (QTL) mapping was performed using 120 Cheongcheong/Nagdong double haploid (CNDH) line after the heading date. A major QTL related to chlorophyll content was detected in the RM26981-RM287 region of chromosome 11. OsbHLHq11 was finally selected through screening of genes related to chlorophyll content in the RM26981-RM287 region. The relative expression level of the gene of OsbHLHq11 was highly expressed in cultivars with low chlorophyll content, and is expected to have a similar function to BHLH62 of the Gramineae genus. OsbHLHq11 is expected to increase photosynthetic efficiency by being involved in the chlorophyll content, and is expected to be utilized as a new genetic resource for breeding high-yield rice.

Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots

Herbicides are key weed-control tools, but their repeated use across large areas has favored the evolution of herbicide resistance. Although target-site has been the most prevalent and studied type of resistance, non-target-site resistance (NTSR) is increasing. However, the genetic factors involved in NTSR are widely unknown. In this study, four gene groups encoding putative NTSR enzymes, namely, cytochrome-P450, glutathione-S-transferase (GST), uridine 5'-diphospho-glucuronosyltransferase (UDPGT), and nitronate monooxygenase (NMO) were analyzed. The monocot and dicot gene sequences were downloaded from publicly available databases. Phylogenetic trees revealed that most of the CYP450 resistance-related sequences belong to CYP81 (5), and in GST, most of the resistance sequences belonged to GSTU18 (9) and GSTF6 (8) groups. In addition, the study of upstream promoter sequences of these NTSR genes revealed stress-related cis-regulatory motifs, as well as eight transcription factor binding sites (TFBS) were identified. The discovered TFBS were commonly present in both monocots and dicots, and the identified motifs are known to play key roles in countering abiotic stress. Further, we predicted the 3D structure for the resistant CYP450 and GST protein and identified the substrate recognition site through the homology approach. Our description of putative NTSR enzymes may be used to develop innovative weed control techniques to delay the evolution of NTSR.

Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum (CER) Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

Plant surfaces are covered with cuticle wax and are the first barrier between a plant and environmental stresses. Eceriferum (CER) is an important gene family involved in wax biosynthesis and stress resistance. In this study, for the first time, 34 CER genes were identified in the passion fruit (Passiflora edulis) genome, and PeCER proteins varied in physicochemical properties. A phylogenetic tree was constructed and divided into seven clades to identify the evolutionary relationship with other plant species. Gene structure analyses revealed that conserved motifs ranged from 1 to 24, and that exons ranged from 1 to 29. The cis-element analysis provides insight into possible roles of PeCER genes in plant growth, development and stress responses. The syntenic analysis revealed that segmental (six gene pairs) and tandem (six gene pairs) gene duplication played an important role in the expansion of PeCER genes and underwent a strong purifying selection. In addition, 12 putative ped-miRNAs were identified to be targeting 16 PeCER genes, and PeCER6 was the most targeted by four miRNAs including ped-miR157a-5p, ped-miR164b-5p, ped-miR319b, and ped-miR319l. Potential transcription factors (TFs) such as ERF, AP2, MYB, and bZIP were predicted and visualized in a TF regulatory network interacting with PeCER genes. GO and KEGG annotation analysis revealed that PeCER genes were highly related to fatty acid, cutin, and wax biosynthesis, plant-pathogen interactions, and stress response pathways. The hypothesis that most PeCER proteins were predicted to localize to the plasma membrane was validated by transient expression assays of PeCER32 protein in onion epidermal cells. qRT-PCR expression results showed that most of the PeCER genes including PeCER1, PeCER11, PeCER15, PeCER17, and PeCER32 were upregulated under drought and Fusarium kyushuense stress conditions compared to controls. These findings provide a foundation for further studies on functions of PeCER genes to further facilitate the genetic modification of passion fruit wax biosynthesis and stress resistance.

CRISPR/Cas9-mediated targeted mutagenesis of GmTCP19L increasing susceptibility to Phytophthora sojae in soybean

The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors is one of the superfamilies of plant-specific transcription factors involved in plant growth, development, and biotic and abiotic stress. However, there is no report on the research of the TCP transcription factors in soybean response to Phytophthora sojae. In this study, Agrobacterium-mediated transformation was used to introduce the CRISPR/Cas9 expression vector into soybean cultivar "Williams 82" and generated targeted mutants of GmTCP19L gene, which was previously related to involve in soybean responses to P. sojae. We obtained the tcp19l mutants with 2-bp deletion at GmTCP19L coding region, and the frameshift mutations produced premature translation termination codons and truncated GmTCP19L proteins, increasing susceptibility to P. sojae in the T2-generation. These results suggest that GmTCP19L encodes a TCP transcription factor that affects plant defense in soybean. The new soybean germplasm with homozygous tcp19l mutations but the BAR and Cas9 sequences were undetectable using strip and PCR methods, respectively, suggesting directions for the breeding or genetic engineering of disease-resistant soybean plants.

Systematic analysis and expression profiles of TCP gene family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stress

Background

As transcription factors, the TCP genes are considered to be promising targets for crop enhancement for their responses to abiotic stresses. However, information on the systematic characterization and functional expression profiles under abiotic stress of TCPs in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is limited.

Results

In this study, we identified 26 FtTCPs and named them according to their position on the chromosomes. Phylogenetic tree, gene structure, duplication events, and cis-acting elements were further studied and syntenic analysis was conducted to explore the bioinformatic traits of the FtTCP gene family. Subsequently, 12 FtTCP genes were selected for expression analysis under cold, dark, heat, salt, UV, and waterlogging (WL) treatments by qRT-PCR. The spatio-temporal specificity, correlation analysis of gene expression levels and interaction network prediction revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stresses. Moreover, subcellular localization confirmed that FtTCP15 and FtTCP18 localized in the nucleus function as transcription factors.

Conclusions

In this research, 26 TCP genes were identified in Tartary buckwheat, and their structures and functions have been systematically explored. Our results reveal that the FtTCP15 and FtTCP18 have special cis-elements in response to abiotic stress and conserved nature in evolution, indicating they could be promising candidates for further functional verification under multiple abiotic stresses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08618-1.

Genome evolution and diversity of wild and cultivated potatoes

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production^1-4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.

Differential gene expression in tall fescue tissues in response to water deficit

Tall fescue (Festuca arundinacea Schreb.) is a popular pasture and turf grass particularly known for drought resistance, allowing for its persistence in locations that are unfavorable for other cool-season grasses. Also, its seed-borne fungal symbiont (endophyte) Epichloë coenophiala, which resides in the crown and pseudostem, can be a contributing factor in its drought tolerance. Because it contains the apical meristems, crown survival under drought stress is critical to plant survival as well as the endophyte. In this study, we subjected tall fescue plants with their endophyte to water-deficit stress or, as controls with normal watering, then compared plant transcriptome responses in four vegetative tissues: leaf blades, pseudostem, crown, and roots. A transcript was designated a differentially expressed gene (DEG) if it exhibited at least a twofold expression difference between stress and control samples with an adjusted p value of .001. Pathway analysis of the DEGs across all tissue types included photosynthesis, carbohydrate metabolism, phytohormone biosynthesis and signaling, cellular organization, and a transcriptional regulation. While no specific pathway was observed to be differentially expressed in the crown, genes encoding auxin response factors, nuclear pore anchors, structural maintenance of chromosomes, and class XI myosin proteins were more highly differentially expressed in crown than in the other vegetative tissues, suggesting that regulation in expression of these genes in the crown may aid in survival of the meristems in the crown.

Passiflora organensis FT/TFL1 gene family and their putative roles in phase transition and floral initiation

Comprehensive analysis of the FT/TFL1 gene family in Passiflora organensis results in understanding how these genes might be involved in the regulation of the typical plant architecture presented by Passiflora species. Passion fruit (Passiflora spp) is an economic tropical fruit crop, but there is hardly any knowledge available about the molecular control of phase transition and flower initiation in this species. The florigen agent FLOWERING LOCUS T (FT) interacts with the bZIP protein FLOWERING LOCUS D (FD) to induce flowering in the model species Arabidopsis thaliana. Current models based on research in rice suggest that this interaction is bridged by 14-3-3 proteins. We identified eight FT/TFL1 family members in Passiflora organensis and characterized them by analyzing their phylogeny, gene structure, expression patterns, protein interactions and putative biological roles by heterologous expression in Arabidopsis. PoFT was highest expressed during the adult vegetative phase and it is supposed to have an important role in flowering induction. In contrast, its paralogs PoTSFs were highest expressed in the reproductive phase. While ectopic expression of PoFT in transgenic Arabidopsis plants induced early flowering and inflorescence determinacy, the ectopic expression of PoTSFa caused a delay in flowering. PoTFL1-like genes were highest expressed during the juvenile phase and their ectopic expression caused delayed flowering in Arabidopsis. Our protein-protein interaction studies indicate that the flowering activation complexes in Passiflora might deviate from the hexameric complex found in the model system rice. Our results provide insights into the potential functions of FT/TFL1 gene family members during floral initiation and their implications in the special plant architecture of Passiflora species, contributing to more detailed studies on the regulation of passion fruit reproduction.

Paradigm shifts in animal epigenetics: Research on non-model species leads to new insights into dependencies, functions and inheritance of DNA methylation

Recent investigations with non-model species and whole-genome approaches have challenged several paradigms in animal epigenetics. They revealed that epigenetic variation in populations is not the mere consequence of genetic variation, but is a semi-independent or independent source of phenotypic variation, depending on mode of reproduction. DNA methylation is not positively correlated with genome size and phylogenetic position as earlier believed, but has evolved differently between and within higher taxa. Epigenetic marks are usually not completely erased in the zygote and germ cells as generalized from mouse, but often persist and can be transgenerationally inherited, making them evolutionarily relevant. Gene body methylation and promoter methylation are similar in vertebrates and invertebrates with well methylated genomes but transposon silencing through methylation is variable. The new data also suggest that animals use epigenetic mechanisms to cope with rapid environmental changes and to adapt to new environments. The main benefiters are asexual populations, invaders, sessile taxa and long-lived species.

Novel QTL Associated with Aerenchyma-Mediated Radial Oxygen Loss (ROL) in Rice (Oryza sativa L.) under Iron (II) Sulfide

In rice, high radial oxygen loss (ROL) has been associated with the reduction in the activity of methanogens, therefore reducing the formation of methane (CH₄) due to the abundance in application of nitrogen (N)-rich fertilizers. In this study, we evaluated the root growth behavior and ROL rate of a doubled haploid (DH) population (n = 117) and parental lines 93-11 (P1, indica) and Milyang352 (P2, japonica) in response to iron (II) sulfide (FeS). In addition, we performed a linkage mapping and quantitative trait locus (QTL) analysis on the same population for the target traits. The results of the phenotypic evaluation revealed that parental lines had distinctive root growth and ROL patterns, with 93-11 (indica) and Milyang352 (japonica) showing low and high ROL rates, respectively. This was also reflected in their derived population, indicating that 93.2% of the DH lines exhibited a high ROL rate and about 6.8% had a low ROL pattern. Furthermore, the QTL and linkage map analysis detected two QTLs associated with the control of ROL and root area on chromosomes 2 (qROL-2-1, 127 cM, logarithm of the odds (LOD) 3.04, phenotypic variation explained (PVE) 11.61%) and 8 (qRA-8-1, 97 cM, LOD 4.394, PVE 15.95%), respectively. The positive additive effect (2.532) of qROL-2-1 indicates that the allele from 93-11 contributed to the observed phenotypic variation for ROL. The breakthrough is that the qROL-2-1 harbors genes proposed to be involved in stress signaling, defense response mechanisms, and transcriptional regulation, among others. The qPCR results revealed that the majority of genes harbored by the qROL-2-1 recorded a higher transcript accumulation level in Milyang352 over time compared to 93-11. Another set of genes exhibited a high transcript abundance in P1 compared to P2, while a few were differentially regulated between both parents. Therefore, OsTCP7 and OsMYB21, OsARF8 genes encoding transcription factors (TFs), coupled with OsTRX, OsWBC8, and OsLRR2 are suggested to play important roles in the positive regulation of ROL in rice. However, the recorded differential expression of OsDEF7 and OsEXPA, and the decrease in OsNIP2, Oscb5, and OsPLIM2a TF expression between parental lines proposes them as being involved in the control of oxygen flux level in rice roots.

Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication

The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family proteins are plant-specific transcription factors that have been well-acknowledged for designing the architectures of plant branch, shoot, and inflorescence. However, evidence for their innovation and emerging role in abiotic stress has been lacking. In this study, we identified a total of 36 TCP genes in Populus trichocarpa, 50% more than that in Arabidopsis (i.e., 24). Comparative intra-genomes showed that such significant innovation was mainly due to the most recent whole genome duplication (rWGD) in Populus lineage around Cretaceous-Paleogene (K-Pg) boundary after the divergence from Arabidopsis. Transcriptome analysis showed that the expressions of PtrTCP genes varied among leaf, stem, and root, and they could also be elaborately regulated by abiotic stresses (e.g., cold and salt). Moreover, co-expression network identified a cold-associated regulatory module including PtrTCP31, PtrTCP10, and PtrTCP36. Of them, PtrTCP10 was rWGD-duplicated from PtrTCP31 and evolved a strong capability of cold induction, which might suggest a neofunctionalization of PtrTCP genes and contribute to the adaptation of Populus lineage during the Cenozoic global cooling. Evidentially, overexpression of PtrTCP10 into Arabidopsis increased freezing tolerance and salt susceptibility. Integrating co-expression network and cis-regulatory element analysis confirmed that PtrTCP10 can regulate the well-known cold- and salt-relevant genes (e.g., ZAT10, GolS2, and SOS1), proving that PtrTCP10 is an evolutionary innovation in P. trichocarpa response to environmental changes. Altogether, our results provide evidence of the rWGD in P. trichocarpa responsible for the innovation of PtrTCP genes and their emerging roles in environmental stresses.

Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication

The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family proteins are plant-specific transcription factors that have been well-acknowledged for designing the architectures of plant branch, shoot, and inflorescence. However, evidence for their innovation and emerging role in abiotic stress has been lacking. In this study, we identified a total of 36 TCP genes in Populus trichocarpa, 50% more than that in Arabidopsis (i.e., 24). Comparative intra-genomes showed that such significant innovation was mainly due to the most recent whole genome duplication (rWGD) in Populus lineage around Cretaceous-Paleogene (K-Pg) boundary after the divergence from Arabidopsis. Transcriptome analysis showed that the expressions of PtrTCP genes varied among leaf, stem, and root, and they could also be elaborately regulated by abiotic stresses (e.g., cold and salt). Moreover, co-expression network identified a cold-associated regulatory module including PtrTCP31, PtrTCP10, and PtrTCP36. Of them, PtrTCP10 was rWGD-duplicated from PtrTCP31 and evolved a strong capability of cold induction, which might suggest a neofunctionalization of PtrTCP genes and contribute to the adaptation of Populus lineage during the Cenozoic global cooling. Evidentially, overexpression of PtrTCP10 into Arabidopsis increased freezing tolerance and salt susceptibility. Integrating co-expression network and cis-regulatory element analysis confirmed that PtrTCP10 can regulate the well-known cold- and salt-relevant genes (e.g., ZAT10, GolS2, and SOS1), proving that PtrTCP10 is an evolutionary innovation in P. trichocarpa response to environmental changes. Altogether, our results provide evidence of the rWGD in P. trichocarpa responsible for the innovation of PtrTCP genes and their emerging roles in environmental stresses.

Functional Antagonism of WRI1 and TCP20 Modulates GH3.3 Expression to Maintain Auxin Homeostasis in Roots

Auxin is a well-studied phytohormone, vital for diverse plant developmental processes. The GH3 genes are one of the major auxin responsive genes, whose expression changes lead to modulation of plant development and auxin homeostasis. However, the transcriptional regulation of these GH3 genes remains largely unknown. WRI1 is an essential transcriptional regulator governing plant fatty acid biosynthesis. Recently, we identified that the expression of GH3.3 is increased in the roots of wri1-1 mutant. Nevertheless, in this study we found that AtWRI1 did not activate or repress the promoter of GH3.3 (proGH3.3) despite of its binding to proGH3.3. Cross-family transcription factor interactions play pivotal roles in plant gene regulatory networks. To explore the molecular mechanism by which WRI1 controls GH3.3 expression, we screened an Arabidopsis transcription factor library and identified TCP20 as a novel AtWRI1-interacting regulator. The interaction between AtWRI1 and TCP20 was further verified by several approaches. Importantly, we found that TCP20 directly regulates GH3.3 expression via binding to TCP binding element. Furthermore, AtWRI1 repressed the TCP20-mediated transactivation of proGH3.3. EMSAs demonstrated that AtWRI1 antagonized TCP20 from binding to proGH3.3. Collectively, we provide new insights that WRI1 attenuates GH3.3 expression through interaction with TCP20, highlighting a new mechanism that contributes to fine-tuning auxin homeostasis.