Transcription Factor Gene Family Research Articles

Crop reproductive meristems in the genomic era: a brief overview.

Modulation of traits beneficial for cultivation and yield is one of the main goals of crop improvement. One of the targets for enhancing productivity is changing the architecture of inflorescences since in many species it determines fruit and seed yield. Inflorescence shape and organization is genetically established during the early stages of reproductive development and depends on the number, arrangement, activities, and duration of meristems during the reproductive phase of the plant life cycle. Despite the variety of inflorescence architectures observable in nature, many key aspects of inflorescence development are conserved among different species. For instance, the genetic network in charge of specifying the identity of the different reproductive meristems, which can be indeterminate or determinate, seems to be similar among distantly related species. The availability of a large number of published transcriptomic datasets for plants with different inflorescence architectures, allowed us to identify transcription factor gene families that are differentially expressed in determinate and indeterminate reproductive meristems. The data that we review here for Arabidopsis, rice, barley, wheat, and maize, particularly deepens our knowledge of their involvement in meristem identity specification.

Transcriptome-wide analysis of the AP2/ERF transcription factor gene family involved in the regulation of gypenoside biosynthesis in Gynostemma pentaphyllum

Gynostemma pentaphyllum is a traditional Chinese medicinal herb, serving as natural source of gypenosides (triterpene saponins). The APETALA2/ethylene response factor (AP2/ERF) transcription factors, playing essential regulation roles in plant biotic and abiotic stress responses and secondary metabolism biosynthesis. However, the regulation roles of AP2/ERF transcription factors in gypenosides biosynthesis in G. pentaphyllum remains little understood. In the present study, 125 AP2/ERF genes were identified from G. pentaphyllum transcriptome datasets. Phylogenetic, conserved motifs and expression pattern were employed to comprehensively analyze the 125 GpAP2/ERF genes. Based on the sequence similarity and phylogeny tree, the 125 GpAP2/ERF genes can be classified into 10 groups. Moreover, the distribution of conserved motifs among GpAP2/ERF proteins in phylogenetic trees was consistent with previous studies, thus supporting the classification. Expression profiling indicated that the 125 GpAP2/ERF genes exhibited distinct tissue-specific expression patterns. As confirmed by qRT-PCR, the four candidate GpAP2/ERF genes and gypenoside biosynthetic genes were highly expressed in leaves and/or flowers, and show similar expression patterns in response to MeJA. Base on the expression patterns and phylogenetic relationships, two GpAP2/ERF genes were considered as potential regulatory genes for gypenoside biosynthesis. Our study enhances understanding roles of GpAP2/ERF genes in regulation of gypenosides biosynthesis.

Genome-wide analysis of evolution and expression profiles of NAC transcription factor gene family in Juglans regia L.

Genome-wide analysis of evolution and expression profiles of NAC transcription factor gene family in Juglans regia L.

Genome-wide analysis of evolution and expression profiles of NAC transcription factor gene family in Juglans regia L.

Genome-wide analysis of evolution and expression profiles of NAC transcription factor gene family in Juglans regia L.

Msx2 plays an important role in BMP6-induced osteogenic differentiation of two mesenchymal cell lines: C3H10T1/2 and C2C12.

Bone morphogenetic proteins (BMPs), have been shown to enhance the osteogenic differentiation of mesenchymal cells (MCs) and to promote bone formation. BMP6 is known to play an important role in the process of MCs towards osteogenic differentiation by virtue of their osteoinductive and cell type specific proliferative activity. However, the molecular mechanism relate to BMP6 osteoinductive activity is still unclear and continues to warrant further investigation. Msx2 is a member of the homeobox gene family of transcription factors and promotes calcification. Hence, we wondered if it might also play a role in BMP6-induced osteogenesis. In this study, two mouse mesenchymal cell lines were treated with BMP6, adenovirus-Msx2 (Ad-Msx2) or adenovirus-siMsx2 (Ad-siMsx2). Based on the results of mRNA and protein expression, it was indicated that BMP6 could enhance the expression of Msx2 and activate the phosphorylation of Smad 1/5/8, p38 and ERK1/2. Being transfected by Ad-Msx2, the BMP6-induced activation of phosphorylation was significantly promoted. On the contrary, two cell lines transfected by Ad-siMsx2 presented an inhibited expression of three phosphorylated proteins even after being induced by BMP6. The evaluation of ALP, OPN, OC and calcium deposits revealed the osteogenic results those were corresponding to the results of mRNA and protein. Taken together, these findings can be a novel viewpoint for the understanding of the mechanisms of BMP6-induced osteogenesis and provide therapeutic targets of bone defect.

First report for availability of HRT-like genes in Eragrostis tef and in silico analysis for elucidating their potential functions

Tef [Eragrostis tef (Zucc.) Troetter] is called ‘super grain’ because of its healthy and nutritious seeds along with compatibility to suboptimal environment. Plant Transcription factors (TFs) are key regulators of gene expression which affect transcription through interaction with proteins and DNA binding. Hordeum Repressor Transcription (HRT) are one of TF gene families with too scanty of information on their abundance, distribution, motifs, phylogenetic relationship among plants, promoter and association network analysis on cereals including tef. CoGeBlast, MEME, MEGA X and PLANTCARE were employed accordingly. Two HRT-like TFs (ET) were identified residing on chromosome 5A and 5B, the proteins exhibit CH residue at the C- terminal end and GIY-YIG domain in the N-terminal. The phylogenetic tree obtained depicted orthology in HRT genes in S. bicolor and Z. mays; O. sativa and O. glaberrima, S. italica and S. virdis; and H. vulgare and T. aestivum and homeologous pairs in E. tef. From the promoter analysis of EtHRTs, CRE elements like ABRE, MYBs, G-box, GC-motif, TC-rich repeats, O2-site were identified known to involve in the control of hormones, sugars and abiotic stresses (ABA, GA, zein and α-amylase) confirming the involvement/role of HRT-like TFs in growth, development and stress response of tef. The study contributes for the understanding of structure and function of HRT-like TFs among plants.

A novel and human-specific CD46-KLF/SP interaction mediates gene expression required for successful Th1 induction

Abstract Signals mediated by autocrine activation of the human-specific complement receptor CD46 during T cell receptor (TCR) stimulation are vital to Th1 induction in human CD4+ T cells, but how exactly CD46 in a molecular level mediates this role is currently undefined. CD46 is expressed in different isoforms that can bear either one of two distinct cytoplasmic tails: CYT-1 or CYT-2. Nuclear translocation of CYT-1 is a critical requirement for the expression of genes coding for nutrient-influx-channels and mTORC1 activity that mediate metabolic adaptations needed for Th1 responses. The lack of a DNA binding domain in CD46-CYT-1 precludes it from acting directly as a transcription factor (TF) and we hence hypothesized that CYT-1 regulates gene expression via direct interaction with specific TF activator and/or repressor complexes. Indeed, CUT&RUN experiments performed using our novel antibody raised against cleaved CYT-1 identified key members of the KLF/SP TFs gene family as potential interacting partners of CD46-CYT-1. Subsequent ELISA and MST experiment confirmed strong, dose-dependent CYT-1/KLF/SP TFs interactions and also demonstrated that CYT-1 fostered KLF/SP TFs binding to appropriate DNA motifs. Genome-wide comparison of the KLF/SP TFs and CYT1 bound genes in T cells revealed their enrichment in crucial basic cell-physiological pathways. Moreover, the CUT&RUN data in conjunction with ATAC-seq analyses indicated that this novel CYT-1/KLF/SP axis may control general chromatin remodeling – a notion we are currently exploring. These data define a novel and critical human-specific pathway of gene regulation and further underpin the vital role of intracellular/autocrine complement in the regulation of normal cellular activity.

FgHtf1 Regulates Global Gene Expression towards Aerial Mycelium and Conidiophore Formation in the Cereal Fungal Pathogen Fusarium graminearum.

The homeobox gene family of transcription factors (HTF) controls many developmental pathways and physiological processes in eukaryotes. We previously showed that a conserved HTF in the plant-pathogenic fungus Fusarium graminearum, Htf1 (FgHtf1), regulates conidium morphology in that organism. This study investigated the mechanism of FgHtf1-mediated regulation and identified putative FgHtf1 target genes by a chromatin immunoprecipitation assay combined with parallel DNA sequencing (ChIP-seq) and RNA sequencing. A total of 186 potential binding peaks, including 142 genes directly regulated by FgHtf1, were identified. Subsequent motif prediction analysis identified two DNA-binding motifs, TAAT and CTTGT. Among the FgHtf1 target genes were FgHTF1 itself and several important conidiation-related genes (e.g., FgCON7), the chitin synthase pathway genes, and the aurofusarin biosynthetic pathway genes. In addition, FgHtf1 may regulate the cAMP-protein kinase A (PKA)-Msn2/4 and Ca2+-calcineurin-Crz1 pathways. Taken together, these results suggest that, in addition to autoregulation, FgHtf1 also controls global gene expression and promotes a shift to aerial growth and conidiation in F. graminearum by activation of FgCON7 or other conidiation-related genes.IMPORTANCE The homeobox gene family of transcription factors is known to be involved in the development and conidiation of filamentous fungi. However, the regulatory mechanisms and downstream targets of homeobox genes remain unclear. FgHtf1 is a homeobox transcription factor that is required for phialide development and conidiogenesis in the plant pathogen F. graminearum In this study, we identified FgHtf1-controlled target genes and binding motifs. We found that, besides autoregulation, FgHtf1 also controls global gene expression and promotes conidiation in F. graminearum by activation of genes necessary for aerial growth, FgCON7, and other conidiation-related genes.

Genome-wide analysis of CsWOX transcription factor gene family in cucumber (Cucumis sativus L.)

WUSCHEL-related homeobox (WOX) transcription factors are plant-specific members that characterized by the presence of a homeodomain. It has been shown that WOX members regulate several aspects of plant development, but the biological functions of this CsWOX gene family remain largely unknown in cucumber (Cucumis sativus L.). In this study, we identified and characterized 11 putative CsWOX genes in cucumber, which are also divided into three major clades (e.g., the Ancient clade, the Intermediate clade and the WUS clade). Expression pattern analysis revealed tissue-specific expression patterns of CsWOX genes, including that CsWOX9 is mainly expressed in developing fruit and also has lower expression in tip and axillary bud, which was further confirmed by in situ hybridization assay. Moreover, overexpression of CsWOX9 in Arabidopsis led to increased branches and rosette leaves, and shorter siliques. Together, these results indicated that CsWOX members may regulate cucumber growth and development.

The bHLH gene family and its response to saline stress in Jilin ginseng, Panax ginseng C.A. Meyer.

Basic helix-loop-helix (bHLH) gene family is a gene family of transcription factors that plays essential roles in plantgrowth and development, secondary metabolism and response to biotic and abiotic stresses. Therefore, a comprehensive knowledge of the bHLH gene family is paramount to understand the molecular mechanisms underlying these processes and develop advanced technologies to manipulate the processes efficiently. Ginseng, Panax ginseng C.A. Meyer, is a well-known medicinal herb; however, little is known about the bHLH genes (PgbHLH) in the species. Here, we identified 137 PgbHLH genes from Jilin ginseng cultivar, Damaya, widely cultivated in Jilin, China, of which 50 are newly identified by pan-genome analysis. These 137 PgbHLH genes were phylogenetically classified into 26 subfamilies, suggesting their sequence diversification. They are alternatively spliced into 366 transcripts in a 4-year-old plant and involved in 11 functional subcategories of the gene ontology, indicating their functional differentiation in ginseng. The expressions of the PgbHLH genes dramatically vary spatio-temporally and across 42 genotypes, but they are still somehow functionally correlated. Moreover, the PgbHLH gene family, at least some of its genes, is shown to have roles in plant response to the abiotic stress of saline. These results provide a new insight into the evolution and functional differentiation of the bHLH gene family in plants, new bHLH genes to the PgbHLH gene family, and saline stress-responsive genes for genetic improvement in ginseng and other plant species.

Association of SOX11 Polymorphisms in distal 3'UTR with Susceptibility for Schizophrenia.

BackgroundDiverse and circumstantial evidence suggests that schizophrenia is a neurodevelopmental disorder. Genes contributing to neurodevelopment may be potential candidates for schizophrenia. The human SOX11 gene is a member of the developmentally essential SOX (Sry‐related HMG box) transcription factor gene family and mapped to chromosome 2p, a potential candidate region for schizophrenia.MethodsOur previous genome‐wide association study (GWAS) implicated an involvement of SOX11 with schizophrenia in a Chinese Han population. To further investigate the association between SOX11 polymorphisms and schizophrenia, we performed an independent replication case‐control association study in a sample including 768 cases and 1348 controls.ResultsAfter Bonferroni correction, four SNPs in SOX11 distal 3′UTR significantly associated with schizophrenia in the allele frequencies: rs16864067 (allelic P = .0022), rs12478711 (allelic P = .0009), rs2564045 (allelic P = .0027), and rs2252087 (allelic P = .0025). The haplotype analysis of the selected SNPs showed different haplotype frequencies for two blocks (rs4371338‐rs7596062‐rs16864067‐rs12478711 and rs2564045‐rs2252087‐rs2564055‐rs1366733) between cases and controls. Further luciferase assay and electrophoretic mobility shift assay (EMSA) revealed the schizophrenia‐associated SOX11 SNPs may influence SOX11 gene expression, and the risk and non‐risk alleles may have different affinity to certain transcription factors and can recruit divergent factors.ConclusionsOur results suggest SOX11 as a susceptibility gene for schizophrenia, and SOX11 polymorphisms and haplotypes in the distal 3′UTR of the gene might modulate transcriptional activity by serving as cis‐regulatory elements and recruiting transcriptional activators or repressors. Also, these SNPs may potentiate as diagnostic markers for the disease.

Genome-Wide Identification and Expression Profile Analysis of the NF-Y Transcription Factor Gene Family in Petunia hybrida.

Nuclear Factor Ys (NF-Ys) are a class of heterotrimeric transcription factors that play key roles in many biological processes, such as abiotic stress responses, flowering time, and root development. The petunia (Petunia hybrida) is a model ornamental plant, and its draft genome has been published. However, no details regarding the NF-Y gene family in petunias are available. Here, 27 NF-Y members from the petunia genome were identified, including 10 PhNF-YAs, 13 PhNF-YBs, and 4 PhNF-YCs. Multiple alignments showed that all PhNF-Y proteins had clear conserved core regions flanked by non-conserved sequences. Phylogenetic analyses identified five pairs of orthologues NF-YB proteins from Petunia and Arabidopsis, and six pairs of paralogues NF-Y proteins in Petunia. Analysis of the gene structure and conserved motifs further confirmed the closer relationship in each subfamily. Bioinformatics analysis revealed that 16 PhNF-Ys could be targeted by 18 miRNA families. RNA-seq results showed that expression patterns of PhNF-Ys among four major organs (leaf, stem, flower, and root) were clustered into six major groups. The stress response pattern of PhNF-Ys was identified under cold, heat, drought, and salinity treatments. Based on the RNA-seq data, we found that 3 genes responded to drought, 4 genes responded to salt, 10 genes responded to cold, and 9 genes responded to hot. In conclusion, this study provides useful information for further studying the functions of NF-Ys in stress response.

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang.

SummaryXinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions of China. But it is unclear how genomic constitutions from foundation parents have been selected and inherited. Here, we deep‐sequenced seven historic foundation parents, comprising four cultivars introduced from the former Soviet Union (108Ф, C1470, 611Б and KK1543) and three from United States and Africa (DPL15, STV2B and UGDM), and re‐sequenced sixty‐nine Xinjiang modern cultivars. Phylogenetic analysis of more than 2 million high‐quality single nucleotide polymorphisms allowed their classification two groups, suggesting that Xinjiang Upland cotton cultivars were not only spawned from 108Ф, C1470, 611Б and KK1543, but also had a close kinship with DPL15, STV2B and UGDM. Notably, identity‐by‐descent (IBD) tracking demonstrated that the former Soviet Union cultivars have made a huge contribution to modern cultivar improvement in Xinjiang. A total of 156 selective sweeps were identified. Among them, apoptosis‐antagonizing transcription factor gene (GhAATF1) and mitochondrial transcription termination factor family protein gene (GhmTERF1) were highly involved in the determination of lint percentage. Additionally, the auxin response factor gene (GhARF3) located in inherited IBD segments from 108Ф and 611Б was highly correlated with fibre quality. These results provide an insight into the genomics of artificial selection for improving cotton production and facilitate next‐generation precision breeding of cotton and other crops.

Efficient Single-Gene and Gene Family Editing in the Apicomplexan Parasite Eimeria tenella Using CRISPR-Cas9.

Eimeria species are pathogenic protozoa with a wide range of hosts and the cause of poultry coccidiosis, which results in huge economic losses to the poultry industry. These parasites encode a genome of ∼8000 genes that control a highly coordinated life cycle of asexual replication and sexual differentiation, transmission, and virulence. However, the function and physiological importance of the large majority of these genes remain unknown mostly due to the lack of tools for systematic analysis of gene functions. Here, we report the first application of CRISPR-Cas9 gene editing technology in Eimeria tenella for analysis of gene function at a single gene level as well as for systematic functional analysis of an entire gene family. Using a transgenic line constitutively expressing Cas9, we demonstrated successful and efficient loss of function through non-homologous end joining as well as guided homologous recombination. Application of this approach to the study of the localization of EtGRA9 revealed that the gene encodes a secreted protein whose cellular distribution varied during the life cycle. Systematic disruption of the ApiAp2 transcription factor gene family using this approach revealed that 23 of the 33 factors expressed by this parasite are essential for development and survival in the host. Our data thus establish CRISPR-Cas9 as a powerful technology for gene editing in Eimeria and will set the stage for systematic functional analysis of its genome to understand its biology and pathogenesis, and will make it possible to identify and validate new targets for coccidiosis therapy.

Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs.

Transcriptomic analysis of the leaves of two grapevine cultivars under high-temperature stress

The frequent occurrence of extremely high temperatures can severely affect agricultural production. In grapevines, elevated temperatures can cause irreversible damage during the fruit ripening period. The suggested main approach for addressing this challenge is breeding high-temperature-resistant varieties, which makes it critical to identify key genes involved in the heat stress molecular regulatory network of grapevines. In this study, we exposed the saplings of two grapevine varieties, “Shenfeng” and “Shenhua,” to 45 °C for 3 and 6 h. After 3 h of temperature stress, the leaves of “Shenfeng” appeared dehydrated, and after 6 h, the whole plants had dried up. In contrast, the leaves and the apex of “Shenhua” stem showed only mild water loss and wilt symptoms after 6 h, indicating that this cultivar has strong heat resistance. In response to the 45 °C high-temperature stress, and compared to their levels at 0 h, 822, 501, and 1161 genes showed differential expression levels in “Shenfeng” after 3 h and in “Shenhua” after 3 and 6 h of treatment, respectively; 233 of these genes showed differential expression patterns in the three comparisons. Statistical analysis of these differentially expressed genes revealed that the most up-regulated metabolic pathways in both cultivars were endoplasmic reticulum protein processing and plant hormone signal transduction. Our data indicates that among heat shock transcription factor (HSF) family genes, the HSFA2 and HSFA7 were the most heat-sensitive, and that HSF and HSP cooperated to response adversity. Photosystem II (PSII) functioned more efficiently in heat-tolerant rather than in heat-sensitive grapevines, leading to differences in the PSII parameters and transcriptional levels of key PSII protein-coding genes between the cultivars. We can conclude that, in response to high-temperature stress, interactions among endogenous hormone-mediated plant defense processes and the ABA response pathway have great research value.

Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.).

The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.

Genome-Wide Analysis of NAC Transcription Factors and Characterization of the Cold Stress Response in Sweet Osmanthus

Sweet osmanthus (Osmanthus fragrans) is an evergreen aromatic woody tree widely used in landscaping. However, O. fragrans is very sensitive to cold stress, which seriously limits its cultivation and application in regions of low temperature. The NAC transcription factor gene family which has been characterized in many plant species could participate in multiple processes and play critical roles in plant response to external stress. However, little is known about this family in O. fragrans, an important woody ornamental plant. Here, the structural characteristics, chromosomal location, evolutionary relationship, cold stress expression patterns, and subcellular localization analysis of NAC family genes in O. fragrans were analyzed on a genome-wide scale. A total of 119 O. fragrans NAC genes were identified, and gene structure analysis showed that most OfNACs contained two introns, suggesting that structural diversity of the O. fragrans NAC family is relatively low. The phylogeny evolutionary tree showed that the NACs of O. fragrans were classified into 13 branches. The transcriptome data suggested that each branch members had different expression patterns in various tissues and a number of OfNACs showed tissue-specific expression profiles. The quantitative real-time PCR and subcellular localization results indicated that expression patterns of most branch ‘5B’ members were significantly induced by cold stress and they were mainly located in the nucleus, especially OfNAC49 and 59, indicating that branch ‘5B’ members could have important roles in cold tolerance in O. fragrans. Remarkably, expression levels of many branch ‘5B’ genes were also significantly changed under waterlogging stress, suggesting that this branch might be widely involved in tolerance to various abiotic stresses. Our study should supply useful gene resources for the cold resistance breeding of O. fragrans.

Extensive intragenic divergences amongst ancient WRKY transcription factor gene family is largely associated with their functional diversity in plants

Diversity at gene sequence and function level is an evolutionary outcome of a constantly expanding gene family in plants. Genome sequences have provided a platform to comprehend the evolutionary architecture of genes and gene families, especially in plant genera. Apparently, regulatory sequences and the selection of trans-binding proteins have massive impressions of gene expression evolution as compared with a transformation at genic-level itself. Therefore, it becomes essential to comprehensively dissect the genome-wide structure-function evolution of regulatory regions'-binding trans-proteins. WRKY gene family members are developmentally and functionally diverged ancient transcription factors that notably regulates numerous cellular as well as stress responsive phenotypes in plant species. To comprehend the evolutionary consequences of WRKY genes during plant development, a meta-phylogenetic analyses of at least 266 WRKY amino acid sequences of alga, monocot and eudicots plant species was accomplished. Phylogenetic clustering identified assorted groups and sub-groups of WRKY orthologous or paralogous sequences. Paralogous gene divergences of monocot and eudicot species showed strong ‘purifying’ selection during the sequence evolution. Evidently, evolutionary exon-intron structural diversification predominantly arose by ‘exon/intron-gain’ and insertion/deletion during primeval sequence-exonization. The structural DNA-binding domain, and global structures of WRKY proteins are exceedingly divergent and also explicit to the classified phylogenetic clusters. Expression profiling displayed that Group IIe WRKY members are profusely expressed in root tissues of the representative species. Remarkably, the spatial and temporal gene expression patterns of WRKY genes in plants apprise our perception about their contributions in the regulation of cellular functions; and structural-functionalism of these members speculate their probable employment into future crop improvement programs.

MiR156a-targeted SBP-Box transcription factor SlSPL13 regulates inflorescence morphogenesis by directly activating SFT in tomato.

The inflorescences and lateral branches of higher plants are generated by lateral meristems. The structure of the inflorescence has a direct effect on fruit yield in tomato (Solanum lycopersicum). We previously demonstrated that miR156a plays important roles in determining the structures of the inflorescences and lateral branches in tomato by suppressing the expression of the SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) transcription factor gene family. However, information on regulatory pathways associated with inflorescence morphogenesis is still lacking. In this study, we demonstrate that SPL13 is the major SPL involved in miR156a‐regulated tomato inflorescence structure determination and lateral branch production. Suppressing the expression of SPL13 in tomato increases the number of inflorescences on vegetative branches and lateral branches, decreases the number of flowers and fruit, and reduces fruit size and yield. Genetic and biochemical evidence indicate that SPL13 controls inflorescence development by positively regulating the expression of the tomato inflorescence‐associated gene SINGLE FLOWER TRUSS (SFT) by directly binding to its promoter region. Thus, our findings provide a major advance to our understanding of the miR156a‐SlSPL‐based mechanism that regulates plant architecture and yield in tomato.