Plant-specific Transcription Factors Research Articles

Genome-Wide Identification of GRAS Gene Family in Cunninghamia lanceolata and Expression Pattern Analysis of ClDELLA Protein Under Abiotic Stresses

The Chinese fir (Cunninghamia lanceolata) is a significant species utilized in afforestation efforts in southern China. It is distinguished by its rapid growth and adaptability to diverse environmental conditions. The GRAS gene family comprises a group of plant-specific transcription factors that play a pivotal role in plant growth and development, response to adversity, and hormone regulatory networks. However, the exploration of the GRAS family in gymnosperm Chinese fir has not yet begun. In this study, a total of 43 GRAS genes were identified in the whole genome of Chinese fir, and a phylogenetic analysis classified them into nine distinct subfamilies. Gene structure analysis revealed that the majority of ClGRAS genes lacked introns. It is notable that among these proteins, both ClGAI and ClGRA possess distinctive DELLA structural domains. Cis-acting element analysis revealed that nearly all ClGRAS genes contained light-responsive elements, while hormone-responsive elements, environmental-responsive elements (low-temperature- or defense-responsive elements), and meristem-organization-related elements were also identified. Based on transcriptome data and RT-qPCR expression patterns, we analyzed the expression of ClGAI and ClRGA genes across different developmental stages, hormones, and three abiotic stresses. Subcellular localization analysis demonstrated that ClGAI and ClRGA were localized to the nucleus. Transcriptional activation assays showed that both genes have self-activating activity. In conclusion, the results of this study indicate that the ClGRAS gene family is involved in the response of Chinese fir to environmental stress. Further research on the ClDELLA genes provides valuable information for exploring the potential regulatory network of DELLA proteins in Chinese fir.

Genome-Wide Identification and Characterization of TCP Genes in Eight Prunus Species and Their Expression Patterns Under Cold Stress in P. tenella var. tenella

Background/Objectives: Teosinte branched1/Cycloidea/Proliferating cell nuclear antigen factors (TCPs) are plant-specific transcription factors involved in leaf development, flowering, branching, hormone signaling, and stress responses. Prunus a key temperate fruit tree with ornamental spring blooms, still lacks comprehensive TCP gene studies across many species. Methods: We identified 154 TCP genes in eight Prunus species: 19 in Prunus tenella var. tenella, 19 in P. amygdalus, 17 in P. armeniaca ‘Rojo Pasion’, 19 in P. mira, 20 in P. jamasakura var. jamasakura, 19 in P. fruticosa, 19 in P. mume var. tortuosa, and 22 in P. × yedoensis ‘Somei-yoshino’. These genes were classified into PCF, CIN, and CYC/TB1 groups. We examined segmental duplication, conserved motifs, and cis-acting elements. Expression patterns of 12 TCPs in P. tenella var. tenella were tested under low-temperature stress (25 °C, 5 °C, −5 °C, and −10 °C), and PtTCP9’s subcellular localization was determined. Results: TCP genes within the same groups showed similar motifs and cis-acting elements. Cold stress analysis identified multiple low-temperature-responsive elements in gene promoters. Four genes (PtTCP2, PtTCP6, PtTCP14, and PtTCP16) increased expression under cold stress, while six genes (PtTCP1, PtTCP5, PtTCP8, PtTCP9, PtTCP17, and PtTCP19) decreased. PtTCP9 was localized to the nucleus. Conclusions: This was the first genome-wide study of the TCP gene family in these eight Prunus species, providing valuable insights into the characteristics and functions of TCP genes within this important genus.

Multifunctional Transcription Factor YABBY6 Regulates Morphogenesis, Drought and Cold Stress Responses in Rice

The roles of plant-specific transcription factor family YABBY may vary among different members. OsYABBY6 is a rice YABBY gene, whose function is not well elucidated so far. In this paper, we show that OsYABBY6 is a nucleus-localized protein with transcriptional activation activity. OsYABBY6 is predominantly expressed in the palea and lemma, as well as in the sheath, culm and node. OsYABBY6 RNA interference (RNAi) plants exhibited altered plant height and larger grain size. Under cold treatment, OsYABBY6 overexpression (OE) plants had up-regulated expression of cold responsive genes, and accumulated less reactive oxygen species but more proline compared to wild type, resulting in improved cold tolerance. On the other hand, RNAi plants showed enhanced drought tolerance compared to the wild type by slower water loss, less reactive oxygen species but more proline and soluble sugar accumulation. In addition, endogenous abscisic acid (ABA) level was reduced in OsYABBY6 RNAi plants, and RNAi and OE plants were more and less sensitive to ABA treatment, respectively. Accordingly, we deduce that OsYABBY6 positively regulates cold response but negatively regulates drought response through different pathways. Our study reveals the crucial roles of OsYABBY6 in plant architecture and grain development, as well as in abiotic stress response, providing new insights into the functions of YABBYs in rice.

Genome-Wide Characterization of Shi-Related Sequence Gene Family and Its Roles in Response to Zn2+ Stress in Cucumber

Shi-related sequence (SRS) proteins, which consist of the RING-like zinc finger domain and IGGH domain, are plant-specific transcription factors that have been well-studied in several plant species. However, information about SRS genes and their roles in cucumber (Cucumis sativus L.) is limited. Therefore, we performed detailed bioinformatic analysis of the SRS gene family, including gene numbers and positions, genes structures, conserved motif distribution patterns, phylogenetic analysis, and promoter cis-element analysis. Eight SRS genes were identified in cucumber and distributed on all seven cucumber chromosomes. SRS genes are conserved in plants and divided into two groups in cucumber based on their protein sequence. In silico analysis predicted that most genes may function in response to abiotic stresses and phytohormones. Gene ontology analysis predicted the possible involvement of genes in development and reproduction, and DNA and protein binding on a molecular level. Furthermore, the differential expression pattern of SRS genes in leaf, stem and root under the condition of Zn2+ stress suggested their roles in response to Zn2+ stress. Furthermore, our metal tolerance assay suggested that CsSRS2 and CsSRS5 mediated enhanced tolerance to Zn2+ stress in Escherichia coli cells. Our study provides a foundation for the functional study of SRS genes in cucumber.

Genome-Wide Identification, Characterization and Expression Patterns of the DBB Transcription Factor Family Genes in Wheat.

Double B-box (DBB) proteins are plant-specific transcription factors (TFs) that play crucial roles in plant growth and stress responses. This study investigated the classification, structure, conserved motifs, chromosomal locations, cis-elements, duplication events, expression levels, and protein interaction network of the DBB TF family genes in common wheat (Triticum aestivum L.). In all, twenty-seven wheat DBB genes (TaDBBs) with two conserved B-box domains were identified and classified into six subgroups based on sequence features. A collinearity analysis of the DBB family genes among wheat, Arabidopsis, and rice revealed some duplicated gene pairs and highly conserved genes in wheat. An expression pattern analysis indicated that wheat TaDBBs were involved in plant growth, responses to drought stress, light/dark, and abscisic acid treatment. A large number of cis-acting regulatory elements related to light response are enriched in the predicted promoter regions of 27 TaDBBs. Furthermore, some of TaDBBs can interact with COP1 or HY5 based on the STRING database prediction and yeast two-hybrid (Y2H) assay, indicating the potential key roles of TaDBBs in the light signaling pathway. Conclusively, our study revealed the potential functions and regulatory mechanisms of TaDBBs in plant growth and development under drought stress, light, and abscisic acid.

GmWRKY33A positively regulates disease resistance in soybean (Glycine max)

The WRKY transcription factor gene family is a plant-specific transcription factor that plays important roles defense responses. Studies in model plant Arabidopsis demonstrated that WRKYs function downstream of mitogen activated-protein kinase (MAPK) signaling cascade and participate in defense responses through activating the expression of defense-related genes. However, the roles of WRKYs in defense responses have not been previously investigated in paleopolyploidy soybean. Bioinfomatic analysis revealed that there are three pair of GmWRKY33 genes in the soybean genome. The identity of first two pair of GmWRKY33 genes is greater than 84% (named as GmWRKY33A). The identity of genes within the same pair is greater than 95%. A 300 bp fragment highly homologous to these four GmWRKY33A was chosen to clone into bean pod mosaic virus (BPMV)-based silencing vector (BPMV-VIGS) to achieve the goal of silencing four GmWRKY33A genes simultaneously. In this study, we simultaneously silenced four homologous genes of GmWRKY33A using a bean pod mottle virus (BPMV) vector carrying a single fragment of GmWRKY33A. Comparing the silenced plants with the vector control plants, no evident morphological phenotypes were observed. However, the GmWRKY33A-silenced plants exhibited significantly reduced resistance to Pseudomonas syringae pv. glycinea (Psg), Xanthomonas axonopodis pv. glycine (Xag), as well as to soybean mosaic virus (SMV). Furthermore, we demonstrated that silencing these GmWRKY33A genes significantly inhibited the activation of GmMPK3/GmMPK6 induced by Psg infection. Collectively, our results suggest that GmWRKY33As are involved in soybean immunity through regulating the transcription of GmMPK3/6 genes or activating the kinase activities of GmMPK3/6. Taken together, our results demonstrated that GmWRKY33As are positive regulators of soybean immune responses.

The GRAS transcription factor PtrPAT1 of Poncirus trifoliata functions in cold tolerance and modulates glycine betaine content by regulating the BADH-like gene

Abstract GRAS, termed after GAI (gibberellic acid insensitive), RGA (repressor of GA1), and SCR (scarecrow), is a plant-specific transcription factor crucial for plant development and stress response. However, understanding of the functions played by the GRAS members and their target genes in citrus is limited. In this study, we identified a cold stress-responsive GRAS gene from Poncirus trifoliate, designated as PtrPAT1, by yeast one-hybrid library screening using the promoter of PtrBADH-l, a betaine aldehyde dehydrogenase (BADH)-like gene. PtrPAT1, belonging to the PAT1 subfamily, was localized in the nucleus and plasma membrane, exhibited transactivation activity and showed a remarkable upregulation under cold stress. Overexpression of PtrPAT1 elevated BADH activity, increased glycine betaine (GB) accumulation and conferred enhanced cold tolerance in transgenic tobacco plants compared with wild type, while downregulation in trifoliate orange by virus-induced gene silencing (VIGS) resulted in opposite trends. Furthermore, the activities of two antioxidant enzymes, including peroxidase (POD) and superoxide dismutase (SOD), were significantly increased in the overexpression plants, but remarkably decreased in the VIGS line, consistent with accumulation patterns of the reactive oxygen species (ROS). PtrPAT1 was demonstrated to interact with and activate the PtrBADH-l promoter through the putative PAT1-binding motif with the core sequence of TTTCATGT, indicating that PtrBADH-l is a target gene of PtrPAT1. Taken together, these results demonstrate that PtrPAT1 positively affects cold tolerance through the regulation of GB biosynthesis by modulating PtrBADH-l expression.

Exploring CDF gene family in wild potato under salinity stress unveils promising candidates for developing climate-resilient crops

The DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors involved in diverse biological processes, including response to biotic and abiotic stresses. Members of this family have been reported in the cultivated potato Solanum tuberosum, but clues to the roles of several Dof genes are still lacking. Potato wild relatives represent a genetic reservoir for breeding as they could provide useful alleles for adaptation to the environment and tolerance to biotic and abiotic stresses. We performed an in silico analysis to identify genes belonging to the Dof family in the wild potato S. commersonii, confirming that the identified Dof genes can be grouped in four classes (A, B, C, D), as reported for cultivated potato. A special focus was dedicated to Cycling Dof Factors (CDFs), which play a crucial role in plant responses to abiotic stresses. Analysis of available RNA-seq data confirmed CDF genes as regulated by stresses and often in a tissue specific manner. To ascertain their involvement in the stress response, S. tuberosum and S. commersonii plantlets growing in vitro were subjected to salt stress (80mM NaCl) for short (2 days) and prolonged (7 days) times. Analysis of phenotypic traits and qRT-PCR expression profiles of target CDF genes in aerial and root tissues showed differences between the two species. In addition, after saline treatment, changes in total phenols, proline, and malondialdehyde suggested a diverse perception of saline stress in S. commersonii vs. S. tuberosum. Overall, this study provided useful clues to the involvement of CDF genes in salt response and promoted the identification of potential candidate genes for further functional studies.

Genome-wide analysis of the WRKY gene family and their response to low-temperature stress in elephant grass.

Elephant grass (Cenchrus purpureus) is a perennial forage grass characterized by tall plants, high biomass and wide adaptability. Low-temperature stress severely limits elephant grass biomass and geographic distribution. WRKY is one of the largest families of plant-specific transcription factors and plays important roles in plant resistance to low-temperature. However, the understanding of the WRKY family in grasses is limited. In this study, we conducted a genome-wide characterization of WRKY proteins in elephant grass, including gene structure, phylogeny, expression, conserved motif organization, and functional annotation, to identify key CpWRKY candidates involved in cold tolerance. In this study, a total of 176 WRKY genes were identified in elephant grass. It was found that 172 were unevenly distributed across its 14 chromosomes, while the remaining 4 genes were not anchored to any chromosome. The genes were classified into three groups based on their WRKY conserved domains and zinc finger motifs. There were 12, 8, 19, 27, 12, 18 and 80 CpWRKYs belonging to group I, group IIa, group IIb, group IIc, group IId, group IIe and group III, respectively. We hypothesized that the ancient subgroup IIc WRKY gene is the ancestor of all WRKY genes in elephant grass. Most CpWRKYs in the same group have similar structure and motif composition. A total of 169 duplicate gene pairs were identified, suggesting that segmental duplication might have contributed to the expansion of the CpWRKY gene family. Ka/Ks analysis revealed that most of the CpWRKYs were subjected to purifying selection during the evolution. It was also found that six genes (CpWRKY51, CpWRKY81, CpWRKY100, CpWRKY101, CpWRKY140 and CpWRKY143) exhibited higher expression in roots compare to leaves, and were significantly induced by low temperature stress. Among them, CpWRKY81 had the highest expression under low-temperature stress, and its over-expression significantly enhanced the cold tolerance in yeast. In this study, we characterized WRKY genes in elephant grass and further investigated their physicochemical properties, evolution, and expression patterns under low-temperature stress. This research provides valuable resources for identifying key CpWRKY genes that contribute to cold tolerance in elephant grass.

Systematic analysis of the ARF gene family in Fagopyrum dibotrys and its potential roles in stress tolerance.

The auxin response factor (ARF) is a plant-specific transcription factor that regulates the expression of auxin response genes by binding directly to their promoters. They play an important role in the regulation of plant growth and development, as well as in the response to biotic and abiotic stresses. However, the identification and functional analysis of ARFs in Fagopyrum dibotrys are still unclear. In this study, a total of 26 FdARF genes were identified using bioinformatic methods. Their chromosomal location, gene structure, physical and chemical properties of their encoded protein, subcellular location, phylogenetic tree, conserved motifs and cis-acting elements in FdARF promoters were analyzed. The results showed that 26 FdARF genes were unevenly distributed on 8 chromosomes, with the largest distribution on chromosome 4 and the least distribution on chromosome 3. Most FdARF proteins are located in the nucleus, except for the proteins FdARF7 and FdARF21 located to the cytoplasm and nucleus, while FdARF14, FdARF16, and FdARF25 proteins are located outside the chloroplast and nucleus. According to phylogenetic analysis, 26 FdARF genes were divided into 6 subgroups. Duplication analysis indicates that the expansion of the FdARF gene family was derived from segmental duplication rather than tandem duplication. The prediction based on cis-elements of the promoter showed that 26 FdARF genes were rich in multiple stress response elements, suggesting that FdARFs may be involved in the response to abiotic stress. Expression profiling analysis showed that most of the FdARF genes were expressed in the roots, stems, leaves, and tubers of F. dibotrys, but their expression exhibits a certain degree of tissue specificity. qRT-PCR analysis revealed that most members of the FdARF gene were up- or down-regulated in response to abiotic stress. The results of this study expand our understanding of the functional role of FdARFs in response to abiotic stress and lay a theoretical foundation for further exploration of other functions of FdARF genes.

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.

PavSPLs are key regulators of growth, development, and stress response in sweet cherry

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes are plant-specific transcription factors essential for plant growth, development, and stress responses; however, their roles in sweet cherry are not well understood. In this study, we identified and isolated 16 SPL genes from the sweet cherry genome, categorizing them into five subfamilies, with 12 PavSPLs predicted as miR156 targets. The promoter regions of PavSPLs contain cis-elements associated with light, stress, and phytohormone responses, indicating their role in biological processes and abiotic stress responses. Seasonal expression analysis showed that PavSPL regulates sweet cherry recovery after dormancy. Gibberellin (GA) treatment reduced PavSPL expression, indicating its role in GA-mediated processes. Overexpression of PavSPL14 in Arabidopsis thaliana resulted in earlier flowering, increased plant height, and enhanced growth. Yeast two-hybrid assays revealed an interaction between PavSPL14 and DELLA protein PavDWARF8, suggesting the involvement of PavSPLs in GA-regulated processes through protein interactions. These findings lay the groundwork for future studies on PavSPL function in sweet cherry.

Genome-Wide Analysis Elucidates the Roles of AhLBD Genes in Different Abiotic Stresses and Growth and Development Stages in the Peanut (Arachis hypogea L.).

The lateral organ boundaries domain (LBD) genes, as the plant-specific transcription factor family, play a crucial role in controlling plant architecture and stress tolerance. However, the functions of AhLBD genes in the peanut plant (Arachis hypogea L.) remain unclear. In this study, 73 AhLBDs were identified in the peanut plant and divided into three groups by phylogenetic tree analysis. Gene structure and conserved protein motif analysis supported the evolutionary conservation of AhLBDs. Tandem and segment duplications contributed to the expansion of AhLBDs. The evolutionary relationship analysis of LBD gene family between A. hypogaea and four other species indicated that the peanut plant had a close relationship with the soybean plant. AhLBDs played a very important role in response to growth and development as well as abiotic stress. Furthermore, gene expression profiling and real-time quantitative qRT-PCR analysis showed that AhLBD16, AhLBD33, AhLBD67, and AhLBD72 were candidate genes for salt stress, while AhLBD24, AhLBD33, AhLBD35, AhLBD52, AhLBD67, and AhLBD71 were candidate genes for drought stress. Our subcellular localization experiment revealed that AhLBD24, AhLBD33, AhLBD67, and AhLBD71 were located in the nucleus. Heterologous overexpression of AhLBD33 and AhLBD67 in Arabidopsis significantly enhanced tolerance to salt stress. Our results provide a theoretical basis and candidate genes for studying the molecular mechanism for abiotic stress in the peanut plant.

Transcription factor ZmNAC19 promotes embryo development in Arabidopsis thaliana.

Overexpression of ZmNAC19, a NAC transcription factor gene from maize, improves embryo development in transgenic Arabidopsis. NAC proteins are plant-specific transcription factors that are involved in multiple aspects of plant growth, development and stress response. Although functions of many NAC transcription factors have been elucidated, little is known about their roles in seed development. In this study, we report the function of a maize NAC transcription factor ZmNAC19 in seed development. ZmNAC19 is highly expressed in embryos of developing maize seeds. ZmNAC19 localizes to nucleus and exhibits transactivation activity in yeast cells. Overexpression of ZmNAC19 in Arabidopsis significantly increases seed size and seed yield. During 3 to 7days after flowering, embryos of ZmNAC19-overexpression Arabidopsis lines developed faster compared to Col-0, while no visible differences were detected for their endosperms. Furthermore, overexpression of ZmNAC19 in Arabidopsis leads to increased transcription levels of two embryo development-related genes YUC1 and RGE1, and several elements proven to be binding sites of NAC transcription factors were observed in promoters of these two genes. Taken together, these results suggest that ZmNAC19 acts as a positive regulator in plant embryo development.

Genomic identification and expression profiles during callus formation of LBD transcription factor genes in sweet orange (Citrus sinensis) and functional characterization of CsLBD17

Lateral organ boundaries domain (LBD) is a plant-specific transcription factor. Here, we identified 37 LBD genes of sweet orange in the CPBD database, which were unevenly distributed on 7 chromosomes, and most of those were located in the nucleus. All CsLBD genes were divided into class I (31) containing five subclasses, and class II (6) containing two subclasses and associated with plant growth and development, plant hormones, defense and stress response. WGD/segmental duplication events primarily were confrimed to promote the development of the CsLBD gene family. CsLBDs were more strongly correlated with dicotyledonous plants than with monocotyledonous plants. Gene expression analysis showed that CsLBD16 and CsLBD17 genes in segment stem cultured in callus induction medium were higher than those in the other two media without auxin throughout the cultivation process. The N-terminal region of the CsLBD17 protein is responsible for the transcriptional activation of CsLBD17. Arabidopsis thaliana with overexpression of CsLBD17 showed stronger callus formation ability on CIM medium and stronger root growth ability on MS medium, indicating that it plays an important role in the development of calluses and roots.

BpTCP19 targets BpWRKY53 to negatively regulate jasmonic acid- and dark-induced leaf senescence in Betula platyphylla

TCP (TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1) is a plant-specific transcription factor that has garnered significant attention due to its wide-ranging involvement in the regulation of plant growth or developmental processes. However, the molecular mechanisms through which TCP genes orchestrate leaf senescence have not been extensively elucidated. BpTCP19, a member of the PCF subfamily in Betula platyphylla, and has high homology to AtTCP19. BpTCP19 displayed pronounced downregulation in response to methyl jasmonate (MeJA) and dark treatment. Overexpressing BpTCP19 in Betula platyphylla led to a delay in leaf senescence, resulting in prolonged leaf greenness under both MeJA and dark conditions. Transcriptome analysis revealed that overexpression of BpTCP19 induced alterations in the expression levels of genes linked to cell proliferation, hormone signaling transduction, and leaf senescence, including the early responsive factor BpWRKY53. Furthermore, through Yeast one-hybrid assays and GUS analysis, BpTCP19 was shown to bind to the promoter region of BpWRKY53, suppressing its expression and thereby retarding leaf senescence. This study elucidates the physiological and molecular functions of BpTCP19 as a central transcriptional regulatory module in leaf senescence and provides a potential target gene for delaying leaf senescence by mitigating sensitivity to external aging signals such as Jasmonic acid (JA) and darkness.

INDETERMINATE DOMAIN Transcription Factors in Crops: Plant Architecture, Disease Resistance, Stress Response, Flowering, and More

INDETERMINATE DOMAIN (IDD) genes encode plant-specific transcription factors containing a conserved IDD domain with four zinc finger motifs. Previous studies on Arabidopsis IDDs (AtIDDs) have demonstrated that these genes play roles in diverse physiological and developmental processes, including plant architecture, seed and root development, flowering, stress responses, and hormone signaling. Recent studies have revealed important functions of IDDs from rice and maize, especially in regulating leaf differentiation, which is related to the evolution of C4 leaves from C3 leaves. Moreover, IDDs in crops are involved in the regulation of agriculturally important traits, including disease and stress resistance, seed development, and flowering. Thus, IDDs are valuable targets for breeding manipulation. This review explores the role of IDDs in plant development, environmental responses, and evolution, which provides idea for agricultural application.

Identification and Functional Characterization of Abiotic Stress Tolerance-Related PLATZ Transcription Factor Family in Barley (Hordeum vulgare L.).

Plant AT-rich sequence and zinc-binding proteins (PLATZs) are a novel category of plant-specific transcription factors involved in growth, development, and abiotic stress responses. However, the PLATZ gene family has not been identified in barley. In this study, a total of 11 HvPLATZs were identified in barley, and they were unevenly distributed on five of the seven chromosomes. The phylogenetic tree, incorporating PLATZs from Arabidopsis, rice, maize, wheat, and barley, could be classified into six clusters, in which HvPLATZs are absent in Cluster VI. HvPLATZs exhibited conserved motif arrangements with a characteristic PLATZ domain. Two segmental duplication events were observed among HvPLATZs. All HvPLATZs were core genes present in 20 genotypes of the barley pan-genome. The HvPLATZ5 coding sequences were conserved among 20 barley genotypes, whereas HvPLATZ4/9/10 exhibited synonymous single nucleotide polymorphisms (SNPs); the remaining ones showed nonsynonymous variations. The expression of HvPLATZ2/3/8 was ubiquitous in various tissues, whereas HvPLATZ7 appeared transcriptionally silent; the remaining genes displayed tissue-specific expression. The expression of HvPLATZs was modulated by salt stress, potassium deficiency, and osmotic stress, with response patterns being time-, tissue-, and stress type-dependent. The heterologous expression of HvPLATZ3/5/6/8/9/10/11 in yeast enhanced tolerance to salt and osmotic stress, whereas the expression of HvPLATZ2 compromised tolerance. These results advance our comprehension and facilitate further functional characterization of HvPLATZs.

A Medicago truncatula HD-ZIP gene MtHB2 is involved in modulation of root development by regulating auxin response.

HD-Zip proteins are plant-specific transcription factors known for their diverse functions in regulating plant growth, development, and responses to environmental stresses. Among the Medicago truncatula HD-Zip II genes, MtHB2 has been previously linked to abiotic stress responses. In this study, we conducted a functional characterization of MtHB2 in the regulation of root growth and development. Upon auxin stimulation, expression of MtHB2 was promptly up-regulated. Overexpression of MtHB2 in Arabidopsis thaliana led to reduced primary root growth and inhibited lateral root formation. Interestingly, the transgenic plants expressing MtHB2 exhibited differential responses to three types of auxins (IAA, NAA, and 2,4-D) in terms of root growth and development compared to the wild-type plants. Specifically, primary root growth was less affected, and lateral root formation was enhanced in the transgenic plants when exposed to auxins. This differential response suggests a potential role for MtHB2 in modulating auxin transport and accumulation, as evidenced by the reduced sensitivity of the transgenic plants to the auxin transport inhibitor NPA and lower expression levels of auxin-related reporters such as PIN-FORMED (PIN1)::PIN1-GFP, PIN3::PIN3-GFP, PIN7::PIN7-GFP, and DR5::GFP compared to wild-type plants. Additionally, microarray analysis of the root tissues revealed down-regulation of several auxin-responsive genes in transgenic seedlings compared to wild-type plants. These findings collectively indicate that MtHB2 plays a critical regulatory role in root growth and development by modulating auxin accumulation and response in the roots.

Genome-wide identification and expression analysis of the SPL gene family and its response to abiotic stress in barley (Hordeum vulgare L.)

BackgroundSquamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that is widely involved in the regulation of plant growth and development, including flower and grain development, stress responses, and secondary metabolite synthesis. However, this gene family has not been comprehensively evaluated in barley, the most adaptable cereal crop with a high nutritional value.ResultsIn this study, a total of 15 HvSPL genes were identified based on the Hordeum vulgare genome. These genes were named HvSPL1 to HvSPL15 based on the chromosomal distribution of the HvSPL genes and were divided into seven groups (I, II, III, V, VI, VII, and VIII) based on the phylogenetic tree analysis. Chromosomal localization revealed one pair of tandem duplicated genes and one pair of segmental duplicated genes. The HvSPL genes exhibited the highest collinearity with the monocotyledonous plant, Zea mays (27 pairs), followed by Oryza sativa (18 pairs), Sorghum bicolor (16 pairs), and Arabidopsis thaliana (3 pairs), and the fewest homologous genes with Solanum lycopersicum (1 pair). The distribution of the HvSPL genes in the evolutionary tree was relatively scattered, and HvSPL proteins tended to cluster with SPL proteins from Z. mays and O. sativa, indicating a close relationship between HvSPL and SPL proteins from monocotyledonous plants. Finally, the spatial and temporal expression patterns of the 14 HvSPL genes from different subfamilies were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the results, the HvSPL gene family exhibited tissue-specific expression and played a regulatory role in grain development and abiotic stress. HvSPL genes are highly expressed in various tissues during seed development. The expression levels of HvSPL genes under the six abiotic stress conditions indicated that many genes responded to stress, especially HvSPL8, which exhibited high expression under multiple stress conditions, thereby warranting further attention.ConclusionIn this study, 15 SPL gene family members were identified in the genome of Hordeum vulgare, and the phylogenetic relationships, gene structure, replication events, gene expression, and potential roles of these genes in millet development were studied. Our findings lay the foundation for exploring the HvSPL genes and performing molecular breeding of barley.