The promiscuous life of plant NUCLEAR FACTOR Y transcription factors

Expression profiling and transcriptional regulation of the SRS transcription factor gene family of common bean (Phaseolus vulgaris) in symbiosis with Rhizobium etli

The SRS/STY transcription factors from the model legumes: Lotus japonicus and Medicago truncatula, are part of regulatory networks that play relevant roles for nodule development during the N-fixing symbiosis with rhizobia. In this work we analyzed the participation of the PvSRS transcription factors from common bean (Phaseolus vulgaris), a most important legume crop, in the symbiosis with Rhizobium etli. Our phylogenetic analysis of SRS TFs across five plant species, including four legumes and Arabidopsis thaliana, identified clades that group SRS proteins that are highly expressed in legume nodules and in Arabidopsis roots. A qRT-PCR expression analysis of the 10 PvSRS in root/nodule of inoculated plants, revealed that all the PvSRS genes are expressed at different stages of the symbiosis, albeit at different levels. Based on what is known for L. japonicus, we demonstrated that the PvSRS10 gene -with highest expression during symbiosis- is transcriptionally activated by NF-Y transcription factor, thus indicating its participation in the NIN-NF-Y regulatory cascade. Based on our previous work about the relevant role of members from the MADS-domain/AGL transcription factors as regulators of the N-fixing symbiosis, in this work we demonstrated the transcriptional regulation of PvSRS10 by the MADS-TF PvFUL-like. Analysis of protein-protein interaction networks predicted thatPvSRS5 and PvSRS6 interact with proteins involved in transcriptional regulation and the auxin-activated signaling pathway. The regulatory mechanisms of PvSRS TF in common bean symbiosis may be related to auxin biosynthesis regulation, that is essential for determinate nodules development. Our study highlights the role of PvSRS TF in the N-/fixing symbiosis, a relevant process for sustainable agriculture.

Impact of molecular regulation on plant oil synthesis

The synthesis of lipids in plants is essential for their growth and development, and it has wide-ranging applications in various fields, including diet and industry. In the majority of plants, the principal unsaturated fatty acids (UFAs) are three C18 varieties: oleic acid (18:1), linoleic acid (18:2), and α-linolenic acid (18:3). Despite the clear delineation of the principal biosynthetic pathways of fatty acids in plants, numerous unresolved issues persist. The regulation of transcription factors can significantly influence the rate of fatty acid synthesis in plants. Consequently, several transcription factors associated with oil synthesis have been identified in recent years, among which the WRINKLED1 (WRI1) and V-myb avian myeloblastosis viral oncogene homolog (MYB) transcription factors play central roles. This study will explain how plants make essential lipids, bring up many unanswered questions, and describe the regulatory network of many transcription factors involved in oil production, with a focus on recent progress in research related to WRI1 and MYB1. The aim is to provide insights for the biological cultivation of high-quality oilseed crops.

Identification and characterization of Eco-miR 169-EcNF-YA13 gene regulatory network reveal their role in conferring tolerance to dehydration and salinity stress in finger millet

The finger millet (Eleusine coracana (L.) Gaertn) genome, comprised 166 conserved microRNAs (miRNAs) belonging to 39 families and three novel miRNAs. The miR169 is one of the most conserved miRNA families, while Eco_N1 is a species-specific miRNA prevalent in finger millet. Its members regulate the expression of genes encoding the Nuclear Factor-Y subunit A (NF-YA) via transcript cleavage. However, the role of miRNA genes in regulating the expression of NF-YA transcription factors in finger millet needs to be deciphered. The present study characterized 166 conserved and novel miRNAs (Eco_N1, Eco_N2 and Eco_N3). Further, secondary structures were predicted, and the potential miR genes targeting the NF-YA transcription factors regulating abiotic stress tolerance were analysed. Twenty-three Eco-miR169 members and one Eco_N1 miRNA targeting EcNF-YA13 were identified in the finger millet genome. The presence of relevant cis-elements such as ABRE (abscisic acid-responsive elements), DRE (dehydration-responsive element), and MYB (myeloblastosis) indicates that the target of Eco-miR169 might be involved in abiotic stress responses. The tissue-specific RNA-seq transcriptomic expression pattern of Eco-miR169 showed variable fold of expression in seedlings compared to the control. At the same time, the expression of EcNF-YA13 (target genes of Eco-miR169 members and Eco_N1) presented a downregulated trend under salinity and dehydration conditions compared to the control. Tissue-specific RNA-seq followed by expression analysis confirmed the antagonistic effect of Eco-miR genes on EcNF-YA13. In a nutshell, the results of this study could be utilized as a platform for further exploration and characterization of finger millet Eco-miR169-EcNF-YA13gene regulatory network.

Overexpression of maize transcription factor ZmNF-YC14 positively regulates drought and salt stress responses in Arabidopsis thaliana

Maize (Zea mays L.) is a food crop with the largest planted area globally and one of the highest total yields worldwide. However, in recent years, deteriorating climate, increasing scarcity of freshwater resources, and rising land salinity have caused drought and salinity stress to be the two major factors that restrict crop growth, development, and yield, significantly affecting crop production and ecological sustainability. Nuclear factor Ys (NF-Ys) are an important class of transcription factors (TFs); however, their roles in plant stress tolerance responses and the underlying molecular mechanisms remain largely unknown. In this study, we conducted a bioinformatic analysis of 17 members of the maize NF-YC family and examined the ZmNF-YC14 gene through multiple sequence alignment among different species and HFD_NF-YC-like functional domains. Reverse transcription quantitative PCR (RT-qPCR) results indicated that ZmNF-YC14 exhibited the highest expression levels in maize leaves and was positively expressed under both drought and salt stress treatments. Western blot analysis revealed a distinct band at 27.68 kDa. Analyses of Escherichia coli BL21 and yeast strains confirmed that ZmNF-YC14 plays a biological role in enhancing tolerance to salt and drought stress. Arabidopsis plants overexpressing ZmNF-YC14 demonstrated reduced levels of hydrogen peroxide, superoxide anion, and malondialdehyde while exhibiting increased peroxidase, catalase, and superoxide dismutase activities after drought and salt stress treatments. This effect was attributed to the reciprocal relationship between ZmNF-YC14 and its downstream target gene ZmCONSTANS-LIKE16. Therefore, ZmNF-YC14 and ZmCONSTANS-LIKE16 may be essential for the response to abiotic stresses such as drought and salt stress in maize. They play a crucial role in the development of new germplasm, cultivation of new maize varieties, addressing the 'necklace' problem in crop breeding, and ensuring national food security.

Mutations in HEADING DATE 1 affect transcription and cell wall composition in rice

Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.

Identification of nuclear factor YA6 genes in sorghum and characterization of their involvement in drought tolerance

Nuclear factor Y alpha proteins (NF-YAs) are conserved transcription factor proteins crucial to plant growth and development that exhibit specific responses to biotic and abiotic stresses. Using bioinformatics approaches to investigate the NF-YA family in sorghum (Sorghum bicolor), we identified nine SbNF-YA genes unevenly distributed on four of the 10 sorghum chromosomes. Despite variations in gene structure, all encode proteins have the characteristic CBFB_NFYA domain and other predicted motifs. The secondary structure of SbNF-YA members is predominantly composed of α-helices and random coils. A phylogenetic analysis of NF-YAs of sorghum and other plant species indicated that SbNF-YAs are closely related to NF-YAs from maize (Zea mays) and distantly related to those in Arabidopsis (Arabidopsis thaliana). A colinearity analysis determined that six of the nine SbNF-YA genes arose from segmental duplication events. Transcriptome and RT-qPCR analyses showed that the expression levels of eight of the SbNF-YA genes (SbNF-YA5 being the exception) are responsive to drought stress to varying degrees. Notably, SbNF-YA1, SbNF-YA4, SbNF-YA6, SbNF-YA8, and SbNF-YA9 expression was significantly upregulated under the stress conditions, suggesting that they participate in drought response. When heterologously expressed in Arabidopsis, SbNF-YA6 conferred greater tolerance of drought stress imposed by treatment with the osmolyte mannitol, with the transgenic Arabidopsis lines showing superior germination rates; longer roots; higher fresh weight; higher activities of the enzymes peroxidase, superoxide dismutase, and catalase; and higher soluble protein and proline contents, compared to the wild type. Additionally, the transgenic Arabidopsis lines accumulated lower levels of hydrogen peroxide, superoxide anion, and malondialdehyde. The expression levels of several drought-responsive genes were elevated in transgenic Arabidopsis seedlings relative to the wild type, indicating that the heterologous expression of SbNF-YA6 enhances the drought tolerance of Arabidopsis.

The role of nuclear factor-Y (NF-Y) transcription factor in plant growth and development

The nuclear factor-Y (NF-Y) transcription factor, also known as heme-activator protein (HAP) or CCAAT-binding factor (CBF), is a critical transcription factor widely present in eukaryotes. The number of NF-Y subunits has significantly increased in higher plants compared to animals and fungi. The NF-Y complex is composed of three subunits: (1) NF-YA; (2) NF-YB; and (3) NF-YC. NF-YB and NF-YC contain histone fold domains (HFDs), which can interact with NF-YA or other transcription factors, or directly bind to the promoter CCAAT box to regulate the transcription of downstream genes. NF-Y plays a significant role in various plant processes, including growth and development. This review elucidates the structural and functional aspects of NF-Y subunits, identified NF-Y complexes, and their molecular regulatory mechanisms. Understanding these facets of NF-Y provides valuable insights into advancing crop genetic improvement and promoting sustainable agricultural practices.

StNF-YA8-YB20-YC5 module regulates potato tuber dormancy by modulating gibberellin and abscisic acid pathways

The molecular mechanisms involved in the regulation of potato tuber dormancy are complex, involving a variety of related genes and enzymes, which modulate multiple signaling pathways. Nuclear factor-Y (NF-Y) transcription factors (TFs) are widely found in eukaryotes and are involved in the regulation of plant embryonic development, seed germination, fruit ripening, and in response to biotic and abiotic stress. Previously, we found that StNF-YA8 gene expression was increasing with the release of potato tuber dormancy. In this study, it was found that StNF-YA8 overexpressed tubers broke dormancy earlier than non-transgenic (NT) and StNF-YA8 downregulated tubers. Changes in abscisic acid (ABA) and gibberellin (GA) content of different types of tubers at different dormancy periods confirmed that both GA and ABA hormones influenced the differences in dormancy time. This was confirmed by the expression of GA pathway genes StGA3ox1 and StGA20ox1 genes and ABA pathway genes StCYP707A2 and StPP2CA1 genes in different tubers. The four genes described above were further shown to be target genes of the StNF-YA8 TF, which transcriptionally activates the expression of these genes. In addition, we verified the involvement of StNF-YA8 in the tuber dormancy release process by the interacting proteins StNF-YB20 and StNF-YC5, which are able to bind to the StNF-YA8-B20-C5 module to activate the transcription of GA and ABA pathway genes. Our study reveals the StNF-YA8-C5 module activates the transcription of the StCYP707A2, StPP2CA1, StGA3ox1, and StGA20ox1 genes and alters GA and ABA content, accelerating the release of dormancy in potato tubers.

The transcription factor NF-YA10 determines the area explored by Arabidopsis thaliana roots and directly regulates LAZY genes

Root developmental plasticity relies on transcriptional reprogramming, which largely depends on the activity of transcription factors (TFs). NF-YA2 and NF-YA10 (nuclear factor A2 and A10) are downregulated by the specific miRNA isoform miR169defg. Here, we analyzed the role of the Arabidopsis thaliana TF NF-YA10 in the regulation of lateral root (LR) development. Plants expressing a version of NF-YA10 resistant to miR169 cleavage showed a perturbation in the LR gravitropic response. By extracting several features of root architecture using an improved version of the ChronoRoot deep-learning-based phenotyping system, we uncovered that these plants showed a differential angle of LRs over time when compared to Col-0. Detailed phenotyping of root growth dynamics revealed that NF-YA10 misregulation modulates the area explored by Arabidopsis roots. Furthermore, we found that NF-YA10 directly regulates LAZY genes, which were previously linked to gravitropism, by targeting their promoter regions. Hence, the TF NF-YA10 is a new element in the control of LR bending and root system architecture.

Aging-dependent temporal regulation of MIR156 epigenetic silencing by CiLDL1 and CiNF-YB8 in chrysanthemum

Temporal decline in microRNA miR156 expression is crucial for the transition to, and maintenance of, the adult phase and flowering competence in flowering plants. However, the molecular mechanisms underlying the temporal regulation of miR156 reduction remain largely unknown. Here, we investigated the epigenetic mechanism regulating the temporal silencing of cin-MIR156 in wild chrysanthemum (Chrysanthemum indicum), focusing on the role of the lysine-specific demethylase CiLDL1 and the nuclear factor Y complex. CiLDL1 and CiNF-YB8 interact with the classical histone-like fold domain (HFD) of CiNF-YC1 and CiNF-YA3, which form distinct heterotrimers binding to the 'CCAAT' box in the promoter region of cin-MIR156ab. CiLDL1 and CiNF-YB8 have opposing effects on cin-MIR156ab expression, with influencing histone 3 lysine 4 demethylation (H3K4me2) levels at the cin-MIR156ab locus. During aging, decreased CiNF-YB8 expression leads to a quantitative switch from the CiNF-YA3-CiNF-YC1-CiNF-YB8 heterotrimer to the CiNF-YA3-CiNF-YC1-CiLDL1 heterotrimer, which reduces H3K4me2 levels at the cin-MIR156ab locus, thus temporal silencing its expression. Our results thus reveal that the dynamic regulatory shift between CiLDL1 and CiNF-YB8 ensures proper aging-dependent flowering in chrysanthemum.

Transcriptome Analysis Revealed the Regulatory Mechanism of DIMBOA Affecting Early Somatic Embryogenesis in Dimocarpus longan Lour

Dimocarpus longan Lour. is an evergreen tree of the genus Longan in the Sapindaceae family, native to tropical and subtropical regions. Longan embryonic development is closely related to fruit set and fruit quality. An in-depth study of the mechanism of longan embryonic development could therefore contribute to the development of the longan industry. DIMBOA is the principal compound representing benzoxazinoids (BXs), and is closely linked to auxin biosynthesis and signal transduction. Auxin is one of the crucial hormones for inducing somatic embryogenesis (SE) in plants. Previous research has shown that DIMBOA promotes morphogenesis in the early somatic embryogenesis of longan, but the specific regulatory mechanism has not yet been clarified. To elucidate the molecular mechanism by which DIMBOA affects early somatic embryogenesis in longan, we chose longan embryogenic cultures grown under 0 mg/L DIMBOA as the control group (the check, CK), and longan embryogenic cultures grown under 0.1 mg/L DIMBOA as the treatment group (D) to be analyzed by transcriptomic sequencing. A total of 478 differentially expressed genes (DEGs) are detected in check vs. D, of which 193 are upregulated and 285 are downregulated. These DEGs are significantly enriched in the biosynthetic and metabolic functions of various substances such as vitamin B6 (VB6) biosynthesis, phenylpropanoid pathways, and carbohydrate metabolism. DIMBOA affects SE processes in longan via TFs, including MYB, ZF, bHLH, LBD, NAC, WRKY, etc. After DIMBOA treatment, the expression of most of the key genes for IAA synthesis was significantly downregulated, VB6 content was significantly reduced, and H2O2 content was significantly increased. Therefore, it is suggested that DIMBOA directly or indirectly affects the H2O2 content through the VB6 metabolic pathway, thereby regulating the endogenous IAA level to modulate the early SE morphogenesis of longan.

Genome-Wide Identification and Expression Pattern Analysis of Nuclear Factor Y B/C Genes in Pinus koraiensis, and Functional Identification of LEAFY COTYLEDON 1

The nuclear factor Y (NF-Y) transcription factor is widely involved in various plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress responses. This study presents a comprehensive genome-wide identification and expression profile of transcription factors NF-YB and NF-YC in Pinus koraiensis. Eight NF-YB and seven NF-YC transcription factors were identified through bioinformatics analysis, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. We evaluate the expression patterns of NF-YB/C genes in various tissues and somatic embryo maturation processes through the transcriptomics of ABA-treated tissues from multiple nutritional tissues, reproductive tissues, and somatic embryo maturation processes. The Leafy cotyledon1 (LEC1) gene belongs to the LEC1-type gene in the NF-YB family, numbered PkNF-YB7. In this study, we characterized the function of PkLEC1 during somatic embryonic development using genetic transformation techniques. The results indicate that PkNF-YB/C transcription factors are involved in the growth and development of nutritional tissues and reproductive organs, with specific high expression in PkNF-YB7 embryogenic callus, somatic embryos, zygotic embryos, and macropores. Most PkNF YB/C genes do not respond to ABA treatment during the maturation culture process. Compared with the absence of ABA, PkNF-YB8 was up-regulated in ABA treatment for one week (4.1 times) and two weeks (11.6 times). However, PkNF-YC5 was down-regulated in both one week (0.6 times) and two weeks (0.36 times) of culture, but the down-regulation trend was weakened in tissues treated with ABA (0.72-0.83 times). In addition, the promoter of PkNF YB/Cs was rich in elements that respond to various plant hormones, indicating their critical role in hormone pathways. The overexpression of PkLEC1 stimulated the generation of early somatic embryos from callus tissue with no potential for embryogenesis, enhancing the somatic embryogenesis ability of P. koraiensis callus tissue.

Increased chloroplast occupancy in bundle sheath cells of rice hap3H mutants revealed by Chloro-Count: a new deep learning-based tool

There is an increasing demand to boost photosynthesis in rice to increase yield potential. Chloroplasts are the site of photosynthesis, and increasing their number and size is a potential route to elevate photosynthetic activity. Notably, bundle sheath cells do not make a significant contribution to overall carbon fixation in rice, and thus, various attempts are being made to increase chloroplast content specifically in this cell type. In this study, we developed and applied a deep learning tool, Chloro-Count, and used it to quantify chloroplast dimensions in bundle sheath cells of OsHAP3H gain- and loss-of-function mutants in rice. Loss of OsHAP3H increased chloroplast occupancy in bundle sheath cells by 50%. When grown in the field, mutants exhibited increased numbers of tillers and panicles. The implementation of Chloro-Count enabled precise quantification of chloroplasts in loss- and gain-of-function OsHAP3H mutants and facilitated a comparison between 2D and 3D quantification methods. Collectively, our observations revealed that a mechanism operates in bundle sheath cells to restrict chloroplast occupancy as cell dimensions increase. That mechanism is unperturbed in Oshap3H mutants but loss of OsHAP3H function leads to an increase in chloroplast numbers. The use of Chloro-Count also revealed that 2D quantification is compromised by the positioning of chloroplasts within the cell.

The Roles of MicroRNAs in the Regulation of Rice-Pathogen Interactions

Rice is exposed to attacks by the three most destructive pathogens, Magnaporthe oryzae (M. oryzae), Xanthomonas oryzae pv. oryzae (Xoo), and Rhizoctonia solani (R. solani), which cause substantial yield losses and severely threaten food security. To cope with pathogenic infections, rice has evolved diverse molecular mechanisms to respond to a wide range of pathogens. Among these strategies, plant microRNAs (miRNAs), endogenous single-stranded short non-coding RNA molecules, have emerged as promising candidates in coordinating plant-pathogen interactions. MiRNAs can modulate target gene expression at the post-transcriptional level through mRNA cleavage and/or translational inhibition. In rare instances, they also influence gene expression at the transcriptional level through DNA methylation. In recent years, substantial advancements have been achieved in the investigation of microRNA-mediated molecular mechanisms in rice immunity. Therefore, we attempt to summarize the current advances of immune signaling mechanisms in rice-pathogen interactions that are regulated by osa-miRNAs, including their functions and molecular mechanisms. We also focus on recent findings concerning the role of osa-miRNAs that respond to M. oryzae, Xoo, and R. solani, respectively. These insights enhance our understanding of how the mechanisms of osa-miRNAs mediate rice immunity and may facilitate the development of improved strategies for breeding pathogen-resistant rice varieties.

Molecular condensation of the CO/NF-YB/NF-YC/FT complex gates floral transition in Arabidopsis

The plant master photoperiodic regulator CONSTANS (CO) interacts with Nuclear Factor-Y subunits B2 (NF-YB2) and C9 (NF-YC9) and transcriptionally activates the florigen gene FLOWERING LOCUS T (FT), regulating floral transition. However, the molecular mechanism of the functional four-component complex assembly in the nucleus remains elusive. We report that co-phase separation of CO with NF-YB2/NF-YC9/FT precisely controls heterogeneous CO assembly and FT transcriptional activation. In response to light signals, CO proteins form functional percolation clusters from a diffuse distribution in a B-box-motif-dependent manner. Multivalent coassembly with NF-YC9 and NF-YB2 prevents inhibitory condensate formation and is necessary to maintain proper CO assembly and material properties. The intrinsically disordered region (IDR) of NF-YC9, containing a polyglutamine motif, fine-tunes the functional properties of CO/NF-YB/NF-YC condensates. Specific FT promoter recognition with polyelectrolyte partitioning also enables the fluidic functional properties of CO/NF-YB/NF-YC/FT condensates. Our findings offer novel insights into the tunable macromolecular condensation of the CO/NF-YB/NF-YC/FT complex in controlling flowering in the photoperiod control.

Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat (Triticum aestivum L.)

The NF-YA gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the NF-YA gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19 TaNF-YA genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of TaNF-YAs. Furthermore, cis-acting elements within the promoters of TaNF-YAs were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the NF-YA gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify TaNF-YAs influencing grain development. Finally, it was found that NF-YAs had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation.

Overexpression of an NF-YB gene family member, EaNF-YB2, enhances drought tolerance in sugarcane (Saccharum Spp. Hybrid)

BACKGROUND

Drought is one of main critical factors that limits sugarcane productivity and juice quality in tropical regions. The unprecedented changes in climate such as monsoon failure, increase in temperature and other factors warrant the need for development of stress tolerant cultivars to sustain sugar production. Plant Nuclear factor (NF-Y) is one of the major classes of transcription factors that have a major role in plant development and abiotic stress response. In our previous studies, we found that under drought conditions, the nuclear factor NF-YB2 was highly expressed in Erianthus arundinaceus, an abiotic stress tolerant wild genus of Saccharum species. In this study, the coding sequence of NF-YB2 gene was isolated from Erianthus arundinaceus and overexpressed in sugarcane to develop drought tolerant lines. RESULTS : EaNF-YB2 overexpressing sugarcane (OE) lines had higher relative water content, chlorophyll content and photosynthetic efficiency compared to non-transgenic (NT) control. In addition, overexpressing lines had higher activity of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR), and higher proline content, lower malondialdehyde (MDA) and peroxide (H2O2) contents. The expression studies revealed that EaNF-YB2 expression was significantly higher in OE lines than NT control under drought stress. The OE lines had an elevated expression of abiotic stress responsive genes such as BRICK, HSP 70, DREB2, EDH45, and LEA3. The morphological analysis revealed that OE lines exhibited less wilting than NT under drought conditions.

CONCLUSION

This study provides insights into the role of the EaNF-YB2 gene in drought tolerance in sugarcane. Based on the findings of this study, the EaNF-YB2 gene can be potentially exploited to produce drought tolerant sugarcane cultivars to sustain sugarcane production under water deficit conditions.

Plant Nuclear Factor Y (NF-Y) Transcription Factors: Evolving Insights into Biological Functions and Gene Expansion

Gene expansion is a common phenomenon in plant transcription factor families; however, the underlying molecular mechanisms remain elusive. Examples of gene expansion in transcription factors are found in all eukaryotes. One example is plant nuclear factor Y (NF-Y) transcription factors. NF-Y is ubiquitous to eukaryotes and comprises three independent protein families: NF-YA, NF-YB, and NF-YC. While animals and fungi mostly have one of each NF-Y subunit, NF-Y is greatly expanded in plants. For example, humans have one each of NF-YA, NF-YB, and NF-YC, while the model plant Arabidopsis has ten each of NF-YA, NF-YB, and NF-YC. Our understanding of the plant NF-Y, including its biological roles, molecular mechanisms, and gene expansion, has improved over the past few years. Here we will review its biological roles and focus on studies demonstrating that NF-Y can serve as a model for plant gene expansion. These studies show that NF-Y can be classified into ancestrally related subclasses. Further, the primary structure of each NF-Y contains a conserved core domain flanked by non-conserved N- and C-termini. The non-conserved N- and C-termini, under pressure for diversifying selection, may provide clues to this gene family's retention and functional diversification following gene duplication. In summary, this review demonstrates that NF-Y expansion has the potential to be used as a model to study the gene expansion and retention of transcription factor families.

A Novel Member of miR169 Family Negatively Regulates Maize Resistance Against Bipolaris maydis

MicroRNAs (miRNAs) have been confirmed to play important roles in plant defense response. However, the key maize miRNAs involved in the defense response against Bipolaris maydis are very limited. In this study, a novel member of the miR169 family in response to B. maydis, named zma-miR169s, was discovered and investigated. The expression levels of pre-miR169s and zma-miR169s were significantly repressed during B. maydis infection. The CRISPR/Cas9-induced zma-miR169s mutant exhibited more resistance against B. maydis, whereas overexpression of zma-miR169s enhanced susceptibility, supporting that zma-miR169s might play a negative role in maize resistance. Moreover, RNA-seq and Gene Ontology analysis showed that differentially expressed genes were highly enriched in the oxidation-reduction process and plant hormone pathway. Hence, reactive oxygen species (ROS) and plant hormone levels were further investigated. ROS detection confirmed that the zma-miR169s mutant accumulated more ROS, while less ROS was detected in transgenic maize OE-miR169s. Furthermore, more remarkable changes in PR-1 expression levels and salicylic acid (SA) contents were detected in the zma-miR169s mutant compared with wild-type and transgenic maize during B. maydis infection. Additionally, nuclear transcription factors (NF-YA1 and NF-YA13) were identified as targets regulated by zma-miR169s through the agrobacterium-mediated transient expression method. Overexpression of ZmNF-YA13 enhanced Arabidopsis resistance to Pseudomonas syringae pv. tomato DC3000. Taken together, our results suggest that zma-miR169s negatively regulates maize defense responses by influencing ROS accumulation and the SA-dependent signaling pathway.

Genome-Wide Identification and Expression Profiles of Nuclear Factor Y A Transcription Factors in Blueberry Under Abiotic Stress

Nuclear Factor Y A (NF-YA) transcription factors are widely involved in multiple plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress response. This study presents a comprehensive genome-wide identification and expression profiling of NF-YA transcription factors in blueberry (Vaccinium corymbosum), an important economic crop with good adaptability, under abiotic stress conditions. Given the economic significance and health benefits of blueberries, understanding their responses to environmental stresses, such as salt, drought, and temperature extremes, is crucial. A total of 24 NF-YA transcription factors were identified through bioinformatics analyses, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. The expression patterns of these NF-YA genes were evaluated in various tissues (roots, stems, and leaves) and under different stress treatments (abscisic acid, salt, and cold) using quantitative real-time PCR (qRT-PCR). The results indicated that most VcNF-YA genes exhibited higher expression levels in stems and leaves compared to roots. Most VcNF-YAs were responsive to the stress treatment. Furthermore, cis-acting element analysis revealed that the promoters of VcNF-YAs were enriched with elements responsive to abiotic stress, suggesting their pivotal role in stress adaptation. This research unveils the expressional responses of NF-YA transcription factors in blueberry upon abiotic stresses and lays the groundwork for future studies on improving crop adaptation.

Integrating gene expression analysis and ecophysiological responses to water deficit in leaves of tomato plants

Soil water deficit (WD) significantly impacts plant survival and crop yields. Many gaps remain in our understanding of the synergistic coordination between molecular and ecophysiological responses delaying substantial drought-induced effects on plant growth. To investigate this synergism in tomato leaves, we combined molecular, ecophysiological, and anatomical methods to examine gene expression patterns and physio-anatomical characteristics during a progressing WD experiment. Four sampling points were selected for transcriptomic analysis based on the key ecophysiological responses of the tomato leaves: 4 and 5 days after WD (d-WD), corresponding to 10% and 90% decrease in leaf stomatal conductance; 8 d-WD, the leaf wilting point; and 10 d-WD, when air embolism blocks 12% of the leaf xylem water transport. At 4 d-WD, upregulated genes were mostly linked to ABA-independent responses, with larger-scale ABA-dependent responses occurring at 5 d-WD. At 8 d-WD, we observed an upregulation of heat shock transcription factors, and two days later (10 d-WD), we found a strong upregulation of oxidative stress transcription factors. Finally, we found that young leaves present a stronger dehydration tolerance than mature leaves at the same drought intensity level, presumably because young leaves upregulate genes related to increased callose deposition resulting in limiting water loss to the phloem, and related to increased cell rigidity by modifying cell wall structures. This combined dataset will serve as a framework for future studies that aim to obtain a more holistic WD plant response at the molecular, ecophysiological and anatomical level.

Nuclear factor-Y-polycomb repressive complex2 dynamically orchestrates starch and seed storage protein biosynthesis in wheat

The endosperm in cereal grains is instrumental in determining grain yield and seed quality, as it controls starch and seed storage protein (SSP) production. In this study, we identified a specific nuclear factor-Y (NF-Y) trimeric complex in wheat (Triticum aestivum L.), consisting of TaNF-YA3-D, TaNF-YB7-B, and TaNF-YC6-B, and exhibiting robust expression within the endosperm during grain filling. Knockdown of either TaNF-YA3 or TaNF-YC6 led to reduced starch but increased gluten protein levels. TaNF-Y indirectly boosted starch biosynthesis genes by repressing TaNAC019, a repressor of cytosolic small ADP-glucose pyrophosphorylase 1a (TacAGPS1a), sucrose synthase 2 (TaSuS2), and other genes involved in starch biosynthesis. Conversely, TaNF-Y directly inhibited the expression of Gliadin-γ-700 (TaGli-γ-700) and low molecular weight-400 (TaLMW-400). Furthermore, TaNF-Y components interacted with SWINGER (TaSWN), the histone methyltransferase subunit of Polycomb repressive complex 2 (PRC2), to repress TaNAC019, TaGli-γ-700, and TaLMW-400 expression through trimethylation of histone H3 at lysine 27 (H3K27me3) modifications. Notably, weak mutation of FERTILIZATION INDEPENDENT ENDOSPERM (TaFIE), a core PRC2 subunit, reduced starch but elevated gliadin and LMW-GS contents. Intriguingly, sequence variation within the TaNF-YB7-B coding region was linked to differences in starch and SSP content. Distinct TaNF-YB7-B haplotypes affect its interaction with TaSWN-B, influencing the repression of targets like TaNAC019 and TaGli-γ-700. Our findings illuminate the intricate molecular mechanisms governing TaNF-Y-PRC2-mediated epigenetic regulation for wheat endosperm development. Manipulating the TaNF-Y complex holds potential for optimizing grain yield and enhancing grain quality.

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.

Genome-wide identification of nuclear factor -Y (NF-Y) transcription factor family in finger millet reveals structural and functional diversity

The Nuclear Factor Y (NF-Y) is one of the widely explored transcription factors (TFs) family for its potential role in regulating molecular mechanisms related to stress response and developmental processes. Finger millet (Eleusine coracana (L.) Gaertn) is a hardy and stress-tolerant crop where partial efforts have been made to characterize a few transcription factors. However, the NF-Y TF is still poorly explored and not well documented. The present study aims to identify and characterize NF-Y genes of finger millet using a bioinformatics approach. Genome mining revealed 57 EcNF-Y (Eleusine coracana Nuclear Factor-Y) genes in finger millet, comprising 18 NF-YA, 23 NF-YB, and 16 NF-YC genes. The gene organization, conserved motif, cis-regulatory elements, miRNA target sites, and three-dimensional structures of these NF-Ys were analyzed. The nucleotide substitution rate and gene duplication analysis showed the presence of 7 EcNF-YA, 10 EcNF-YB, and 8 EcNF-YC paralogous genes and revealed the possibilities of synonymous substitution and stabilizing selection during evolution. The role of NF-Ys of finger millet in abiotic stress tolerance was evident by the presence of relevant cis-elements such as ABRE (abscisic acid-responsive elements), DRE (dehydration-responsive element), MYB (myeloblastosis) or MYC (myelocytomatosis). Twenty-three isoforms of miR169, mainly targeting a single NF-Y gene, i.e., the EcNF-YA13 gene, were observed. This interaction could be targeted for finger millet improvement against Magnaporthe oryzae (blast fungus). Therefore, by this study, the putative functions related to biotic and abiotic stress tolerance for many of the EcNF-Y genes could be explored in finger millet.

Nematode-resistance loci in upland cotton genomes are associated with structural differences

Reniform and root-knot nematode are two of the most destructive pests of conventional upland cotton, Gossypium hirsutum L., and continue to be a major threat to cotton fiber production in semiarid regions of the Southern United States and Central America. Fortunately, naturally occurring tolerance to these nematodes has been identified in the Pima cotton species (Gossypium barbadense) and several upland cotton varieties (G. hirsutum), which has led to a robust breeding program that has successfully introgressed and stacked these independent resistant traits into several upland cotton lineages with superior agronomic traits, e.g. BAR 32-30 and BARBREN-713. This work identifies the genomic variations of these nematode-tolerant accessions by comparing their respective genomes to the susceptible, high-quality fiber-producing parental line of this lineage: Phytogen 355 (PSC355). We discover several large genomic differences within marker regions that harbor putative resistance genes as well as expression mechanisms shared by the two resistant lines, with respect to the susceptible PSC355 parental line. This work emphasizes the utility of whole-genome comparisons as a means of elucidating large and small nuclear differences by lineage and phenotype.

Expression of AtNF-YB1 activates early flowering, showing potential in breeding hybrid rice

The nuclear factor Y (NF-Y) has been shown to be involved in plant growth and development in response to various environmental signals. However, the integration of these mechanisms into breeding practices for new cultivars has not been extensively investigated. In this study, the Arabidopsis gene AtNF-YB1 was introduced into rice, including inbred Kasalath and the hybrids Jinfeng × Chenghui 727 and Jinfeng × Chuanhui 907. The obtained transgenic rice showed early flowering under both natural long day (NLD) and natural short day (NSD) conditions. For the inbred Kasalath, the transgenic lines clearly showed a shorter plant height and lower grain yield, with a decrease in spike length and grain number but more productive panicles. However, the hybrids with AtNF-YB1 had much smaller or even zero reduction in spike length and grain number and more productive panicles. Thus, maintained or even increased grain yields of the transgenic hybrids were recorded under the NLD conditions. Quantitative PCR analysis indicated that the rice flowering initiation pathways were early activated via the suppression of Ghd7 induction in the transgenic rice. RNA-Seq further demonstrated that three pathways related to plant photosynthesis were markedly upregulated in both Jinfeng B and the hybrid Jinfeng × Chuanhui 907 with AtNF-YB1 expression. Moreover, physiological experiments showed an upregulation of photosynthetic rates in the transgenic lines. Taken together, this study suggests that AtNF-YB1 expression in rice not only induces early flowering but also benefits photosynthesis, which might be used to develop hybrid varieties with early ripening.

A pair of nuclear factor Y transcription factors act as positive regulators in jasmonate signaling and disease resistance in Arabidopsis

The plant hormone jasmonate (JA) regulates plant growth and immunity by orchestrating a genome-wide transcriptional reprogramming. In the resting stage, JASMONATE-ZIM DOMAIN (JAZ) proteins act as main repressors to regulate the expression of JA-responsive genes in the JA signaling pathway. However, the mechanisms underlying de-repression of JA-responsive genes in response to JA treatment remain elusive. Here, we report two nuclear factor Y transcription factors NF-YB2 and NF-YB3 (thereafter YB2 and YB3) play key roles in such de-repression in Arabidopsis. YB2 and YB3 function redundantly and positively regulate plant resistance against the necrotrophic pathogen Botrytis cinerea, which are specially required for transcriptional activation of a set of JA-responsive genes following inoculation. Furthermore, YB2 and YB3 modulated their expression through direct occupancy and interaction with histone demethylase Ref6 to remove repressive histone modifications. Moreover, YB2 and YB3 physically interacted with JAZ repressors and negatively modulated their abundance, which in turn attenuated the inhibition of JAZ proteins on the transcription of JA-responsive genes, thereby activating JA response and promoting disease resistance. Overall, our study reveals the positive regulators of YB2 and YB3 in JA signaling by positively regulating transcription of JA-responsive genes and negatively modulating the abundance of JAZ proteins.

Genome-wide investigation of the nuclear factor Y gene family in Ginger (Zingiber officinale Roscoe): evolution and expression profiling during development and abiotic stresses

BACKGROUND

Nuclear factor Y (NF-Y) plays a vital role in numerous biological processes as well as responses to biotic and abiotic stresses. However, its function in ginger (Zingiber officinale Roscoe), a significant medicinal and dietary vegetable, remains largely unexplored. Although the NF-Y family has been thoroughly identified in many plant species, and the function of individual NF-Y TFs has been characterized, there is a paucity of knowledge concerning this family in ginger.

METHODS

We identified the largest number of NF-Y genes in the ginger genome using two BLASTP methods as part of our ginger genome research project. The conserved motifs of NF-Y proteins were analyzed through this process. To examine gene duplication events, we employed the Multiple Collinearity Scan toolkit (MCScanX). Syntenic relationships of NF-Y genes were mapped using the Dual Synteny Plotter software. Multiple sequence alignments were performed with MUSCLE under default parameters, and the resulting alignments were used to generate a maximum likelihood (ML) phylogenetic tree with the MEGA X program. RNA-seq analysis was conducted on collected samples, and statistical analyses were performed using Sigma Plot v14.0 (SYSTAT Software, USA).

RESULTS

In this study, the ginger genome was utilized to identify 36 NF-Y genes (10 ZoNF-YAs, 16 ZoNF-YBs, and 10 ZoNF-YCs), which were renamed based on their chromosomal distribution. Ten distinct motifs were identified within the ZoNF-Y genes, with certain unique motifs being vital for gene function. By analyzing their chromosomal location, gene structure, conserved protein motifs, and gene duplication events, we gained a deeper understanding of the evolutionary characteristics of these ZoNF-Y genes. Detailed analysis of ZoNF-Y gene expression patterns across various tissues, performed through RNA-seq and qRT-PCR, revealed their significant role in regulating ginger rhizome and flower growth and development. Additionally, we identified the ZoNF-Y family genes that responded to abiotic stresses.

CONCLUSION

This study represents the first identification of the ZoNF-Y family in ginger. Our findings contribute to research on evolutionary characteristics and provide a better understanding of the molecular basis for development and abiotic stress response. Furthermore, it lays the foundation for further functional characterization of ZoNF-Y genes with an aim of ginger crop improvement.

miR156-SPL and miR169-NF-YA Modules Regulate the Induction of Somatic Embryogenesis in Arabidopsis via LEC- and Auxin-Related Pathways

The embryogenic transition of plant somatic cells to produce somatic embryos requires extensive reprogramming of the cell transcriptome. The prominent role of transcription factors (TFs) and miRNAs in controlling somatic embryogenesis (SE) induction in plants was documented. The profiling of MIRNA expression in the embryogenic culture of Arabidopsis implied the contribution of the miR156 and miR169 to the embryogenic induction. In the present study, the function of miR156 and miR169 and the candidate targets, SPL and NF-YA genes, were investigated in Arabidopsis SE. The results showed that misexpression of MIRNA156 and candidate SPL target genes (SPL2, 3, 4, 5, 9, 10, 11, 13, 15) negatively affected the embryogenic potential of transgenic explants, suggesting that specific fine-tuning of the miR156 and target genes expression levels seems essential for efficient SE induction. The results revealed that SPL11 under the control of miR156 might contribute to SE induction by regulating the master regulators of SE, the LEC (LEAFY COTYLEDON) genes (LEC1, LEC2, FUS3). Moreover, the role of miR169 and its candidate NF-YA targets in SE induction was demonstrated. The results showed that several miR169 targets, including NF-YA1, 3, 5, 8, and 10, positively regulated SE. We found, that miR169 via NF-YA5 seems to modulate the expression of a master SE regulator LEC1/NF-YA and other auxin-related genes: YUCCA (YUC4, 10) and PIN1 in SE induction. The study provided new insights into miR156-SPL and miR169-NF-YA functions in the auxin-related and LEC-controlled regulatory network of SE.

Identification and expression analysis of nuclear factor Y transcription factor genes under drought, cold and Eldana infestation in sugarcane (Saccharum spp. hybrid)

BACKGROUND

The Nuclear Factor Y (NF-Y) transcription factor (TF) gene family plays a crucial role in plant development and response to stress. Limited information is available on this gene family in sugarcane.

OBJECTIVES

To identify sugarcane NF-Y genes through bioinformatic analysis and phylogenetic association and investigate the expression of these genes in response to abiotic and biotic stress.

METHODS

Sugarcane NF-Y genes were identified using comparative genomics from functionally annotated Poaceae and Arabidopsis species. Quantitative PCR and transcriptome analysis assigned preliminary functional roles to these genes in response to water deficit, cold and African sugarcane borer (Eldana saccharina) infestation.

RESULTS

We identify 21 NF-Y genes in sugarcane. Phylogenetic analysis revealed three main branches representing the subunits with potential discrepancies present in the assignment of numerical names of some NF-Y putative orthologs across the different species. Gene expression analysis indicated that three genes, ShNF-YA1, A3 and B3 were upregulated and two genes, NF-YA4 and A7 were downregulated, while three genes were upregulated, ShNF-YB2, B3 and C4, in the plants exposed to water deficit and cold stress, respectively. Functional involvement of NF-Y genes in the biotic stress response were also detected where three genes, ShNF-YA6, A3 and A7 were downregulated in the early resistant (cv. N33) response to Eldana infestation whilst only ShNF-YA6 was downregulated in the susceptible (cv. N11) early response.

CONCLUSIONS

Our research findings establish a foundation for investigating the function of ShNF-Ys and offer candidate genes for stress-resistant breeding and improvement in sugarcane.

Transcription factor TaNF-YB2 interacts with partners TaNF-YA7/YC7 and transcriptionally activates distinct stress-defensive genes to modulate drought tolerance in T. Aestivum

BACKGROUND

Drought stress limits significantly the crop productivity. However, plants have evolved various strategies to cope with the drought conditions by adopting complex molecular, biochemical, and physiological mechanisms. Members of the nuclear factor Y (NF-Y) transcription factor (TF) family constitute one of the largest TF classes and are involved in plant responses to abiotic stresses.

RESULTS

TaNF-YB2, a NY-YB subfamily gene in T. aestivum, was characterized in this study focusing on its role in mediating plant adaptation to drought stress. Yeast two-hybrid (Y-2 H), biomolecular fluoresence complementation (BiFC), and Co-immunoprecipitation (Co-IP) assays indicated that TaNF-YB2 interacts with the NF-YA member TaNF-YA7 and NF-YC family member TaNF-YC7, which constitutes a heterotrimer TaNF-YB2/TaNF-YA7/TaNF-YC7. The TaNF-YB2 transcripts are induced in roots and aerial tissues upon drought signaling; GUS histochemical staining analysis demonstrated the roles of cis-regulatory elements ABRE and MYB situated in TaNF-YB2 promoter to contribute to target gene response to drought. Transgene analysis on TaNF-YB2 confirmed its functions in regulating drought adaptation via modulating stomata movement, osmolyte biosynthesis, and reactive oxygen species (ROS) homeostasis. TaNF-YB2 possessed the abilities in transcriptionally activating TaP5CS2, the P5CS family gene involving proline biosynthesis and TaSOD1, TaCAT5, and TaPOD5, the genes encoding antioxidant enzymes. Positive correlations were found between yield and the TaNF-YB2 transcripts in a core panel constituting 45 wheat cultivars under drought condition, in which two types of major haplotypes including TaNF-YB2-Hap1 and -Hap2 were included, with the former conferring more TaNF-YB2 transcripts and stronger plant drought tolerance.

CONCLUSIONS

TaNF-YB2 is transcriptional response to drought stress. It is an essential regulator in mediating plant drought adaptation by modulating the physiological processes associated with stomatal movement, osmolyte biosynthesis, and reactive oxygen species (ROS) homeostasis, depending on its role in transcriptionally regulating stress response genes. Our research deepens the understanding of plant drought stress underlying NF-Y TF family and provides gene resource in efforts for molecular breeding the drought-tolerant cultivars in T. aestivum.

Genome-Wide Identification of Sorghum Paclobutrazol-Resistance Gene Family and Functional Characterization of SbPRE4 in Response to Aphid Stress

Sorghum (Sorghum bicolor), the fifth most important cereal crop globally, serves as a staple food, animal feed, and a bioenergy source. Paclobutrazol-Resistance (PRE) genes play a pivotal role in the response to environmental stress, yet the understanding of their involvement in pest resistance remains limited. In the present study, a total of seven SbPRE genes were found within the sorghum BTx623 genome. Subsequently, their genomic location was studied, and they were distributed on four chromosomes. An analysis of cis-acting elements in SbPRE promoters revealed that various elements were associated with hormones and stress responses. Expression pattern analysis showed differentially tissue-specific expression profiles among SbPRE genes. The expression of some SbPRE genes can be induced by abiotic stress and aphid treatments. Furthermore, through phytohormones and transgenic analyses, we demonstrated that SbPRE4 improves sorghum resistance to aphids by accumulating jasmonic acids (JAs) in transgenic Arabidopsis, giving insights into the molecular and biological function of atypical basic helix-loop-helix (bHLH) transcription factors in sorghum pest resistance.

ZmNF-YA1 Contributes to Maize Thermotolerance by Regulating Heat Shock Response

Zea mays (maize) is a staple food, feed, and industrial crop. Heat stress is one of the major stresses affecting maize production and is usually accompanied by other stresses, such as drought. Our previous study identified a heterotrimer complex, ZmNF-YA1-YB16-YC17, in maize. ZmNF-YA1 and ZmNF-YB16 were positive regulators of the drought stress response and were involved in maize root development. In this study, we investigated whether ZmNF-YA1 confers heat stress tolerance in maize. The nf-ya1 mutant and overexpression lines were used to test the role of ZmNF-YA1 in maize thermotolerance. The nf-ya1 mutant was more temperature-sensitive than the wild-type (WT), while the ZmNF-YA1 overexpression lines showed a thermotolerant phenotype. Higher malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation were observed in the mutant, followed by WT and overexpression lines after heat stress treatment, while an opposite trend was observed for chlorophyll content. RNA-seq was used to analyze transcriptome changes in nf-ya1 and its wild-type control W22 in response to heat stress. Based on their expression profiles, the heat stress response-related differentially expressed genes (DEGs) in nf-ya1 compared to WT were grouped into seven clusters via k-means clustering. Gene Ontology (GO) enrichment analysis of the DEGs in different clades was performed to elucidate the roles of ZmNF-YA1-mediated transcriptional regulation and their contribution to maize thermotolerance. The loss function of ZmNF-YA1 led to the failure induction of DEGs in GO terms of protein refolding, protein stabilization, and GO terms for various stress responses. Thus, the contribution of ZmNF-YA1 to protein stabilization, refolding, and regulation of abscisic acid (ABA), ROS, and heat/temperature signaling may be the major reason why ZmNF-YA1 overexpression enhanced heat tolerance, and the mutant showed a heat-sensitive phenotype.

Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar

The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.

Nuclear factor Y-A3b binds to the SINGLE FLOWER TRUSS promoter and regulates flowering time in tomato

The control of flowering time is essential for reproductive success and has a major effect on seed and fruit yield and other important agricultural traits in crops. Nuclear factors Y (NF-Ys) are transcription factors that form heterotrimeric protein complexes to regulate gene expression required for diverse biological processes, including flowering time control in plants. However, to our knowledge, there has been no report on mutants of individual NF-YA subunits that promote early flowering phenotype in plants. In this study, we identified SlNF-YA3b, encoding a member of the NF-Y transcription factor family, as a key gene regulating flowering time in tomato. Knockout of NF-YA3b resulted in an early flowering phenotype in tomato, whereas overexpression of NF-YA3b delayed flowering in transgenic tomato plants. NF-YA3b was demonstrated to form heterotrimeric protein complexes with multiple NF-YB/NF-YC heterodimers in yeast three-hybrid assays. Biochemical evidence indicated that NF-YA3b directly binds to the CCAAT cis-elements of the SINGLE FLOWER TRUSS (SFT) promoter to suppress its gene expression. These findings uncovered a critical role of NF-YA3b in regulating flowering time in tomato and could be applied to the management of flowering time in crops.

Expression profiling of Nuclear Factor-Y (NF-Y) transcription factors during dehydration and salt stress in finger millet reveals potential candidate genes for multiple stress tolerance

MAIN CONCLUSION

Expression profiling of NF-Y transcription factors during dehydration and salt stress in finger millet genotypes contrastingly differing in tolerance levels identifies candidate genes for further characterization and functional studies. The Nuclear Factor-Y (NF-Y) transcription factors are known for imparting abiotic stress tolerance in different plant species. However, there is no information on the role of this transcription factor family in naturally drought-tolerant crop finger millet (Eleusine coracana L.). Therefore, interpretation of expression profiles against drought and salinity stress may provide valuable insights into specific and/or overlapping expression patterns of Eleusine coracana Nuclear Factor-Y (EcNF-Y) genes. Given this, we identified 59 NF-Y (18 NF-YA, 23 NF-YB, and 18 NF-YC) encoding genes and designated them EcNF-Y genes. Expression profiling of these genes was performed in two finger millet genotypes, PES400 (dehydration and salt stress tolerant) and VR708 (dehydration and salt stress sensitive), subjected to PEG-induced dehydration and salt (NaCl) stresses at different time intervals (0, 6, and 12 h). The qRT-PCR expression analysis reveals that the six EcNF-Y genes namely EcNF-YA1, EcNF-YA5, EcNF-YA16, EcNF-YB6, EcNF-YB10, and EcNF-YC2 might be associated with tolerance to both dehydration and salinity stress in early stress condition (6 h), suggesting the involvement of these genes in multiple stress responses in tolerant genotype. In contrast, the transcript abundance of finger millet EcNF-YA5 genes was also observed in the sensitive genotype VR708 under late stress conditions (12 h) of both dehydration and salinity stress. Therefore, the EcNF-YA5 gene might be important for adaptation to salinity and dehydration stress in sensitive finger millet genotypes. Therefore, this gene could be considered as a susceptibility determinant, which can be edited to impart tolerance. The phylogenetic analyses revealed that finger millet NF-Y genes share strong evolutionary and functional relationship to NF-Ys governing response to abiotic stresses in rice, sorghum, maize, and wheat. This is the first report of expression profiling of EcNF-Ys genes identified from the finger millet genome and reveals potential candidate for enhancing dehydration and salt tolerance.

Jasmonate signaling pathway confers salt tolerance through a NUCLEAR FACTOR-Y trimeric transcription factor complex in Arabidopsis

Jasmonate (JA) is a well-known phytohormone essential for plant response to biotic stress. Recently, a crucial role of JA signaling in salt resistance has been highlighted; however, the specific regulatory mechanism remains largely unknown. In this study, we found that the NUCLEAR FACTOR-Y (NF-Y) subunits NF-YA1, NF-YB2, and NF-YC9 form a trimeric complex that positively regulates the expression of salinity-responsive genes, whereas JASMONATE-ZIM DOMAIN protein 8 (JAZ8) directly interacts with three subunits and acts as the key repressor to suppress both the assembly of the NF-YA1-YB2-YC9 trimeric complex and the transcriptional activation activity of the complex. When plants encounter high salinity, JA levels are elevated and perceived by the CORONATINE INSENSITIVE (COI) 1 receptor, leading to the degradation of JAZ8 via the 26S proteasome pathway, thereby releasing the activity of the NF-YA1-YB2-YC9 complex, initiating the activation of salinity-responsive genes, such as MYB75, and thus enhancing the salinity tolerance of plants.

Mining Heat-Resistant Key Genes of Peony Based on Weighted Gene Co-Expression Network Analysis

The RNA-Seq and gene expression data of mature leaves under high temperature stress of Paeonia suffruticosa 'Hu Hong' were used to explore the key genes of heat tolerance of peony. The weighted gene co-expression network analysis (WGCNA) method was used to construct the network, and the main modules and core genes of co-expression were screened according to the results of gene expression and module function enrichment analysis. According to the correlation of gene expression, the network was divided into 19 modules. By analyzing the expression patterns of each module gene, Blue, Salmon and Yellow were identified as the key modules of peony heat response related functions. GO and KEGG functional enrichment analysis was performed on the genes in the three modules and a network diagram was constructed. Based on this, two key genes PsWRKY53 (TRINITY_DN60998_c1_g2, TRINITY_DN71537_c0_g1) and PsHsfB2b (TRINITY_DN56794_c0_g1) were excavated, which may play a key role in the heat shock response of peony. The three co-expression modules and two key genes were helpful to further elucidate the heat resistance mechanism of P. suffruticosa 'Hu Hong'.

Genome-Wide Identification and Drought Stress Response Pattern of the NF-Y Gene Family in Cymbidium sinense

Cymbidium sinense, a type of orchid plant, is more drought-resistant and ornamental than other terrestrial orchids. Research has shown that many members of the NUCLEAR FACTOR Y (NF-Y) transcription factor family are responsive to plant growth, development, and abiotic stress. However, the mechanism of the NF-Y gene family's response to abiotic stress in orchids has not yet been reported. In this study, phylogenetic analysis allowed for 27 CsNF-Y genes to be identified (5 CsNF-YAs, 9 CsNF-YBs, and 13 CsNF-YC subunits), and the CsNF-Ys were homologous to those in Arabidopsis and Oryza. Protein structure analysis revealed that different subfamilies contained different motifs, but all of them contained Motif 2. Secondary and tertiary protein structure analysis indicated that the CsNF-YB and CsNF-YC subfamilies had a high content of alpha helix structures. Cis-element analysis showed that elements related to drought stress were mainly concentrated in the CsNF-YB and CsNF-YC subfamilies, with CsNF-YB3 and CsNF-YC12 having the highest content. The results of a transcriptome analysis showed that there was a trend of downregulation of almost all CsNF-Ys in leaves under drought stress, while in roots, most members of the CsNF-YB subfamily showed a trend of upregulation. Additionally, seven genes were selected for real-time reverse transcription quantitative PCR (qRT-PCR) experiments. The results were generally consistent with those of the transcriptome analysis. The regulatory roles of CsNF-YB 1, 2, and 4 were particularly evident in the roots. The findings of our study may make a great contribution to the understanding of the role of CsNF-Ys in stress-related metabolic processes.

Genome-wide identification and expression analysis of NF-Y gene family in tobacco (Nicotiana tabacum L.)

Nuclear factor Y (NF-Y) gene family is an important transcription factor composed of three subfamilies of NF-YA, NF-YB and NF-YC, which is involved in plant growth, development and stress response. In this study, 63 tobacco NF-Y genes (NtNF-Ys) were identified in Nicotiana tabacum L., including 17 NtNF-YAs, 30 NtNF-YBs and 16 NtNF-YCs. Phylogenetic analysis revealed ten pairs of orthologues from tomato and tobacco and 25 pairs of paralogues from tobacco. The gene structure of NtNF-YAs exhibited similarities, whereas the gene structure of NtNF-YBs and NtNF-YCs displayed significant differences. The NtNF-Ys of the same subfamily exhibited a consistent distribution of motifs and protein 3D structure. The protein interaction network revealed that NtNF-YC12 and NtNF-YC5 exhibited the highest connectivity. Many cis-acting elements related to light, stress and hormone response were found in the promoter of NtNF-Ys. Transcriptome analysis showed that more than half of the NtNF-Y genes were expressed in all tissues, and NtNF-YB9/B14/B15/B16/B17/B29 were specifically expressed in roots. A total of 15, 12, 5, and 6 NtNF-Y genes were found to respond to cold, drought, salt, and alkali stresses, respectively. The results of this study will lay a foundation for further study of NF-Y genes in tobacco and other Solanaceae plants.

Genome-wide identification and characterization of flowering genes in Citrus sinensis (L.) Osbeck: a comparison among C. Medica L., C. Reticulata Blanco, C. Grandis (L.) Osbeck and C. Clementina

BACKGROUND

Flowering plays an important role in completing the reproductive cycle of plants and obtaining next generation of plants. In case of citrus, it may take more than a year to achieve progeny. Therefore, in order to fasten the breeding processes, the juvenility period needs to be reduced. The juvenility in plants is regulated by set of various flowering genes. The citrus fruit and leaves possess various medicinal properties and are subjected to intensive breeding programs to produce hybrids with improved quality traits. In order to break juvenility in Citrus, it is important to study the role of flowering genes. The present study involved identification of genes regulating flowering in Citrus sinensis L. Osbeck via homology based approach. The structural and functional characterization of these genes would help in targeting genome editing techniques to induce mutations in these genes for producing desirable results.

RESULTS

A total of 43 genes were identified which were located on all the 9 chromosomes of citrus. The in-silico analysis was performed to determine the genetic structure, conserved motifs, cis-regulatory elements (CREs) and phylogenetic relationship of the genes. A total of 10 CREs responsible for flowering were detected in 33 genes and 8 conserved motifs were identified in all the genes. The protein structure, protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to study the functioning of these genes which revealed the involvement of flowering proteins in circadian rhythm pathways. The gene ontology (GO) and gene function analysis was performed to functionally annotate the genes. The structure of the genes and proteins were also compared among other Citrus species to study the evolutionary relationship among them. The expression study revealed the expression of flowering genes in floral buds and ovaries. The qRT-PCR analysis revealed that the flowering genes were highly expressed in bud stage, fully grown flower and early stage of fruit development.

CONCLUSIONS

The findings suggested that the flowering genes were highly conserved in citrus species. The qRT-PCR analysis revealed the tissue specific expression of flowering genes (CsFT, CsCO, CsSOC, CsAP, CsSEP and CsLFY) which would help in easy detection and targeting of genes through various forward and reverse genetic approaches.

A member of NF-Y family, OsNF-YC5 negatively regulates salt tolerance in rice

NF-Y, a critical transcription factor, binds to the CCAAT-box in target gene promoters, playing a pivotal role in plant development and abiotic stress response. OsNF-YC5, encodes a putative subunit of the NF-Y transcription factor in rice, had an undetermined function. Our research revealed that OsNF-YC5 is induced by high salinity and exogenous abscisic acid (ABA). Subcellular localization studies showed that OsNF-YC5 is nuclear- and cytoplasm-localized. Using CRISPR-Cas9 to disrupt OsNF-YC5, we observed significantly enhanced rice salinity tolerance and ABA-hypersensitivity. Compared to the wild-type, osnf-yc5 mutants exhibited reduced H2O2 and malondialdehyde (MDA) levels, increased catalase (CAT) activity, and elevated OsCATA transcripts under salt stress. Moreover, ABA-dependent (OsABI2 and OsLEA3) and ABA-independent (OsDREB1A, OsDREB1B, and OsDREB2A) marker genes were upregulated in mutant lines in response to salinity. These results indicate that disrupting OsNF-YC5 enhances rice salinity tolerance, potentially by boosting CAT enzyme activity and modulating gene expression in both ABA-dependent and ABA-independent pathways. Therefore, this study provides a valuable theoretical foundation and genetic resources for developing novel salt-tolerant rice varieties.

Multifaceted roles of transcription factors during plant embryogenesis

Transcription factors (TFs) are diverse groups of regulatory proteins. Through their specific binding domains, TFs bind to their target genes and regulate their expression, therefore TFs play important roles in various growth and developmental processes. Plant embryogenesis is a highly regulated and intricate process during which embryos arise from various sources and undergo development; it can be further divided into zygotic embryogenesis (ZE) and somatic embryogenesis (SE). TFs play a crucial role in the process of plant embryogenesis with a number of them acting as master regulators in both ZE and SE. In this review, we focus on the master TFs involved in embryogenesis such as BABY BOOM (BBM) from the APETALA2/Ethylene-Responsive Factor (AP2/ERF) family, WUSCHEL and WUSCHEL-related homeobox (WOX) from the homeobox family, LEAFY COTYLEDON 2 (LEC2) from the B3 family, AGAMOUS-Like 15 (AGL15) from the MADS family and LEAFY COTYLEDON 1 (LEC1) from the Nuclear Factor Y (NF-Y) family. We aim to present the recent progress pertaining to the diverse roles these master TFs play in both ZE and SE in Arabidopsis, as well as other plant species including crops. We also discuss future perspectives in this context.

Evolutionary insights and expression dynamics of the CaNFYB transcription factor gene family in pepper (Capsicum annuum) under salinity stress

Introduction: The Capsicum annuum nuclear factor Y subunit B (CaNFYB) gene family plays a significant role in diverse biological processes, including plant responses to abiotic stressors such as salinity. Methods: In this study, we provide a comprehensive analysis of the CaNFYB gene family in pepper, encompassing their identification, structural details, evolutionary relationships, regulatory elements in promoter regions, and expression profiles under salinity stress. Results and discussion: A total of 19 CaNFYB genes were identified and subsequently characterized based on their secondary protein structures, revealing conserved domains essential for their functionality. Chromosomal distribution showed a non-random localization of these genes, suggesting potential clusters or hotspots for NFYB genes on specific chromosomes. The evolutionary analysis focused on pepper and comparison with other plant species indicated a complex tapestry of relationships with distinct evolutionary events, including gene duplication. Moreover, promoter cis-element analysis highlighted potential regulatory intricacies, with notable occurrences of light-responsive and stress-responsive binding sites. In response to salinity stress, several CaNFYB genes demonstrated significant temporal expression variations, particularly in the roots, elucidating their role in stress adaptation. Particularly CaNFYB01, CaNFYB18, and CaNFYB19, play a pivotal role in early salinity stress response, potentially through specific regulatory mechanisms elucidated by their cis-elements. Their evolutionary clustering with other Solanaceae family members suggests conserved ancestral functions vital for the family's survival under stress. This study provides foundational knowledge on the CaNFYB gene family in C. annuum, paving the way for further research to understand their functional implications in pepper plants and relative species and their potential utilization in breeding programs to enhance salinity tolerance.

Granule-bound starch synthase in plants: Towards an understanding of their evolution, regulatory mechanisms, applications, and perspectives

Amylose content (AC) is a significant quality trait in starchy crops, affecting their processing and application by the food and non-food industries. Therefore, fine-tuning AC in these crops has become a focus for breeders. Granule-bound starch synthase (GBSS) is the core enzyme that directly determines the AC levels. Several excellent reviews have summarized key progress in various aspects of GBSS research in recent years, but they mostly focus on cereals. Herein, we provide an in-depth review of GBSS research in monocots and dicots, focusing on the molecular characteristics, evolutionary relationships, expression patterns, molecular regulation mechanisms, and applications. We also discuss future challenges and directions for controlling AC in starchy crops, and found simultaneously increasing both the PTST and GBSS gene expression levels may be an effective strategy to increase amylose content.

Characterization of NF-Y gene family and their expression and interaction analysis in Phalaenopsis orchid

The complex of Nuclear Factor Ys (NF-Ys), a family of heterotrimeric transcription factors composed of three unique subunits (NF-YA, NF-YB, and NF-YC), binds to the CCAAT box of eukaryotic promoters to activate or repress transcription of the downstream genes involved into various biological processes in plants. However, the systematic characterization of NF-Y gene family has not been elucidated in Phalaenopsis. A total of 24 NF-Y subunits (4 NF-YA, 9 NF-YB, and 11 NF-YC subunits) were identified in Phalaenopsis genome, whose exon/intron structures were highly differentiated among the PhNF-Y subunits. The distribution of motifs between coding regions of PhNF-YA and PhNF-YB/C was distinct. Segmental and tandem duplication events among paralogous PhNF-Ys were occurred. Six pairs of orthologous NF-Ys from Phalaenopsis and Arabidopsis and five pairs of orthologous NF-Ys from Phalaenopsis and rice involved in the phylogenetic gene synteny were identified. The various cis-elements being responsive to low-temperature, drought and ABA were distributed in the promoters of PhNF-Ys. qRT-PCR analysis indicated all of PhNF-Ys displayed the spatial specificity of expression in different tissues. Moreover, the expression levels of multiple PhNF-Ys significantly changed responding to low-temperature and ABA treatment. Yeast two hybrid and bimolecular fluorescence complementation assays approved the interaction of PhNF-YA1/3 with PhNF-YB6/PhNF-YC7, respectively, as well as PhNF-YB6 with PhNF-YC7. PhNF-YA1/3, PhNF-YB6, and PhNF-YC7 proteins were all localized in the nucleus. Further, transient overexpression of PhNF-YB6 and PhNF-YC7 promoted PhFT3 and repressed PhSVP expression in Phalaenopsis. These findings will facilitate to explore the role of PhNF-Ys in floral transition in Phalaenopsis orchid.

Ralstonia solanacearum Suppresses Tomato Root Growth by Downregulation of a Wall-Associated Receptor Kinase

The root architecture of a range of host plants is altered in response to Ralstonia solanacearum infection. This work aimed to identify host genes involved in root development during R. solanacearum infection. A deficient mutant of the type III secretion system regulator hrpB was created in R. solanacearum GMI1000. The hrpB mutant was impaired in virulence but showed a similar suppressive effect as wild-type GMI1000 on tomato root development. Based on comparative transcriptome analysis, 209 genes were found that showed the same changed expression pattern in GMI1000 and hrpB mutant infected roots relative to uninoculated roots. Among them, the wall-associated receptor kinase WAKL20 was substantially downregulated in GMI1000 and hrpB mutant infected roots. Knockdown of WAKL20 led to a shorter primary root length and fewer lateral roots in tomato as well as in Nicotiana benthamiana. The WAKL20 is a pivotal target suppressed by R. solanacearum to shape the altered root development during infection.

It is time to move: Heat-induced translocation events

Climate change-induced temperature fluctuations impact agricultural productivity through short-term intense heat waves or long-term heat stress. Plants have evolved sophisticated strategies to deal with heat stress. Understanding perception and transduction of heat signals from outside to inside cells is essential to improve plant thermotolerance. In this review, we will focus on translocation of molecules and proteins associated with signal transduction to understand how plant cells decode signals from the environment to trigger a suitable response.

Integration of eQTL and machine learning to dissect causal genes with pleiotropic effects in genetic regulation networks of seed cotton yield

The dissection of a gene regulatory network (GRN) that complements the genome-wide association study (GWAS) locus and the crosstalk underlying multiple agronomical traits remains a major challenge. In this study, we generate 558 transcriptional profiles of lint-bearing ovules at one day post-anthesis from a selective core cotton germplasm, from which 12,207 expression quantitative trait loci (eQTLs) are identified. Sixty-six known phenotypic GWAS loci are colocalized with 1,090 eQTLs, forming 38 functional GRNs associated predominantly with seed yield. Of the eGenes, 34 exhibit pleiotropic effects. Combining the eQTLs within the seed yield GRNs significantly increases the portion of narrow-sense heritability. The extreme gradient boosting (XGBoost) machine learning approach is applied to predict seed cotton yield phenotypes on the basis of gene expression. Top-ranking eGenes (NF-YB3, FLA2, and GRDP1) derived with pleiotropic effects on yield traits are validated, along with their potential roles by correlation analysis, domestication selection analysis, and transgenic plants.