miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis

Genome-Wide Identification and Expression Pattern Analysis of SBP Gene Family in Neolamarckia cadamba

Background: SQUAMOSA promoter-binding protein (SBP) genes encode a group of plant-specific transcription factors that play crucial roles in plant growth, development, and stress responses. To date, SBP genes have been reported in a number of plant species, but the SBP gene family has not been identified in Neolamarckia cadamba, an important fast-growing species referred to as a 'miracle tree' and recognized for its potential medicinal value in Southeast Asia. Methods: Bioinformatics approaches were employed to conduct a comprehensive analysis of the NcSBP gene family, including investigations into physicochemical characteristics, phylogenetic relationships, gene structure, chromosomal localization, conserved motifs, cis-acting elements, and expression patterns. Results: A total of 27 NcSBP members were identified in the N. cadamba genome, encoding proteins ranging from 148 to 1038 amino acids in length, with molecular weights between 16,714.34 and 114,331.61 Da. They were classified into eight clades according to phylogenetic analysis, and unevenly distributed across 17 chromosomes, with 4 tandem gene duplication pairs and 27 fragment duplication events. In addition, cis-acting elements associated with hormone and light responses were most presented in the promoters of NcSBP genes. The transcript levels of NcSBP were investigated through RNA-seq and qRT-PCR, indicating distinct expression patterns across various tissues and under different hormone and stress conditions. Conclusions: In summary, this study comprehensively identified and characterized the SBP gene family in N. cadamba, providing a significant foundation for further functional investigation into NcSBP genes.

Functional Characterization of MaSPL8 Reveals Its Different Roles in Biotic and Abiotic Stress Responses in Mulberry

The Squamosa promoter-binding protein-like (SPL) family proteins plays pivotal roles in plant development and stress adaptation. In this study, we functionally characterized MaSPL8 in mulberry (Morus alba) and investigated its regulatory roles in biotic and abiotic stress responses. MaSPL8 encodes a 364-amino acid protein with a conserved SBP domain and lacks miR156/157 binding sites. Phylogenetic analysis confirmed its orthology to Arabidopsis AtSPL8, albeit with functional divergence. Downregulation of MaSPL8 via virus-induced gene silencing (VIGS) resulted in more susceptibility to Ciboria shiraiana infection, but significantly enhanced resistance to drought and salt stress, as evidenced by reduced oxidative damage, elevated proline accumulation, and increased antioxidant enzyme activities. Transcriptomic profiling of MaSPL8-silenced plants revealed enrichment of differentially expressed genes (DEGs) in brassinosteroid biosynthesis, jasmonic acid metabolism, and oxidative stress responses, suggesting hormone signaling interplay. Furthermore, bioinformatic predictions identified miR5658 and miR4221 as potential post-transcriptional regulators of MaSPL8. This study highlights MaSPL8 as a negative regulator of abiotic stress tolerance and positive regulator of biotic (C. shiraiana) stress tolerance in mulberry and provides insights into its integration with phytohormone pathways. Our findings underscore the evolutionary plasticity of SPL8 genes and propose MaSPL8 as a target for enhancing mulberry's resilience in challenging environments.

An organ-specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways

Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome-wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ-specifically expressed, and 13 of these miRNAs could perform organ-specific target regulation. More than 80% of the phasiRNA loci were organ-specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ-specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber-specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme-coding genes of the β-elemene biosynthetic pathway showed that the downstream genes were tuber-specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β-elemene biosynthesis. Summarily, our report provided an organ-specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.

Identification and functional analysis of strigolactone pathway genes regulating tillering traits in sugarcane

Saccharum officinarum and Saccharum spontaneum are two fundamental species of modern sugarcane cultivars, exhibiting divergent tillering patterns crucial for sugarcane architecture and yield. Strigolactones (SLs), a class of plant hormones, are considered to play a central role in shaping plant form and regulating tillering. Our study highlights the distinct tillering patterns observed between S. officinarum and S. spontaneum and implicates significant differences in SL levels in root exudates between the two species. Treatment with rac-GR24 (an artificial SL analog) suppressed tillering in S. spontaneum. Based on transcriptome analysis, we focused on two genes, TRANSCRIPTION ELONGATION FACTOR 1 (TEF1) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which show higher expression in S. spontaneum or S. officinarum, respectively. While the overexpression of SoCCA1 did not lead to significant phenotypic differences, overexpression of SsTEF1 in rice stimulated tillering and inhibited plant height, demonstrating its role in tillering regulation. However, the overexpression of suggests that SoCCA1 may not be the key regulator of sugarcane tillering. Yeast one-hybrid assays identified four transcription factors (TFs) regulating SsTEF1 and four and five TFs regulating SsCCA1 and SoCCA1. This study provides a theoretical foundation for deciphering the molecular mechanisms underlying the different tillering behaviors between S. officinarum and S. spontaneum, providing valuable insights for the molecular-based design of sugarcane breeding strategies.

Overexpression of TCP5 or Its Dominant Repressor Form, TCP5-SRDX, Causes Male Infertility in Arabidopsis

TCP transcription factors have long been known to play a crucial role in leaf development, but their significance in reproduction has recently been revealed. TCP5 is a member of class II of the TCP family, which predominantly regulates cell differentiation. This study used overexpression and SRDX fusion to evaluate the role of TCP5 in anther development. TCP5 overexpression resulted in lower fertility, primarily due to anther non-dehiscence. We also observed reduced lignin accumulation in the anther endothecium. In addition, TCP5 overexpression resulted in smaller anthers with fewer pollen sacs and pollen due to early-anther defects before meiosis. TCP5 showed expression in early anthers, including the epidermis, endothecium, middle layer, tapetum, sporogenous cells (pollen mother cells), and vascular bundles. Conversely, during meiosis, the TCP5 signal was only detected in the tapetum, PMCs, and vascular bundles. The TCP5 signal disappeared after meiosis, and no signal was observed in mature anthers. Interestingly, the TCP5-SRDX transgenic plants were also sterile, at least for the early-arising flowers, if not all of them. TCP5-SRDX expression also resulted in undersized anthers with fewer pollen sacs and pollen. However, the lignin accumulation in most of these anthers was comparable to that of the wild type, allowing these anthers to open. The qRT-PCR results revealed that several genes associated with secondary cell wall thickening had altered expression profiles in TCP5 overexpression transgenics, which supported the non-dehiscent anther phenotype. Furthermore, the expression levels of numerous critical anther genes were down-regulated in both TCP5 overexpression and TCP5-SRDX plants, indicating a comparable anther phenotype in these transgenic plants. These findings not only suggest that an appropriate TCP5 expression level is essential for anther development and plant fertility, but also improve our understanding of TCP transcription factor functioning in plant male reproduction and contribute information that may allow us to manipulate fertility and breeding in crops.

Phylogenetic and Expression Analysis of SBP-Box Gene Family to Enhance Environmental Resilience and Productivity in Camellia sinensis cv. Tie-guanyin

Tieguanyin tea, a renowned oolong tea, is one of the ten most famous teas in China. The Squamosa Promoter Binding Protein (SBP)-box transcription factor family, widely present in plants, plays a crucial role in plant development, growth, and stress responses. In this study, we identify and analyze 22 CsSBP genes at the genome-wide level. These genes were distributed unevenly across 11 chromosomes. Using Arabidopsis thaliana and Solanum lycopersicum L. as model organisms, we constructed a phylogenetic tree to classify these genes into six distinct subfamilies. Collinearity analysis revealed 20 homologous gene pairs between AtSBP and CsSBP, 21 pairs between SiSBP and CsSBP, and 14 pairs between OsSBP and CsSBP. Cis-acting element analysis indicated that light-responsive elements were the most abundant among the CsSBP genes. Protein motif, domain, and gene architecture analyses demonstrated that members of the same subgroup shared similar exon-intron structures and motif arrangements. Furthermore, we evaluated the expression profiles of nine CsSBP genes under light, shade, and cold stress using qRT-PCR analysis. Notably, CsSBP1, CsSBP17, and CsSBP19 were significantly upregulated under all three stresses. This study provides fundamental insights into the CsSBP gene family and offers a novel perspective on the mechanisms of SBP transcription factor-mediated stress responses, as well as Tieguanyin tea's adaptation to environmental variations.

SlTDF1: A key regulator of tapetum degradation and pollen development in tomato

Pollen formation and development during the life cycle of flowering plant are crucial for maintaining reproductive and genetic diversity. In this study, an R2R3MYB family transcription factor, SlTDF1 (SlMYB35), was predominantly expressed in stamens. Repressed expression of SlTDF1 results in a delay in the degradation of the anther tapetum in tomatoes, which in turn leads to the formation of abnormal pollen, including a reduction in the number of single-fruit seeds and fertility when compared to wild-type plants. Analysis of paraffin sections demonstrated that SlTDF1 is a crucial factor in the maturation of tomato pollen. Further analysis of the transcriptomic data revealed that downregulation of the SlTDF1 gene significantly suppressed the expression of genes related to sugar metabolism and anther development. The findings of this study indicated that SlTDF1 plays a pivotal role in regulating tomato pollen development. Moreover, these findings provide a genetic resource for male sterility in tomato plants.

Identification and expression analysis of the SPL gene family during flower bud differentiation in Rhododendron molle

BACKGROUND

The family of SQUAMOSA promoter binding protein-like (SPL) transcription factors is essential for regulating plant growth and development. While this SPL gene functional research has been limited in Rhododendron molle (R. molle).

OBJECTIVE

To preliminarily explore the regulatory mechanism of the SPL gene in flower bud development of R. molle.

METHODS

In this study, for R. molle, the flower bud differentiation period was determined by observing the morphological anatomy of the flower bud. The SPL gene family members were identified based on the R. molle genome, Additionally, the expressions of RmSPL genes at five flower bud differentiation stages were analyzed via Quantitative reverse transcription PCR (RT-qPCR).

RESULTS

We first characterized 20 SPL family members in the reference genome of R. molle. The phylogenetic analysis of plant SPL proteins separated them into eight subfamilies (G1-G8) according to conserved gene structures and protein motifs. Cis-elements of promoter region analysis showed that RmSPL genes were regulated by light, phytohormones, stress response, and plant growth and development and may play a critical role in the photoresponse, abasic acid, anaerobic induction, and meristematic expression. Gene expression analysis showed that 18 RmSPL genes were differentially expressed in different developing flower buds. In particular, RmSPL1/7/8/12/13 exhibited significantly different expressions, suggesting that they were likely essential genes for regulating the differentiation of flower buds.

CONCLUSION

In conclusion, our analysis of RmSPL genes provides a theoretical basis and reference for future functional analysis of RmSPL genes in the flower bud differentiation of R. molle.

Global identification and regulatory network analysis reveal the significant roles of lncRNAs during anther and pollen development in Arabidopsis

KEY MESSAGE

A high-throughput sequencing identified 1283 lncRNAs in anthers at different stages in Arabidopsis and their relationship with protein-coding genes and miRNAs during anther and pollen development were analyzed. Long non-coding RNAs (lncRNAs) are important regulatory molecules involved in various biological processes. However, their roles in male reproductive development and interactions with miRNAs remained elusive. In this study, a high-throughput sequencing of anthers at different developmental stages in Arabidopsis identified 1283 lncRNAs including 524 differentially expressed lncRNAs (DELs). Most of these DELs exhibited positive correlations with the expression patterns of adjacent protein-coding genes. Weighted gene co-expression network analysis (WGCNA) revealed that protein-coding genes targeted by DELs in four modules related to the tetrad stage were associated with functions such as pollen wall formation, pollen germination, or pollen tube growth, respectively. Furthermore, five, 10, and 11 lncRNAs were predicted as miRNAs' endogenous target mimics (eTMs), precursors, and natural antisense transcripts of pri-miRNA, respectively. Remarkably, the lncRNA, host gene of ath-miR167a (ath-miR167aHG), predicted as the precursor of miR167a, was selected for function validation. Its overexpression resulted in the up-regulation of miR167a and the subsequent down-regulation of miR167a's target genes ARF6 and ARF8, demonstrating a functional interaction between ath-miR167aHG and miR167a. The transgenic plants showed delayed flowering, shorter filaments, abnormal anther dehiscence, and undeveloped siliques ultimately, suggesting a role of ath-miR167aHG in male reproductive development. Collectively, our research shed new light on the functions of lncRNAs in male reproductive development and uncovered the unique interactions between lncRNAs and miRNAs.

Transcriptional regulation of miR528-PPO module by miR156 targeted SPLs orchestrates chilling response in banana

Banana is sensitive to cold stress and often suffers from chilling injury with browning peel and failure to normal ripening. We have previously reported that banana chilling injury is accompanied by a reduction of miR528 accumulation, alleviating the degradation of its target gene MaPPO and raising ROS levels that cause peel browning. Here, we further revealed that the miR528-MaPPO cold-responsive module was regulated by miR156-targeted SPL transcription factors, and the miR156c-MaSPL4 module was also responsive to cold stress in banana. Transient overexpression of miR156c resulted in a more severe chilling phenotype by decreasing the expression of MaSPL4 and miR528. Conversely, the browning was alleviated in STTM-miR156c silencing and OE-MaSPL4 samples. Furthermore, DNA affinity purification sequencing and MaSPL4-overexpressing transcriptome jointly revealed that MaSPL4 may mediate the transcription of genes related to lipid metabolism and antioxidation, in addition to the miR528-MaPPO module, demonstrating MaSPL4 as a master regulator in the fruit cold response network. In summary, our results suggest that the miR156c-MaSPL4 module can mediate the chilling response in banana by regulating the miR528-MaPPO module and multiple other pathways, which provides evidence for the crosstalk between TFs and miRNAs that can be used for the molecular breeding of fruit cold tolerance.

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. 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 5 subfamilies, with 12 PavSPLs predicted as miR156 targets. 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. PavSPL14 overexpression in Arabidopsis thaliana resulted in earlier flowering and increased plant height and growth. Yeast two-hybrid assays showed an interaction between PavSPL14 and DELLA protein PavDWARF8, suggesting PavSPL14 and PavDWARF8 co-regulate growth and development. These findings lay the groundwork for further research on PavSPL function in sweet cherry.

SPL13 controls a root apical meristem phase change by triggering oriented cell divisions

Oriented cell divisions are crucial for determining the overall morphology and size of plants, but what controls the onset and duration of this process remains largely unknown. Here, we identified a small molecule that activates root apical meristem (RAM) expression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13 (SPL13) a known player in the shoot's juvenile-to-adult transition. This expression leads to oriented cell divisions in the RAM through SHORT ROOT (SHR) and cell cycle regulators. We further show that the RAM has distinct juvenile and adult phases typed by morphological and molecular characteristics and that SPL factors are crucially required for this transition in Arabidopsis and rice (Oryza sativa). In summary, we provide molecular insights into the age-dependent morphological changes occurring in the RAM during phase change.

Identification of differentially expressed miRNAs between male sterile and fertile floral buds in watermelon (Citrullus lanatus L.) via high-throughput sequencing

This experiment used floral buds from watermelon genic male sterile dual-purpose lines as materials to explore the differentially expressed miRNAs (DEMs) between male fertile and sterile floral buds of watermelon. Paraffin sectioning technology was employed for a cytological analysis, and small RNA sequencing was used to explore miRNAs related to anther or pollen development. Cytological analysis indicated that the abnormal development of tapetal cells may cause microspore abortion. Small RNA sequencing identified a total of 314 miRNAs (29 known and 285 novel, which belonged to 12 and 61 miRNA families, respectively) in floral buds. Differential expression revealed 36 (5 known and 31 novel) DEMs between male fertile and sterile buds, 7 and 29 of which were up-regulated and down-regulated, respectively. Target genes analysis showed that the 36 DEMs were predicted to target 577 genes, and these targets might participate in various biological processes, such as response to metal ions, floral organ development, stamen development, anther development, pollen maturation, and programmed cell death. Moreover, pathway analysis indicated that these genes were mainly enriched in purine metabolism, starch and sucrose metabolism, RNA transport, and other pathways. In addition, the 55 miRNA-target modules, including 3 known and 16 novel miRNAs with 30 target genes, might be related to anther or pollen development in watermelon. Our findings provide important miRNA-target modules related to watermelon anther or pollen development and can lay the foundation for biological functional analysis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04084-6.

CpSPL10-CpELF4 module involves in the negative regulation of flower bud differentiation in Chinese cherry

SQUAMOSA promoter-binding protein-like (SPL) genes play a crucial role in regulating floral induction. Despite such importance, a comprehensive study of SPLs in Chinese cherry flower bud development has been absent. In this study, 32 CpSPL genes were identified. According to expression profiling, CpSPLs exhibited tissue-specific expression and distinct trends throughout flower bud differentiation. Specifically, CpSPL10 was greatly expressed at the beginning of the differentiation, and its role was further investigated. Its overexpression extended the vegetative growth of transgenic tobacco plants, delayed flowering by about 20 days. Moreover, the accumulation of NbELF4 (Early flowering 4) transcripts was enhanced due to the up-regulated levels of CpSPL10 in tobacco plants. ELF4 functions as a major element of the circadian clock; its high expression typically delays the transition from vegetative-to-reproductive growth. Further experiments revealed that CpSPL10 interacts with CpSPL9 or a transposase-derived transcription factor CpFRS5 (FAR1-RELATED SEQUENCE 5) and activates the expression of the downstream gene CpELF4. Notably, the GUS fusing reporter assay detected the activation of CpSPL10 and CpELF4 promoters in shoot apical meristems of transgenic Arabidopsis. These findings revealed the negative regulation of the CpSPL10-CpELF4 module in flower bud differentiation, providing references for supplementing the specific relationships among SPL, FRS, and ELF4.

Genome-Wide Characterization and Analysis of the SPL Gene Family in Eucalyptus grandis

SQUAMOSA promoter-binding protein-like (SPL) gene family, a group of plant-specific transcription factors, played crucial roles in regulating plant growth, development, signal transduction, and stress response. This study focuses on the SPL gene family in the fast-growing Eucalyptus grandis, employing bioinformatics approaches to identify and analyze the gene physiochemical characteristics, conserved domains, structural composition, chromosomal distribution, phylogenetic relationships, cis-acting elements, and their expression patterns in various tissues and stress treatments. Twenty-three SPL genes were identified in E. grandis, which uneven distributed across seven chromosomes and classified into five groups. Prediction of cis-acting elements revealed that these genes might be related to light, hormone, and stress responses. Furthermore, EgSPL9 and EgSPL23, mainly expressed in the stem apex and lateral branches, seem to be involved in hormone stress resistance. Our study provides insights into the potential functions of the EgSPL genes in plant growth, stress response, and hormone transduction, offering valuable perspectives for subsequent research into their biological roles.

TaSPL6B, a member of the Squamosa promoter binding protein-like family, regulates shoot branching and florescence in Arabidopsis thaliana

BACKGROUND

Squamosa promoter-binding protein-like (SPL) proteins are essential to plant growth and development as plant-specific transcription factors. However, the functions of SPL proteins in wheat need to be further explored.

RESULTS

We cloned and characterized TaSPL6B of wheat in this study. Analysis of physicochemical properties revealed that it contained 961 amino acids and had a molecular weight of 105 kDa. Full-length TaSPL6B transcription activity was not validated in yeast and subcellular localization analysis revealed that TaSPL6B was distributed in the nucleus. Ectopic expression of TaSPL6B in Arabidopsis led to increasing number of branches and early flowering. TaSPL6B was highly transcribed in internodes of transgenic Arabidopsis. The expression of AtSMXL6/AtSMXL7/AtSMXL8 (homologous genes of TaD53) was markedly increased, whereas the expression of AtSPL2 (homologous genes of TaSPL3) and AtBRC1 (homologous genes of TaTB1) was markedly reduced in the internodes of transgenic Arabidopsis. Besides, TaSPL6B, TaSPL3 and TaD53 interacted with one another, as demonstrated by yeast two-hybrid and bimolecular fluorescence complementation assays. Therefore, we speculated that TaSPL6B brought together TaD53 and TaSPL3 and enhanced the inhibition effect of TaD53 on TaSPL3 through integrating light and strigolactone signaling pathways, followed by suppression of TaTB1, a key repressor of tillering.

CONCLUSIONS

As a whole, our findings contribute to a better understanding of how SPL genes work in wheat and will be useful for further research into how TaSPL6B affects yield-related traits in wheat.

Genome-wide identification and analysis of SPL gene family in chickpea (Cicer arietinum L.)

A transcription factor in plants encodes SQUAMOSA promoter binding protein-like (SPL) serves a broad spectrum of important roles for the plant, like, growth, flowering, and signal transduction. A gene family that encodes SPL proteins is documented in various model plant species, including Arabidopsis thaliana and Oryza sativa. Chickpea (Cicer arietinum), a leguminous crop, has not been thoroughly explored with regard to the SPL protein-encoding gene family. Chickpea SPL family genes were located and characterized computationally using a genomic database. Gene data of chickpea were obtained from the phytozome repository and was examined using bioinformatics methods. For investigating the possible roles of SPLs in chickpea, genome-wide characterization, expression, as well as structural analyses of this SPL gene family were performed. Cicer arietinum genome had 19 SPL genes, whereas, according to phylogenetic analysis, the SPLs in chickpea are segregated among four categories: Group-I has 2 introns, Group-II and IV have 1-2 introns (except CaSPL13 and CaSPL15 having 3 introns), and Group-III has 9 introns (except CaSPL1 and CaSPL11 with 1 and 8 introns, respectively). The SBP domain revealed that SPL proteins featured two zinc-binding sites, i.e., C3H and C2HC and one nuclear localization signal. All CaSPL proteins are found to contain highly conserved motifs, i.e., Motifs 1, 2, and 4, except CaSPL10 in which Motifs 1 and 4 were absent. Following analysis, it was found that Motifs 1 and 2 of the chickpea SBP domain are Zinc finger motifs, and Motif 4 includes a nuclear localization signal. All pairs of CaSPL paralogs developed by purifying selection. The CaSPL promoter investigation discovered cis-elements that are responsive to stress, light, and phytohormones. Examination of their expression patterns highlighted major CaSPLs to be evinced primarily among younger pods and flowers. Indicating their involvement in the plant's growth as well as development, along with their capacity to react as per different situations by handling the regulation of target gene's expression, several CaSPL genes are also expressed under certain stress conditions, namely, cold, salt, and drought. The majority of the CaSPL genes are widely expressed and play crucial roles in terms of the plant's growth, development, and responses to the environmental-stress conditions. Our work provides extensive insight into the gene family CaSPL, which might facilitate further studies related to the evolution and functions of the SPL genes for chickpea and other plant species.

Flowering time: From physiology, through genetics to mechanism

Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.

Differential expression and global analysis of miR156/SQUAMOSA promoter binding-like proteins (SPL) module in oat

SQUAMOSA promoter binding-like proteins (SPLs) are important transcription factors that influence growth phase transition and reproduction in plants. SPLs are targeted by miR156 but the SPL/miR156 module is completely unknown in oat. We identified 28 oat SPL genes (AsSPLs) distributed across all 21 oat chromosomes except for 4C and 6D. The oat- SPL gene family represented six of eight SPL phylogenetic groups, with no AsSPLs in groups 3 and 7. A novel oat miR156 (AsmiR156) family with 21 precursors divided into 7 groups was characterized. A total of 16 AsSPLs were found to be targeted by AsmiR156. Intriguingly, AsSPL3s showed high transcript abundance during early inflorescence (GS-54), as compared to the lower abundance of AsmiR156, indicating their role in reproductive development. Unravelling the SPL/miR156 regulatory hub and alterations in expression patterns of AsSPLs could provide an essential toolbox for genetic improvement in the cultivated oat.

A Regulatory Mechanism on Pathways: Modulating Roles of MYC2 and BBX21 in the Flavonoid Network

Genes of metabolic pathways are individually or collectively regulated, often via unclear mechanisms. The anthocyanin pathway, well known for its regulation by the MYB/bHLH/WDR (MBW) complex but less well understood in its connections to MYC2, BBX21, SPL9, PIF3, and HY5, is investigated here for its direct links to the regulators. We show that MYC2 can activate the structural genes of the anthocyanin pathway but also suppress them (except F3'H) in both Arabidopsis and Oryza when a local MBW complex is present. BBX21 or SPL9 can activate all or part of the structural genes, respectively, but the effects can be largely overwritten by the local MBW complex. HY5 primarily influences expressions of the early genes (CHS, CHI, and F3H). TF-TF relationships can be complex here: PIF3, BBX21, or SPL9 can mildly activate MYC2; MYC2 physically interacts with the bHLH (GL3) of the MBW complex and/or competes with strong actions of BBX21 to lessen a stimulus to the anthocyanin pathway. The dual role of MYC2 in regulating the anthocyanin pathway and a similar role of BBX21 in regulating BAN reveal a network-level mechanism, in which pathways are modulated locally and competing interactions between modulators may tone down strong environmental signals before they reach the network.

A Comprehensive Analysis of the Peanut SQUAMOSA Promoter Binding Protein-like Gene Family and How AhSPL5 Enhances Salt Tolerance in Transgenic Arabidopsis

SPL (SQUAMOSA promoter binding protein-like), as one family of plant transcription factors, plays an important function in plant growth and development and in response to environmental stresses. Despite SPL gene families having been identified in various plant species, the understanding of this gene family in peanuts remains insufficient. In this study, thirty-eight genes (AhSPL1-AhSPL38) were identified and classified into seven groups based on a phylogenetic analysis. In addition, a thorough analysis indicated that the AhSPL genes experienced segmental duplications. The analysis of the gene structure and protein motif patterns revealed similarities in the structure of exons and introns, as well as the organization of the motifs within the same group, thereby providing additional support to the conclusions drawn from the phylogenetic analysis. The analysis of the regulatory elements and RNA-seq data suggested that the AhSPL genes might be widely involved in peanut growth and development, as well as in response to environmental stresses. Furthermore, the expression of some AhSPL genes, including AhSPL5, AhSPL16, AhSPL25, and AhSPL36, were induced by drought and salt stresses. Notably, the expression of the AhSPL genes might potentially be regulated by regulatory factors with distinct functionalities, such as transcription factors ERF, WRKY, MYB, and Dof, and microRNAs, like ahy-miR156. Notably, the overexpression of AhSPL5 can enhance salt tolerance in transgenic Arabidopsis by enhancing its ROS-scavenging capability and positively regulating the expression of stress-responsive genes. These results provide insight into the evolutionary origin of plant SPL genes and how they enhance plant tolerance to salt stress.

The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants

Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.

Plant age-dependent dynamics of annatto pigment (bixin) biosynthesis in Bixa orellana

Age affects the production of secondary metabolites, but how developmental cues regulate secondary metabolism remains poorly understood. The achiote tree (Bixa orellana L.) is a source of bixin, an apocarotenoid used in diverse industries worldwide. Understanding how age-dependent mechanisms control bixin biosynthesis is of great interest for plant biology and for economic reasons. Here we overexpressed miRNA156 (miR156) in B. orellana to comprehensively study the effects of the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module on age-dependent bixin biosynthesis in leaves. Overexpression of miR156 in annatto plants (miR156ox) reduced BoSPL transcript levels, impacted leaf ontogeny, lessened bixin production, and increased abscisic acid levels. Modulation of expression of BoCCD4-4 and BoCCD1, key genes in carotenoid biosynthesis, was associated with diverting the carbon flux from bixin to abscisic acid in miR156ox leaves. Proteomic analyses revealed an overall low accumulation of most secondary metabolite-related enzymes in miR156ox leaves, suggesting that miR156-targeted BoSPLs may be required to activate several secondary metabolic pathways. Our findings suggest that the conserved BomiR156-BoSPL module is deployed to regulate leaf dynamics of bixin biosynthesis, and may create novel opportunities to fine-tune bixin output in B. orellana breeding programs.

Cell-cycle-linked growth reprogramming encodes developmental time into leaf morphogenesis

How is time encoded into organ growth and morphogenesis? We address this question by investigating heteroblasty, where leaf development and form are modified with progressing plant age. By combining morphometric analyses, fate-mapping through live-imaging, computational analyses, and genetics, we identify age-dependent changes in cell-cycle-associated growth and histogenesis that underpin leaf heteroblasty. We show that in juvenile leaves, cell proliferation competence is rapidly released in a "proliferation burst" coupled with fast growth, whereas in adult leaves, proliferative growth is sustained for longer and at a slower rate. These effects are mediated by the SPL9 transcription factor in response to inputs from both shoot age and individual leaf maturation along the proximodistal axis. SPL9 acts by activating CyclinD3 family genes, which are sufficient to bypass the requirement for SPL9 in the control of leaf shape and in heteroblastic reprogramming of cellular growth. In conclusion, we have identified a mechanism that bridges across cell, tissue, and whole-organism scales by linking cell-cycle-associated growth control to age-dependent changes in organ geometry.

Plant biology: Managing age-related bursts during leaf development

Age-dependent control of the miR165-regulated SPL transcription factor circuitry is responsible for the variation in leaf morphology over time. A new study reveals the underlying morphogenetic dynamics.

Genome-wide investigation of SQUAMOSA promoter binding protein-like genes in Liriodendron and functional characterization of LcSPL2

The plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play a pivotal role in various developmental processes, including leaf morphogenesis and vegetative to reproductive phase transition. Liriodendron chinense and Liriodendron tulipifera are widely used in landscaping due to their tulip-like flowers and peculiar leaves. However, the SPL gene family in Liriodendron has not been identified and systematically characterized. We systematically identified and characterized the SPL family members in Liriodendron, including phylogeny, gene structure and syntenic analyses. Subsequently, we quantified the expression patterns of LcSPLs across various tissue sites through transcription-quantitative polymerase chain reaction (RT-qPCR) assays and identified the target gene, LcSPL2. Finally, we characterized the functions of LcSPL2 via ectopic transformation. Altogether, 17 LcSPL and 18 LtSPL genes were genome-widely identified in L. chinense and L. tulipifera, respectively. All the 35 SPLs were grouped into 9 clades. Both species had three SPL gene pairs arising from segmental duplication events, and the LcSPLs displayed high collinearity with the L. tulipifera genome. RT-qPCR assays showed that SPL genes were differentially expressed in different tissues, especially. Because LcSPL2 is highly expressed in pistils and leaves, it was selected to describe the SPL gene family of L. chinense by ectopic expression. We showed that overexpression of LcSPL2 in Arabidopsis thaliana resulted in earlier flowering and fewer rosette leaves. Moreover, we observed that overexpression of LcSPL2 in A. thaliana up-regulated the expression levels of four genes related to flower development. This study identified SPL genes in Liriodendron and characterized the function of LcSPL2 in advancing flower development.

miR156b-targeted VvSBP8/13 functions downstream of the abscisic acid signal to regulate anthocyanins biosynthesis in grapevine fruit under drought

Anthocyanins are the primary color components of grapevine berries and wines. In cultivation practices, a moderate water deficit can promote anthocyanin accumulation in red grape skins. Our previous study showed that abscisic acid (ABA) plays a key role in this process. Herein, we identified a microRNA, vv-miR156b, that is generated in grapevine berries in response to drought stress, along with increasing anthocyanin content and biosynthetic structural gene transcripts. In contrast, vv-miR156b short tandem target mimic (STTM) function-loss callus exhibits the opposite phenotype. Results from in vivo and in vitro experiments revealed that the ABA-signaling-regulated transcription factor VvAREB2 binds directly to the ABA-responsive element (ABRE) of the MIR156b promoter and activates miR156b expression. Furthermore, two miR156b downstream targets, VvSBP8 and VvSBP13, exhibited reduced grape anthocyanin content in their overexpressors but there was a contrary result in their CRISPR-edited lines, the decrease in anthocyanin content was rescued in miR156b and SBP8/13 double overexpressors. We further demonstrated that both VvSBP8 and VvSBP13, encoding transcriptional repressors, displayed sufficient ability to interact with VvMYC1 and VvMYBA1, thereby interfering with MYB-bHLH-WD (MBW) repeat transcriptional complex formation, resulting in the repression of anthocyanin biosynthesis. Our findings demonstrate a direct functional relationship between ABA signaling and the miR156-SBP-MBW complex regulatory module in driving drought-induced anthocyanin accumulation in grape berries.

The miR156-SPL4/SPL9 module regulates leaf and lateral branch development in Betula platyphylla

The miR156 gene is known to play an important role in regulating growth and development in plants. This gene is involved in the transition from juvenile to adult stages, leaf morphology, and root development, among other processes. While the function of miR156 is similar in many plants, there are also differences in the function of this gene between herbaceous and native species. We obtained BpmiR156 overexpression transgenic lines in Betula platyphylla, and the transgenic lines exhibited traits such as delayed development, dwarfism, increased leaf epidermal hairs, larger leaf basal angle and altered stem curvature, which were highly consistent with the overexpression miR156 in Arabidopsis, rice and tomato. However, we also observed a lack of apical dominance, increased number of lateral branches and increased diameter of lateral branches in transgenic B. platyphylla, which is different from the effects reported in other plants. Transgenic plants showed changes in the distribution of IAA, GA3, and Zeatin in lateral branches and main stem, and the ratio of the content of the three hormones was significantly higher than in the non-transgenic plants served as control. Additionally, overexpression of BpmiR156 caused down-regulation of BpSPL4 and BpSPL9 expression, as well as differential expression of genes involved in auxin and cytokinin synthesis such as BpARR3, BpARR11 and BpmiR172.

Comparative analysis of the Squamosa Promoter Binding-Like (SPL) gene family in Nicotiana benthamiana and Nicotiana tabacum

SQUAMOSA PROMOTER BINDING-LIKE (SPL) proteins constitute a large family of transcription factors known to play key roles in growth and developmental processes, including juvenile-to-adult and vegetative-to-reproductive phase transitions. This makes SPLs interesting targets for precision breeding in plants of the Nicotiana genus used as e.g. recombinant biofactories. We report the identification of 49 SPL genes in Nicotiana tabacum cv. K326 and 43 SPL genes in Nicotiana benthamiana LAB strain, which were classified into eight phylogenetic groups according to the SPL classification in Arabidopsis. Exon-intron gene structure and DNA-binding domains were highly conserved between homeologues and orthologues. Thirty of the NbSPL genes and 33 of the NtSPL genes were found to be possible targets of microRNA 156. The expression of SPL genes in leaves was analysed by RNA-seq at three different stages, revealing that genes not under miR156 control were in general constitutively expressed at high levels, whereas miR156-regulated genes showed lower expression, often developmentally regulated. We selected the N. benthamiana SPL13_1a gene as target for a CRISPR/Cas9 knock-out experiment. We show here that a full knock-out in this single gene leads to a significant delay in flowering time, a trait that could be exploited to increase biomass for recombinant protein production.

Evolutionary assessment of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in citrus relatives with a specific focus on flowering

Phase transition and floral induction in citrus requires several years of juvenility after germination. Such a long period of juvenility has been a major hindrance to its genetic improvement program. Studies have shown that miR156 along with its downstream genes SQUAMOSA PROMOTER BINDING PROTEINS (SBP) and SBP-LIKE (SPL) mediate the phase transition and floral induction process in plants. Our current study has systematically analyzed SPLs in 15 different citrus-related species, systematically annotated them based on their close homology to their respective Arabidopsis orthologs, and confirmed the functional attributes of the selected members in floral precocity. The majority of the species harbored 15 SPLs. Their cis-element assessment suggested the involvement of the SPLs in diverse developmental and physiological processes in response to different biotic and abiotic cues. Among all, SPL5, SPL9, and SPL11 stood out as consistently differentially expressed SPLs in the adult and young tissues of different citrus-related species. Independent overexpression of their F. hindsii orthologs (FhSPL5, FhSPL9, and FhSPL11) brought an enhanced expression of endogenous FLOWERING LOCUS T leading to the significantly precocious flowering in transgenic Arabidopsis lines. Future study of the genes in the citrus plant itself is expected to conclude the assessments made in the current study.

Molecular Cues for Phenological Events in the Flowering Cycle in Avocado

Reproductively mature horticultural trees undergo an annual flowering cycle that repeats each year of their reproductive life. This annual flowering cycle is critical for horticultural tree productivity. However, the molecular events underlying the regulation of flowering in tropical tree crops such as avocado are not fully understood or documented. In this study, we investigated the potential molecular cues regulating the yearly flowering cycle in avocado for two consecutive crop cycles. Homologues of flowering-related genes were identified and assessed for their expression profiles in various tissues throughout the year. Avocado homologues of known floral genes FT, AP1, LFY, FUL, SPL9, CO and SEP2/AGL4 were upregulated at the typical time of floral induction for avocado trees growing in Queensland, Australia. We suggest these are potential candidate markers for floral initiation in these crops. In addition, DAM and DRM1, which are associated with endodormancy, were downregulated at the time of floral bud break. In this study, a positive correlation between CO activation and FT in avocado leaves to regulate flowering was not seen. Furthermore, the SOC1-SPL4 model described in annual plants appears to be conserved in avocado. Lastly, no correlation of juvenility-related miRNAs miR156, miR172 with any phenological event was observed.

Molecular and functional dissection of LIGULELESS1 (LG1) in plants

Plant architecture is a culmination of the features necessary for capturing light energy and adapting to the environment. An ideal architecture can promote an increase in planting density, light penetration to the lower canopy, airflow as well as heat distribution to achieve an increase in crop yield. A number of plant architecture-related genes have been identified by map cloning, quantitative trait locus (QTL) and genome-wide association study (GWAS) analysis. LIGULELESS1 (LG1) belongs to the squamosa promoter-binding protein (SBP) family of transcription factors (TFs) that are key regulators for plant growth and development, especially leaf angle (LA) and flower development. The DRL1/2-LG1-RAVL pathway is involved in brassinosteroid (BR) signaling to regulate the LA in maize, which has facilitated the regulation of plant architecture. Therefore, exploring the gene regulatory functions of LG1, especially its relationship with LA genes, can help achieve the precise regulation of plant phenotypes adapted to varied environments, thereby increasing the yield. This review comprehensively summarizes the advances in LG1 research, including its effect on LA and flower development. Finally, we discuss the current challenges and future research goals associate with LG1.

Differentially Expressed Conserved Plant Vegetative Phase-Change-Related microRNAs in Mature and Rejuvenated Silver Birch In Vitro Propagated Tissues

In plants, phase change from the juvenile stage to maturity involves physiological and anatomical changes, which are initiated and controlled by evolutionary highly conserved microRNAs. This process is of particular significance for the in vitro propagation of woody plant species, as individuals or tissues that have undergone the transition to vegetative maturity are recalcitrant to propagation. Conserved miRNAs differentially expressed between juvenile (including rejuvenated) and mature silver birch tissues were identified using high-throughput sequencing of small RNA libraries. Expression of some miR156 isoforms was high in juvenile tissues and has been previously reported to regulate phase transitions in a range of species. Additional miRNAs, such as miR394 and miR396, that were previously reported to be highly expressed in juvenile woody plant tissues were also differentially expressed in this study. However, expression of miR172, previously reported to be highly expressed in mature tissues, was low in all sample types in this study. The obtained results will provide insight for further investigation of the molecular mechanisms regulating vegetative phase change in silver birch and other perennial woody plant species, by analysing a wider range of genotypes, tissue types and maturation stages. This knowledge can potentially assist in identification of rejuvenated material at an earlier stage than currently possible, increasing the efficiency of silver birch in vitro propagation.

Effects of differentially expressed microRNAs induced by rootstocks and silicon on improving chilling tolerance of cucumber seedlings (Cucumis sativus L.)

BACKGROUND

Rootstocks can improve the chilling tolerance of grafted cucumbers, but their effectiveness varies. Rootstocks with strong de-blooming capacity may result in lower chilling tolerance of grafted cucumbers compared to those with weak de-blooming capacity, while also reducing the silicon absorption. However, it remains unclear whether this reduction in chilling tolerance is due to differences in rootstock genotypes or the reduction in silicon absorption.

RESULTS

The chilling tolerance of cucumber seedlings was improved by using rootstocks and silicon nutrition. Rootstocks had a more significant effect than silicon nutrition, and the weak de-blooming rootstock 'Yunnan figleaf gourd' was superior to the strong de-blooming rootstock 'Huangchenggen No. 2'. Compared to self-rooted cucumber, twelve miRNAs were regulated by two rootstocks, including seven identical miRNAs (novel-mir23, novel-mir26, novel-mir30, novel-mir37, novel-mir46, miR395a and miR398a-3p) and five different miRNAs (novel-mir32, novel-mir38, novel-mir65, novel-mir78 and miR397a). Notably, four of these miRNAs (novel-mir38, novel-mir65, novel-mir78 and miR397a) were only identified in 'Yunnan figleaf gourd'-grafted cucumbers. Furthermore, six miRNAs (miR168a-5p, miR390a-5p, novel-mir26, novel-mir55, novel-mir67 and novel-mir70) were found to be responsive to exogenous silicon. Target gene prediction for 20 miRNAs resulted in 520 genes. Functional analysis of these target genes showed that 'Yunnan figleaf gourd' improves the chilling tolerance of cucumber by regulating laccase synthesis and sulfate metabolism, while 'Huangchenggen No. 2' and exogenous silicon reduced chilling stress damage to cucumber by regulating ROS scavenging and protein protection, respectively.

CONCLUSION

Among the identified miRNAs, novel-mir46 and miR398a-3p were found in cucumbers in response to chilling stress and two types of rootstocks. However, no identical miRNAs were identified in response to chilling stress and silicon. In addition, the differential expression of novel-mir38, novel-mir65, novel-mir78 and miR397a may be one of the important reasons for the differences in chilling tolerance of grafted cucumbers caused by two types of rootstocks.

Variations in OsSPL10 confer drought tolerance by directly regulating OsNAC2 expression and ROS production in rice

Drought is a major factor restricting the production of rice (Oryza sativa L.). The identification of natural variants for drought stress-related genes is an important step toward developing genetically improved rice varieties. Here, we characterized a member of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family, OsSPL10, as a transcription factor involved in the regulation of drought tolerance in rice. OsSPL10 appears to play a vital role in drought tolerance by controlling reactive oxygen species (ROS) production and stomatal movements. Haplotype and allele frequency analyses of OsSPL10 indicated that most upland rice and improved lowland rice varieties harbor the OsSPL10^Hap1 allele, whereas the OsSPL10^Hap2 allele was mainly present in lowland and landrace rice varieties. Importantly, we demonstrated that the varieties with the OsSPL10^Hap1 allele showed low expression levels of OsSPL10 and its downstream gene, OsNAC2, which decreases the expression of OsAP37 and increases the expression of OsCOX11, thus preventing ROS accumulation and programmed cell death (PCD). Furthermore, the knockdown or knockout of OsSPL10 induced fast stomatal closure and prevented water loss, thereby improving drought tolerance in rice. Based on these observations, we propose that OsSPL10 confers drought tolerance by regulating OsNAC2 expression and that OsSPL10^Hap1 could be a valuable haplotype for the genetic improvement of drought tolerance in rice.

SlMYB72 affects pollen development by regulating autophagy in tomato

The formation and development of pollen are among the most critical processes for reproduction and genetic diversity in the life cycle of flowering plants. The present study found that SlMYB72 was highly expressed in the pollen and tapetum of tomato flowers. Downregulation of SlMYB72 led to a decrease in the amounts of seeds due to abnormal pollen development compared with wild-type plants. Downregulation of SlMYB72 delayed tapetum degradation and inhibited autophagy in tomato anther. Overexpression of SlMYB72 led to abnormal pollen development and delayed tapetum degradation. Expression levels of some autophagy-related genes (ATGs) were decreased in SlMYB72 downregulated plants and increased in overexpression plants. SlMYB72 was directly bound to ACCAAC/ACCAAA motif of the SlATG7 promoter and activated its expression. Downregulation of SlATG7 inhibited the autophagy process and tapetum degradation, resulting in abnormal pollen development in tomatoes. These results indicated SlMYB72 affects the tapetum degradation and pollen development by transcriptional activation of SlATG7 and autophagy in tomato anther. The study expands the understanding of the regulation of autophagy by SlMYB72, uncovers the critical role that autophagy plays in pollen development, and provides potential candidate genes for the production of male-sterility in plants.

Fire frequency, as well as stress response and developmental gene control serotiny level variation in a widespread pioneer Mediterranean conifer, Pinus halepensis

Many plants undergo adaptation to fire. Yet, as global change is increasing fire frequency worldwide, our understanding of the genetics of adaptation to fire is still limited. We studied the genetic basis of serotiny (the ability to disseminate seeds exclusively after fire) in the widespread, pioneer Mediterranean conifer Pinus halepensis Mill., by linking individual variation in serotiny presence and level to fire frequency and to genetic polymorphism in natural populations. After filtering steps, 885 single nucleotide polymorphisms (SNPs) out of 8000 SNPs used for genotyping were implemented to perform an in situ association study between genotypes and serotiny presence and level. To identify serotiny-associated loci, we performed random forest analyses of the effect of SNPs on serotiny levels, while controlling for tree size, frequency of wildfires, and background environmental parameters. Serotiny showed a bimodal distribution, with serotinous trees more frequent in populations exposed to fire in their recent history. Twenty-two SNPs found in genes involved in stress tolerance were associated with the presence-absence of serotiny while 37 found in genes controlling for flowering were associated with continuous serotiny variation. This study shows the high potential of P. halepensis to adapt to changing fire regimes, benefiting from a large and flexible genetic basis of trait variation.

Plant non-coding RNAs function in pollen development and male sterility

Male sterility is classified as either cytoplasmic male sterility (CMS) or genic male sterility (GMS). Generally, CMS involves mitochondrial genomes interacting with the nuclear genome, while GMS is caused by nuclear genes alone. Male sterility is regulated by multilevel mechanisms in which non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and phased small interfering RNAs (phasiRNAs), which have been proven to be critical elements. The development of high-throughput sequencing technology offers new opportunities to evaluate the genetic mechanism of ncRNAs in plant male sterility. In this review, we summarize the critical ncRNAs that regulate gene expression in ways dependent on or independent of hormones, which involve the differentiation of the stamen primordia, degradation of the tapetum, formation of microspores, and the release of pollen. In addition, the key mechanisms of the miRNA-lncRNA-mRNA interaction networks mediating male sterility in plants are elaborated. We present a different perspective on exploring the ncRNA-mediated regulatory pathways that control CMS in plants and create male-sterile lines through hormones or genome editing. A refined understanding of the ncRNA regulatory mechanisms in plant male sterility for the development of new sterile lines would be conducive to improve hybridization breeding.

Molecular characterization of SPL gene family during flower morphogenesis and regulation in blueberry

The SPL gene is a plant-specific transcription factor involved in the regulation of plant growth and development, which have been identified in woody plants. The process of floral bud differentiation affects the timing of flowering and fruit set and regulates plant growth, however, the mechanism of regulation of flower development by SPL genes is less studied. In this study, 56 VcSPL genes were identified in the tetraploid blueberry. The VcSPL gene family was classified into six subfamilies, and analysis of cis-elements showed that VcSPL genes were regulated by light, phytohormones (abscisic acid, MeJA), and low temperature. In the evolutionary analysis, segmental replication may play an important role in VcSPL gene amplification. Interestingly, we also studied diploid blueberry (Bilberry), in which 24 SPL genes were identified, and 36 homologous pairs were found, suggesting a high degree of convergence in the syntenic relationship between blueberry (Vaccinium corymbosum L) and bilberry (Vaccinium darrowii). Based on the expression profile, VcSPL genes were expressed at high levels in flowers, shoots, and roots, indicating a diversity of gene functions. Then we selected 20 differentially-expressed SPL genes to further investigate the role of VcSPL in floral induction and initiation. It showed that the genes VcSPL40, VcSPL35, VcSPL45, and VcSPL53 may play a crucial role in the blueberry floral transition phase (from vegetative growth to flower initiation). These results provided important information for understanding and exploring the role of VcSPLs in flower morphogenesis and plant growth.

Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

The SQUAMOSA promoter binding-like protein (SPL) is a specific transcription factor that affects plant growth and development. The SPL gene family has been explored in various plants, but information about these genes in alfalfa is limited. This study, based on the whole genome data of alfalfa SPL, the fundamental physicochemical properties, phylogenetic evolution, gene structure, cis-acting elements, and gene expression of members of the MsSPL gene family were analyzed by bioinformatics methods. We identified 82 SPL sequences in the alfalfa, which were annotated into 23 genes, including 7 (30.43%) genes with four alleles, 10 (43.47%) with three, 3 (13.04%) with two, 3 (13.04%) with one allele. These SPL genes were divided into six groups, that are constructed from A. thaliana, M. truncatula and alfalfa. Chromosomal localization of the identified SPL genes showed arbitary distribution. The subcellular localization predictions showed that all MsSPL proteins were located in the nucleus. A total of 71 pairs of duplicated genes were identified, and segmental duplication mainly contributed to the expansion of the MsSPL gene family. Analysis of the Ka/Ks ratios indicated that paralogs of the MsSPL gene family principally underwent purifying selection. Protein-protein interaction analysis of MsSPL proteins were performed to predict their roles in potential regulatory networks. Twelve cis-acting elements including phytohormone and stress elements were detected in the regions of MsSPL genes. We further analyzed that the MsSPLs had apparent responses to abiotic stresses such as drought and salt and the biotic stress of methyl jasmonate. These results provide comprehensive information on the MsSPL gene family in alfalfa and lay a solid foundation for elucidating the biological functions of MsSPLs. This study also provides valuable on the regulation mechanism and function of MsSPLs in response to biotic and abiotic stresses.

What Do We Know about Barley miRNAs?

Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.

Genome-Wide Analysis of SQUAMOSA-Promoter-Binding Protein-like Family in Flowering Pleioblastus pygmaeus

SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL genes in reproductive growth are undisclosed in bamboo plants. In the study, a total of 28 SPLs were screened from an ornamental dwarf bamboo species, Pleioblastus pygmaeus. Phylogenetic analysis indicates that 183 SPLs from eight plant species can be classified into nine subfamilies, and the 28 PpSPLs are distributed among eight subfamilies. Homologous analysis shows that as many as 32 pairs of homologous genes were found between P. pygmaeus and rice, and 83 pairs were found between P. pygmaeus and Moso bamboo, whose Ka/Ks values are all <1. MiRNA target prediction reveals that 13 out of the 28 PpSPLs have recognition sites complementary to miRNA156. To screen the SPLs involved in the reproductive growth of bamboo plants, the mRNA abundance of the 28 PpSPLs was profiled in the different tissues of flowering P. pygmaeus and non-flowering plants by RNA-Seq. Moreover, the relative expression level of eight PpSPLs is significantly higher in flowering P. pygmaeus than that in non-flowering plants, which was also validated by RT-qPCR. Combined with phylogenetic analysis and homologous analysis, the eight significant, differentially expressed PpSPLs were identified to be associated with the reproductive process and flower organ development. Among them, there are four potential miRNA156-targeting PpSPLs involved in the flowering process. Of significant interest in the study is the identification of 28 SPLs and the exploration of four key flowering-related SPLs from P. pygmaeus, which provides a theoretic basis for revealing the underlying functions of SPLs in the reproductive growth of bamboo plants.

Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense

SQUAMOSA promoter-binding-protein (SBP)-box family proteins are a class of plant-specific transcription factors, and widely regulate the development of floral and leaf morphology in plant growth and involve in environment and hormone signal response. In this study, we isolated and identified 21 non-redundant SBP-box genes in Chrysanthemum nankingense with bioinformatics analysis. Sequence alignments of 21 CnSBP proteins discovered a highly conserved SBP domain including two zinc finger-like structures and a nuclear localization signal region. According to the amino acid sequence alignments, 67 SBP-box genes from Arabidopsis thaliana, rice, Artemisia annua and C. nankingense were clustered into eight groups, and the motif and gene structure analysis also sustained this classification. The gene evolution analysis indicated the CnSBP genes experienced a duplication event about 10 million years ago (Mya), and the CnSBP and AtSPL genes occurred a divergence at 24 Mya. Transcriptome data provided valuable information for tissue-specific expression profiles of the CnSBPs, which highly expressed in floral tissues and differentially expressed in leaf, root and stem organs. Quantitative Real-time Polymerase Chain Reaction data showed expression patterns of the CnSBPs under exogenous hormone and abiotic stress treatments, separately abscisic acid, salicylic acid, gibberellin A3, methyl jasmonate and ethylene spraying as well as salt and drought stresses, indicating that the candidate CnSBP genes showed differentiated spatiotemporal expression patterns in response to hormone and abiotic stresses. Our study provides a systematic genome-wide analysis of the SBP-box gene family in C. nankingense. In general, it provides a fundamental theoretical basis that SBP-box genes may regulate the resistance of stress physiology in chrysanthemum via exogenous hormone pathways.

miR156 regulates somatic embryogenesis by modulating starch accumulation in citrus

Somatic embryogenesis (SE) is a major regeneration approach for in vitro cultured tissues of plants, including citrus. However, SE capability is difficult to maintain, and recalcitrance to SE has become a major obstacle to plant biotechnology. We previously reported that miR156-SPL modules regulate SE in citrus callus. However, the downstream regulatory pathway of the miR156-SPL module in SE remains unclear. In this study, we found that transcription factors CsAGL15 and CsFUS3 bind to the CsMIR156A promoter and activate its expression. Suppression of csi-miR156a function leads to up-regulation of four target genes, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (CsSPL) genes, and reduction of SE efficiency. In the short tandem target mimic (STTM)-miR156a overexpression callus (MIM156), the number of amyloplasts and starch content were significantly reduced, and genes involved in starch synthesis and transport were down-regulated. csi-miR172d was down-regulated, whereas the target genes, CsTOE1.1 and CsTOE1.2, which inhibit the expression of starch biosynthesis genes, were up-regulated. In our working model, CsAGL15 and CsFUS3 activate csi-miR156a, which represses CsSPLs and further regulates csi-miR172d and CsTOEs, thus altering starch accumulation in callus cells and regulating SE in citrus. This study elucidates the pathway of miR156-SPLs and miR172-TOEs-mediated regulation of SE, and provides new insights into enhancing SE capability in citrus.

The miR156-Targeted SQUAMOSA PROMOTER BINDING PROTEIN (PmSBP) Transcription Factor Regulates the Flowering Time by Binding to the Promoter of SUPPRESSOR OF OVEREXPRESSION OF CO1 (PmSOC1) in Prunus mume

Prunus mume, a famous perennial ornamental plant and fruit tree in Asia, blooms in winter or early spring in the Yangtze River area. The flowering time directly determines its ornamental and economic value, so it is of great significance to study the molecular mechanism of flowering time. SQUAMOSA PROMOTER BINDING PROTEIN (SBP), often regulated by miR156, is an important flowering regulator, although its function is unknown in P. mume. Here, 11 miR156 precursors were analyzed and located in five chromosomes of the P. mume genome. The expression pattern showed that PmSBP1/6 was negatively correlated with miR156. The promoters of PmSBP1/6 were specifically expressed in the apical meristem. Overexpression of PmSBP1/6 in tobacco promoted flowering and changed the length ratio of pistil and stamen. Moreover, PmSBP1 also affected the number and vitality of pollen and reduced the fertility of transgenic tobacco. Furthermore, ectopic expression of PmSBP1/6 caused up-regulated expression of endogenous SUPPRESSOR OF OVEREXPRESSION OF CO1 (NtSOC1). The yeast-one hybrid assay showed that PmSBP1 was bonded to the promoters of PmSOC1s. In conclusion, a miR156-PmSBP1-PmSOC1s pathway was formed to participate in the regulation of flowering time in P. mume, which provided references for the molecular mechanism of flowering time regulation and molecular breeding of P. mume.

Energy status-promoted growth and development of Arabidopsis require copper deficiency response transcriptional regulator SPL7

Copper (Cu) is a cofactor of around 300 Arabidopsis proteins, including photosynthetic and mitochondrial electron transfer chain enzymes critical for adenosine triphosphate (ATP) production and carbon fixation. Plant acclimation to Cu deficiency requires the transcription factor SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 (SPL7). We report that in the wild type (WT) and in the spl7-1 mutant, respiratory electron flux via Cu-dependent cytochrome c oxidase is unaffected under both normal and low-Cu cultivation conditions. Supplementing Cu-deficient medium with exogenous sugar stimulated growth of the WT, but not of spl7 mutants. Instead, these mutants accumulated carbohydrates, including the signaling sugar trehalose 6-phosphate, as well as ATP and NADH, even under normal Cu supply and without sugar supplementation. Delayed spl7-1 development was in agreement with its attenuated sugar responsiveness. Functional TARGET OF RAPAMYCIN and SNF1-RELATED KINASE1 signaling in spl7-1 argued against fundamental defects in these energy-signaling hubs. Sequencing of chromatin immunoprecipitates combined with transcriptome profiling identified direct targets of SPL7-mediated positive regulation, including Fe SUPEROXIDE DISMUTASE1 (FSD1), COPPER-DEFICIENCY-INDUCED TRANSCRIPTION FACTOR1 (CITF1), and the uncharacterized bHLH23 (CITF2), as well as an enriched upstream GTACTRC motif. In summary, transducing energy availability into growth and reproductive development requires the function of SPL7. Our results could help increase crop yields, especially on Cu-deficient soils.

Genome-wide analysis and molecular dissection of the SPL gene family in Fraxinus mandshurica

BACKGROUND

SQUAMOSA promoter binding protein-like (SPL) is a unique family of transcription factors in plants, which is engaged in regulating plant growth and development, physiological and biochemical processes. Fraxinus mandshurica is an excellent timber species with a wide range of uses in northeastern China and enjoys a high reputation in the international market. SPL family analysis has been reported in some plants while SPL family analysis of Fraxinus mandshurica has not been reported.

RESULTS

We used phylogeny, conserved motifs, gene structure, secondary structure prediction, miR156 binding sites, promoter cis elements and GO annotation to systematically analyze the FmSPLs family. This was followed by expression analysis by subcellular localization, expression patterns at various tissue sites, abiotic stress and hormone induction. Because FmSPL2 is highly expressed in flowers it was selected to describe the SPL gene family of Fraxinus mandshurica by ectopic expression. Among them, 10 FmSPL genes that were highly expressed at different loci were selected for expression analysis under abiotic stress (NaCl and Cold) and hormone induction (IAA and ABA). These 10 FmSPL genes showed corresponding trends in response to both abiotic stress and hormone induction. We showed that overexpression of FmSPL2 in transgenic Nicotiana tabacum L. resulted in taller plants, shorter root length, increased root number, rounded leaves, and earlier flowering time.

CONCLUSIONS

We identified 36 SPL genes, which were classified into seven subfamilies based on sequence analysis. FmSPL2 was selected for subsequent heterologous expression by analysis of expression patterns in various tissues and under abiotic stress and hormone induction, and significant phenotypic changes were observed in the transgenic Nicotiana tabacum L. These results provide insight into the evolutionary origin and biological significance of plant SPL. The aim of this study was to lay the foundation for the genetic improvement of Fraxinus mandshurica and the subsequent functional analysis of FmSPL2.

Genome-Wide Analysis of the SPL Gene Family and Expression Analysis during Flowering Induction in Prunus × yedoensis 'Somei-yoshino'

SQUAMOSA Promoter-Binding Protein-Like (SPL) genes encode plant-specific transcription factors which bind to the SQUAMOSA promoter of the MADS-box genes to regulate its expression. It plays important regulatory roles in floral induction and development, fertility, light signals and hormonal transduction, and stress response in plants. In this study, 32 PySPL genes with complete SBP (squamosa promoter binding protein) conserved domain were identified from the genome of Prunus × yedoensis ‘Somei-yoshino’ and analyzed by bioinformatics. 32 PySPLs were distributed on 13 chromosomes, encoding 32 PySPL proteins with different physical and chemical properties. The phylogenetic tree constructed with Arabidopsis thaliana and Oryza sativa can be divided into 10 subtribes, indicating PySPLs of different clusters have different biological functions. The conserved motif prediction showed that the number and distribution of motifs on each PySPL is varied. The gene structure analysis revealed that PySPLs harbored exons ranging from 2 to 10. The predictive analysis of acting elements showed that the promoter of PySPLs contain a large number of light-responsive elements, as well as response elements related to hormone response, growth and development and stress response. The analysis of the PySPLs expressions in flower induction and flower organs based on qRT-PCR showed that PySPL06/22 may be the key genes of flower development, PySPL01/06 and PySPL22 may play a role in the development of sepal and pistil, respectively. The results provide a foundation for the study of SPL transcription factors of Prunus × yedoensis ‘Somei-yoshino’ and provide more reference information of the function of SPL gene in flowering.

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

BACKGROUND

Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively.

RESULTS

These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development.

CONCLUSIONS

This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.