Molecular characterisation of the Arabidopsis SBP-box genes

A regulatory network controlling developmental boundaries and meristem fates contributed to maize domestication

During domestication, early farmers selected different vegetative and reproductive traits, but identifying the causative loci has been hampered by their epistasis and functional redundancy. Using chromatin immunoprecipitation sequencing combined with genome-wide association analysis, we uncovered a developmental regulator that controls both types of trait while acting upstream of multiple domestication loci. tasselsheath4 (tsh4) is a new maize domestication gene that establishes developmental boundaries and specifies meristem fates despite not being expressed within them. TSH4 accomplishes this by using a double-negative feedback loop that targets and represses the very same microRNAs that negatively regulate it. TSH4 functions redundantly with a pair of homologs to positively regulate a suite of domestication loci while specifying the meristem that doubled seed yield in modern maize. TSH4 has a critical role in yield gain and helped generate ideal crop plant architecture, thus explaining why it was a major domestication target.

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.

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

BACKGROUND

Squamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that is widely involved in the regulation of plant growth and development, including flower and grain development, stress responses, and secondary metabolite synthesis. However, this gene family has not been comprehensively evaluated in barley, the most adaptable cereal crop with a high nutritional value.

RESULTS

In this study, a total of 15 HvSPL genes were identified based on the Hordeum vulgare genome. These genes were named HvSPL1 to HvSPL15 based on the chromosomal distribution of the HvSPL genes and were divided into seven groups (I, II, III, V, VI, VII, and VIII) based on the phylogenetic tree analysis. Chromosomal localization revealed one pair of tandem duplicated genes and one pair of segmental duplicated genes. The HvSPL genes exhibited the highest collinearity with the monocotyledonous plant, Zea mays (27 pairs), followed by Oryza sativa (18 pairs), Sorghum bicolor (16 pairs), and Arabidopsis thaliana (3 pairs), and the fewest homologous genes with Solanum lycopersicum (1 pair). The distribution of the HvSPL genes in the evolutionary tree was relatively scattered, and HvSPL proteins tended to cluster with SPL proteins from Z. mays and O. sativa, indicating a close relationship between HvSPL and SPL proteins from monocotyledonous plants. Finally, the spatial and temporal expression patterns of the 14 HvSPL genes from different subfamilies were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the results, the HvSPL gene family exhibited tissue-specific expression and played a regulatory role in grain development and abiotic stress. HvSPL genes are highly expressed in various tissues during seed development. The expression levels of HvSPL genes under the six abiotic stress conditions indicated that many genes responded to stress, especially HvSPL8, which exhibited high expression under multiple stress conditions, thereby warranting further attention.

CONCLUSION

In this study, 15 SPL gene family members were identified in the genome of Hordeum vulgare, and the phylogenetic relationships, gene structure, replication events, gene expression, and potential roles of these genes in millet development were studied. Our findings lay the foundation for exploring the HvSPL genes and performing molecular breeding of barley.

Identification and Functional Studies on the Role of PlSPL14 in Herbaceous Peony Stem Development

Stem strength plays a crucial role in the growth and development of plants, as well as in their flowering and fruiting. It not only impacts the lodging resistance of crops, but also influences the ornamental value of ornamental plants. Stem development is closely linked to stem strength; however, the roles of the SPL transcription factors in the stem development of herbaceous peony (Paeonia lactiflora Pall.) are not yet fully elucidated. In this study, we obtained and cloned the full-length sequence of PlSPL14, encoding 1085 amino acids. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression level of PlSPL14 gradually increased with the stem development of P. lactiflora and was significantly expressed in vascular bundles. Subsequently, utilizing the techniques of virus-induced gene silencing (VIGS) and heterologous overexpression in tobacco (Nicotiana tabacum L.), it was determined that PlSPL14-silenced P. lactiflora had a thinner xylem thickness, a decreased stem diameter, and weakened stem strength, while PlSPL14-overexpressing tobacco resulted in a thicker xylem thickness, an increased stem diameter, and enhanced stem strength. Further screening of the interacting proteins of PlSPL14 using a yeast two-hybrid (Y2H) assay revealed an interactive relationship between PlSPL14 and PlSLR1 protein, which acts as a negative regulator of gibberellin (GA). Additionally, the expression level of PlSLR1 gradually decreased during the stem development of P. lactiflora. The above results suggest that PlSPL14 may play a positive regulatory role in stem development and act in the xylem, making it a potential candidate gene for enhancing stem straightness in plants.

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.

Pepper SBP-box transcription factor, CaSBP13, plays a negatively role in drought response

The SBP-box gene significantly influences plant growth, development, and stress responses, yet its function in pepper plants during drought stress remains unexplored. Using virus-induced gene silencing and overexpression strategies, we examined the role of CaSBP13 during drought stress in plants. The results revealed that the expression of CaSBP13 can be induced by drought stress. Silencing of CaSBP13 in pepper notably boosted drought resistance, as evident by decreased active oxygen levels. Furthermore, the water loss rate, relative electrical conductivity, malondialdehyde content, and stomatal density were reduced in CaSBP13-silenced plants compared to controls. In contrast, CaSBP13 overexpression in Nicotiana benthamiana decreased drought tolerance with elevated reactive oxygen levels and stomatal density. Additionally, ABA signaling pathway genes (CaPP2C, CaAREB) exhibited reduced expression levels in CaSBP13-silenced plants post drought stress, as compared to control plants. On the contrary, CaPYL9 and CaSNRK2.4 showed heightened expression in CaSBP13-sienced plants under the same conditions. However, a converse trend for NbAREB, NbSNRK2.4, and NbPYL9 was observed post-four day drought in CaSBP13-overexpression plants. These findings suggest that CaSBP13 negatively regulates drought tolerance in pepper, potentially via ROS and ABA signaling pathways.

Genetic Analysis of Soybean Flower Size Phenotypes Based on Computer Vision and Genome-Wide Association Studies

The dimensions of organs such as flowers, leaves, and seeds are governed by processes of cellular proliferation and expansion. In soybeans, the dimensions of these organs exhibit a strong correlation with crop yield, quality, and other phenotypic traits. Nevertheless, there exists a scarcity of research concerning the regulatory genes influencing flower size, particularly within the soybean species. In this study, 309 samples of 3 soybean types (123 cultivar, 90 landrace, and 96 wild) were re-sequenced. The microscopic phenotype of soybean flower organs was photographed using a three-eye microscope, and the phenotypic data were extracted by means of computer vision. Pearson correlation analysis was employed to assess the relationship between petal and seed phenotypes, revealing a strong correlation between the sizes of these two organs. Through GWASs, SNP loci significantly associated with flower organ size were identified. Subsequently, haplotype analysis was conducted to screen for upstream and downstream genes of these loci, thereby identifying potential candidate genes. In total, 77 significant SNPs associated with vexil petals, 562 significant SNPs associated with wing petals, and 34 significant SNPs associated with keel petals were found. Candidate genes were screened by candidate sites, and haplotype analysis was performed on the candidate genes. Finally, the present investigation yielded 25 and 10 genes of notable significance through haplotype analysis in the vexil and wing regions, respectively. Notably, Glyma.07G234200, previously documented for its high expression across various plant organs, including flowers, pods, leaves, roots, and seeds, was among these identified genes. The research contributes novel insights to soybean breeding endeavors, particularly in the exploration of genes governing organ development, the selection of field materials, and the enhancement of crop yield. It played a role in the process of material selection during the growth period and further accelerated the process of soybean breeding material selection.

Delineation of loci governing an extra-earliness trait in lentil (Lens culinaris Medik.) using the QTL-Seq approach

Developing early maturing lentil has the potential to minimize yield losses, mainly during terminal drought. Whole-genome resequencing (WGRS) based QTL-seq identified the loci governing earliness in lentil. The genetic analysis for maturity duration provided a good fit to 3:1 segregation (F2), indicating earliness as a recessive trait. WGRS of Globe Mutant (late parent), late-flowering, and early-flowering bulks (from RILs) has generated 1124.57, 1052.24 million raw and clean reads, respectively. The QTL-Seq identified three QTLs (LcqDTF3.1, LcqDTF3.2, and LcqDTF3.3) on chromosome 3 having 246244 SNPs and 15577 insertions/deletions (InDels) and 13 flowering pathway genes. Of these, 11 exhibited sequence variations between bulks and validation (qPCR) revealed a significant difference in the expression of nine candidate genes (LcGA20oxG, LcFRI, LcLFY, LcSPL13a, Lcu.2RBY.3g060720, Lcu.2RBY.3g062540, Lcu.2RBY.3g062760, LcELF3a, and LcEMF1). Interestingly, the LcELF3a gene showed significantly higher expression in late-flowering genotype and exhibited substantial involvement in promoting lateness. Subsequently, an InDel marker (I-SP-383.9; LcELF3a gene) developed from LcqDTF3.2 QTL region showed 82.35% PVE (phenotypic variation explained) for earliness. The cloning, sequencing, and comparative analysis of the LcELF3a gene from both parents revealed 23 SNPs and InDels. Interestingly, a 52 bp deletion was recorded in the LcELF3a gene of L4775, predicted to cause premature termination of protein synthesis after 4 missense amino acids beyond the 351st amino acid due to the frameshift during translation. The identified InDel marker holds significant potential for breeding early maturing lentil varieties.

Research on drought stress in Medicago sativa L. from 1998 to 2023: a bibliometric analysis

Alfalfa (Medicago sativa L.) is one of the most important forage crops in the world. Drought is recognized as a major challenge limiting alfalfa production and threatening food security. Although some literature reviews have been conducted in this area, bibliometric reviews based on large amounts of published data are still lacking. In this paper, a bibliometric analysis of alfalfa drought stress from 1998-2023 was conducted using the Web of Science Core Collection database in order to assess global trends in alfalfa drought stress research and to provide new directions for future research. The results showed that the annual publication output maintained an increase in most years, with China and the United States contributing significantly to the field. Most of the journals published are specialized journals in botany, environmental science, soil science and crop science, as well as related agribusiness journals. "plant growth" and "yield" were the most frequently used keywords, reflecting the important purpose of research in this field. And two main research directions were identified: research on drought response mechanism of alfalfa and exploration of drought-resistant technology. In addition, physiological, biochemical, and molecular responses of drought tolerance and high yield in alfalfa, transgenics, and microbial fertilizer research have been hot research topics in recent years and may continue in the future. The ultimate goal of this paper is to provide a foundational reference for future research on alfalfa's drought resistance and yield optimization mechanisms, thereby enhancing the crop's application in agricultural production.

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.

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.

Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.

Identification and expression analysis of SBP-Box-like (SPL) gene family disclose their contribution to abiotic stress and flower budding in pigeon pea (Cajanus cajan)

The SPL gene family (for Squamosa Promoter-binding like Proteins) represents specific transcription factors that have significant roles in abiotic stress tolerance, development and the growth processes of different plants, including initiation of the leaf, branching and development of shoot and fruits. The SPL gene family has been studied in different plant species; however, its role is not yet fully explored in pigeon pea (Cajanus cajan ). In the present study, 11 members of the CcSPL gene family were identified in C. cajan . The identified SPLs were classified into nine groups based on a phylogenetic analysis involving SPL protein sequences from C. cajan , Arabidopsis thaliana , Cicer arietinum , Glycine max , Phaseolus vulgaris , Vigna unguiculata and Arachis hypogaea . Further, the identification of gene structure, motif analysis, domain analysis and presence of cis -regulatory elements in the SPL family members were studied. Based on RNA-sequencing data, gene expression analysis was performed, revealing that CcSPL2.1, 3 and 13A were significantly upregulated for salt-tolerance and CcSPL14 and 15 were upregulated in a salt-susceptible cultivar. Real-time qPCR validation indicated that CcSPL3, 4, 6 and 13A were upregulated under salt stress conditions. Therefore, molecular docking was performed against the proteins of two highly expressed genes (CcSPL3 and CcSPL14 ) with three ligands: abscisic acid, gibberellic acid and indole-3-acetic acid. Afterward, their binding affinity was obtained and three-dimensional structures were predicted. In the future, our study may open avenues for harnessing CcSPL genes in pigeon pea for enhanced abiotic stress resistance and developmental traits.

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.

CsSPL13A directly binds and positively regulates CsFT and CsBAM to accelerate flowering in cucumber

Flowering is an important developmental transition that greatly affects the yield of many vegetable crops. In cucumber (Cucumis sativus), flowering is regulated by various factors including squamosa promoter-binding-like (SPL) family proteins. However, the role of CsSPL genes in cucumber flowering remains largely unknown. In this study, we cloned the squamosa promoter-binding-like protein 13A (CsSPL13A) gene, which encodes a highly conserved SBP-domain protein that acts as a transcription factor and localizes to the nucleus. Quantitative real-time PCR (qRT-PCR) analysis showed that CsSPL13A was mainly expressed in flowers, and its expression level increased significantly nearing the flowering stage. Additionally, compared with the wild type(WT), CsSPL13A-overexpressing transgenic cucumber plants (CsSPL13A-OE) showed considerable differences in flowering phenotypes, such as early flowering, increased number of male flowers, and longer flower stalks. CsSPL13A upregulated the expression of the flowering integrator gene Flowering Locus T (CsFT) and the sugar-mediated flowering gene β-amylase (CsBAM) in cucumber. Yeast one-hybrid and firefly enzyme reporter assays confirmed that the CsSPL13A protein could directly bind to the promoters of CsFT and CsBAM, suggesting that CsSPL13A works together with CsFT and CsBAM to mediate flowering in cucumber. Overall, our results provide novel insights into the regulatory network of flowering in cucumber as well as new ideas for the genetic improvement of cucumber varieties.

Genome-wide identification, evolution, and role of SPL gene family in beet (Beta vulgaris L.) under cold stress

BACKGROUND

SPL transcription factors play vital roles in regulating plant growth, development, and abiotic stress responses. Sugar beet (Beta vulgaris L.), one of the world's main sugar-producing crops, is a major source of edible and industrial sugars for humans. Although the SPL gene family has been extensively identified in other species, no reports on the SPL gene family in sugar beet are available.

RESULTS

Eight BvSPL genes were identified at the whole-genome level and were renamed based on their positions on the chromosome. The gene structure, SBP domain sequences, and phylogenetic relationship with Arabidopsis were analyzed for the sugar beet SPL gene family. The eight BvSPL genes were divided into six groups (II, IV, V, VI, VII, and VIII). Of the BvSPL genes, no tandem duplication events were found, but one pair of segmental duplications was present. Multiple cis-regulatory elements related to growth and development were identified in the 2000-bp region upstream of the BvSPL gene start codon (ATG). Using quantitative real-time polymerase chain reaction (qRT-PCR), the expression profiles of the eight BvSPL genes were examined under eight types of abiotic stress and during the maturation stage. BvSPL transcription factors played a vital role in abiotic stress, with BvSPL3 and BvSPL6 being particularly noteworthy.

CONCLUSION

Eight sugar beet SPL genes were identified at the whole-genome level. Phylogenetic trees, gene structures, gene duplication events, and expression profiles were investigated. The qRT-PCR analysis indicated that BvSPLs play a substantial role in the growth and development of sugar beet, potentially participating in the regulation of root expansion and sugar accumulation.

Comparative analysis of SPL transcription factors from streptophyte algae and embryophytes reveals evolutionary trajectories of SPL family in streptophytes

SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon-intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes.

Temporal regulation of vegetative phase change in plants

During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.

Genome-Wide Identification and Expression Analysis of the SQUAMOSA Promoter-Binding Protein-like (SPL) Transcription Factor Family in Catalpabungei

As a plant-specific transcription factor, the SPL gene family plays a critical role in plant growth and development. Although the SPL gene family has been identified in diverse plant species, there have been no genome-wide identification or systematic study reports on the SPL gene family in Catalpa bungei. In this study, we identified 19 putative SPL gene family members in the C. bungei genome. According to the phylogenetic relationship, they can be divided into eight groups, and the genes in the same group have a similar gene structure and conserved motifs. Synteny analysis showed that fragment duplication played an important role in the expansion of the CbuSPL gene family. At the same time, CbuSPL genes have cis-acting elements and functions related to light response, hormone response, growth and development, and stress response. Tissue-specific expression and developmental period-specific expression analysis showed that CbuSPL may be involved in flowering initiation and development, flowering transition, and leaf development. In addition, the ectopic expression of CbuSPL4 in Arabidopsis confirmed that it can promote early flowering and induce the expression of related flowering genes. These systematic research results will lay a foundation for further study on the functional analysis of SPL genes in C. bungei.

Genome-wide identification and analysis of the evolution and expression pattern of the SBP gene family in two Chimonanthus species

BACKGROUND

Chimonanthus praecox and Chimonanthus salicifolius are closely related species that diverged approximately six million years ago. While both C. praecox and C. salicifolius could withstand brief periods of low temperatures of - 15 °C. Their flowering times are different, C. praecox blooms in early spring, whereas C. salicifolius blooms in autumn. The SBP-box (SQUAMOSA promoter-binding protein) is a plant-specific gene family that plays a crucial vital role in regulating plant flowering. Although extensively studied in various plants, the SBP gene family remains uncharacterized in Calycanthaceae.

METHODS AND RESULTS

We conducted genome-wide identification of SBP genes in both C. praecox and C. salicifolius and comprehensively characterized the chromosomal localization, gene structure, conserved motifs, and domains of the identified SBP genes. In total, 15 and 18 SBP genes were identified in C. praecox and C. salicifolius, respectively. According to phylogenetic analysis, the SBP genes from Arabidopsis, C. praecox, and C. salicifolius were clustered into eight groups. Analysis of the gene structure and conserved protein motifs showed that SBP proteins of the same subfamily have similar motif structures. The expression patterns of SBP genes were analyzed using transcriptome data. The results revealed that more than half of the genes exhibited lower expression levels in leaves than in flowers, suggesting their potential involvement in the flower development process and may be linked to the winter and autumn flowering of C. praecox and C. salicifolius.

CONCLUSION

Thirty-three SBPs were identified in C. praecox and C. salicifolius. The evolutionary characteristics and expression patterns were examined in this study. These results provide valuable information to elucidate the evolutionary relationships of the SBP family and help determine the functional characteristics of the SBP genes in subsequent studies.

Genome-wide analysis of the SPL transcription factor family and its response to water stress in sunflower (Helianthus annuus)

SPL (SQUAMOSA promoter binding proteins-like) are plant-specific transcription factors that play essential roles in a variety of developmental processes as well as the ability to withstand biotic and abiotic stresses. To date, numerous species have been investigated for the SPL gene family, but so far, no SPL family genes have been thoroughly identified and characterized in the sunflower (Helianthus annuus). In this study, 25 SPL genes were identified in the sunflower genome and were unevenly distributed on 11 chromosomes. According to phylogeny analysis, 59 SPL genes from H. annuus, O. sativa, and A. thaliana were clustered into seven groups. Furthermore, the SPL genes in groups-I and II were demonstrated to be potential targets of miR156. Synteny analysis showed that 7 paralogous gene pairs exist in HaSPL genes and 26 orthologous gene pairs exist between sunflower and rice, whereas 21 orthologous gene pairs were found between sunflower and Arabidopsis. Segmental duplication appears to have played a vital role in the expansion processes of sunflower SPL genes, and because of selection pressure, all duplicated genes have undergone purifying selection. Tissue-specific gene expression analysis of the HaSBP genes proved their diverse spatiotemporal expression patterns, which were predominantly expressed in floral organs and differentially expressed in stem, axil, and root tissues. The expression pattern of HaSPL genes under water stress showed broad involvement of HaSPLs in the response to flood and drought stresses. This genome-wide identification investigation provides detailed information on the sunflower SPL transcription factor gene family and establishes a strong platform for future research on sunflower responses to abiotic stress tolerance.

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.

Genome-Wide Analysis of SPL/miR156 Module and Its Expression Analysis in Vegetative and Reproductive Organs of Oil Palm (Elaeis guineensis)

The SPL (SQUAMOSA-promoter binding protein-like) gene family is one of the largest plant transcription factors and is known to be involved in the regulation of plant growth, development, and stress responses. The genome-wide analysis of SPL gene members in a diverse range of crops has been elucidated. However, none of the genome-wide studies on the SPL gene family have been carried out for oil palm, an important oil-yielding plant. In this research, a total of 24 EgSPL genes were identified via a genome-wide approach. Phylogenetic analysis revealed that most of the EgSPLs are closely related to the Arabidopsis and rice SPL gene members. EgSPL genes were mapped onto the only nine chromosomes of the oil palm genome. Motif analysis revealed conservation of the SBP domain and the occurrence of 1-10 motifs in EgSPL gene members. Gene duplication analysis demonstrated the tandem duplication of SPL members in the oil palm genome. Heatmap analysis indicated the significant expression of SPL genes in shoot and flower organs of oil palm plants. Among the identified EgSPL genes, a total 14 EgSPLs were shown to be targets of miR156. Real-time PCR analysis of 14 SPL genes showed that most of the EgSPL genes were more highly expressed in female and male inflorescences of oil palm plants than in vegetative tissues. Altogether, the present study revealed the significant role of EgSPL genes in inflorescence development.

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.

Comparative Analysis Based on Physiological and Transcriptomic Data between Juvenile and Adult Tree Peony (Paeonia delavayi)

A long juvenile period limits the breeding process of many woody plants including tree peony. To investigate the physiological and transcriptomic differences between juvenile and adult plants of tree peony and to explore the key SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, which are vital in age-dependent pathways, 1-year-old and 3-year-old Paeonia delavayi plants were used to compare the relevant physiological parameters and transcriptomic profiles of the leaves in two phases of plants. The results of the physiological parameters showed that the starch content in the leaves of adult plants remained unchanged and that the soluble sugar content significantly increased compared with those in the juvenile plants. In terms of plant hormones, the contents of cytokinin-like hormone (N6-isopentenyladenine (iP)) and jasmonic acid (JA) significantly decreased, whereas the contents of auxin (indole-3-acetic acid, IAA), abscisic acid (ABA), cytokinin-like hormone (N6-isopentenyladenenosine (iPR)), and ethylene precursor (1-aminocyclopropane-1-carboxylic acid, ACC) showed no statistic difference. Transcriptome sequencing results showed that there were 194 differentially expressed genes (DEGs) between juvenile and adult plants, including 171 up-regulated DEGs and 23 down-regulated DEGs. Circadian rhythm, plant hormone signal transduction, and sugar metabolism were closely related to the juvenile-to-adult transition in P. delavayi, involving a total of 12 DEGs. In addition, a total of 13 SPL genes were identified in the transcriptome data, but only PdSPL10 (c71307.graph_c0) was differentially expressed. It was further validated via qRT-PCR analysis, indicating that PdSPL10 might be a key gene regulating the process of juvenile-to-adult in P. delavayi. Based on the above results, a hypothetical transcriptional network regulating juvenile-to-adult transition and flowering in P. delavayi was proposed. These findings provide a reference for understanding the mechanism of juvenile-to-adult transition in tree peony.

Integrated transcriptome and microRNA sequencing analyses reveal gene responses in poplar leaves infected by the novel pathogen bean common mosaic virus (BCMV)

Recently, a novel poplar mosaic disease caused by bean common mosaic virus (BCMV) was investigated in Populus alba var. pyramidalis in China. Symptom characteristics, physiological performance of the host, histopathology, genome sequences and vectors, and gene regulation at the transcriptional and posttranscriptional levels were analyzed and RT-qPCR (quantitative reverse transcription PCR) validation of expression was performed in our experiments. In this work, the mechanisms by which the BCMV pathogen impacts physiological performance and the molecular mechanisms of the poplar response to viral infection were reported. The results showed that BCMV infection decreased the chlorophyll content, inhibited the net photosynthesis rate (Pn) and stomatal conductance (Gs), and significantly changed chlorophyll fluorescence parameters in diseased leaves. Transcriptome analysis revealed that the expression of the majority of DEGs (differentially expressed genes) involved in the flavonoid biosynthesis pathway was promoted, but the expression of all or almost all DEGs associated with photosynthesis-antenna proteins and the photosynthesis pathway was inhibited in poplar leaves, suggesting that BCMV infection increased the accumulation of flavonoids but decreased photosynthesis in hosts. Gene set enrichment analysis (GSEA) illustrated that viral infection promoted the expression of genes involved in the defense response or plant-pathogen interaction. MicroRNA-seq analysis illustrated that 10 miRNA families were upregulated while 6 families were downregulated in diseased poplar leaves; moreover, miR156, the largest family with the most miRNA members and target genes, was only differentially upregulated in long-period disease (LD) poplar leaves. Integrated transcriptome and miRNA-seq analyses revealed 29 and 145 candidate miRNA-target gene pairs; however, only 17 and 76 pairs, accounting for 2.2% and 3.2% of all DEGs, were authentically negatively regulated in short-period disease (SD) and LD leaves, respectively. Interestingly, 4 miR156/SPL (squamosa promoter-binding-like protein) miRNA-target gene pairs were identified in LD leaves: the miR156 molecules were upregulated, but SPL genes were downregulated. In conclusion, BCMV infection significantly changed transcriptional and posttranscriptional gene expression in poplar leaves, inhibited photosynthesis, increased the accumulation of flavonoids, induced systematic mosaic symptoms, and decreased physiological performance in diseased poplar leaves. This study elucidated the fine-tuned regulation of poplar gene expression by BCMV; moreover, the results also suggested that miR156/SPL modules played important roles in the virus response and development of viral systematic symptoms in plant virus disease.

Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Three Orchids

SPL transcription factors regulate important processes such as plant growth and development, metabolic regulation, and abiotic stress. They play crucial roles in the development of flower organs. However, little is known about the characteristics and functions of the SPLs in the Orchidaceae. In this study, Cymbidium goeringii Rchb. f., Dendrobium chrysotoxum Lindl., and Gastrodia elata BI. were used as research objects. The SPL gene family of these orchids was analyzed on a genome-wide scale, and their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns were studied. Transcriptome and qRT-PCR methods were combined to investigate the regulatory effect of SPLs on the development of flower organs during the flowering process (bud, initial bloom, and full bloom). This study identifies a total of 43 SPLs from C. goeringii (16), D. chrysotoxum (17), and G. elata (10) and divides them into eight subfamilies according to the phylogenetic tree. Most SPL proteins contained conserved SBP domains and complex gene structures; half of the genes had introns longer than 10 kb. The largest number and variety of cis-acting elements associated with light reactions were enriched, accounting for about 45% of the total (444/985); 13/43 SPLs contain response elements of miRNA156. GO enrichment analysis showed that the functions of most SPLs were mainly enriched in the development of plant flower organs and stems. In addition, expression patterns and qRT-PCR analysis suggested the involvement of SPL genes in the regulation of flower organ development in orchids. There was little change in the expression of the CgoSPL in C. goeringii, but DchSPL9 and GelSPL2 showed significant expression during the flowering process of D. chrysotoxum and G. elata, respectively. In summary, this paper provides a reference for exploring the regulation of the SPL gene family in orchids.

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.

Genome-Wide Identification of miR156 and SPL family genes and phenotypic analysis of vegetative phase change in Pepper (Capsicum annuum L.)

After germination, plants through two phases of vegetative development - juvenile and adult - before entering the reproductive phase. These phases have varying characteristics and timing across plant species, making it challenging to determine if different vegetative traits correspond to the same or distinct developmental processes. miR156 has been identified as the primary regulator of vegetative phase change in plants, with the miR156-SPLs (SQUAMOSA Promoter Binding Protein-Likes) module playing a crucial role in regulating age-related agronomic traits in various crops. Such traits include disease resistance, optimal plant breeding, and secondary metabolism regulation. However, it is unknown whether miR156-SPLs contribute to the critical agronomic traits of pepper (Capsicum annuum L.). Thus, this study seeks to identify miR156 and SPLs genes in pepper, analyze their evolutionary links with model plants, and confirm their expression patterns using gene expression assays. The study also examines the relationship between miR156 expression levels in two cultivars of pepper and specific traits associated with the juvenile-to-adult transition. The results indicate that leaf shape and the number of leaf veins are correlated to the timing expression of miR156. Our study represents an important resource for identifying age-dependent agronomic traits in pepper and lays the foundation for future systematic regulation of miR156-SPLs to advance pepper development.

MsSPL9 Modulates Nodulation under Nitrate Sufficiency Condition in Medicago sativa

Nodulation in Leguminous spp. is induced by common environmental cues, such as low nitrogen availability conditions, in the presence of the specific Rhizobium spp. in the rhizosphere. Medicago sativa (alfalfa) is an important nitrogen-fixing forage crop that is widely cultivated around the world and relied upon as a staple source of forage in livestock feed. Although alfalfa's relationship with these bacteria is one of the most efficient between rhizobia and legume plants, breeding for nitrogen-related traits in this crop has received little attention. In this report, we investigate the role of Squamosa-Promoter Binding Protein-Like 9 (SPL9), a target of miR156, in nodulation in alfalfa. Transgenic alfalfa plants with SPL9-silenced (SPL9-RNAi) and overexpressed (35S::SPL9) were compared to wild-type (WT) alfalfa for phenotypic changes in nodulation in the presence and absence of nitrogen. Phenotypic analyses showed that silencing of MsSPL9 in alfalfa caused an increase in the number of nodules. Moreover, the characterization of phenotypic and molecular parameters revealed that MsSPL9 regulates nodulation under a high concentration of nitrate (10 mM KNO₃) by regulating the transcription levels of the nitrate-responsive genes Nitrate Reductase1 (NR1), NR2, Nitrate transporter 2.5 (NRT2.5), and a shoot-controlled autoregulation of nodulation (AON) gene, Super numeric nodules (SUNN). While MsSPL9-overexpressing transgenic plants have dramatically increased transcript levels of SUNN, NR1, NR2, and NRT2.5, reducing MsSPL9 caused downregulation of these genes and displayed a nitrogen-starved phenotype, as downregulation of the MsSPL9 transcript levels caused a nitrate-tolerant nodulation phenotype. Taken together, our results suggest that MsSPL9 regulates nodulation in alfalfa in response to nitrate.

Distinct function of SPL genes in age-related resistance in Arabidopsis

In plants, age-related resistance (ARR) refers to a gain of disease resistance during shoot or organ maturation. ARR associated with vegetative phase change, a transition from juvenile to adult stage, is a widespread agronomic trait affecting resistance against multiple pathogens. How innate immunity in a plant is differentially regulated during successive stages of shoot maturation is unclear. In this work, we found that Arabidopsis thaliana showed ARR against its bacterial pathogen Pseudomonas syringae pv. tomato DC3000 during vegetative phase change. The timing of the ARR activation was associated with a temporal drop of miR156 level. The microRNA miR156 maintains juvenile phase by inhibiting the accumulation and translation of SPL transcripts. A systematic inspection of the loss- and gain-of-function mutants of 11 SPL genes revealed that a subset of SPL genes, notably SPL2, SPL10, and SPL11, activated ARR in adult stage. The immune function of SPL10 was independent of its role in morphogenesis. Furthermore, the SPL10 mediated an age-dependent augmentation of the salicylic acid (SA) pathway partially by direct activation of PAD4. Disrupting SA biosynthesis or signaling abolished the ARR against Pto DC3000. Our work demonstrated that the miR156-SPL10 module in Arabidopsis is deployed to operate immune outputs over developmental timing.

Genome-Wide Identification of the SQUAMOSA Promoter-Binding Protein-like (SPL) Transcription Factor Family in Sweet Cherry Fruit

Plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play important regulatory roles during plant growth and development, fruit ripening, inflorescence branching, and biotic and abiotic stresses. However, there have been no identification or systematic studies of the SPL gene family in the sweet cherry. In this study, 12 SPL genes were identified in the sweet cherry reference genome, which were distributed over 6 chromosomes and classified into six groups according to phylogenetic relationships with other SPL gene families. Nine PavSPLs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, which implied that they were important regulators during fruit development and ripening. The expression patterns of PavSPL genes under ABA, GA, and MeJA treatments showed that the PavSPLs were involved in the process of fruit ripening. A subcellular localization experiment proved that PavSPL4 and PavSPL7 proteins were localized in the nucleus. The genome-wide identification of the SPL gene family provided new insights while establishing an important foundation for sweet cherry studies.

Comprehensive analyses of the SPL transcription factor family in Paulownia fortunei and their responses to biotic and abiotic stresses

To study the molecular characteristics, phylogenetic evolution, and gene functions of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes in Paulownia fortunei, a whole genome sequence analysis was carried out, and a total of 23 PfSPL genes were identified. Tandem duplication and fragment replication were the main patterns of gene expansion in the PfSPL family. Phylogenetic analysis showed that the 23 identified PfSPLs formed seven subgroups, and the structures of the proteins in the same subgroup were similar. Functional analysis indicated that PfSPL11 may regulate flowering, PfSPL5 was involved in gibberellin signaling, PfSPL1/4/23 regulated branching, and PfSPL9/16/18 were related to pathogen resistance. Yeast one hybrid technology confirmed that PfSPL4 and PfSP23 can bind to the promoter of PfTCPa. The transcriptome analysis indicated that PfSPL10 was sensitive to both drought and salt stress. Ten PfSPLs that responded to phytoplasma infection were identified. Molecular docking showed that PfSPL10 and PfSPL 4/5/9/10/11/13 formed active pockets in the conserved SBP domain that could bind methyl methane sulfonate (MMS) and rifampicin (Rif) through stable hydrogen bonds, respectively. This study provides a basis for further studies on the functions of the PfSPL transcription factor family, and for genetic improvement and breeding of trees resistant to PaWB disease.

Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Quinoa (Chenopodium quinoa)

BACKGROUND

Squamous promoter binding protein-like (SPL) proteins are a class of transcription factors that play essential roles in plant growth and development, signal transduction, and responses to biotic and abiotic stresses. The rapid development of whole genome sequencing has enabled the identification and characterization of SPL gene families in many plant species, but to date this has not been performed in quinoa (Chenopodium quinoa).

RESULTS

This study identified 23 SPL genes in quinoa, which were unevenly distributed on 18 quinoa chromosomes. Quinoa SPL genes were then classified into eight subfamilies based on homology to Arabidopsis thaliana SPL genes. We selected three dicotyledonous and monocotyledonous representative species, each associated with C. quinoa, for comparative sympatric mapping to better understand the evolution of the developmental mechanisms of the CqSPL family. Furthermore, we also used 15 representative genes from eight subfamilies to characterize CqSPLs gene expression in different tissues and at different fruit developmental stages under six different abiotic stress conditions.

CONCLUSIONS

This study, the first to identify and characterize SPL genes in quinoa, reported that CqSPL genes, especially CqSPL1, play a critical role in quinoa development and in its response to various abiotic stresses.

Root colonization by the endophytic fungus Piriformospora indica shortens the juvenile phase of Piper nigrum L. by fine tuning the floral promotion pathways

Piriformospora indica, the mutualistic biotrophic root colonizing endosymbiotic fungus belonging to the order Sebacinales, offers host plants various benefits and enhances its growth and performance. The effect of colonization of P. indica in Piper nigrum L. cv. Panniyur1 on growth advantages, floral induction and evocation was investigated. Growth and yield benefits are credited to the alteration in the phytohormone levels fine-tuned by plants in response to the fungal colonization and perpetuation. The remarkable upregulation in the phytohormone levels, as estimated by LC- MS/MS and quantified by qRT-PCR, revealed the effectual contribution by the endophyte. qRT-PCR results revealed a significant shift in the expression of putative flowering regulatory genes in the photoperiod induction pathway (FLOWERING LOCUS T, LEAFY, APETALA1, AGAMOUS, SUPPRESSOR OF CONSTANS 1, GIGANTEA, PHYTOCHROMEA, and CRYPTOCHROME1) gibberellin biosynthetic pathway genes (GIBBERELLIN 20-OXIDASE2, GIBBERELLIN 2-OXIDASE, DELLA PROTEIN REPRESSOR OF GA1-3 1) autonomous (FLOWERING LOCUS C, FLOWERING LOCUS VE, FLOWERING LOCUS CA), and age pathway (SQUAMOSA PROMOTER LIKE9, APETALA2). The endophytic colonization had no effect on vernalization (FLOWERING LOCUS C) or biotic stress pathways (SALICYLIC ACID INDUCTION DEFICIENT 2, WRKY family transcription factor 22). The data suggest that P. nigrum responds positively to P. indica colonization, affecting preponement in floral induction as well as evocation, and thereby shortening the juvenile phase of the crop.

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.

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 Identification and Characterization of SPL Family Genes in Chenopodium quinoa

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode a large family of plant-specific transcription factors that play important roles in plant growth, development, and stress responses. However, there is little information available on SPL genes in Chenopodiaceae. Here, 23 SPL genes were identified and characterized in the highly nutritious crop Chenopodium quinoa. Chromosome localization analysis indicated that the 23 CqSPL genes were unevenly distributed on 12 of 18 chromosomes. Two zinc finger-like structures and a nuclear location signal were present in the SBP domains of all CqSPLs, with the exception of CqSPL21/22. Phylogenetic analysis revealed that these genes were classified into eight groups (group I–VIII). The exon–intron structure and motif composition of the genes in each group were similar. Of the 23 CqSPLs, 13 were potential targets of miR156/7. In addition, 5 putative miR156-encoding loci and 13 putative miR157-encoding loci were predicted in the quinoa genome, and they were unevenly distributed on chromosome 1–4. The expression of several Cqu-MIR156/7 loci was confirmed by reverse transcription polymerase chain reaction in seedlings. Many putative cis-elements associated with light, stress, and phytohormone responses were identified in the promoter regions of CqSPLs, suggesting that CqSPL genes are likely involved in the regulation of key developmental processes and stress responses. Expression analysis revealed highly diverse expression patterns of CqSPLs among tissues. Many CqSPLs were highly expressed in leaves, flowers, and seeds, and their expression levels were low in the roots, suggesting that CqSPLs play distinct roles in the development and growth of quinoa. The expression of 13 of 23 CqSPL genes responded to salt treatment (11 up-regulated and 2 down-regulated). A total of 22 of 23 CqSPL genes responded to drought stress (21 up-regulated and 1 down-regulated). Moreover, the expression of 14 CqSPL genes was significantly altered following cadmium treatment (3 up-regulated and 11 down-regulated). CqSPL genes are thus involved in quinoa responses to salt/drought and cadmium stresses. These findings provide new insights that will aid future studies of the biological functions of CqSPLs in C. quinoa.

Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

BACKGROUND

Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited.  RESULTS: In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention.

CONCLUSIONS

In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.

Genome-Wide Identification, Characterization, and Expression Profiling Analysis of SPL Gene Family during the Inflorescence Development in Trifolium repens

Trifolium repens is the most widely cultivated perennial legume forage in temperate region around the world. It has rich nutritional value and good palatability, seasonal complementarity with grasses, and can improve the feed intake and digestibility of livestock. However, flowering time and inflorescence development directly affects the quality and yield of T. repens, as well as seed production. The Squa promoter binding protein-like (SPL) gene family is a plant specific transcription factor family, which has been proved to play a critical role in regulating plant formation time and development of flowers. In this study, a total of 37 TrSPL genes were identified from the whole genome of T. repens and were divided into nine clades based on phylogenetic tree. Seventeen TrSPL genes have potential target sites for miR156. The conserved motif of squamosa promoter binding protein (SBP) contains two zinc finger structures and one NLS structure. Gene structure analysis showed that all TrSPL genes contained SBP domain, while ankyrin repeat region was just distributed in part of genes. 37 TrSPL genes were relatively dispersedly distributed on 16 chromosomes, and 5 pairs of segmental repeat genes were found, which indicated that segmental duplication was the main way of gene expansion. Furthermore, the gene expression profiling showed that TrSPL11, TrSPL13, TrSPL22, and TrSPL26 were highly expressed only in the early stage of inflorescence development, while TrSPL1 and TrSPL6 are highly expressed only in the mature inflorescence. Significantly, the expression of TrSPL4 and TrSPL12 increased gradually with the development of inflorescences. The results of this study will provide valuable clues for candidate gene selection and elucidating the molecular mechanism of T. repens flowering regulation.

Deciphering Pleiotropic Signatures of Regulatory SNPs in Zea mays L. Using Multi-Omics Data and Machine Learning Algorithms

Maize is one of the most widely grown cereals in the world. However, to address the challenges in maize breeding arising from climatic anomalies, there is a need for developing novel strategies to harness the power of multi-omics technologies. In this regard, pleiotropy is an important genetic phenomenon that can be utilized to simultaneously enhance multiple agronomic phenotypes in maize. In addition to pleiotropy, another aspect is the consideration of the regulatory SNPs (rSNPs) that are likely to have causal effects in phenotypic development. By incorporating both aspects in our study, we performed a systematic analysis based on multi-omics data to reveal the novel pleiotropic signatures of rSNPs in a global maize population. For this purpose, we first applied Random Forests and then Markov clustering algorithms to decipher the pleiotropic signatures of rSNPs, based on which hierarchical network models are constructed to elucidate the complex interplay among transcription factors, rSNPs, and phenotypes. The results obtained in our study could help to understand the genetic programs orchestrating multiple phenotypes and thus could provide novel breeding targets for the simultaneous improvement of several agronomic traits.

Osa-miR535 targets SQUAMOSA promoter binding protein-like 4 to regulate blast disease resistance in rice

Many rice microRNAs have been identified as fine-tuning factors in the regulation of agronomic traits and immunity. Among them, Osa-miR535 targets SQUAMOSA promoter binding protein-like 14 (OsSPL14) to positively regulate tillers but negatively regulate yield and immunity. Here, we uncovered that Osa-miR535 targets another SPL gene, OsSPL4, to suppress rice immunity against Magnaporthe oryzae. Overexpression of Osa-miR535 significantly decreased the accumulation of the fusion protein SPL4_TBS -YFP that contains the target site of Osa-miR535 in OsSPL4. Consistently, Osa-miR535 mediated the cleavage of OsSPL4 mRNA between the 10th and 11th base pair of the predicted binding site at the 3' untranslated region. Transgenic rice lines overexpressing OsSPL4 (OXSPL4) displayed enhanced blast disease resistance accompanied by enhanced immune responses, including increased expression of defense-relative genes and up-accumulated H₂ O₂ . By contrast, the knockout mutant osspl4 exhibited susceptibility. Moreover, OsSPL4 binds to the promoter of GH3.2, an indole-3-acetic acid-amido synthetase, and promotes its expression. Together, these data indicate that Os-miR535 targets OsSPL4 and OsSPL4-GH3.2, which may parallel the OsSPL14-WRKY45 module in rice blast disease resistance.

MiR172-APETALA2-like genes integrate vernalization and plant age to control flowering time in wheat

Plants possess regulatory mechanisms that allow them to flower under conditions that maximize reproductive success. Selection of natural variants affecting those mechanisms has been critical in agriculture to modulate the flowering response of crops to specific environments and to increase yield. In the temperate cereals, wheat and barley, the photoperiod and vernalization pathways explain most of the natural variation in flowering time. However, other pathways also participate in fine-tuning the flowering response. In this work, we integrate the conserved microRNA miR172 and its targets APETALA2-like (AP2L) genes into the temperate grass flowering network involving VERNALIZATION 1 (VRN1), VRN2 and FLOWERING LOCUS T 1 (FT1 = VRN3) genes. Using mutants, transgenics and different growing conditions, we show that miR172 promotes flowering in wheat, while its target genes AP2L1 (TaTOE1) and AP2L5 (Q) act as flowering repressors. Moreover, we reveal that the miR172-AP2L pathway regulates FT1 expression in the leaves, and that this regulation is independent of VRN2 and VRN1. In addition, we show that the miR172-AP2L module and flowering are both controlled by plant age through miR156 in spring cultivars. However, in winter cultivars, flowering and the regulation of AP2L1 expression are decoupled from miR156 downregulation with age, and induction of VRN1 by vernalization is required to repress AP2L1 in the leaves and promote flowering. Interestingly, the levels of miR172 and both AP2L genes modulate the flowering response to different vernalization treatments in winter cultivars. In summary, our results show that conserved and grass specific gene networks interact to modulate the flowering response, and that natural or induced mutations in AP2L genes are useful tools for fine-tuning wheat flowering time in a changing environment.

Silencing of MsD14 Resulted in Enhanced Forage Biomass through Increasing Shoot Branching in Alfalfa (Medicago sativa L.)

Branching is one of the key determinants of plant architecture that dramatically affects crop yield. As alfalfa is the most important forage crop, understanding the genetic basis of branching in this plant can facilitate breeding for a high biomass yield. In this study, we characterized the strigolactone receptor gene MsD14 in alfalfa and demonstrated that MsD14 was predominantly expressed in flowers, roots, and seedpods. Furthermore, we found that MsD14 expression could significantly respond to strigolactone in alfalfa seedlings, and its protein was located in the nucleus, cytoplasm, and cytomembrane. Most importantly, transformation assays demonstrated that silencing of MsD14 in alfalfa resulted in increased shoot branching and forage biomass. Significantly, MsD14 could physically interact with AtMAX2 and MsMAX2 in the presence of strigolactone, suggesting a similarity between MsD14 and AtD14. Together, our results revealed the conserved D14-MAX2 module in alfalfa branching regulation and provided candidate genes for alfalfa high-yield molecular breeding.

OsSPLs Regulate Male Fertility in Response to Different Temperatures by Flavonoid Biosynthesis and Tapetum PCD in PTGMS Rice

Photoperiod and thermo-sensitive genic male sterile (PTGMS) rice is an important resource for two line hybrid rice production. The SQUAMOSA–promoter binding, such as the (SPL) gene family, encode the plant specific transcription factors that regulate development and defense responses in plants. However, the reports about SPLs participating in male fertility regulation are limited. Here, we identified 19 OsSPL family members and investigated their involvement in the fertility regulation of the PTGMS rice lines, PA2364S and PA2864S, with different fertility transition temperatures. The results demonstrated that OsSPL2, OsSPL4, OsSPL16 and OsSPL17 affect male fertility in response to temperature changes through the MiR156-SPL module. WGCNA (weighted gene co-expression network analysis) revealed that CHI and APX1 were co-expressed with OsSPL17. Targeted metabolite and flavonoid biosynthetic gene expression analysis revealed that OsSPL17 regulates the expression of flavonoid biosynthesis genes CHI, and the up regulation of flavanones (eriodictvol and naringenin) and flavones (apigenin and luteolin) content contributed to plant fertility. Meanwhile, OsSPL17 negatively regulates APX1 to affect APX (ascorbate peroxidase) activity, thereby regulating ROS (reactive oxygen species) content in the tapetum, controlling the PCD (programmed cell death) process and regulating male fertility in rice. Overall, this report highlights the potential role of OsSPL for the regulation of male fertility in rice and provides a new insight for the further understanding of fertility molecular mechanisms in PTGMS rice.

Conservation and Divergence of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family between Wheat and Rice

The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family affects plant architecture, panicle structure, and grain development, representing key genes for crop improvements. The objective of the present study is to utilize the well characterized SPLs' functions in rice to facilitate the functional genomics of TaSPL genes. To achieve these goals, we combined several approaches, including genome-wide analysis of TaSPLs, comparative genomic analysis, expression profiling, and functional study of TaSPL3 in rice. We established the orthologous relationships of 56 TaSPL genes with the corresponding OsSPLs, laying a foundation for the comparison of known SPL functions between wheat and rice. Some TaSPLs exhibited different spatial-temporal expression patterns when compared to their rice orthologs, thus implicating functional divergence. TaSPL2/6/8/10 were identified to respond to different abiotic stresses through the combination of RNA-seq and qPCR expression analysis. Additionally, ectopic expression of TaSPL3 in rice promotes heading dates, affects leaf and stem development, and leads to smaller panicles and decreased yields per panicle. In conclusion, our work provides useful information toward cataloging of the functions of TaSPLs, emphasized the conservation and divergence between TaSPLs and OsSPLs, and identified the important SPL genes for wheat improvement.

Molecular Characterization of the miR156/MsSPL Model in Regulating the Compound Leaf Development and Abiotic Stress Response in Alfalfa

Plant leaf patterns and shapes are spectacularly diverse. Changing the complexity of leaflet numbers is a valuable approach to increase its nutrition and photosynthesis. Alfalfa (Medicago sativa) is the most important forage legume species and has diversified compound leaf patterns, which makes it a model species for studying compound leaf development. However, transcriptomic information from alfalfa remains limited. In this study, RNA-Seq technology was used to identify 3746 differentially expressed genes (DEGs) between multifoliate and trifoliate alfalfa. Through an analysis of annotation information and expression data, SPL, one of the key regulators in modifiable plant development and abiotic stress response, was further analyzed. Here, thirty MsSPL genes were obtained from the alfalfa genome, of which 16 had the putative miR156 binding site. A tissue expression pattern analysis showed that the miR156-targeted MsSPLs were divided into two classes, namely, either tissue-specific or widely expressed in all tissues. All miR156-targeted SPLs strongly showed diversification and positive roles under drought and salt conditions. Importantly, miR156/MsSPL08 was significantly suppressed in multifoliate alfalfa. Furthermore, in the paralogous mutant of MsSPL08 isolated from Medicago truncatula, the phenotypes of mutant plants reveal that miR156/MsSPL08 is involved not only involved the branches but also especially regulates the number of leaflets. The legume is a typical compound leaf plant; the ratio of the leaflet often affects the quality of the forage. This study sheds light on new functions of SPL genes that regulate leaflet number development.

The Mulberry SPL Gene Family and the Response of MnSPL7 to Silkworm Herbivory through Activating the Transcription of MnTT2L2 in the Catechin Biosynthesis Pathway

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, as unique plant transcription factors, play important roles in plant developmental regulation and stress response adaptation. Although mulberry is a commercially valuable tree species, there have been few systematic studies on SPL genes. In this work, we identified 15 full-length SPL genes in the mulberry genome, which were distributed on 4 Morus notabilis chromosomes. Phylogenetic analysis clustered the SPL genes from five plants (Malus × domestica Borkh, Populus trichocarpa, M. notabilis, Arabidopsis thaliana, and Oryza sativa) into five groups. Two zinc fingers (Zn1 and Zn2) were found in the conserved SBP domain in all of the MnSPLs. Comparative analyses of gene structures and conserved motifs revealed the conservation of MnSPLs within a group, whereas there were significant structure differences among groups. Gene quantitative analysis showed that the expression of MnSPLs had tissue specificity, and MnSPLs had much higher expression levels in older mulberry leaves. Furthermore, transcriptome data showed that the expression levels of MnSPL7 and MnSPL14 were significantly increased under silkworm herbivory. Molecular experiments revealed that MnSPL7 responded to herbivory treatment through promoting the transcription of MnTT2L2 and further upregulating the expression levels of catechin synthesis genes (F3′H, DFR, and LAR).