The D-type cyclin CYCD3;1 is limiting for the G1-to-S-phase transition in Arabidopsis

Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells

Brassinosteroid hormones are positive regulators of plant organ growth, yet their function in proliferating tissues remains unclear. Here, through integrating single-cell RNA sequencing with long-term live-cell imaging of the Arabidopsis root, we reveal that brassinosteroid activity fluctuates throughout the cell cycle, decreasing during mitotic divisions and increasing during the G1 phase. The post-mitotic recovery of brassinosteroid activity is driven by the intrinsic polarity of the mother cell, resulting in one daughter cell with enhanced brassinosteroid signaling, while the other supports brassinosteroid biosynthesis. The coexistence of these distinct daughter cell states during the G1 phase circumvents a negative feedback loop to facilitate brassinosteroid production while signaling increases. Our findings uncover polarity-guided, uneven mitotic divisions in the meristem, which control brassinosteroid hormone activity to ensure optimal root growth.

A retinoblastoma-related protein promotes adventitious root development and secondary wall formation in Populus through the SHR/SCR network

Retinoblastoma-Related (RBR) proteins, evolutionarily conserved homologs of animal RB tumor suppressor, are involved in cell cycle regulation, differentiation, and stress responses. This study systematically investigates the functional characterization of PeRBR in hybrid poplar (Populus deltoides × P. euramericana, clone "Nanlin 895") and its regulatory interactions with the SHR/SCR network governing adventitious root (AR) morphogenesis and secondary wall biogenesis. Transgenic poplar overexpressing PeRBR exhibited significant enhancement in AR system architecture and secondary xylem development, manifesting increased cambial cell layers (1.5-2.2 fold) and elevated lignin deposition (35% increase). Molecular analyses employing bimolecular fluorescence complementation (BiFC) and quantitative real-time PCR (qRT-PCR) revealed that PeRBR directly interacts with PeSCR in the nucleus while transcriptionally upregulating PeSHR, PeCYCD6;1, and PeWOX5 expression. Transcriptomic profiling identified 817 differentially expressed genes (DEGs) between WT plants and overexpression transgenic lines (OE_PeRBR), with notable enrichment in phenylpropanoid biosynthesis pathways. Key lignin biosynthesis genes (PAL, 4CL, CAD) and cellulose synthase (CesA) family members showed significant upregulation in OE_PeRBR lines compared to WT. These findings establish PeRBR as a central regulatory node within the SHR/SCR network, coordinating both AR development and secondary wall formation through transcriptional reprogramming of cell cycle regulators and cell wall biosynthesis machinery in woody species.

Unraveling Morphological, Physiological, and Transcriptomic Alterations Underlying the Formation of Little Leaves in Phytoplasma-Infected Sweet Cherry Trees

Phytoplasmas are minute phytopathogenic bacteria that induce excessive vegetative growth, known as witches' broom (WB), in many infected plant species during the later stages of infection. The WB structure is characterized by densely clustered little (small) leaves, which are frequently accompanied by chlorosis (yellowing). The mechanisms behind the formation of little leaves within WB structures (LL-WB) are poorly understood. To address this gap, the LL-WB formation was extensively studied using sweet cherry virescence (SCV) phytoplasma-infected sweet cherry plants. Based on morphological examinations, signs of premature leaf senescence were observed in LL-WB samples, including reduced leaf size, chlorosis, and alterations in shape. Subsequent physiological analyses indicated decreased sucrose and glucose levels and changes in hormone concentrations in LL-WB samples. Additionally, the transcriptomic analysis revealed impaired ribosome biogenesis and DNA replication. As an essential process in protein production, the compromised ribosome biogenesis and the inhibited DNA replication led to cell cycle arrest, thus affecting leaf morphogenesis and further plant development. Moreover, the expression of marker genes involved in premature leaf senescence was significantly altered. These results indicate a complicated interplay between the development of leaves, premature leaf senescence, and pathogen-induced stress responses in SCV phytoplasma-infected sweet cherry trees. The results of this study provide insight into understanding the underlying molecular mechanisms driving the formation of little leaves and interactions between plants and pathogens. The findings might help control phytoplasma diseases in sweet cherry cultivation.

Transcriptome Analysis Reveals Sugar and Hormone Signaling Pathways Mediating Flower Induction in Pitaya (Hylocereus polyrhizus)

Flower induction in pitaya (Hylocereus polyrhizus) is regulated by complex gene networks involving multiple signaling pathways that ensure flower bud (FB) formation, but its molecular determinants remain largely unknown. In this study, we aimed to identify key genes and pathways involved in pitaya flower induction by analyzing transcriptomics profiles from differentiating buds. Our results indicate that the flower induction process is driven by a combination of sugar, hormone, transcription factor (TF), and flowering-related genes. We found that during the FB induction period, the levels of sugar, starch, auxin (AUX), cytokinin (CTK) active forms dihydrozeatin riboside (dhZR), zeatin riboside (ZR), N6-isopentenyladenosine (iPA), and brassinosteroid (BR) increase in the late stage (LS), while active gibberellins (GA3, GA4) decrease, signaling a metabolic and hormonal shift essential for flowering. Differential gene expression analysis identified key genes involved in starch and sugar metabolism, AUX, CTK, BR synthesis, and (GA) degradation, with notable differential expression in photoperiod (COL, CDF, TCP), age-related (SPL), and key flowering pathways (FT, FTIP, AGL, SOC1). This study reveals a multidimensional regulatory network for FB formation in pitaya, primarily mediated by the crosstalk between sugar and hormone signaling pathways, providing new insights into the molecular mechanism of FB formation in pitaya.

Sucrose induces flowering by degradation of the floral repressor Ghd7 via K48-linked polyubiquitination in rice

Sucrose functions as a signaling molecule in several metabolic pathways as well as in various developmental processes. However, the molecular mechanisms by which sucrose regulates these processes remain largely unknown. In the present study, we demonstrate that sucrose promotes flowering by mediating the stability of a regulatory protein that represses flowering in rice. Exogenous application of sucrose promoted flowering by inducing florigen gene expression. Reduction of sucrose levels in the phloem through genetic modifications, such as the overexpression of the vacuolar invertase OsVIN2 or the mutation of OsSUT2, a sucrose transporter, delayed flowering. Analysis of relative transcript levels of floral regulatory genes showed that sucrose activated Ehd1 upstream of the florigen, with no significant effect on the expression of other upstream genes. Examination of protein stability after sucrose treatment of major floral repressors revealed that the Ghd7 protein was specifically degraded. The Ghd7 protein interacted with the E3 ligase IPA INTERACTING PROTEIN1 (IPI1), and sucrose-induced K48-linked polyubiquitination of Ghd7 via IPI1, leading to protein degradation. Mutants defective in IPI1 delayed flowering, confirming its role in modulating proteins involved in flowering. We conclude that sucrose acts as a signaling molecule to induce flowering by promoting Ghd7 degradation via IPI1.

Chrysanthemum lavandulifolium homolog CYCLIN A2;1 modulates cell division in ray florets

The morphology of ray florets in chrysanthemums is tightly associated with cell division and expansion, both of which require proper progression of the cell cycle. Here, we identified a Chrysanthemum lavandulifolium homolog, CYCLIN A2;1 (CYCA2;1), the expression of which in ray florets is negatively correlated with petal width. We found that CYC2a, a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor in the CYCLOIDEA2 (CYC2) family, interacts with and stabilizes CYC2b, and the latter can bind to the promoter of CYCA2;1 to activate its transcription. Overexpression of CYCA2;1 in C. lavandulifolium reduced the size of capitula and ray florets. Cytological analysis revealed that CYCA2;1 overexpression inhibited both cell division and expansion via repression of the mitotic cell cycle in ray florets, the latitudinal development of which was more relatively negatively influenced, thereby leading to increased ratios of petal length to width at later developmental stages. Yeast two-hybrid library screening revealed multiple proteins that interacted with CYCA2;1 including ACTIN-RELATED PROTEIN7 (ARP7), and silencing ARP7 inhibited the development of ray florets. Co-immunoprecipitation assays confirmed that CYCA2;1 could induce the degradation of ARP7 to inhibit the development of ray florets. Taken together, our results indicate the presence of a regulatory network in ray floret development in chrysanthemum consisting of CYC2b-CYCA2;1-ARP7 that acts via governing mitosis. The identification of this network has the potential to facilitate breeding efforts targeted at producing novel ornamental traits in the flowers.

An incoherent feed-forward loop involving bHLH transcription factors, Auxin and CYCLIN-Ds regulates style radial symmetry establishment in Arabidopsis

The bilateral-to-radial symmetry transition occurring during the development of the Arabidopsis thaliana female reproductive organ (gynoecium) is a crucial biological process linked to plant fertilization and seed production. Despite its significance, the cellular mechanisms governing the establishment and breaking of radial symmetry at the gynoecium apex (style) remain unknown. To fill this gap, we employed quantitative confocal imaging coupled with MorphoGraphX analysis, in vivo and in vitro transcriptional experiments, and genetic analysis encompassing mutants in two bHLH transcription factors necessary and sufficient to promote transition to radial symmetry, SPATULA (SPT) and INDEHISCENT (IND). Here, we show that defects in style morphogenesis correlate with defects in cell-division orientation and rate. We showed that the SPT-mediated accumulation of auxin in the medial-apical cells undergoing symmetry transition is required to maintain cell-division-oriented perpendicular to the direction of organ growth (anticlinal, transversal cell division). In addition, SPT and IND promote the expression of specific core cell-cycle regulators, CYCLIN-D1;1 (CYC-D1;1) and CYC-D3;3, to support progression through the G1 phase of the cell cycle. This transcriptional regulation is repressed by auxin, thus forming an incoherent feed-forward loop mechanism. We propose that this mechanism fine-tunes cell division rate and orientation with the morphogenic signal provided by auxin, during patterning of radial symmetry at the style.

RNA-seq reveals the gene expression in patterns in Populus × euramericana 'Neva' plantation under different precision water and fertilizer-intensive management

BACKGROUND

Populus spp. is a crucial fast-growing and productive tree species extensively cultivated in the mid-latitude plains of the world. However, the impact of intensive cultivation management on gene expression in plantation remains largely unexplored.

RESULTS

Precision water and fertilizer-intensive management substantially increased key enzyme activities of nitrogen transport, assimilation, and photosynthesis (1.12-2.63 times than CK) in Populus × euramericana 'Neva' plantation. Meanwhile, this management approach had a significant regulatory effect on the gene expression of poplar plantations. 1554 differential expression genes (DEGs)were identified in drip irrigation (ND) compared with conventional irrigation. Relative to ND, 2761-4116 DEGs, predominantly up-regulated, were identified under three drip fertilization combinations, among which 202 DEGs were mainly regulated by fertilization. Moreover, drip irrigation reduced the expression of cell wall synthesis-related genes to reduce unnecessary water transport. Precision drip and fertilizer-intensive management promotes the synergistic regulation of carbon and nitrogen metabolism and up-regulates the expression of major genes in nitrogen transport and assimilation processes (5 DEGs), photosynthesis (15 DEGs), and plant hormone signal transduction (11 DEGs). The incorporation of trace elements further enhanced the up-regulation of secondary metabolic process genes. In addition, the co-expression network identified nine hub genes regulated by precision water and fertilizer-intensive management, suggesting a pivotal role in regulating the growth of poplar.

CONCLUSION

Precision water and fertilizer-intensive management demonstrated the ability to regulate the expression of key genes and transcription factor genes involved in carbon and nitrogen metabolism pathways, plant hormone signal transduction, and enhance the activity of key enzymes involved in related processes. This regulation facilitated nitrogen absorption and utilization, and photosynthetic abilities such as light capture, light transport, and electron transport, which faintly synergistically regulate the growth of poplar plantations. These results provide a reference for proposing highly efficient precision intensive management to optimize the expression of target genes.

Ontogenic stage-associated SA response contributes to leaf age-dependent resistance in Arabidopsis and cotton

Introduction

As leaves grow, they transition from a low-microbe environment embedded in shoot apex to a more complex one exposed to phyllosphere microbiomes. Such change requires a coordinated reprogramming of cellular responses to biotic stresses. It remains unclear how plants shift from fast growth to robust resistance during organ development.

Results

Here, we reported that salicylic acid (SA) accumulation and response were temporarily increased during leaf maturation in herbaceous annual Arabidopsis. Leaf primordia undergoing active cell division were insensitive to the elicitor-induced SA response. This age-dependent increase in SA response was not due to prolonged exposure to environmental microbes. Autoimmune mutants with elevated SA levels did not alter the temporal pattern dependent on ontogenic stage. Young Arabidopsis leaves were more susceptible than mature leaves to Pseudomonas syringae pv. tomato (Pto) DC3000 cor- infection. Finally, we showed a broadly similar pattern in cotton, a woody perennial, where young leaves with reduced SA signaling were preferentially invaded by a Xanthomonas pathogen after leaf surface infection.

Discussion

Through this work, we provided insights in the SA-mediated ontogenic resistance in Arabidopsis and tomato.

The role of D3-type cyclins is related to cytokinin and the bHLH transcription factor SPATULA in Arabidopsis gynoecium development

MAIN CONCLUSION

We studied the D3-type cyclin function during gynoecium development in Arabidopsis and how they are related to the hormone cytokinin and the transcription factor SPATULA. Growth throughout the life of plants is sustained by cell division and differentiation processes in meristematic tissues. In Arabidopsis, gynoecium development implies a multiphasic process where the tissues required for pollination, fertilization, and seed development form. The Carpel Margin Meristem (CMM) is a mass of undifferentiated cells that gives rise to the gynoecium internal tissues, such as septum, ovules, placenta, funiculus, transmitting tract, style, and stigma. Different genetic and hormonal factors, including cytokinin, control the CMM function. Cytokinin regulates the cell cycle transitions through the activation of cell cycle regulators as cyclin genes. D3-type cyclins are expressed in proliferative tissues, favoring the mitotic cell cycle over the endoreduplication. Though the role of cytokinin in CMM and gynoecium development is highly studied, its specific role in regulating the cell cycle in this tissue remains unclear. Additionally, despite extensive research on the relationship between CYCD3 genes and cytokinin, the regulatory mechanism that connects them remains elusive. Here, we found that D3-type cyclins are expressed in proliferative medial and lateral tissues. Conversely, the depletion of the three CYCD3 genes showed that they are not essential for gynoecium development. However, the addition of exogenous cytokinin showed that they could control the division/differentiation balance in gynoecium internal tissues and outgrowths. Finally, we found that SPATULA can be a mechanistic link between cytokinin and the D3-type cyclins. The data suggest that the role of D3-type cyclins in gynoecium development is related to the cytokinin response, and they might be activated by the transcription factor SPATULA.

Phenotypic and transcriptome profiling of spikes reveals the regulation of light regimens on spike growth and fertile floret number in wheat

The spike growth phase is critical for the establishment of fertile floret (grain) numbers in wheat (Triticum aestivum L.). Then, how to shorten the spike growth phase and increase grain number synergistically? Here, we showed high-resolution analyses of floret primordia (FP) number, morphology and spike transcriptomes during the spike growth phase under three light regimens. The development of all FP in a spike could be divided into four distinct stages: differentiation (Stage I), differentiation and morphology development concurrently (Stage II), morphology development (Stage III), and polarization (Stage IV). Compared to the short photoperiod, the long photoperiod shortened spike growth and stimulated early flowering by shortening Stage III; however, this reduced assimilate accumulation, resulting in fertile floret loss. Interestingly, long photoperiod supplemented with red light shortened the time required to complete Stages I-II, then raised assimilates supply in the spike and promoted anther development before polarization initiation, thereby increasing fertile FP number during Stage III, and finally maintained fertile FP development during Stage IV until they became fertile florets via a predicted dynamic gene network. Our findings proposed a light regimen, critical stages and candidate regulators that achieved a shorter spike growth phase and a higher fertile floret number in wheat.

Sugar signals pedal the cell cycle!

Cell cycle involves the sequential and reiterative progression of important events leading to cell division. Progression through a specific phase of the cell cycle is under the control of various factors. Since the cell cycle in multicellular eukaryotes responds to multiple extracellular mitogenic cues, its study in higher forms of life becomes all the more important. One such factor regulating cell cycle progression in plants is sugar signalling. Because the growth of organs depends on both cell growth and proliferation, sugars sensing and signalling are key control points linking sugar perception to regulation of downstream factors which facilitate these key developmental transitions. However, the basis of cell cycle control via sugars is intricate and demands exploration. This review deals with the information on sugar and TOR-SnRK1 signalling and how they manoeuvre various events of the cell cycle to ensure proper growth and development.

Overexpression of a TaATL1 encoding RING-type E3 ligase negatively regulates cell division and flowering time in Arabidopsis thaliana

The transition of food crops from the vegetative to reproductive stages is an important process that affects the final yield. Despite extensive characterization of E3 ligases in model plants, their roles in wheat development remain unknown. In this study, we elucidated the molecular function of wheat TaATL1 (Arabidopsis thaliana Toxicos EN Levadura), which acts as a negative regulator of flowering time and cell division. TaATL1 amino acid residues contain a RING domain and exist mainly in a beta-turn form. The expression level of TaATL1 was highly reduced during the transition from vegetative to reproductive stages. TaATL1 is localized in the nucleus and exhibits E3 ligase activity. Transgenic Arabidopsis plants, in which the TaATL1 gene is constitutively overexpressed under the control of the cauliflower mosaic virus 35 S promoter, exhibited regulation of cell numbers, thereby influencing both leaf and root growth. Moreover, TaATL1 overexpression plants showed a late-flowering phenotype compared to wild-type (WT) plants. Following transcriptome analysis, it was discovered that 1661 and 901 differentially expressed genes were down- or up- regulated, respectively, in seedling stages between WT and TaATL1 overexpression. TaATL1 transcripts are involved in cell division, flowering, and signaling. Overall, our findings demonstrated that the regulatory mechanism of wheat TaATL1 gene plays a significant role in cell division-mediated flowering in Arabidopsis.

Functional characterization of D-type cyclins involved in cell division in rice

BACKGROUND

D-type cyclins (CYCD) regulate the cell cycle G1/S transition and are thus closely involved in cell cycle progression. However, little is known about their functions in rice.

RESULTS

We identified 14 CYCD genes in the rice genome and confirmed the presence of characteristic cyclin domains in each. The expression of the OsCYCD genes in different tissues was investigated. Most OsCYCD genes were expressed at least in one of the analyzed tissues, with varying degrees of expression. Ten OsCYCD proteins could interact with both retinoblastoma-related protein (RBR) and A-type cyclin-dependent kinases (CDKA) forming holistic complexes, while OsCYCD3;1, OsCYCD6;1, and OsCYCD7;1 bound only one component, and OsCYCD4;2 bound to neither protein. Interestingly, all OsCYCD genes except OsCYCD7;1, were able to induce tobacco pavement cells to re-enter mitosis with different efficiencies. Transgenic rice plants overexpressing OsCYCD2;2, OsCYCD6;1, and OsCYCD7;1 (which induced cell division in tobacco with high-, low-, and zero-efficiency, respectively) were created. Higher levels of cell division were observed in both the stomatal lineage and epidermal cells of the OsCYCD2;2- and OsCYCD6;1-overexpressing plants, with lower levels seen in OsCYCD7;1-overexpressing plants.

CONCLUSIONS

The distinct expression patterns and varying effects on the cell cycle suggest different functions for the various OsCYCD proteins. Our findings will enhance understanding of the CYCD family in rice and provide a preliminary foundation for the future functional verification of these genes.

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.

OsMED16, a tail subunit of Mediator complex, interacts with OsE2Fa to synergistically regulate rice leaf development and blast resistance

Mediator, a universal eukaryotic coactivator, is a multiprotein complex to transduce information from the DNA-bound transcription factors to the RNA polymerase II transcriptional machinery. In this study, the biofunctions of a rice mediator subunit OsMED16 in leaf development and blast resistance were characterized. OsMED16 encodes a putative protein of 1170 amino acids, which is 393 bp shorted than the version in Rice Genome Annotation Project databases. Overexpression of OsMED16 plants exhibited wider leaves with larger and more numerous cells in lateral axis, and enhanced resistance to M. oryzae with hyperaccumulated salicylic acid. Further analysis revealed that OsMED16 interacts with OsE2Fa in nuclei, and the complex could directly regulate the transcriptional levels of several genes involved in cell cycle regulation and SA mediated blast resistance, such as OsCC52A1, OsCDKA1, OsCDKB2;2, OsICS1 and OsWRKY45. Altogether, this study proved that OsMED16 is a positive regulator of rice leaf development and blast resistance, and providing new insights into the crosstalk between cell cycle regulation and immunity.

Increase in ENHANCER OF SHOOT REGENERATION2 expression by treatment with strigolactone-related inhibitors and kinetin during adventitious shoot formation in ipecac

KEY MESSAGE

Increase of ENHANCER OF SHOOT REGENERATION 2 expression was consistent to treatment with kinetin, TIS108, and KK094 in adventitious shoot formation of ipecac. Unlike many plant species, ipecac (Carapichea ipecacuanha (Brot.) L. Andersson) can form adventitious shoots in tissue culture without cytokinin (CK) treatment. Strigolactone (SL) biosynthesis and signaling inhibitors stimulate adventitious shoot formation in ipecac, suggesting their potential use as novel growth regulators in plant tissue culture, but the molecular mechanism of their action is unclear. In this study, we compared the effects of SL-related inhibitors (TIS108 and KK094) and CKs (2iP, tZ, and kinetin) on adventitious shoot formation in ipecac. Exogenously applied SL-related inhibitors and CKs stimulated adventitious shoot formation. Combinations of SL-related inhibitors and kinetin also promoted adventitious shoot formation, but without additive effects. We also analyzed the expression of CK biosynthesis genes in ipecac. TIS108 increased the expression of the ipecac homolog of ISOPENTENYL TRANSFERASE 3 (CiIPT3) but decreased that of LONELY GUY 7 homolog (CiLOG7), presumably resulting in no change in 2iP-type CK levels. KK094 and kinetin increased CiLOG7 expression, elevating 2iP-type CK levels. Among pluripotency- and meristem-related genes, TIS108, KK094, and kinetin consistently increased the expression of ENHANCER OF SHOOT REGENERATION 2 homolog (CiESR2), which has a key role in shoot regeneration, in the internodal segment region that formed adventitious shoots. We propose that CiESR2 might be a key stimulator of adventitious shoot formation in ipecac.

Thinking outside the F-box: how UFO controls angiosperm development

The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.

Spatiotemporal formation of the large vacuole regulated by the BIN2-VLG module is required for female gametophyte development in Arabidopsis

In Arabidopsis thaliana, female gametophyte (FG) development is accompanied by the formation and expansion of the large vacuole in the FG; this is essential for FG expansion, nuclear polar localization, and cell fate determination. Arabidopsis VACUOLELESS GAMETOPHYTES (VLG) facilitates vesicular fusion to form large vacuole in the FG, but the regulation of VLG remains largely unknown. Here, we found that gain-of-function mutation of BRASSINOSTEROID INSENSITIVE2 (BIN2) (bin2-1) increases VLG abundance to induce the vacuole formation at stage FG1, and leads to abortion of FG. Loss-of-function mutation of BIN2 and its homologs (bin2-3 bil1 bil2) reduced VLG abundance and mimicked vlg/VLG phenotypes. Knocking down VLG in bin2-1 decreased the ratio of aberrant vacuole formation at stage FG1, whereas FG1-specific overexpression of VLG mimicked the bin2-1 phenotype. VLG partially rescued the bin2-3 bil1 bil2 phenotype, demonstrating that VLG acts downstream of BIN2. Mutation of VLG residues that are phosphorylated by BIN2 altered VLG stability and a phosphorylation mimic of VLG causes similar defects as did bin2-1. Therefore, BIN2 may function by interacting with and phosphorylating VLG in the FG to enhance its stability and abundance, thus facilitating vacuole formation. Our findings provide mechanistic insight into how the BIN2-VLG module regulates the spatiotemporal formation of the large vacuole in FG development.

The selection and application of peduncle length QTL QPL_6D.1 in modern wheat (Triticum aestivum L.) breeding

QPL_6D.1b displayed an additive effect with Rht-B1b and Rht-D1b in reducing wheat plant height and peduncle length, which confers shorter peduncle length and more kernels per spike, and had been broadly selected by Chinese modern wheat cultivars. Peduncle length (PL), as the key component of wheat plant height (PH), plays critical role in determining wheat lodging resistance and wheat pathogen resistance; then, its breeding selection and genetic basis remain largely unclear. Here the PH and PL were investigated in 406 wheat accessions in eight environments. In this study, a PL preferentially QTL QPL_6D.1 was identified in six environments by GWAS, which explained 13.6-24.2% of wheat PL variations in natural population. The allele QPL_6D.1b displayed a significantly additive effect with Rht-B1b and Rht-D1b in controlling PH and PL and could freely combined with Rht-B1b and Rht-D1b in current wheat cultivars. Haplotypic analysis demonstrates the QPL_6D.1b has been selected by Chinese modern wheat cultivar and confers shorter PL and more kernels per spike, highlighting its potentials in wheat breeding.

Cowpea NAC1/NAC2 transcription factors improve growth and tolerance to drought and heat in transgenic cowpea through combined activation of photosynthetic and antioxidant mechanisms

NAC (NAM/ATAF1/2/CUC2) transcription factors are central switches of growth and stress responses in plants. However, unpredictable interspecies conservation of function and regulatory targets makes the well-studied NAC orthologs inapt for pulse engineering. The knowledge of suitable NAC candidates in hardy pulses like cowpea (Vigna unguiculata (L.) Walp.) is still in infancy, hence warrants immediate biotechnological intervention. Here, we showed that overexpression of two native NAC genes (VuNAC1 and VuNAC2) promoted germinative, vegetative, and reproductive growth and conferred multiple abiotic stress tolerance in a commercial cowpea variety. The transgenic lines displayed increased leaf area, thicker stem, nodule-rich denser root system, early flowering, higher pod production (∼3.2-fold and ∼2.1-fold), and greater seed weight (10.3% and 6.0%). In contrast, transient suppression of VuNAC1/2 caused severe growth retardation and flower inhibition. The overexpressor lines showed remarkable tolerance to major yield-declining terminal stresses, such as drought, salinity, heat, and cold, and recovered growth and seed production by boosting photosynthetic activity, water use efficiency, membrane integrity, Na⁺ /K⁺ homeostasis, and antioxidant activity. The comparative transcriptome study indicated consolidated activation of genes involved in chloroplast development, photosynthetic complexes, cell division and expansion, cell wall biogenesis, nutrient uptake and metabolism, stress response, abscisic acid, and auxin signaling. Unlike their orthologs, VuNAC1/2 direct synergistic transcriptional tuning of stress and developmental signaling to avoid unwanted trade-offs. Their overexpression governs the favorable interplay of photosynthesis and reactive oxygen species regulation to improve stress recovery, nutritional sufficiency, biomass, and production. This unconventional balance of strong stress tolerance and agronomic quality is useful for translational crop research and molecular breeding of pulses.

Genome-Wide Identification, Characterization, and Transcriptomic Analysis of the Cyclin Gene Family in Brassica rapa

Cyclins are involved in cell division and proliferation by activating enzymes required for the cell cycle progression. Our genome-wide analysis identified 76 cyclin genes in Brassica rapa, which were divided into nine different types (A-, B-, C-, D-, H-, L-, P-, T-, and SDS-type). Cyclin genes were unevenly scattered on all chromosomes, with a maximum of 10 on A08 and a minimum of 2 on A04. The gene structure and conserved motif analysis showed that the cyclins which belonged to the same type or subgroup have a comparable intron/exon pattern or motif. A total of 14 collinear gene pairs suggested that the B. rapa cyclin genes experienced a mass of segmental duplication. The Ka/Ks analysis revealed that the Brcyclin gene family has undergone an extensive purifying pressure. By analyzing the cis-elements in the promoters, we identified 11 cis-elements and five of them are related to the hormone response. We observed 48 potential miRNAs targeting 44 Brcyclin genes, which highlighted the involvement of miRNAs in the regulation of cyclin genes. An association analysis between the leaf size and SNPs in mutants and a transcriptome analysis of two Chinese cabbage-cabbage translocation lines also showed that the Brcyclin gene family was involved in the development of the leaves. The functional characterization of the B. rapa cyclin gene family will provide the foundation for future physiological and genetic studies in the regulation of leaf growth.

Genome-wide characterization of AINTEGUMENTA-LIKE family in Medicago truncatula reveals the significant roles of AINTEGUMENTAs in leaf growth

AINTEGUMENTA-LIKE (AIL) transcription factors are widely studied and play crucial roles in plant growth and development. However, the functions of the AIL family in legume species are largely unknown. In this study, 11 MtAIL genes were identified in the model legume Medicago truncatula, of which four of them are MtANTs. In situ analysis showed that MtANT1 was highly expressed in the shoot apical meristem (SAM) and leaf primordium. Characterization of mtant1 mtant2 mtant3 mtant4 quadruple mutants and MtANT1-overexpressing plants revealed that MtANTs were not only necessary but also sufficient for the regulation of leaf size, and indicated that they mainly function in the regulation of cell proliferation during secondary morphogenesis of leaves in M. truncatula. This study systematically analyzed the MtAIL family at the genome-wide level and revealed the functions of MtANTs in leaf growth. Thus, these genes may provide a potential application for promoting the biomass of legume forages.

MAX2-dependent competence for callus formation and shoot regeneration from Arabidopsis thaliana root explants

Although the division of the pericycle cells initiates both lateral root development and root-derived callus formation, these developmental processes are affected differently in the strigolactone and karrikin/KARRIKIN INSENSITIVE 2 (KAI2) ligand signalling mutant more axillary growth 2 (max2). Whereas max2 produces more lateral roots than the wild type, it is defective in the regeneration of shoots from root explants. We suggest that the decreased shoot regeneration of max2 originates from delayed formation of callus primordium, yielding less callus material to regenerate shoots. Indeed, when incubated on callus-inducing medium, the pericycle cell division was reduced in max2 and the early gene expression varied when compared with the wild type, as determined by a transcriptomics analysis. Furthermore, the expression of the LATERAL ORGAN BOUNDARIES DOMAIN genes and of callus-induction genes was modified in correlation with the max2 phenotype, suggesting a role for MAX2 in the regulation of the interplay between cytokinin, auxin, and light signalling in callus initiation. Additionally, we found that the in vitro shoot regeneration phenotype of max2 might be caused by a defect in KAI2, rather than in DWARF14, signalling. Nevertheless, the shoot regeneration assays revealed that the strigolactone biosynthesis mutants max3 and max4 also play a minor role.

Gene expression profiling before and after internode culture for adventitious shoot formation in ipecac

BACKGROUND

In ipecac (Carapichea ipecacuanha (Brot.) L. Andersson), adventitious shoots can be induced simply by placing internodal segments on phytohormone-free culture medium. The shoots form locally on the epidermis of the apical region of the segments, but not the basal region. Levels of endogenous auxin and cytokinin transiently increase in the segments after 1 week of culture.

RESULTS

Here, we conducted RNA-seq analysis to compare gene expression patterns in apical and basal regions of segments before culture and after 1 week of culture for adventitious shoot formation. The results revealed 8987 differentially expressed genes in a de novo assembly of 76,684 genes. Among them, 276 genes were upregulated in the apical region after 1 week of culture relative to before culture and the basal region after 1 week of culture. These genes include 18 phytohormone-response genes and shoot-formation-related genes. Validation of the gene expression by quantitative real-time PCR assay confirmed that the expression patterns were similar to those of the RNA-seq data.

CONCLUSIONS

The transcriptome data show that expression of cytokinin biosynthesis genes is induced along with the acquisition of cellular pluripotency and the initiation of cell division by wounding in the apical region of internodal segments, that trigger adventitious shoot formation without callusing.

The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume

Plant with naturally twisted branches is referred to as a tortuous-branch plant, which have extremely high ornamental value due to their zigzag shape and the natural twisting of their branches. Prunus mume is an important woody ornamental plant. However, the molecular mechanism underlying this unique trait in Prunus genus is unknown. Here, we present a chromosome-level genome assembly of the cultivated P. mume var. tortuosa created using Oxford Nanopore combined with Hi-C scaffolding, which resulted in a 237.8 Mb genome assembly being anchored onto eight pseudochromosomes. Molecular dating indicated that P. mume is the most recently differentiated species in Prunus. Genes associated with cell division, development and plant hormones play essential roles in the formation of tortuous branch trait. A putative regulatory pathway for the tortuous branch trait was constructed based on gene expression levels. Furthermore, after transferring candidate PmCYCD genes into Arabidopsis thaliana, we found that seedlings overexpressing these genes exhibited curled rosette leaves. Our results provide insights into the evolutionary history of recently differentiated species in Prunus genus, the molecular basis of stem morphology, and the molecular mechanism underlying the tortuous branch trait and highlight the utility of multi-omics in deciphering the properties of P. mume plant architecture.

The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions

BACKGROUND

To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia.

RESULTS

Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species.

CONCLUSION

Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.

Ectopic Expression of Poplar PsnCYCD1;1 Reduces Cell Size and Regulates Flower Organ Development in Nicotiana tabacum

The D-type cyclin (CYCD) gene, as the rate-limiting enzyme in the G1 phase of cell cycle, plays a vital role in the process of plant growth and development. Early studies on plant cyclin mostly focused on herbs, such as Arabidopsis thaliana. The sustainable growth ability of woody plants is a unique characteristic in the study of plant cyclin. Here, the promoter of PsnCYCD1;1 was cloned from poplar by PCR and genetically transformed into tobacco. A strong GUS activity was observed in the areas with vigorous cell division, such as stem tips, lateral buds, and young leaves. The PsnCYCD1;1-GFP fusion expression vector was transformed into tobacco, and the green fluorescence signal was observed in the nucleus. Compared with the control plant, the transgenic tobacco showed significant changes in the flower organs, such as enlargement of sepals, petals, and fruits. Furthermore, the stems of transgenic plants were slightly curved at each stem node, the leaves were curled on the adaxial side, and the fruits were seriously aborted after artificial pollination. Microscopic observation showed that the epidermal cells of petals, leaves, and seed coats of transgenic plants became smaller. The transcriptional levels of endogenous genes, such as NtCYCDs, NtSTM, NtKNAT1, and NtASs, were upregulated by PsnCYCD1;1. Therefore, PsnCYCD1;1 gene played an important role in the regulation of flower organ and stem development, providing new understanding for the functional characterization of CYCD gene and new resources for improving the ornamental value of horticultural plants.

Cellular and molecular characterizations of the irregular internode division zone formation of a slow-growing bamboo variant

The key molecular mechanisms underlying the sectionalized growth within bamboo or other grass internodes remain largely unknown. Here, we genetically and morphologically compared the culm and rhizome internode division zones (DZs) of a slow-growing bamboo variant (sgv) having dwarf internodes, with those of the corresponding wild type (WT). Histological analysis discovers that the sgv has an irregular internode DZ. However, the shoot apical meristems in height, width, outside shape, cell number and cell width of the sgv and the WT were all similar. The DZ irregularities first appeared post apical meristem development, in 1-mm sgv rhizome internodes. Thus, the sgv is a DZ irregularity bamboo variant, which has been first reported in bamboo according to our investigation. Transcriptome sequencing analysis finds that a number of cell wall biogenesis and cell division-related genes are dramatically downregulated in the sgv DZ. Interestingly, both transcriptomic and brassinosteroid (BR) contents detection, as well as quantitative real-time PCR analyses show that these irregularities have resulted from the BR signaling pathway defects. Brassinosteroid defect might also cause the erect leaves and branches as well as the irregular epidermis of the sgv. These results suggest that BR signaling pathway plays critical roles in bamboo internode DZ and leaf development from a mutant perspective and also explain the upstream mechanisms causing the dwarf internode of the sgv bamboo.

Hormone analysis and candidate genes identification associated with seed size in Camellia oleifera

Camellia oleifera is an important woody oil species in China. Its seed oil has been widely used as a cooking oil. Seed size is a crucial factor influencing the yield of seed oil. In this study, the horizontal diameter, vertical diameter and volume of C. oleifera seeds showed a rapid growth tendency from 235 days after pollination (DAP) to 258 DAP but had a slight increase at seed maturity. During seed development, the expression of genes related to cell proliferation and expansion differ greatly. Auxin plays an important role in C. oleifera seeds; YUC4 and IAA17 were significantly downregulated. Weighted gene co-expression network analysis screened 21 hub transcription factors for C. oleifera seed horizontal diameter, vertical diameter and volume. Among them, SPL4 was significantly decreased and associated with all these three traits, while ABI4 and YAB1 were significantly increased and associated with horizontal diameter of C. oleifera seeds. Additionally, KLU significantly decreased (2040-fold). Collectively, our data advances the knowledge of factors related to seed size and provides a theoretical basis for improving the yield of C. oleifera seeds.

Electrophysiological, Morphologic, and Transcriptomic Profiling of the Ogura-CMS, DGMS and Maintainer Broccoli Lines

To better serve breeding of broccoli, the electrophysiological, morphological and transcriptomic profiling of the isogenic Ogura-CMS, DGMS and their maintainer fertile lines, were carried out by scanning electron microscopy, investigation of agronomic traits and RNA-sequencing analysis. The agronomic traits of plant height, length of the largest leaf, plant spread angle, single head weight, head width and stem diameter showed stronger performance in Ogura-CMS broccoli than in DGMS line or maintainer fertile line. However, the Ogura-CMS broccoli was poorer in the seed yield and seed germination than in the DGMS line and maintainer fertile line. Additionally, the DGMS broccoli had longer maturation and flowering periods than the Ogura-CMS and maintainer fertile lines. There were obvious differences in the honey gland, happening in the male sterility and fertile lines of broccoli. Additionally, the mechanism regulating Ogura-CMS and DGMS in broccoli was investigated using florets transcriptome analyses of the Ogura-CMS, DGMS and maintainer fertile lines. As a result, a total of 2670 differentially expressed genes (DEGs) were detected, including 1054 up- and 1616 downregulated genes in the Ogura-CMS and DGMS lines compared to the maintainer fertile line. A number of functionally known genes involved in plant hormones (auxin, salicylic acid and brassinosteroid), five Mitochondrial Oxidative Phosphorylation (OXPHOS) genes of atp8, LOC106319879, LOC106324734, LOC106314622 and LOC106298585, and three upregulated genes (Lhcb1, Lhcb3 and Lhcb5) associated with the photosynthesis-antenna protein pathway, were obviously detected to be highly associated with reproductive development including flowering time, maturity and reproductive period in the Ogura-CMS and DGMS broccoli comparing to their maintainer fertile line. Our research would provide a comprehensive foundation for understanding the differences of electrophysiological, morphological and transcriptomic profiles in the Ogura-CMS, DGMS and maintainer broccoli, and as well as being beneficial to exploring the mechanism of male sterility in Brassica crops.

SAMBA controls cell division rate during maize development

SAMBA has been identified as a plant-specific regulator of the anaphase-promoting complex/cyclosome (APC/C) that controls unidirectional cell cycle progression in Arabidopsis (Arabidopsis thaliana), but so far its role has not been studied in monocots. Here, we show the association of SAMBA with the APC/C is conserved in maize (Zea mays). Two samba genome edited mutants showed growth defects, such as reduced internode length, shortened upper leaves with erect leaf architecture, and reduced leaf size due to an altered cell division rate and cell expansion, which aggravated with plant age. The two mutants differed in the severity and developmental onset of the phenotypes, because samba-1 represented a knockout allele, while translation re-initiation in samba-3 resulted in a truncated protein that was still able to interact with the APC/C and regulate its function, albeit with altered APC/C activity and efficiency. Our data are consistent with a dosage-dependent role for SAMBA to control developmental processes for which a change in growth rate is pivotal.

Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages

Background

MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes.

Methods

To answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data.

Results

Overexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the families of hormone synthesis, signaling pathways, and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit and a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.

Plant casein kinases phosphorylate and destabilize a cyclin-dependent kinase inhibitor to promote cell division

Cell cycle is one of the most fundamentally conserved biological processes of plants and mammals. Casein kinase1s (CK1s) are critical for cell proliferation in mammalian cells; however, how CK1s coordinate cell division in plants remains unknown. Through genetic and biochemical studies, here we demonstrated that plant CK1, Arabidopsis (Arabidopsis thaliana) EL1-like (AELs), regulate cell cycle/division by modulating the stability and inhibitory effects of Kip-related protein6 (KRP6) through phosphorylation. Cytological analysis showed that AELs deficiency results in suppressed cell-cycle progression mainly due to the decreased DNA replication rate at S phase and increased period of G2 phase. AELs interact with and phosphorylate KRP6 at serines 75 and 109 to stimulate KRP6's interaction with E3 ligases, thus facilitating the KRP6 degradation through the proteasome. These results demonstrate the crucial roles of CK1s/AELs in regulating cell division through modulating cell-cycle rates and elucidate how CK1s/AELs regulate cell division by destabilizing the stability of cyclin-dependent kinase inhibitor KRP6 through phosphorylation, providing insights into the plant cell-cycle regulation through CK1s-mediated posttranslational modification.

The GpIA7 effector from the potato cyst nematode Globodera pallida targets potato EBP1 and interferes with the plant cell cycle programme

The potato cyst nematode Globodera pallida acquires all of its nutrients from an elaborate feeding site that it establishes in a host plant root. Normal development of the root cells is re-programmed in a process coordinated by secreted nematode effector proteins. The biological function of the G. pallida GpIA7 effector was investigated in this study. GpIA7 is specifically expressed in the subventral pharyngeal glands of pre-parasitic stage nematodes. Ectopic expression of GpIA7 in potato plants affected plant growth and development, suggesting a potential role for this effector in feeding site establishment. Potato plants overexpressing GpIA7 were shorter, with reduced tuber weight and delayed flowering. We provide evidence that GpIA7 associates with the plant growth regulator StEBP1 (ErbB-3 epidermal growth factor receptor-binding protein 1). GpIA7 modulates the regulatory function of StEBP1, altering the expression level of downstream target genes, including ribonucleotide reductase 2, cyclin D3;1 and retinoblastoma related 1, which are downregulated in plants overexpressing GpIA7. We provide an insight into the molecular mechanism used by the nematode to manipulate the host cell cycle and provide evidence that this may rely, at least in part, on hindering the function of host EBP1.

GmMs1 encodes a kinesin-like protein essential for male fertility in soybean (Glycine max L.)

The application of heterosis is a promising approach for greatly increasing yield in soybean (Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Here we report the cloning of the gene underlying the soybean male-sterile mutant ms-1, which has been widely used for recurrent selection in soybean breeding programs. We initially delimited the ms1 locus to a 16.15 kb region on chromosome 13, based on SLAF_BSA sequencing followed by genotyping of an F2 population segregating for the locus. Compared with the same region in fertile plants, the mutant region lacks a sequence of approximately 38.7 kb containing five protein-coding genes, including an ortholog of the kinesin-like protein gene NACK2, named GmMs1. The GmMs1 knockout plants generated via CRISPR/Cas-mediated gene editing displayed a complete male-sterile phenotype. Metabolic profiling showed that fertile anthers accumulated starch and sucrose normally, whereas sterile anthers had higher anthocyanin levels and lower flavonoid levels and lower antioxidant enzyme activities. These results provide insights into the molecular mechanisms governing male sterility and demonstrate that GmMs1 could be used to create male-sterile lines through targeted mutagenesis. These findings pave the way for designing seed production technology and an intelligent male-sterile line system to utilize heterosis in soybean.

Overexpression Populus d-Type Cyclin Gene PsnCYCD1;1 Influences Cell Division and Produces Curved Leaf in Arabidopsis thaliana

d-type cyclins (CYCDs) are a special class of cyclins and play extremely important roles in plant growth and development. In the plant kingdom, most of the existing studies on CYCDs have been done on herbaceous plants, with few on perennial woody plants. Here, we identified a Populus d-type cyclin gene, PsnCYCD1;1, which is mainly transcribed in leaf buds and stems. The promoter of PsnCYCD1;1 activated GUS gene expression and transgenic Arabidopsis lines were strongly GUS stained in whole seedlings and mature anthers. Moreover, subcellular localization analysis showed the fluorescence signal of PsnCYCD1;1-GFP fusion protein is present in the nucleus. Furthermore, overexpression of the PsnCYCD1;1 gene in Arabidopsis can promote cell division and lead to small cell generation and cytokinin response, resulting in curved leaves and twisted inflorescence stems. Moreover, the transcriptional levels of endogenous genes, such as ASs, KNATs, EXP10, and PHB, were upregulated by PsnCYCD1;1. Together, our results indicated that PsnCYCD1;1 participates in cell division by cytokinin response, providing new information on controlling plant architecture in woody plants.

A conservative pathway for coordination of cell wall biosynthesis and cell cycle progression in plants

The mechanism that coordinates cell growth and cell cycle progression remains poorly understood; in particular, whether the cell cycle and cell wall biosynthesis are coordinated remains unclear. Recently, cell wall biosynthesis and cell cycle progression were reported to respond to wounding. Nonetheless, no genes are reported to synchronize the biosynthesis of the cell wall and the cell cycle. Here, we report that wounding induces the expression of genes associated with cell wall biosynthesis and the cell cycle, and that two genes, AtMYB46 in Arabidopsis thaliana and RrMYB18 in Rosa rugosa, are induced by wounding. We found that AtMYB46 and RrMYB18 promote the biosynthesis of the cell wall by upregulating the expression of cell wall-associated genes, and that both of them also upregulate the expression of a battery of genes associated with cell cycle progression. Ultimately, this response leads to the development of curled leaves of reduced size. We also found that the coordination of cell wall biosynthesis and cell cycle progression by AtMYB46 and RrMYB18 is evolutionarily conservative in multiple species. In accordance with wounding promoting cell regeneration by regulating the cell cycle, these findings also provide novel insight into the coordination between cell growth and cell cycle progression and a method for producing miniature plants.

Hydroxyurea and Caffeine Impact pRb-like Protein-Dependent Chromatin Architecture Profiles in Interphase Cells of Vicia faba

The survival of cells depends on their ability to replicate correctly genetic material. Cells exposed to replication stress can experience a number of problems that may lead to deregulated proliferation, the development of cancer, and/or programmed cell death. In this article, we have induced prolonged replication arrest via hydroxyurea (HU) treatment and also premature chromosome condensation (PCC) by co-treatment with HU and caffeine (CF) in the root meristem cells of Vicia faba. We have analyzed the changes in the activities of retinoblastoma-like protein (RbS807/811ph). Results obtained from the immunocytochemical detection of RbS807/811ph allowed us to distinguish five unique activity profiles of pRb. We have also performed detailed 3D modeling using Blender 2.9.1., based on the original data and some final conclusions. 3D models helped us to visualize better the events occurring within the nuclei and acted as a high-resolution aid for presenting the results. We have found that, despite the decrease in pRb activity, its activity profiles were mostly intact and clearly recognizable, with some local alterations that may correspond to the increased demand in transcriptional activity. Our findings suggest that Vicia faba’s ability to withstand harsh environments may come from its well-developed and highly effective response to replication stress.

The ATR-WEE1 kinase module inhibits the MAC complex to regulate replication stress response

DNA damage response is a fundamental mechanism to maintain genome stability. The ATR-WEE1 kinase module plays a central role in response to replication stress. Although the ATR-WEE1 pathway has been well studied in yeasts and animals, how ATR-WEE1 functions in plants remains unclear. Through a genetic screen for suppressors of the Arabidopsis atr mutant, we found that loss of function of PRL1, a core subunit of the evolutionarily conserved MAC complex involved in alternative splicing, suppresses the hypersensitivity of atr and wee1 to replication stress. Biochemical studies revealed that WEE1 directly interacts with and phosphorylates PRL1 at Serine 145, which promotes PRL1 ubiquitination and subsequent degradation. In line with the genetic and biochemical data, replication stress induces intron retention of cell cycle genes including CYCD1;1 and CYCD3;1, which is abolished in wee1 but restored in wee1 prl1. Remarkably, co-expressing the coding sequences of CYCD1;1 and CYCD3;1 partially restores the root length and HU response in wee1 prl1. These data suggested that the ATR-WEE1 module inhibits the MAC complex to regulate replication stress responses. Our study discovered PRL1 or the MAC complex as a key downstream regulator of the ATR-WEE1 module and revealed a novel cell cycle control mechanism.

Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq

Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.

Phytohormone-Based Regulation of Trichome Development

Phytohormones affect plant growth and development. Many phytohormones are involved in the initiation of trichome development, which can help prevent damage from UV radiation and insect bites and produce fragrance, flavors, and compounds used as pharmaceuticals. Phytohormones promote the participation of transcription factors in the initiation of trichome development; for example, the transcription factors HDZIP, bHLH and MYB interact and form transcriptional complexes to regulate trichome development. Jasmonic acid (JA) mediates the progression of the endoreduplication cycle to increase the number of multicellular trichomes or trichome size. Moreover, there is crosstalk between phytohormones, and some phytohormones interact with each other to affect trichome development. Several new techniques, such as the CRISPR-Cas9 system and single-cell transcriptomics, are available for investigating gene function, determining the trajectory of individual trichome cells and elucidating the regulatory network underlying trichome cell lineages. This review discusses recent advances in the modulation of trichome development by phytohormones, emphasizes the differences and similarities between phytohormones initially present in trichomes and provides suggestions for future research.

1H NMR metabolic phenotyping of Dipterocarpus alatus as a novel tool for age and growth determination

Dipterocarpus alatus belongs to Family Dipterocarpaceae that can be commonly found in Southeast Asian countries. It is a perennial plant with oval-shaped leaves and oleoresin-rich wood. It has been considered as a multipurpose plant since all parts can be practically utilized. One of the major problems for utilizing Dipterocarpus alatus is the difficulty knowing the exact age as this kind of plant is ready for multipurpose use after 20 years of age. At present, the most commonly used method for determining age of Dipterocarpus alatus is the annual ring estimation. However, this conventional method is unable to provide the high precision and accuracy of age determination due to its limitation including blurry annual rings caused by enriched oleoresin in the wood. The current study aimed to investigate the differences of 1H -NMR spectroscopy-based metabolic profiles from bark and leaf of Dipterocarpus alatus at different ages including 2, 7, 15 and 25 years. Our findings demonstrated that there is a total of 56 metabolites shared between bark and leaf. It is noticeable that bark at different ages exhibited the strongest variation and sugar or sugar derivatives that were found in higher concentrations in bark compared with those in leaf. We found that decreasing levels of certain metabolites including tagatose, 1'kestose and 2'-fucosyllactose exhibited the promising patterns. In conclusion, panel metabolites involved in the sucrose biosynthesis can precisely determine the age and growth of Dipterocarpus alatus.

Genome-Wide Analysis of the Cyclin Gene Family and Their Expression Profile in Medicago truncatula

Cyclins, together with highly conserved cyclin-dependent kinases (CDKs), play an important role in the process of cell cycle in plants, but less is known about the functions of cyclins in legume plants, especially Medicago truncatula. Our genome-wide analysis identified 58, 103, and 51 cyclin members in the M. truncatula, Glycine max, and Phaseolus vulgaris genomes. Phylogenetic analysis suggested that these cyclins could be classified into 10 types, and the CycB-like types (CycBL1-BL8) were the specific subgroups in M. truncatula, which was one reason for the expansion of the B-type in M. truncatula. All putative cyclin genes were mapped onto their own chromosomes of each genome, and 9 segmental duplication gene pairs involving 20 genes were identified in M. truncatula cyclins. Determined by quantitative real-time PCR, the expression profiling suggested that 57 cyclins in M. truncatula were differentially expressed in 9 different tissues, while a few genes were expressed in some specific tissues. Using the publicly available RNAseq data, the expression of Mtcyclins in the wild-type strain A17 and three nodule mutants during rhizobial infection showed that 23 cyclins were highly upregulated in the nodulation (Nod) factor-hypersensitive mutant sickle (skl) mutant after 12 h of rhizobium inoculation. Among these cyclins, six cyclin genes were also specifically expressed in roots and nodules, which might play specific roles in the various phases of Nod factor-mediated cell cycle activation and nodule development. Our results provide information about the cyclin gene family in legume plants, serving as a guide for further functional research on plant cyclins.

Transcriptome analysis of diploid and triploid Populus tomentosa

Triploid Chinese white poplar (Populus tomentosa Carr., Salicaceae) has stronger advantages in growth and better stress resistance and wood quality than diploid P. tomentosa. Using transcriptome sequencing technology to identify candidate transcriptome-based markers for growth vigor in young tree tissue is of great significance for the breeding of P. tomentosa varieties in the future. In this study, the cuttings of diploid and triploid P. tomentosa were used as plant materials, transcriptome sequencing was carried out, and their tissue culture materials were used for RT-qPCR verification of the expression of genes. The results showed that 12,240 differentially expressed genes in diploid and triploid P. tomentosa transcripts were annotated and enriched into 135 metabolic pathways. The top six pathways that enriched the most significantly different genes were plant-pathogen interaction, phenylpropanoid biosynthesis, MAPK signalling pathway-plant, ascorbate and aldarate metabolism, diterpenoid biosynthesis, and the betalain biosynthesis pathway. Ten growth-related genes were selected from pathways of plant hormone signal transduction and carbon fixation in photosynthetic organisms for RT-qPCR verification. The expression levels of MDH and CYCD3 in tissue-cultured and greenhouse planted triploid P. tomentosa were higher than those in tissue-cultured diploid P. tomentosa, which was consist ent with the TMM values calculated by transcriptome.

Investigation of genes associated with petal variations between diploid and autotetraploid in Chinese cabbage (Brassica rapa L. ssp. pekinensis) by RNA-seq and sRNA-seq

Polyploidy promotes morphological, physiological, and reproductive diversity in plants. The imminent effect of chromosome doubling in plants is the enlargement of organs such as flowers and fruits, which increases the commercial value of crops. Flowering plays a vital role in the growth and development of angiosperms. Here, we prepared an isolated microspore culture of 'FT', a doubled haploid (DH) line of Chinese cabbage (Brassica rapa L. ssp. pekinensis), and obtained diploid and autotetraploid plants with the same genetic background. Compared with diploids, the autotetraploids were characterized by large floral organs, dark petals, delayed flowering, and reduced fertility. The indole-3-acetic acid (IAA) and jasmonic acid (JA) levels in autotetraploid petals were significantly higher and the abscisic acid (ABA) level was significantly lower than those in the diploid petals. The lutein level in autotetraploid petals was nearly two times higher than that in the diploid petals. A comparative transcriptome analysis revealed 14,412 differentially expressed genes (DEGs) between the diploids and autotetraploids, and they were enriched in 117 Gene Ontology terms and 110 Kyoto Encyclopedia of Genes and Genomes pathways. We detected 231 DEGs related to phytohormone signal transduction and 29 DEGs involved in carotenoid biosynthesis. An miRNA-target mRNA analysis showed that 32 DEGs regulated by 16 DEMs were associated with flowering timing (BraA03000336, BraA09004319, and BraA09000515), petal development (BraA05002408, BraA01004006, BraA09004069, and BraA04000966), flower opening (BraA07000350), and pollen development (BraA01000720, BraA09005727, and BraA01000253). This study provides information to help elucidate the molecular mechanisms underlying phenotypic variations induced by autopolyploidy in Chinese cabbage.

Establishment of a mitotic model system by transient expression of the D-type cyclin in differentiated leaf cells of tobacco (Nicotiana benthamiana)

Investigations of plant cell division would greatly benefit from a fast, inducible system. Therefore, we aimed to establish a mitotic model by transiently expressing D-type cyclins in tobacco leaf cells. Two different D-type cyclins, CYCD3;1 and CYCD4;2 from Arabidopsis thaliana, were expressed by agrobacterial infiltration in the cells of expanded leaves in tobacco (Nicotiana benthamiana). Leaf pavement cells were examined after cyclin expression while target and reference (histone or tubulin) proteins were marked by fluorescent protein-tagging. Ectopic expression of the D-type cyclin induced pavement cells to re-enter cell division by establishing mitotic microtubule arrays. The induced leaf cells expressed M phase-specific genes of Arabidopsis encoding the mitotic kinase AtAurora 1, the microtubule-associated proteins AtEDE1 and AtMAP65-4, and the vesicle fusion protein AtKNOLLE by recognizing their genomic elements. Their distinct localizations at spindle poles (AtAurora1), spindle microtubules (AtEDE1), phragmoplast microtubules (AtMAP65-4) and the cell plate (AtKNOLLE) were indistinguishable from those in their native Arabidopsis cells. The dividing cells also revealed two rice (Oryza sativa) microtubule-associated proteins in the phragmoplast and uncovered a novel spindle-associated microtubule motor protein. Hence, this cell division-enabled leaf system predicts hypothesized cell cycle-dependent functions of heterologous genes by reporting the dynamics of encoded proteins.

Cyclin-Dependent Kinase Inhibitor Gene TaICK1 acts as a Potential Contributor to Wheat Male Sterility induced by a Chemical Hybridizing Agent

Heterosis has been widely accepted as an effective strategy to increase yields in plant breeding. Notably, the chemical hybridization agent SQ-1 induces male sterility in wheat, representing a critical potential tool in hybrid seed production. However, the mechanisms underlying the male sterility induced by SQ-1 still remain poorly understood. In this study, a cyclin-dependent kinase inhibitor gene, TaICK1, which encodes a 229 amino acid protein, was identified as a potential contributor to male sterility in common wheat. The expression of TaICK1 was upregulated during the development of anthers in Xinong1376 wheat treated with SQ-1. Meanwhile, the seed setting rate was found to be significantly decreased in TaICK1 transgenic rice. Furthermore, we identified two cyclin proteins, TaCYCD2;1 and TaCYCD6;1, as interactors through yeast two-hybrid screening using TaICK1 as the bait, which were validated using bimolecular fluorescence complementation. Subcellular localization revealed that the proteins encoded by TaICK1, TaCYCD2;1, and TaCYCD6;1 were localized in the cell nucleus. The expression levels of TaCYCD2;1 and TaCYCD6;1 were lower in Xinong1376 treated with SQ-1. A further analysis demonstrated that the expression levels of OsCYCD2;1 and OsCYCD6;1 were lower in transgenic TaICK1 rice lines as well. Taken together, these results suggest that the upregulation of TaICK1, induced by SQ-1, may subsequently suppress the expression of TaCYCD2;1 and TaCYCD6;1 in anthers, resulting in male sterility. This study provides new insights into the understanding of SQ-1-induced wheat male sterility, as well as the developmental mechanisms of anthers.

Double or Nothing? Cell Division and Cell Size Control

Size is a fundamental property that must be tightly regulated to ensure that cells and tissues function efficiently. Dynamic size control allows unicellular organisms to adapt to environmental changes, but cell size is also integral to multicellular development, affecting tissue size and structure. Despite clear evidence for homeostatic cell size maintenance, we are only now beginning to understand cell size regulation in the actively dividing meristematic tissues of higher plants. We discuss here how coupled advances in live cell imaging and modelling are uncovering dynamic mechanisms for size control mediated at the cellular level. We argue that integrated models of cell growth and division will be necessary to predict cell size and fully understand multicellular growth and development.