The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves

The LOB domain protein, a novel transcription factor with multiple functions: A review

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein, named for its LATERAL ORGAN BOUNDARIES (LOB) domain, is a member of a class of specific transcription factors commonly found in plants and is absent from all other groups of organisms. LBD TFs have been systematically identified in about 35 plant species and are involved in regulating various aspects of plant growth and development. However, research on the signaling network and regulatory functions of LBD TFs is insufficient, and only a few members have been studied. Moreover, a comprehensive review of these existing studies is lacking. In this review, the structure, regulatory mechanism and function of LBD TFs in recent years were reviewed in order to better understand the role of LBD TFs in plant growth and development, and to provide a new perspective for the follow-up study of LBD TFs.

AINTEGUMENTA and redundant AINTEGUMENTA-LIKE6 are required for bract outgrowth in Arabidopsis

Plants consist of fundamental units of growth called phytomers (leaf or bract, axillary bud, node, and internode), which are repeated and modified throughout shoot development to give plants plasticity for survival and adaptation. One phytomer modification is the suppression or outgrowth of bracts, the leaves subtending the flowers. The floral meristem identity regulator LEAFY (LFY) and the organ boundary genes BLADE-ON-PETIOLE1 (BOP1) and BOP2 have been shown to suppress bract development in Arabidopsis, as mutations in these genes result in bract outgrowth. However, much less is known about the mechanisms that promote bract outgrowth in Arabidopsis mutants such as these. Further understanding of this mechanism may provide a potential tool for modifying leaf development. Here, we showed that the MADS-box genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), FRUITFUL (FUL), and AGAMOUS-LIKE24 (AGL24) play more important roles than BOP1/2 and LFY in bract suppression, and that AINTEGUMENTA (ANT) and the partially redundant AINTEGUMENTA-LIKE6 (AIL6) are necessary for bract outgrowth in these mutant backgrounds. We also demonstrated that misexpression of AIL6 alone is sufficient for bract outgrowth. Our data reveal a mechanism for bract suppression and outgrowth and provide insight into phytomer plasticity.

Genome-wide transcript expression analysis reveals major chickpea and lentil genes associated with plant branching

The search for elite cultivars with better architecture has been a demand by farmers of the chickpea and lentil crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. Herein, this work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested. A total of 1,624 and 2,512 transcripts were identified as differentially expressed among different tissues and contrasting cultivars of chickpea and lentil, respectively. Several gene categories were significantly modulated such as cell cycle, DNA transcription, energy metabolism, hormonal biosynthesis and signaling, proteolysis, and vegetative development between apical and axillary tissues and contrasting cultivars of chickpea and lentil. Based on differential expression and branching-associated biological function, ten chickpea genes and seven lentil genes were considered the main players involved in differentially regulating the plant branching between contrasting cultivars. These collective data putatively revealed the general mechanism and high-effect genes associated with the regulation of branching in chickpea and lentil, which are potential targets for manipulation through genome editing and transgenesis aiming to improve plant architecture.

Shaping leaves through TALE homeodomain transcription factors

The first TALE homeodomain transcription factor gene to be described in plants was maize knotted1 (kn1). Dominant mutations in kn1 disrupt leaf development, with abnormal knots of tissue forming in the leaf blade. kn1 was found to be expressed in the shoot meristem but not in a peripheral region that gives rise to leaves. Furthermore, KN1 and closely related proteins were excluded from initiating and developing leaves. These findings were a prelude to a large body of work wherein TALE homeodomain proteins have been identified as vital regulators of meristem homeostasis and organ development in plants. KN1 homologues are widely represented across land plant taxa. Thus, studying the regulation and mechanistic action of this gene class has allowed investigations into the evolution of diverse plant morphologies. This review will focus on the function of TALE homeodomain transcription factors in leaf development in eudicots. Here, we discuss how TALE homeodomain proteins contribute to a spectrum of leaf forms, from the simple leaves of Arabidopsis thaliana to the compound leaves of Cardamine hirsuta and species beyond the Brassicaceae.

Conserved functions of chromatin regulators in basal Archaeplastida

Chromatin is a dynamic network that regulates genome organization and gene expression. Different types of chromatin regulators are highly conserved among Archaeplastida, including unicellular algae, while some chromatin genes are only present in land plant genomes. Here, we review recent advances in understanding the function of conserved chromatin factors in basal land plants and algae. We focus on the role of Polycomb-group genes which mediate H3K27me3-based silencing and play a role in balancing gene dosage and regulating haploid-to-diploid transitions by tissue-specific repression of the transcription factors KNOX and BELL in many representatives of the green lineage. Moreover, H3K27me3 predominantly occupies repetitive elements which can lead to their silencing in a unicellular alga and basal land plants, while it covers mostly protein-coding genes in higher land plants. In addition, we discuss the role of nuclear matrix constituent proteins as putative functional lamin analogs that are highly conserved among land plants and might have an ancestral function in stress response regulation. In summary, our review highlights the importance of studying chromatin regulation in a wide range of organisms in the Archaeplastida.

Cloning and functional identification of apple LATERAL ORGAN BOUNDARY DOMAIN 3 (LBD3) transcription factor in the regulation of drought and salt stress

MAIN CONCLUSION

Overexpression of MdLBD3 in Arabidopsis reduced sensitivity to salt and drought stresses and was instrumental in promoting early flowering. Salt and drought stresses have serious effects on plant growth. LATERAL ORGAN BOUNDARY DOMAIN (LBD) proteins are a plant-specific transcription factors (TFs) family and play important roles in plants in resisting to abiotic stress. However, about the function of LBDs in apple and other woody plants is little known. In this study, protein sequences of the LBD family TFs in apples were identified which contained conserved LOB domains. The qRT-PCR analysis showed that the MdLBD3 gene was widely expressed in various tissues and organs. The subcellular localization assay showed that the MdLBD3 protein was localized in the nucleus. Ectopic expression of MdLBD3 in Arabidopsis positively regulated its salt and drought resistance, and promoted early flowering. Collectively, these results showed that MdLBD3 improved the abiotic stress resistance, plant growth and development. Overall, this study provided a new gene for breeding that can increase the abiotic stress tolerance in apple.

Overview of molecular mechanisms of plant leaf development: a systematic review

Leaf growth initiates in the peripheral region of the meristem at the apex of the stem, eventually forming flat structures. Leaves are pivotal organs in plants, serving as the primary sites for photosynthesis, respiration, and transpiration. Their development is intricately governed by complex regulatory networks. Leaf development encompasses five processes: the leaf primordium initiation, the leaf polarity establishment, leaf size expansion, shaping of leaf, and leaf senescence. The leaf primordia starts from the side of the growth cone at the apex of the stem. Under the precise regulation of a series of genes, the leaf primordia establishes adaxial-abaxial axes, proximal-distal axes and medio-lateral axes polarity, guides the primordia cells to divide and differentiate in a specific direction, and finally develops into leaves of a certain shape and size. Leaf senescence is a kind of programmed cell death that occurs in plants, and as it is the last stage of leaf development. Each of these processes is meticulously coordinated through the intricate interplay among transcriptional regulatory factors, microRNAs, and plant hormones. This review is dedicated to examining the regulatory influences of major regulatory factors and plant hormones on these five developmental aspects of leaves.

Pick a side: Integrating gene expression and mechanical forces to polarize aerial organs

How organs acquire their shapes is a central question in developmental biology. In plants, aerial lateral organs such as leaves initiate at the flanks of the growing meristem as dome-shaped primordia. These simple structures then grow out along multiple polarity axes to achieve a dizzying array of final shapes. Many of the hormone signaling pathways and genetic interactions that influence growth along these axes have been identified in the past few decades. Open questions include how and when initial gene expression patterns are set in organ primordia, and how these patterns are translated into the physical outcomes observed at the cellular and tissue levels. In this review, we highlight recent studies into the auxin signaling and gene expression dynamics that govern adaxial-abaxial patterning, and the contributions of mechanical forces to the development of flattened structures.

Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development

Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants.

Genome-wide identification and analysis of Lateral Organ Boundaries Domain (LBD) transcription factor gene family in melon (Cucumis melo L.)

Background

Lateral Organ Boundaries Domain (LBD) transcription factor (TF) gene family members play very critical roles in several biological processes like plant-spesific development and growth process, tissue regeneration, different biotic and abiotic stress responses in plant tissues and organs. The LBD genes have been analyzed in various species. Melon (Cucumis melo L.), a member of the Cucurbitaceae family, is economically important and contains important molecules for nutrition and human health such as vitamins A and C, β-carotenes, phenolic acids, phenolic acids, minerals and folic acid. However, no studies have been reported so far about LBD genes in melon hence this is the first study for LBD genes in this plant.

Results

In this study, 40 melon CmLBD TF genes were identified, which were separated into seven groups through phylogenetic analysis. Cis-acting elements showed that these genes were associated with plant growth and development, phytohormone and abiotic stress responses. Gene Ontology (GO) analysis revealed that of CmLBD genes especially function in regulation and developmental processes. The in silico and qRT-PCR expression patterns demonstrated that CmLBD01 and CmLBD18 are highly expressed in root and leaf tissues, CmLBD03 and CmLBD14 displayed a high expression in male-female flower and ovary tissues.

Conclusions

These results may provide important contributions for future research on the functional characterization of the melon LBD gene family and the outputs of this study can provide information about the evolution and characteristics of melon LBD gene family for next studies.

Genome-Wide Identification and Expression Analysis of AS2 Genes in Brassica rapa Reveal Their Potential Roles in Abiotic Stress

The ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) gene family plays a pivotal role in plant growth, induction of phytohormones, and the abiotic stress response. However, the AS2 gene family in Brassica rapa has yet to be investigated. In this study, we identified 62 AS2 genes in the B. rapa genome, which were classified into six subfamilies and distributed across 10 chromosomes. Sequence analysis of BrAS2 promotors showed that there are several typical cis-elements involved in abiotic stress tolerance and stress-related hormone response. Tissue-specific expression analysis showed that BrAS2-47 exhibited ubiquitous expression in all tissues, indicating it may be involved in many biological processes. Gene expression analysis showed that the expressions of BrAS2-47 and BrAS2-10 were significantly downregulated under cold stress, heat stress, drought stress, and salt stress, while BrAS2-58 expression was significantly upregulated under heat stress. RT-qPCR also confirmed that the expression of BrAS2-47 and BrAS2-10 was significantly downregulated under cold stress, drought stress, and salt stress, and in addition BrAS2-56 and BrAS2-4 also changed significantly under the three stresses. In addition, protein-protein interaction (PPI) network analysis revealed that the Arabidopsis thaliana genes AT5G67420 (homologous gene of BrAS2-47 and BrAS2-10) and AT3G49940 (homologous gene of BrAS2-58) can interact with NIN-like protein 7 (NLP7), which has been previously reported to play a role in resistance to adverse environments. In summary, our findings suggest that among the BrAS2 gene family, BrAS2-47 and BrAS2-10 have the most potential for the regulation of abiotic stress tolerance. These results will facilitate future functional investigations of BrAS2 genes in B. rapa.

ASYMMETRIC LEAVES 2 and ASYMMETRIC LEAVES 2-LIKE are partially redundant genes and essential for fruit development in tomato

Fruit size and shape are controlled by genes expressed during the early developmental stages of fruit. Although the function of ASYMMETRIC LEAVES 2 (AS2) in promoting leaf adaxial cell fates has been well characterized in Arabidopsis thaliana, the molecular mechanisms conferring freshy fruit development as a spatial-temporal expression gene in tomato pericarp remain unclear. In the present study, we verified the transcription of SlAS2 and SlAS2L, two homologs of AS2, in the pericarp during early fruit development. Disruption of SlAS2 or SlAS2L caused a significant decrease in pericarp thickness as a result of a reduction in the number of pericarp cell layers and cell area, leading to smaller tomato fruit size, which revealed their critical roles in tomato fruit development. In addition, leaves and stamens exhibited severe morphological defects in slas2 and slas2l single mutants, as well as in the double mutants. These results demonstrated the redundant and pleiotropic functions of SlAS2 and SlAS2L in tomato fruit development. Yeast two-hybrid and split-luciferase complementation assays showed that both SlAS2 and SlAS2L physically interact with SlAS1. Molecular analyses further indicated that SlAS2 and SlAS2L regulate various downstream genes in leaf and fruit development, and that some genes participating in the regulation of cell division and cell differentiation in the tomato pericarp are affected by these genes. Our findings demonstrate that SlAS2 and SlAS2L are vital transcription factors required for tomato fruit development.

Growth-regulating factors: conserved and divergent roles in plant growth and development and potential value for crop improvement

High yield and stress resistance are the major prerequisites for successful crop cultivation, and can be achieved by modifying plant architecture. Evolutionarily conserved growth-regulating factors (GRFs) control the growth of different tissues and organs of plants. Here, we provide a systematic overview of the expression patterns of GRF genes and the structural features of GRF proteins in different plant species. Moreover, we illustrate the conserved and divergent roles of GRFs, microRNA396 (miR396), and GRF-interacting factors (GIFs) in leaf, root, and flower development. We also describe the molecular networks involving the miR396-GRF-GIF module, and illustrate how this module coordinates with different signaling molecules and transcriptional regulators to control development of different plant species. GRFs promote leaf growth, accelerate grain filling, and increase grain size and weight. We also provide some molecular insight into how coordination between GRFs and other signaling modules enhances crop productivity; for instance, how the GRF-DELLA interaction confers yield-enhancing dwarfism while increasing grain yield. Finally, we discuss how the GRF-GIF chimera substantially improves plant transformation efficiency by accelerating shoot formation. Overall, we systematically review the conserved and divergent roles of GRFs and the miR396-GRF-GIF module in growth regulation, and also provide insights into how GRFs can be utilized to improve the productivity and nutrient content of crop plants.

Targeted mutagenesis of BnaSTM leads to abnormal shoot apex development and cotyledon petiole fusion at the seedling stage in Brassica napus L

The Arabidopsis homeodomain transcription factor SHOOT MERISTEMLESS (STM) is crucial for shoot apical meristem (SAM) function, which cooperates with CLAVATA3 (CLV3)/WUSCHEL (WUS) feedback regulation loops to maintain the homeostasis of stem cells in SAM. STM also interacts with the boundary genes to regulate the tissue boundary formation. However, there are still few studies on the function of STM in Brassica napus, an important oil crop. There are two homologs of STM in B. napus (BnaA09g13310D and BnaC09g13580D). In the present study, CRISPR/Cas9 technology was employed to create the stable site-directed single and double mutants of the BnaSTM genes in B. napus. The absence of SAM could be observed only in the BnaSTM double mutants at the mature embryo of seed, indicating that the redundant roles of BnaA09.STM and BnaC09.STM are vital for regulating SAM development. However, different from Arabidopsis, the SAM gradually recovered on the third day after seed germination in Bnastm double mutants, resulting in delayed true leaves development but normal late vegetative and reproductive growth in B. napus. The Bnastm double mutant displayed a fused cotyledon petiole phenotype at the seedling stage, which was similar but not identical to the Atstm in Arabidopsis. Further, transcriptome analysis showed that targeted mutation of BnaSTM caused significant changes for genes involved in the SAM boundary formation (CUC2, CUC3, LBDs). In addition, Bnastm also caused significant changes of a sets of genes related to organogenesis. Our findings reveal that the BnaSTM plays an important yet distinct role during SAM maintenance as compared to Arabidopsis.

Is auxin enough? Cytokinins and margin patterning in simple leaves

The interplay between auxin and cytokinins affects facets of plant development as different as ovule formation and lateral root initiation. Moreover, cytokinins favor complexity in the development of Solanum lycopersicum and Cardamine hirsuta compound leaves. Nevertheless, no role has been proposed for cytokinins in patterning the margins of the simple leaves of Arabidopsis thaliana, a process that is assumed to be sufficiently explained by auxin localization. Here, we discuss evidence supporting the hypothesis that cytokinins play a role in simple leaf margin morphogenesis via crosstalk with auxin, as occurs in other plant developmental events. Indeed, mutant or transgenic arabidopsis plants defective in cytokinin biosynthesis or signaling, or with increased cytokinin degradation have leaf margins less serrated than the wild type.

ZmLBD5, a class-II LBD gene, negatively regulates drought tolerance by impairing abscisic acid synthesis

Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors. Class-I LBD genes have been widely demonstrated to play pivotal roles in organ development; however, knowledge on class-II genes remains limited. Here, we report that ZmLBD5, a class-II LBD gene, is involved in the regulation of maize (Zea mays) growth and the drought response by affecting gibberellin (GA) and abscisic acid (ABA) synthesis. ZmLBD5 is mainly involved in regulation of the TPS-KS-GA2ox gene module, which is comprised of key enzyme-encoding genes involved in GA and ABA biosynthesis. ABA insufficiency increases stomatal density and aperture in overexpression plants and causes a drought-sensitive phenotype by promoting water transpiration. Increased GA₁ levels promotes seedling growth in overexpression plants. Accordingly, CRISPR/Cas9 knockout lbd5 seedlings are dwarf but drought-tolerant. Moreover, lbd5 has a higher grain yield under drought stress conditions and shows no penalty in well-watered conditions compared to the wild type. On the whole, ZmLBD5 is a negative regulator of maize drought tolerance, and it is a potentially useful target for drought resistance breeding.

Genome-wide identification of the KNOTTED HOMEOBOX gene family and their involvement in stalk development in flowering Chinese cabbage

Gibberellin and cytokinin synergistically regulate the stalk development in flowering Chinese cabbage. KNOX proteins were reported to function as important regulators of the shoot apex to promote meristem activity by synchronously inducing CTK and suppressing GA biosynthesis, while their regulatory mechanism in the bolting and flowering is unknown. In this study, 9 BcKNOX genes were identified and mapped unevenly on 6 out of 10 flowering Chinese cabbage chromosomes. The BcKNOXs were divided into three subfamilies on the basis of sequences and gene structure. The proteins contain four conserved domains except for BcKNATM. Three BcKNOX TFs (BcKNOX1, BcKNOX3, and BcKNOX5) displayed high transcription levels on tested tissues at various stages. The major part of BcKNOX genes showed preferential expression patterns in response to low-temperature, zeatin (ZT), and GA₃ treatment, indicating that they were involved in bud differentiation and bolting. BcKNOX1 and BcKNOX5 showed high correlation level with gibberellins synthetase, and CTK metabolic genes. BcKONX1 also showed high correlation coefficients within BcRGA1 and BcRGL1 which are negative regulators of GA signaling. In addition, BcKNOX1 interacted with BcRGA1 and BcRGL1, as confirmed by yeast two-hybrid (Y2H) and biomolecular fluorescence complementation assay (BiFC). This analysis has provided useful foundation for the future functional roles' analysis of flowering Chinese cabbage KNOX genes.

Overexpression of LtuHB6 from Liriodendron tulipifera causes lobed-leaf formation in Arabidopsis thaliana

Liriodendron tulipifera L. is an ornamental tree species with extraordinarily lobed leaves. However, the mechanisms underlying lobed leaf formation in plants remain unclear. The transcription factor, ARABIDOPSIS THALIANA HOMEBOX 6 (HB6), plays a role in regulating leaf margin development. HB6 is involved in cell division and differentiation of developmental organs and negatively regulates abscisic acid (ABA) signal transmission under external abiotic stress; it is unclear whether HB6 performs a pivotal role in leaf morphogenesis in L. tulipifera. In this study, full-length LtuHB6 from L. tulipifera was heterologously expressed in tobacco and Arabidopsis thaliana; its expression pattern was analyzed to determine its potential role in leaf development. In addition, LtuHB6 is localized in the nucleus and cell membrane of tobacco leaves. The expression of LtuHB6 was highest in mature leaves compared to the other stages of leaf development (bud growth, young leaves, and leaf senescence). Transgenic A. thaliana plants overexpressing LtuHB6 exhibited an abnormal phenotype with lobed leaves. Moreover, LtuHB6 overexpression significantly affected the expression of seven genes related to leaf serration in the initial stage of leaf primordia and altered the expression levels of hormonal genes. Our findings indicate that LtuHB6 is an essential regulatory factor in L. tulipifera lobed-leaf formation and is involved in regulating and responding to hormones.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01254-9.

Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat

Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.

Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in Jatropha curcas and Related Species

Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play important roles in organ development and stress response. However, the function of LBD genes has not been reported in Euphorbiaceae. In this paper, we used Jatropha curcas as the main study object and added rubber tree (Hevea brasiliensis), cassava (Manihot esculenta Crantz) and castor (Ricinus communis L.) to take a phylogenetic analysis of LBD genes. Of LBD, 33, 58, 54 and 30 members were identified in J. curcas, rubber tree, cassava and castor, respectively. The phylogenetic analysis showed that LBD members of Euphorbiaceae could be classified into two major classes and seven subclasses (Ia-Ie,IIa-IIb), and LBD genes of Euphorbiaceae tended to cluster in the same branch. Further analysis showed that the LBD genes of Euphorbiaceae in the same clade usually had similar protein motifs and gene structures, and tissue expression patterns showed that they also have similar expression profiles. JcLBDs in class Ia and Ie are mainly expressed in male and female flowers, and there are multiple duplication genes with similar expression profiles in these clades. It was speculated that they are likely to play important regulatory roles in flower development. Our study provided a solid foundation for further investigation of the role of LBD genes in the sexual differentiaion of J. curcas.

The cellular basis for synergy between RCO and KNOX1 homeobox genes in leaf shape diversity

Leaves of seed plants provide an attractive system to study the development and evolution of form. Leaves show varying degrees of margin complexity ranging from simple, as in Arabidopsis thaliana, to fully dissected into leaflets in the closely related species Cardamine hirsuta. Leaflet formation requires actions of Class I KNOTTED1-LIKE HOMEOBOX (KNOX1) and REDUCED COMPLEXITY (RCO) homeobox genes, which are expressed in the leaves of C. hirsuta but not A. thaliana. Evolutionary studies indicate that diversification of KNOX1 and RCO genes was repeatedly associated with increased leaf complexity. However, whether this gene combination represents a developmentally favored avenue for leaflet formation remains unknown, and the cell-level events through which the combined action of these genes drives leaflet formation are also poorly understood. Here we show, through a genetic screen, that when a C. hirsuta RCO transgene is expressed in A. thaliana, then ectopic KNOX1 expression in leaves represents a preferred developmental path for leaflet formation. Using time-lapse growth analysis, we demonstrate that KNOX1 expression in the basal domain of leaves leads to prolonged and anisotropic cell growth. This KNOX1 action, in synergy with local growth repression by RCO, is instrumental in generating rachises and petiolules, the linear geometrical elements, that bear leaflets in complex leaves. Our results show how the combination of cell-level growth analyses and genetics can help us understand how evolutionary modifications in expression of developmentally important genes are translated into diverse leaf shapes.

Leaf Development in Medicago truncatula

Forage yield is largely dependent on leaf development, during which the number of leaves, leaflets, leaf size, and shape are determined. In this mini-review, we briefly summarize recent studies of leaf development in Medicago truncatula, a model plant for legumes, with a focus on factors that could affect biomass of leaves. These include: floral development and related genes, lateral organ boundary genes, auxin biosynthesis, transportation and signaling genes, and WOX related genes.

Epigenetic mechanisms affect the curled leaf phenotype in the hypomethylated ddc mutant of Arabidopsis thaliana

The ddc mutant of Arabidopsis thaliana is characterized by pleiotropic phenotypic alterations including a curl-shaped leaf, previously explained by disturbed auxin metabolism and transport. The present study was aimed at further explore the molecular bases underlying the abnormal phenotype of the ddc leaf. We demonstrated that genes specifically related to leaf fate commitment and morphogenesis were misexpressed on developing ddc leaves, such as upregulation of CURLY LEAF (CLF) and downregulation of ASYMMETRIC LEAVES2 (AS2), KNOTTED-like gene from A. thaliana (KNAT6), TEOSINTE-LIKE1 CYCLOIDEA and PROLIFERATING CELL FACTOR 2 (TCP2) and others. The CLF gene, encoding a component of Polycomb repressive complex 2 (PRC2) which adds trimethylation marks at Lys27 of histone H3, was overexpressed in the ddc mutant and concomitantly was correlated with DNA methylation-dependent repression of its negative regulator UCL1. KNAT6, encoding a class 1 KNOX homeotic gene, had increased H3K27me3 trimethylation levels, suggesting it is a target gene of the CLF containing PRC2 complex in the ddc mutant. We postulate that different epigenetic mechanisms modulate expression of genes related to auxin pathways as well as gene targets of Polycomb repressive action, during leaf morphogenesis.

ZmLBD5 Increases Drought Sensitivity by Suppressing ROS Accumulation in Arabidopsis

Drought stress is known to significantly limit crop growth and productivity. Lateral organ boundary domain (LBD) transcription factors-particularly class-I members-play essential roles in plant development and biotic stress. However, little information is available on class-II LBD genes related to abiotic stress in maize. Here, we cloned a maize class-II LBD transcription factor, ZmLBD5, and identified its function in drought stress. Transient expression, transactivation, and dimerization assays demonstrated that ZmLBD5 was localized in the nucleus, without transactivation, and could form a homodimer or heterodimer. Promoter analysis demonstrated that multiple drought-stress-related and ABA response cis-acting elements are present in the promoter region of ZmLBD5. Overexpression of ZmLBD5 in Arabidopsis promotes plant growth under normal conditions, and suppresses drought tolerance under drought conditions. Furthermore, the overexpression of ZmLBD5 increased the water loss rate, stomatal number, and stomatal apertures. DAB and NBT staining demonstrated that the reactive oxygen species (ROS) decreased in ZmLBD5-overexpressed Arabidopsis. A physiological index assay also revealed that SOD and POD activities in ZmLBD5-overexpressed Arabidopsis were higher than those in wild-type Arabidopsis. These results revealed the role of ZmLBD5 in drought stress by regulating ROS levels.

CRISPR-Cas9-mediated mutagenesis of the SlSRM1-like gene leads to abnormal leaf development in tomatoes

BACKGROUND

Leaves, which are the most important organs of plants, can not only fix carbon sources through photosynthesis, but also absorb nutrients through transpiration. Leaf development directly determines the growth, flowering and fruiting of plants. There are many factors that affect leaf development, such as the growth environment, gene expression, and hormone synthesis. In this study, tomatoes were used to study the role of the transcription factor Solanum lycopersicum salt-related MYB1-like (SlSRM1-like) in the development of tomato leaves.

RESULTS

Loss-of-function of the SlSRM1-like gene mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) resulted in abnormal tomato leaf morphology, including thinner leaves, wrinkled edges, raised veins, disordered edge veins, and left and right asymmetry. An analysis of the transcription levels of genes related to leaf development revealed that the expression of these genes was significantly altered in the SlSRM1-like mutants (SlSRM1-like-Ms). Moreover, the SlSRM1-like gene was expressed at higher transcription levels in young tissues than in old tissues, and its expression was also induced in response to auxin. In addition, the transcription levels of genes related to the auxin pathway, which regulates tomato growth and development, were severely affected in the SlSRM1-like-Ms. Therefore, it is hypothesized that the SlSRM1-like gene functions in the regulation of tomato leaf development through the auxin-related pathway.

CONCLUSIONS

In this study, we successfully knocked out the SlSRM1-like gene in the tomato variety Ailsa Craig using CRISPR technology and found that knockout of the SlSRM1-like gene resulted in abnormal development of tomato leaves. Further research indicated that SlSRM1-like regulated tomato leaf development through auxin-related pathways. The results provide an important reference for the functional study of other SRM1-like genes in plants and provide new insights into the regulation of leaf development in tomato and other plants.

Arabidopsis ASYMMETRIC LEAVES2 (AS2): roles in plant morphogenesis, cell division, and pathogenesis

The ASYMMETRIC LEAVES2 (AS2) gene in Arabidopsis thaliana is responsible for the development of flat, symmetric, and extended leaf laminae and their vein systems. AS2 protein is a member of the plant-specific AS2/LOB protein family, which includes 42 members comprising the conserved amino-terminal domain referred to as the AS2/LOB domain, and the variable carboxyl-terminal region. Among the members, AS2 has been most intensively investigated on both genetic and molecular levels. AS2 forms a complex with the myb protein AS1, and is involved in epigenetic repression of the abaxial genes ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3), ARF4, and class 1 KNOX homeobox genes. The repressed expression of these genes by AS2 is markedly enhanced by the cooperative action of various modifier genes, some of which encode nucleolar proteins. Further downstream, progression of the cell division cycle in the developing organs is stimulated; meristematic states are suppressed in determinate leaf primordia; and the extension of leaf primordia is induced. AS2 binds the specific sequence in exon 1 of ETT/ARF3 and maintains methylated CpGs in several exons of ETT/ARF3. AS2 forms bodies (designated as AS2 bodies) at nucleolar peripheries. AS2 bodies partially overlap chromocenters, including inactive 45S ribosomal DNA repeats, suggesting the presence of molecular and functional links among AS2, the 45S rDNAs, and the nucleolus to exert the repressive regulation of ETT/ARF3. The AS2/LOB domain is characterized by three subdomains, the zinc finger (ZF) motif, the internally conserved-glycine containing (ICG) region, and the leucine-zipper-like (LZL) region. Each of these subdomains is essential for the formation of AS2 bodies. ICG to LZL are required for nuclear localization, but ZF is not. LZL intrinsically has the potential to be exported to the cytoplasm. In addition to its nuclear function, it has been reported that AS2 plays a positive role in geminivirus infection: its protein BV1 stimulates the expression of AS2 and recruits AS2 to the cytoplasm, which enhances virus infectivity by suppression of cytoplasmic post transcriptional gene silencing.

Insights into Regulation of C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq

Amaranthaceae (incl. Chenopodiaceae) shows an immense diversity of C₄ syndromes. More than 15 independent origins of C₄ photosynthesis, and the largest number of C₄ species in eudicots signify the importance of this angiosperm lineage in C₄ evolution. Here, we conduct RNA-Seq followed by comparative transcriptome analysis of three species from Camphorosmeae representing related clades with different photosynthetic types: Threlkeldia diffusa (C₃), Sedobassia sedoides (C₂), and Bassia prostrata (C₄). Results show that B. prostrata belongs to the NADP-ME type and core genes encoding for C₄ cycle are significantly upregulated when compared with Sed. sedoides and T. diffusa. Sedobassia sedoides and B. prostrata share a number of upregulated C₄-related genes; however, two C₄ transporters (DIT and TPT) are found significantly upregulated only in Sed. sedoides. Combined analysis of transcription factors (TFs) of the closely related lineages (Camphorosmeae and Salsoleae) revealed that no C₃-specific TFs are higher in C₂ species compared with C₄ species; instead, the C₂ species show their own set of upregulated TFs. Taken together, our study indicates that the hypothesis of the C₂ photosynthesis as a proxy towards C₄ photosynthesis is questionable in Sed. sedoides and more in favour of an independent evolutionary stable state.

The transcription factor PagLBD3 contributes to the regulation of secondary growth in Populus

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes encode plant-specific transcription factors that participate in regulating various developmental processes. In this study, we genetically characterized PagLBD3 encoding an important regulator of secondary growth in poplar (Populus alba × Populus glandulosa). Overexpression of PagLBD3 increased stem secondary growth in Populus with a significantly higher rate of cambial cell differentiation into phloem, while dominant repression of PagLBD3 significantly decreased the rate of cambial cell differentiation into phloem. Furthermore, we identified 1756 PagLBD3 genome-wide putative direct target genes (DTGs) through RNA sequencing (RNA-seq)-coupled DNA affinity purification followed by sequencing (DAP-seq) assays. Gene Ontology analysis revealed that genes regulated by PagLBD3 were enriched in biological pathways regulating meristem development, xylem development, and auxin transport. Several central regulator genes for vascular development, including PHLOEM INTERCALATED WITH XYLEM (PXY), WUSCHEL RELATED HOMEOBOX4 (WOX4), Secondary Wall-Associated NAC Domain 1s (SND1-B2), and Vascular-Related NAC-Domain 6s (VND6-B1), were identified as PagLBD3 DTGs. Together, our results indicate that PagLBD3 and its DTGs form a complex transcriptional network to modulate cambium activity and phloem/xylem differentiation.

Genome-Wide Identification of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) Transcription Factors and Screening of Salt Stress Candidates of Rosa rugosa Thunb

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are regulators of lateral organ morphogenesis, boundary establishment, and secondary metabolism in plants. The responsive role of LBD gene family in plant abiotic stress is emerging, whereas its salt stress responsive mechanism in Rosa spp. is still unclear. The wild plant of Rosa rugosa Thunb., which exhibits strong salt tolerance to stress, is an ideal material to explore the salt-responsive LBD genes. In our study, we identified 41 RrLBD genes based on the R. rugosa genome. According to phylogenetic analysis, all RrLBD genes were categorized into Classes I and II with conserved domains and motifs. The cis-acting element prediction revealed that the promoter regions of most RrLBD genes contain defense and stress responsiveness and plant hormone response elements. Gene expression patterns under salt stress indicated that RrLBD12c, RrLBD25, RrLBD39, and RrLBD40 may be potential regulators of salt stress signaling. Our analysis provides useful information on the evolution and development of RrLBD gene family and indicates that the candidate RrLBD genes are involved in salt stress signaling, laying a foundation for the exploration of the mechanism of LBD genes in regulating abiotic stress.

Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development

KEY MESSAGE

Developmental and transcriptomic analysis of Brachypodium embryogenesis and comparison with Arabidopsis identifies conserved and divergent phases of embryogenesis and reveals widespread heterochrony of developmental gene expression. Embryogenesis, transforming the zygote into the mature embryo, represents a fundamental process for all flowering plants. Current knowledge of cell specification and differentiation during plant embryogenesis is largely based on studies of the dicot model plant Arabidopsis thaliana. However, the major crops are monocots and the transcriptional programs associated with the differentiation processes during embryogenesis in this clade were largely unknown. Here, we combined analysis of cell division patterns with development of a temporal transcriptomic resource during embryogenesis of the monocot model plant Brachypodium distachyon. We found that early divisions of the Brachypodium embryo were highly regular, while later stages were marked by less stereotypic patterns. Comparative transcriptomic analysis between Brachypodium and Arabidopsis revealed that early and late embryogenesis shared a common transcriptional program, whereas mid-embryogenesis was divergent between species. Analysis of orthology groups revealed widespread heterochronic expression of potential developmental regulators between the species. Interestingly, Brachypodium genes tend to be expressed at earlier stages than Arabidopsis counterparts, which suggests that embryo patterning may occur early during Brachypodium embryogenesis. Detailed investigation of auxin-related genes shows that the capacity to synthesize, transport and respond to auxin is established early in the embryo. However, while early PIN1 polarity could be confirmed, it is unclear if an active response is mounted. This study presents a resource for studying Brachypodium and grass embryogenesis and shows that divergent angiosperms share a conserved genetic program that is marked by heterochronic gene expression.

From genes to networks: The genetic control of leaf development

Substantial diversity exists for both the size and shape of the leaf, the main photosynthetic organ of flowering plants. The two major forms of leaf are simple leaves, in which the leaf blade is undivided, and compound leaves, which comprise several leaflets. Leaves form at the shoot apical meristem from a group of undifferentiated cells, which first establish polarity, then grow and differentiate. Each of these processes is controlled by a combination of transcriptional regulators, microRNAs and phytohormones. The present review documents recent advances in our understanding of how these various factors modulate the development of both simple leaves (focusing mainly on the model plant Arabidopsis thaliana) and compound leaves (focusing mainly on the model legume species Medicago truncatula).

Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)

BACKGROUND

Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription factors unique to plants, are involved in multiple transcriptional regulatory pathways and play important roles in lateral organ development, pathogen response, secondary growth, and hormone response. The LBD gene family has not previously been characterized in moso bamboo (Phyllostachys edulis).

RESULTS

In this study, we identified 55 members of the LBD gene family from moso bamboo and found that they were distributed non-uniformly across its 18 chromosomes. Phylogenetic analysis showed that the moso bamboo LBD genes could be divided into two classes. LBDs from the same class share relatively conserved gene structures and sequences encoding similar amino acids. A large number of hormone response-associated cis-regulatory elements were identified in the LBD upstream promoter sequences. Synteny analysis indicated that LBDs in the moso bamboo genome showed greater collinearity with those of O. sativa (rice) and Zea mays (maize) than with those of Arabidopsis and Capsicum annuum (pepper). Numerous segmental duplicates were found in the moso bamboo LBD gene family. Gene expression profiles in four tissues showed that the LBD genes had different spatial expression patterns. qRT-PCR assays with the Short Time-series Expression Miner (STEM) temporal expression analysis demonstrated that six genes (PeLBD20, PeLBD29, PeLBD46, PeLBD10, PeLBD38, and PeLBD06) were consistently up-regulated during the rapid growth and development of bamboo shoots. In addition, 248 candidate target genes that function in a variety of pathways were identified based on consensus LBD binding motifs.

CONCLUSIONS

In the current study, we identified 55 members of the moso bamboo transcription factor LBD and characterized for the first time. Based on the short-time sequence expression software and RNA-seq data, the PeLBD gene expression was analyzed. We also investigated the functional annotation of all PeLBDs, including PPI network, GO, and KEGG enrichment based on String database. These results provide a theoretical basis and candidate genes for studying the molecular breeding mechanism of rapid growth of moso bamboo.

Leaf Shape Diversity: From Genetic Modules to Computational Models

Plant leaves display considerable variation in shape. Here, we introduce key aspects of leaf development, focusing on the morphogenetic basis of leaf shape diversity. We discuss the importance of the genetic control of the amount, duration, and direction of cellular growth for the emergence of leaf form. We highlight how the combined use of live imaging and computational frameworks can help conceptualize how regulated cellular growth is translated into different leaf shapes. In particular, we focus on the morphogenetic differences between simple and complex leaves and how carnivorous plants form three-dimensional insect traps. We discuss how evolution has shaped leaf diversity in the case of complex leaves, by tinkering with organ-wide growth and local growth repression, and in carnivorous plants, by modifying the relative growth of the lower and upper sides of the leaf primordium to create insect-digesting traps.

RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy

Downy mildew, caused by the oomycete Plasmopara viticola, is one of the diseases causing the most severe economic losses to grapevine (Vitis vinifera) production. To date, the application of fungicides is the most efficient method to control the pathogen and the implementation of novel and sustainable disease control methods is a major challenge. RNA interference (RNAi) represents a novel biotechnological tool with a great potential for controlling fungal pathogens. Recently, a candidate susceptibility gene (VviLBDIf7) to downy mildew has been identified in V. vinifera. In this work, the efficacy of RNAi triggered by exogenous double-stranded RNA (dsRNA) in controlling P. viticola infections has been assessed in a highly susceptible grapevine cultivar (Pinot noir) by knocking down VviLBDIf7 gene. The effects of dsRNA treatment on this target gene were assessed by evaluating gene expression, disease severity, and development of vegetative and reproductive structures of P. viticola in the leaf tissues. Furthermore, the effects of dsRNA treatment on off-target (EF1α, GAPDH, PEPC, and PEPCK) and jasmonic acid metabolism (COI1) genes have been evaluated. Exogenous application of dsRNA led to significant reductions both in VviLBDIf7 gene expression, 5 days after the treatment, and in the disease severity when artificial inoculation was carried out 7 days after dsRNA treatments. The pathogen showed clear alterations to both vegetative (hyphae and haustoria) and reproductive structures (sporangiophores) that resulted in stunted growth and reduced sporulation. Treatment with dsRNA showed signatures of systemic activity and no deleterious off-target effects. These results demonstrated the potential of RNAi for silencing susceptibility factors in grapevine as a sustainable strategy for pathogen control, underlying the possibility to adopt this promising biotechnological tool in disease management strategies.

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype

Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale, we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNA-seq experiments were used to understand the global pattern of expressed genes during a mixture of stages at one time in kale, cabbage, and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plant architecture, defense, and nutrition were differentially expressed in kale. This allowed us to identify a set of candidate genes we suggest may be important in the kale domestication syndrome. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.

SAW homeodomain transcription factors regulate initiation of leaf margin serrations

Plant leaves are the main photosynthetic organ of plants and they occur in an array of different shapes. Leaf shape is determined by morphogenesis whereby patterning of the leaf margin can result in interspaced leaf serrations, lobes, or leaflets, depending on the species, developmental stage, and in some instances the environment. In Arabidopsis, mutations in the homeodomain transcription factors SAW1 and SAW2 result in more prominent leaf margin serrations. Here we show that serrations appear precociously in the saw1 saw2 mutant. The pattern of auxin maxima, and of PIN1 and CUC2 expression, which form a feedback loop that drives serration outgrowth, is altered in saw1 saw2 and correlates with precocious serration initiation. SAW1 is not expressed in the outer epidermal cell layer where PIN1 convergence points generate auxin maxima. Instead, SAW1 is expressed on the adaxial side of the leaf and expression in this domain is sufficient for function. We suggest that SAW1 and SAW2 repress serration initiation and outgrowth by promoting the transition to a determinate fate in the leaf margin.

Genome-Wide Identification, Evolution, and Expression Analysis of LBD Transcription Factor Family in Bread Wheat (Triticum aestivum L.)

The lateral organ boundaries domain (LBD) genes, as the plant-specific transcription factor family, play a crucial role in controlling plant architecture and stress tolerance. Although it has been thoroughly characterized in many species, the LBD family was not well studied in wheat. Here, the wheat LBD family was systematically investigated through an in silico genome-wide search method. A total of 90 wheat LBD genes (TaLBDs) were identified, which were classified into class I containing seven subfamilies, and class II containing two subfamilies. Exon-intron structure, conserved protein motif, and cis-regulatory elements analysis showed that the members in the same subfamily shared similar gene structure organizations, supporting the classification. Furthermore, the expression patterns of these TaLBDs in different types of tissues and under diverse stresses were identified through public RNA-seq data analysis, and the regulation networks of TaLBDs involved were predicted. Finally, the expression levels of 12 TaLBDs were validated by quantitative PCR (qPCR) analysis and the homoeologous genes showed differential expression. Additionally, the genetic diversity of TaLBDs in the landrace population showed slightly higher than that of the genetically improved germplasm population while obvious asymmetry at the subgenome level. This study not only provided the potential targets for further functional analysis but also contributed to better understand the roles of LBD genes in regulating development and stress tolerance in wheat and beyond.

Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides

PREMISE

Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question.

METHODS

ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF.

RESULTS

ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it.

CONCLUSIONS

Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.

Patterning a Leaf by Establishing Polarities

Leaves are the major organ for photosynthesis in most land plants, and leaf structure is optimized for the maximum capture of sunlight and gas exchange. Three polarity axes, the adaxial-abaxial axis, the proximal-distal axis, and the medial-lateral axis are established during leaf development to give rise to a flattened lamina with a large area for photosynthesis and blades that are extended on petioles for maximum sunlight. Adaxial cells are elongated, tightly packed cells with many chloroplasts, and their fate is specified by HD-ZIP III and related factors. Abaxial cells are rounder and loosely packed cells and their fate is established and maintained by YABBY family and KANADI family proteins. The activities of adaxial and abaxial regulators are coordinated by ASYMMETRIC LEAVES2 and auxin. Establishment of the proximodistal axis involves the BTB/POZ domain proteins BLADE-ON-PETIOLE1 and 2, whereas homeobox genes PRESSED FLOWER and WUSCHEL-RELATED HOMEOBOX1 mediate leaf development along the mediolateral axis. This review summarizes recent advances in leaf polarity establishment with a focus on the regulatory networks involved.

Irregular adaxial-abaxial polarity rearrangement contributes to the monosymmetric-to-asymmetric transformation of Canna indica stamen

In flowering plants, lateral organs including stamens develop according to the precise regulation of adaxial-abaxial polarity. However, the polarity establishment process is poorly understood in asymmetric stamens. Canna indica (Zingiberales: Cannaceae) is a common ornamental plant with an asymmetric stamen comprising a one-theca anther and a petaloid appendage. In this study, we depicted the monosymmetric-to-asymmetric morphogenesis of C. indica stamen, and the morphogenesis of the monosymmetric stamen of a sister species was used as a contrast. We chose a HD-ZIP III gene family member and a YABBY family member as the adaxial and abaxial polarity marker genes, respectively, and tested their expression using mRNA in situ hybridization. The expression patterns of the two genes changed dynamically and asymmetrically during the stamen development process. Compared with their homologues in Arabidopsis thaliana, these two genes exhibited some specific expression patterns. We hypothesize that the distinctive adaxial-abaxial polarity participates in the irregular morphogenesis of C. indica stamen, which mediates the putative stamen-to-petaloid staminode conversion in this species.

Identification of the target genes of AqAPETALA3-3 (AqAP3-3) in Aquilegia coerulea (Ranunculaceae) helps understand the molecular bases of the conserved and nonconserved features of petals

Identification and comparison of the conserved and variable downstream genes of floral organ identity regulators are critical to understanding the mechanisms underlying the commonalities and peculiarities of floral organs. Yet, because of the lack of studies in nonmodel species, a general picture of the regulatory evolution between floral organ identity genes and their targets is still lacking. Here, by conducting extensive chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), electrophoretic mobility shift assay and bioinformatic analyses, we identify and predict the target genes of a petal identity gene, AqAPETALA3-3 (AqAP3-3), in Aquilegia coerulea (Ranunculaceae) and compare them with those of its counterpart in Arabidopsis thaliana, AP3. In total, 7049 direct target genes are identified for AqAP3-3, of which 2394 are highly confident and 1085 are shared with AP3. Gene Ontology enrichment analyses further indicate that conserved targets are largely involved in the formation of identity-related features, whereas nonconserved targets are mostly required for the formation of species-specific features. These results not only help understand the molecular bases of the conserved and nonconserved features of petals, but also pave the way to studying the regulatory evolution between floral organ identity genes and their targets.

Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium

A comprehensive account of the LBD gene family of Gossypium was provided in this work. Expression analysis and functional characterization revealed that LBD genes might play different roles in G. hirsutum and G. barbadense. The Lateral Organ Boundaries Domain (LBD) proteins comprise a plant-specific transcription factor family, which plays crucial roles in physiological processes of plant growth, development, and stress tolerance. In the present work, a systematical analysis of LBD gene family from two allotetraploid cotton species, G. hirsutum and G. barbadense, together with their genomic donor species, G. arboreum and G. raimondii, was conducted. There were 131, 128, 62, and 68 LBDs identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. The LBD proteins could be classified into two main classes, class I and class II, based on the structure of their lateral organ boundaries domain and traits of phylogenetic tree, and class I was further divided into five subgroups. The gene structure and motif composition analyses conducted in both G. hirsutum and G. barbadense revealed that LBD genes kept relatively conserved within the subfamilies. Synteny analysis suggested that segmental duplication acted as an important mechanism in expansion of the cotton LBD gene family. Cis-element analysis predicated the possible functions of LBD genes. Public RNA-seq data were investigated to analyze the expression patterns of cotton LBD genes in various tissues as well as gene expression under abiotic stress treatments. Furthermore, RT-qPCR results found that GhLBDs had various expression regulation under MeJA treatments. Expression analysis indicated the differential functions of cotton LBD genes in response to abiotic stress and hormones.

The formation of perinucleolar bodies is important for normal leaf development and requires the zinc-finger DNA-binding motif in Arabidopsis ASYMMETRIC LEAVES2

In Arabidopsis, the ASYMMETRIC LEAVES2 (AS2) protein plays a key role in the formation of flat symmetric leaves via direct repression of the abaxial gene ETT/ARF3. AS2 encodes a plant-specific nuclear protein that contains the AS2/LOB domain, which includes a zinc-finger (ZF) motif that is conserved in the AS2/LOB family. We have shown that AS2 binds to the coding DNA of ETT/ARF3, which requires the ZF motif. AS2 is co-localized with AS1 in perinucleolar bodies (AS2 bodies). To identify the amino acid signals in AS2 required for formation of AS2 bodies and function(s) in leaf formation, we constructed recombinant DNAs that encoded mutant AS2 proteins fused to yellow fluorescent protein. We examined the subcellular localization of these proteins in cells of cotyledons and leaf primordia of transgenic plants and cultured cells. The amino acid signals essential for formation of AS2 bodies were located within and adjacent to the ZF motif. Mutant AS2 that failed to form AS2 bodies also failed to rescue the as2-1 mutation. Our results suggest the importance of the formation of AS2 bodies and the nature of interactions of AS2 with its target DNA and nucleolar factors including NUCLEOLIN1. The partial overlap of AS2 bodies with perinucleolar chromocenters with condensed ribosomal RNA genes implies a correlation between AS2 bodies and the chromatin state. Patterns of AS2 bodies in cells during interphase and mitosis in leaf primordia were distinct from those in cultured cells, suggesting that the formation and distribution of AS2 bodies are developmentally modulated in plants.

SIMON: Simple methods for analyzing DNA methylation by targeted bisulfite next-generation sequencing

DNA methylation in higher organisms has become an expanding field of study as it often involves the regulation of gene expression. Although Whole Genome Bisulfite Sequencing (WG-BS) based on next-generation sequencing (NGS) is the most versatile method, this is a costly technique that lacks in-depth analytic power. There are no conventional methods based on NGS that enable researchers to easily compare the level of DNA methylation from the practical number of samples handled in the laboratory. Although the targeted BS method based on Sanger sequencing is generally used in this case, it lacks in-depth analytic power. Therefore, we propose a new method that combines the high throughput analytic power of NGS and bioinformatics with the specificity and focus offered by PCR-amplification-based bisulfite sequencing methods. We use in silico size sieving of DNA-fragments and primer matchings instead of whole-fragment alignment in our bioinformatics analyses, and named our method SIMON (Simple Inference for Methylome based On NGS). The results of our targeted BS method based on NGS (SIMON method) show that small variations in DNA methylation patterns can be precisely and efficiently measured at a single nucleotide resolution. SIMON method combines pre-existing techniques to provide a cost-effective technique for in-depth studies that focus on pre-identified loci. It offers significant improvements with regard to workflow and the quality of the acquired DNA methylation information. Because of the high accuracy of the analysis, small variations of DNA methylation levels can be precisely determined even with large numbers of samples and loci.

Comprehensive characterization of a floral mutant reveals the mechanism of hooked petal morphogenesis in Chrysanthemum morifolium

The diversity of form of the chrysanthemum flower makes this species an ideal model for studying petal morphogenesis, but as yet, the molecular mechanisms underlying petal shape development remain largely unexplored. Here, a floral mutant, which arose as a bud sport in a plant of the variety 'Anastasia Dark Green', and formed straight, rather than hooked petals, was subjected to both comparative morphological analysis and transcriptome profiling. The hooked petals only became discernible during a late stage of flower development. At the late stage of 'Anastasia Dark Green', genes related to chloroplast, hormone metabolism, cell wall and microtubules were active, as were cell division-promoting factors. Auxin concentration was significantly reduced, and a positive regulator of cell expansion was down-regulated. Two types of critical candidates, boundary genes and adaxial-abaxial regulators, were identified from 7937 differentially expressed genes in pairwise comparisons, which were up-regulated at the late stage in 'Anastasia Dark Green' and another two hooked varieties. Ectopic expression of a candidate abaxial gene, CmYAB1, in chrysanthemum led to changes in petal curvature and inflorescence morphology. Our findings provide new insights into the regulatory networks underlying chrysanthemum petal morphogenesis.

TCP7 functions redundantly with several Class I TCPs and regulates endoreplication in Arabidopsis

TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR) proteins, a family of plant-specific transcription factors, play important roles in many developmental processes. However, genetic and functional redundancy among class I TCP limits the analysis of their biological roles. Here, we identified a dominant-negative mutant of Arabidopsis thaliana TCP7 named leaf curling-upward (lcu), which exhibits smaller leaf cells and shorter hypocotyls than the wild type, due to defective endoreplication. A septuple loss-of-function mutant of TCP7, TCP8, TCP14, TCP15, TCP21, TCP22, and TCP23 displayed similar developmental defects to those of lcu. Genome-wide RNA-sequencing showed that lcu and the septuple mutant share many misexpressed genes. Intriguingly, TCP7 directly targets the CYCLIN D1;1 (CYCD1;1) locus and activates its transcription. We determined that the C-terminus of TCP7 accounts for its transcriptional activation activity. Furthermore, the mutant protein LCU exhibited reduced transcriptional activation activity due to the introduction of an EAR-like repressive domain at its C-terminus. Together, these observations indicate that TCP7 plays important roles during leaf and hypocotyl development, redundantly, with at least six class I TCPs, and regulates the expression of CYCD1;1 to affect endoreplication in Arabidopsis.

Nonsense-Mediated mRNA Decay Deficiency Affects the Auxin Response and Shoot Regeneration in Arabidopsis

Plants generally possess a strong ability to regenerate organs; for example, in tissue culture, shoots can regenerate from callus, a clump of actively proliferating, undifferentiated cells. Processing of pre-mRNA and ribosomal RNAs is important for callus formation and shoot regeneration. However, our knowledge of the roles of RNA quality control via the nonsense-mediated mRNA decay (NMD) pathway in shoot regeneration is limited. Here, we examined the shoot regeneration phenotypes of the low-beta-amylase1 (lba1)/upstream frame shift1-1 (upf1-1) and upf3-1 mutants, in which the core NMD components UPF1 and UPF3 are defective. These mutants formed callus from hypocotyl explants normally, but this callus behaved abnormally during shoot regeneration: the mutant callus generated numerous adventitious root structures instead of adventitious shoots in an auxin-dependent manner. Quantitative RT-PCR and microarray analyses showed that the upf mutations had widespread effects during culture on shoot-induction medium. In particular, the expression patterns of early auxin response genes, including those encoding AUXIN/INDOLE ACETIC ACID (AUX/IAA) family members, were significantly affected in the upf mutants. Also, the upregulation of shoot apical meristem-related transcription factor genes, such as CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, was inhibited in the mutants. Taken together, these results indicate that NMD-mediated transcriptomic regulation modulates the auxin response in plants and thus plays crucial roles in the early stages of shoot regeneration.

tRNA Wobble Modification Affects Leaf Cell Development in Arabidopsis thaliana

The tRNA modification at the wobble position of Lys, Glu and Gln (wobbleU* modification) is responsible for the fine-tuning of protein translation efficiency and translation rate. This modification influences organism function in accordance with growth and environmental changes. However, the effects of wobbleU* modification at the cellular, tissue, or individual level have not yet been elucidated. In this study, we show that sulfur modification of wobbleU* of the tRNAs affects leaf development in Arabidopsis thaliana. The sulfur modification was impaired in the two wobbleU*-modification mutants: the URM1-like protein-defective mutant and the Elongator complex-defective mutants. Analyses of the mutant phenotypes revealed that the deficiency in the wobbleU* modification increased the airspaces in the leaves and the leaf size without affecting the number and the area of palisade mesophyll cells. On the other hand, both mutants exhibited increased number of leaf epidermal pavement cells but with reduced cell size. The deficiency in the wobbleU* modification also delayed the initiation of the endoreduplication processes of mesophyll cells. The phenotype of ASYMMETRIC LEAVES2-defective mutant was enhanced in the Elongator-defective mutants, while it was unchanged in the URM1-like protein-defective mutant. Collectively, the findings of this study suggest that the tRNA wobbleU* modification plays an important role in leaf morphogenesis by balancing the development between epidermal and mesophyll tissues.

The Evolution of the KANADI Gene Family and Leaf Development in Lycophytes and Ferns

Leaves constitute the main photosynthetic plant organ and even though their importance is not debated, the origin and development of leaves still is. The leaf developmental network has been elucidated for angiosperms, from genes controlling leaf initiation, to leaf polarity and shape. There are four KANADI (KAN) paralogs in Arabidopsisthaliana needed for organ polarity with KAN1 and KAN2 specifying abaxial leaf identity. Yet, studies of this gene lineage outside angiosperms are required to better understand the evolutionary patterns of leaf development and the role of KAN homologs. We studied the evolution of KAN genes across vascular plants and their expression by in situ hybridization in the fern, Equisetum hyemale and the lycophyte Selaginella moellendorffii. Our results show that the expression of KAN genes in leaves is similar between ferns and angiosperms. However, the expression patterns observed in the lycophyte S. moellendorffii are significantly different compared to all other vascular plants, suggesting that the KAN function in leaf polarity is likely only conserved across ferns, gymnosperms, and angiosperms. This study indicates that mechanisms for leaf development are different in lycophytes compared to other vascular plants.