Molecular and Hormonal Regulation of Leaf Morphogenesis in Arabidopsis

Genome-wide association study uncovers key genomic regions governing agro-morphological and quality traits in Indian mustard [Brassica juncea (L.) Czern. and Coss.]

In Indian mustard, improving agro-morphological and quality traits through conventional methods are both cumbersome and resource-intensive. Marker-aided breeding presents a promising solution to these challenges. Hence, the present research aimed to identify genomic regions governing agro-morphological and quality traits using genome-wide association studies (GWAS). The GWAS panel comprised 142 diverse genotypes of Indian mustard were evaluated for 20 different agro-morphological and quality traits, revealing significant difference among genotypes. Subsequently, the GWAS panel genotyped using the Brassica 90K SNP array (Illumina). Structure and diversity analysis grouped the GWAS panel into 3 sub-populations or groups, and LD decay of 1.05 Mb was confirmed through genotypic analysis. GWAS using the BLINK model revealed a total of 49 marker-trait associations (MTAs), in which 28 and 21 MTAs were observed during rabi 2020-21 and rabi 2021-22 for various agro-morphological and quality traits, respectively. Amongst them, twelve MTAs demonstrated stable associations with the studied traits, including days to 50% flowering (DF), days to 100% flower termination (DFT), days to maturity (DM), plant height (PH), main shoot length (MSL), siliqua length (SL), seeds per siliqua (SPS), oil content (OC), and glucosinolates content (Glu) in both years. Moreover, in silico analysis of nearby regions of these stable SNPs revealed their association with 31 candidate genes known to be involved in various molecular, physiological, and biochemical pathways relevant to the studied traits. These genes can be further characterized and deciphered for more precise utilization in breeding programs in the future.

SlTCP29 and SlTCP24 participate in the morphological development of tomato compound leaves by integrating multiple pathways

Leaves are the primary vegetative organs of plants, and their morphology is an important trait affecting plant architecture, light energy utilization, environmental adaptation, and fruit quality and yield. Leaf development is highly flexible; however, understanding the regulatory mechanisms of factors coordinating leaf morphogenesis and differentiation remains limited. In this study, we obtained a double mutant for SlTCP29 and SlTCP24 genes from the CRISPR/Cas9 mutant population, both belonging to the CINCINNATA-like TCP (TEOSINTE BRANCHED, CYCLOIDEA and PCF1/2) transcription factor subfamily. Simultaneous mutations of SlTCP29 and SlTCP24 genes increase the complexity of tomato leaves, characterized by deeper leaf margin notches and increased number of leaflets. In conjunction with RNA-seq analysis, determination of plant hormone content, and molecular interaction assays, we identified the KNOXII gene SlTKNII5, SlMIR164a, and 1-aminocyclopropane-1-carboxylic acid synthase gene SlACS1A as direct downstream targets of SlTCP29 and SlTCP24, among which SlTKNII5 can physically interact with other KNOXII members to form heterodimers. Our study provides insight into the mechanisms by which SlTCP29 and SlTCP24 are involved in the morphological development of tomato compound leaves by integrating multiple pathways, including transcription factor, microRNA, and phytohormone.

Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean

BACKGROUND

Calmodulin-binding transcription activator (CAMTA) is comprised of a group of transcription factors and plays an important role in the Ca2+ signaling pathway, mediating various molecular responses via interactions with other transcription factors and binding to the promoter region of specific genes. Mung beans (Vigna radiata) are one of the most commonly consumed commodities in Asia. To date, CAMTA proteins have not been characterized in this important crop plant.

RESULTS

Eight paralogous VrCAMTA genes were identified and found to be distributed on five of the 11 chromosomes. The proteins possessed CG-1 DNA-binding domains with bipartite NLS signals, ankyrin domains, CaM-binding IQ motifs, and CaM-binding domain (CaMBD). The 2 kb upstream regions of VrCAMTA genes contained sequence motifs of abscisic acid-responsive elements (ABRE) and ethylene-responsive elements (ERE), and binding sites for transcription factors of the bZIP and bHLH domains. Analysis of RNA-seq data from a public repository revealed ubiquitous expression of the VrCAMTA genes, as VrCAMTA1 was expressed at the highest level in seedling leaves, whereas VrCAMTA8 was expressed at the lowest level, which agreed with the RT-qPCR analysis performed on the first true leaves. On day four after leaf emergence, all VrCAMTA genes were upregulated, with VrCAMTA1 exhibiting the highest degree of upregulation. In darkness on day 4, upregulation was not observed in most VrCAMTA genes, except VrCAMTA7, for which a low degree of upregulation was found, whereas no difference was found in VrCAMTA8 expression between light and dark conditions. Treatment with calcium ionophores enhanced VrCAMTA expression under light and/or dark conditions at different times after leaf emergence, suggesting that calcium signaling is involved in the light-induced upregulation of VrCAMTA gene expression.

CONCLUSIONS

The expression dependence of nearly all VrCAMTA genes on light and calcium signaling suggests their possible differential but likely complementary roles during the early stages of mung bean growth and development.

Integratedly analyzed quantitative proteomics with transcriptomics to discover key genes via fg-1 non-heading mutant in the early heading stage of Chinese cabbage

Leaf heading is an important agronomic trait of Chinese cabbage, which directly affects its yield. Leaf heading formation in Chinese cabbage is controlled by its internal genotype and external environmental factors, the underlying mechanism of which remains poorly understood. To discover the leaf heading formation mechanism more deeply, this study analyzed the correlation between proteomic and transcriptomic data in the leaf heading formation mutant fg-1 generated by EMS. iTRAQ-based quantitative proteomics techniques were performed to identify the protein expression profiles during the key periods of the early heading stage in the section of the soft leaf apical region (section a) and the whole leaf basal region (section d). We first identified 1,246 differentially expressed proteins (DEPs) in section a and 1,055 DEPs in section d. Notably, transcriptome-proteome integrated analysis revealed that 207 and 278 genes showed consistent trends at the genes' and proteins' expression levels in section a and section d, respectively. KEGG analyses showed that the phenylpropanoid biosynthesis pathway was enriched in both sections a and d. Furthermore, 86 TFs exhibited co-upregulation or co-downregulation, and seven out of 86 were involved in plant hormone synthesis and signal transduction pathways. This indicates that they are potentially related to the leaf heading formation in Chinese cabbage. Taken together, we have identified several key early-heading-formation-related factors via integration analysis of the transcriptomics and proteomics data. This provides sufficient gene resources to discover the molecular mechanism of leaf heading formation.

Chemical free, bio-Intercalation of selenium nanoparticles for highly accelerated photo-responsive of organic contaminants debasement and their in-vitro anti-bacterial agents, anti-oxidants effect, cyto-toxic analysis

This study investigates the use of Excoecaria agallocha leaves as a bio-template for the intercalation of Selenium nanoparticles (SeNPs). The synthesized SeNPs were characterized using techniques like SEM-EDX, TEM/HR-TEM, and XRD spectroscopic studies. The study found that SeNPs showed maximum cleaning ability at a dosage of 50 μl/mL, with 95% inhibition of DPPH radicals. However, cellular absorption was limited to 55% at concentrations of 300 μg/L over a 72-h period. The synthesized SeNPs also demonstrated a strong cytotoxic effect on MCF-7 breast cancer cell lines, indicating their potential as anti-cancer agents. Further research is needed to fully explore the potential of these novel nanocomposites.

Morphological characterization and transcriptome analysis of rolled and narrow leaf mutant in soybean

BACKGROUND

In plants, the leaf functions as a solar panel, where photosynthesis converts carbon dioxide and water into carbohydrates and oxygen. In soybean, leaf type traits, including leaf shape, leaf area, leaf width, and leaf width so on, are considered to be associated with yield. In this study, we performed morphological characterization, transcriptome analysis, and endogenous hormone analysis of a rolled and narrow leaf mutant line (rl) in soybean.

RESULTS

Compared with wild type HX3, mutant line rl showed rolled and narrower leaflet, and smaller leaf, meanwhile rl also performed narrower pod and narrower seed. Anatomical analysis of leaflet demonstrated that cell area of upper epidermis was bigger than the cell area of lower epidermis in rl, which may lead rolled and narrow leaf. Transcriptome analysis revealed that several cytokinin oxidase/dehydrogenase (CKX) genes (Glyma.06G028900, Glyma.09G225400, Glyma.13G104700, Glyma.14G099000, and Glyma.17G054500) were up-regulation dramatically, which may cause lower cytokinin level in rl. Endogenous hormone analysis verified that cytokinin content of rl was lower. Hormone treatment results indicated that 6-BA rescued rolled leaf enough, rescued partly narrow leaf. And after 6-BA treatment, the cell area was similar between upper epidermis and lower epidermis in rl. Although IAA content and ABA content were reduced in rl, but exogenous IAA and ABA didn't affect leaf type of HX3 and rl.

CONCLUSIONS

Our results suggest abnormal cytokinin metabolism caused rolled and narrow leaf in rl, and provide valuable clues for further understanding the mechanisms underlying leaf development in soybean.

Temporal dynamics of genetic architecture governing leaf development in Populus

Leaf development is a multifaceted and dynamic process orchestrated by a myriad of genes to shape the proper size and morphology. The dynamic genetic network underlying leaf development remains largely unknown. Utilizing a synergistic genetic approach encompassing dynamic genome-wide association study (GWAS), time-ordered gene co-expression network (TO-GCN) analyses and gene manipulation, we explored the temporal genetic architecture and regulatory network governing leaf development in Populus. We identified 42 time-specific and 18 consecutive genes that displayed different patterns of expression at various time points. We then constructed eight TO-GCNs that covered the cell proliferation, transition, and cell expansion stages of leaf development. Integrating GWAS and TO-GCN, we postulated the functions of 27 causative genes for GWAS and identified PtoGRF9 as a key player in leaf development. Genetic manipulation via overexpression and suppression of PtoGRF9 revealed its primary influence on leaf development by modulating cell proliferation. Furthermore, we elucidated that PtoGRF9 governs leaf development by activating PtoHB21 during the cell proliferation stage and attenuating PtoLD during the transition stage. Our study provides insights into the dynamic genetic underpinnings of leaf development and understanding the regulatory mechanism of PtoGRF9 in this dynamic process.

A mutation in CsGME encoding GDP-mannose 3,5-epimerase results in little and wrinkled leaf in cucumber

KEY MESSAGE

Map-based cloning revealed that a mutation in a highly conserved amino acid of the CsGME gene encoding GDP-mannose 3,5-epimerase, causes the phenotype of little and wrinkled leaves in cucumbers. Leaf size is a critical determinant of plant architecture in cucumbers, yet only a few genes associated with this trait have been mapped or cloned. Here, we identified and characterized a mutant with little and wrinkled leaves, named lwl-1. Genetic analysis revealed that the phenotype of the lwl-1 was controlled by a single recessive gene. Through map-based cloning, the lwl-1 locus was narrowed down to a 12.22-kb region exclusively containing one fully annotated gene CsGME (CsaV3_2G004170). CsGME encodes GDP-mannose 3,5-epimerase, which is involved in the synthesis of ascorbic acid (ASA) and one of the components of pectin, RG-II. Whole-length sequencing of the 12.22 kb DNA fragment revealed the presence of only a non-synonymous mutation located in the sixth exon of CsGME in lwl-1, resulting in an amino acid alteration from Pro363 to Leu363. This mutation was unique among 118 inbred lines from cucumber natural populations. CsGME expression significantly reduced in various organs of lwl-1, accompanied by a significant decrease in ASA and pectin content in leaves. Both CsGME and Csgme proteins were localized to the cytoplasm. The mutant phenotype exhibited partial recovery after the application of exogenous boric acid. Silencing CsGME in cucumber through VIGS confirmed its role as the causal gene for lwl-1. Transcriptome profiling revealed that CsGME greatly affected the expression of genes related to the cell division process and cell plate formation. This study represents the first report to characterize and clone the CsGME in cucumber, indicating its crucial role in regulating leaf size and development.

Transcriptomic analyses to summarize gene expression patterns that occur during leaf initiation of Chinese cabbage

In Chinese cabbage, rosette leaves expose their adaxial side to the light converting light energy into chemical energy, acting as a source for the growth of the leafy head. In the leafy head, the outer heading leaves expose their abaxial side to the light while the inner leaves are shielded from the light and have become a sink organ of the growing Chinese cabbage plant. Interestingly, variation in several ad/abaxial polarity genes is associated with the typical leafy head morphotype. The initiation of leaf primordia and the establishment of leaf ad/abaxial polarity are essential steps in the initiation of marginal meristem activity leading to leaf formation. Understanding the molecular genetic mechanisms of leaf primordia formation, polar differentiation, and leaf expansion is thus relevant to understand leafy head formation. As Brassica's are mesa-hexaploids, many genes have multiple paralogues, complicating analysis of the genetic regulation of leaf development. In this study, we used laser dissection of Chinese cabbage leaf primordia and the shoot apical meristem (SAM) to compare gene expression profiles between both adaxial and abaxial sides and the SAM aiming to capture transcriptome changes underlying leaf primordia development. We highlight genes with roles in hormone pathways and transcription factors. We also assessed gene expression gradients along expanded leaf blades from the same plants to analyze regulatory links between SAM, leaf primordia and the expanding rosette leaf. The catalogue of differentially expressed genes provides insights in gene expression patterns involved in leaf development and form a starting point to unravel leafy head formation.

Transcriptomics of Leaf Development in the Endangered Dioecious Magnolia kwangsiensis: Molecular Basis Underpinning Specialized Metabolism Genes

Magnolia kwangsiensis, a dioecious tree native to China, is recognized not only for its status as an at-risk species but also for its potential in therapeutic applications courtesy of its bioactive compounds. However, the genetic underpinnings of its leaf development and compound biosynthesis are not well documented. Our study aims to bridge this knowledge gap through comparative transcriptomics, analyzing gene expression through different leaf maturation stages. We studied the transcriptome of M. kwangsiensis leaves by applying RNA sequencing at juvenile, tender, and mature phases. We identified differentially expressed genes (DEGs) to explore transcriptional changes accompanying the developmental trajectory. Our analysis delineates the transcriptional landscape of over 20,000 genes with over 6000 DEGs highlighting significant transcriptional shifts throughout leaf maturation. Mature leaves demonstrated upregulation in pathways related to photosynthesis, cell wall formation, and polysaccharide production, affirming their structural integrity and specialized metabolic functions. Our GO and KEGG enrichment analyses underpin these findings. Furthermore, we unveiled coordinated gene activity correlating development with synthesizing therapeutically relevant polysaccharides. We identified four novel glycosyltransferases potentially pivotal in this synergistic mechanism. Our study uncovers the complementary evolutionary forces that concurrently sculpt structural and chemical defenses. These genetic mechanisms calibrate leaf tissue resilience and biochemical efficacy.

Physiological Control and Genetic Basis of Leaf Curvature and Heading in Brassica rapa L

BACKGROUND

Heading is an important agronomic feature for Chinese cabbage, cabbage, and lettuce. The heading leaves function as nutrition storage organs, which contribute to the high quality and economic worth of leafy heads. Leaf development is crucial during the heading stage, most genes previously predicted to be involved in the heading process are based on Arabidopsis leaf development studies.

AIM OF REVIEW

Till date, there is no published review article that demonstrated a complete layout of all the identified regulators of leaf curvature and heading. In this review, we have summarized all the identified physiological and genetic regulators that are directly or indirectly involved in leaf curvature and heading in Brassica crops. By integrating all identified regulators that provide a coherent logic of leaf incurvature and heading, we proposed a molecular mechanism in Brassica crops with graphical illustrations. This review adds value to future breeding of distinct heading kinds of cabbage and Chinese cabbage by providing unique insights into leaf development.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Leaf curvature and heading are established by synergistic interactions among genes, transcription factors, microRNAs, phytohormones, and environmental stimuli that regulate primary and secondary morphogenesis. Various genes have been identified using transformation and genome editing that are responsible for the formation of leaf curvature and heading in Brassica crops. A range of leaf morphologies have been observed in Brassica, which are established because of the mutated determinants that are responsible for cell division and leaf polarity.

Selenium nanoparticles based on Amphipterygium glaucum extract with antibacterial, antioxidant, and plant biostimulant properties

BACKGROUND

In recent years, crop production has expanded due to the variety of commercially available species. This increase in production has led to global competition and the search for biostimulant products that improve crop quality and yield. At the same time, agricultural products that protect against diseases caused by phytopathogenic microorganisms are needed. Thus, the green synthesis of selenium nanoparticles (SeNPs) is a proposal for achieving these needs. In this research, SeNPs were synthesized from methanolic extract of Amphipterygium glaucum leaves, and chemically and biologically characterized.

RESULTS

The characterization of SeNPs was conducted by ultraviolet-visible spectrophotometry (UV-Vis), scanning electron microscopy (SEM), electron microscopy transmission (TEM), Dynamic Light Scattering (DLS), energy dispersion X-ray spectroscopy (EDX), and infrared spectrophotometry (FTIR) techniques. SeNPs with an average size of 40-60 nm and spherical and needle-shaped morphologies were obtained. The antibacterial activity of SeNPs against Serratia marcescens, Enterobacter cloacae, and Alcaligenes faecalis was evaluated. The results indicate that the methanolic extracts of A. glaucum and SeNPs presented a high antioxidant activity. The biostimulant effect of SeNPs (10, 20, 50, and 100 µM) was evaluated in vinca (Catharanthus roseus), and calendula (Calendula officinalis) plants under greenhouse conditions, and they improved growth parameters such as the height, the fresh and dry weight of roots, stems, and leaves; and the number of flowers of vinca and calendula.

CONCLUSIONS

The antibacterial, antioxidant, and biostimulant properties of SeNPs synthesized from A. glaucum extract demonstrated in this study support their use as a promising tool in crop production.

"Pathomorphogenic" Changes Caused by Citrus Bark Cracking Viroid and Transcription Factor TFIIIA-7ZF Variants Support Viroid Propagation in Tobacco

Viroids are small, non-coding, pathogenic RNAs with the ability to disturb plant developmental processes. This dysregulation redirects the morphogenesis of plant organs, significantly impairing their functionality. Citrus bark cracking viroid (CBCVd) causes detrimental developmental distortions in infected hops (Humulus lupulus) and causes significant economic losses. CBCVd can infect cells and tissues of the model plant tobacco (Nicotiana tabacum), provided it is delivered via transgenesis. The levels of CBCVd in tobacco were enhanced in plant hybrids expressing CBCVd cDNAs and either the tobacco or hop variant of TFIIIA-7ZF, a viroid-mediated splicing derivative of transcription factor IIIA, which is important for viroid replication by DNA-dependent RNA polymerase II. The TFIIIA-7ZF variants can change the tobacco morphogenesis if expressed in leaves and shoots. In addition to the splitting of shoots, the "pathomorphogenic" network in hybrid plants expressing CBCVd and HlTFIIIA-7ZF induced leaf fusions and malformations. Moreover, CBCVd can dramatically change another morphogenesis into teratomic and petal-like tissues if propagated above some limit in young transgenic tobacco microspores and anthers. By comparative RNA profiling of transgenic tobacco shoots bearing TFIIIA-7ZFs and CBCVd-transformed/infected anthers, we found a differential expression of many genes at p < 0.05. As the main common factor showing the differential up-regulation in shoot and anther tissues, a LITTLE ZIPPER 2-like transcription factor was found. We propose that this factor, which can interact as a competitive inhibitor of the also dysregulated homeobox-leucin zipper family protein (HD-ZIPIII) in apical meristem, is essential for a network responsible for some morphological changes and modifications of plant degradome within shoot meristem regulation and secondary xylem differentiation.

Leaf-size control beyond transcription factors: Compensatory mechanisms

Plant leaves display abundant morphological richness yet grow to characteristic sizes and shapes. Beginning with a small number of undifferentiated founder cells, leaves evolve via a complex interplay of regulatory factors that ultimately influence cell proliferation and subsequent post-mitotic cell enlargement. During their development, a sequence of key events that shape leaves is both robustly executed spatiotemporally following a genomic molecular network and flexibly tuned by a variety of environmental stimuli. Decades of work on Arabidopsis thaliana have revisited the compensatory phenomena that might reflect a general and primary size-regulatory mechanism in leaves. This review focuses on key molecular and cellular events behind the organ-wide scale regulation of compensatory mechanisms. Lastly, emerging novel mechanisms of metabolic and hormonal regulation are discussed, based on recent advances in the field that have provided insights into, among other phenomena, leaf-size regulation.

Independent Responses of Photosynthesis and Plant Morphology to Alterations of PIF Proteins and Light-Dependent MicroRNA Contents in Arabidopsis thaliana&nbsp;pif Mutants Grown under Lights of Different Spectral Compositions

The effects of the quality of light on the content of phytochrome interacting factors (PIFs) such as PIF3, PIF4 and PIF5, as well as the expression of various light-dependent microRNAs, in adult Arabidopsis thaliana pif mutant plants (pif4, pif5, pif3pif5, pif4pif5, pif3pif4pif5) were studied. We demonstrate that under blue light, the pif4 mutant had maximal expression of most of the studied microRNAs (miR163, miR319, miR398, miR408, miR833) when the PIF4 protein in plants was reduced. This finding indicates that the PIF4 protein is involved in the downregulation of this group of microRNAs. This assumption is additionally confirmed by the fact that under the RL spectrum in pif5 mutants, practically the same miRNAs decrease expression against the background of an increase in the amount of PIF4 protein. Unlike the WT and other mutants, the pif4 mutant responded to the BL spectrum not only by activating the expression of light-dependent miRNAs, but also by a significant increase in the expression of transcription factors and key light signalling genes. These molecular reactions do not affect the activity of photosynthesis but may be involved in the formation of a light quality-dependent phenotype.

Morphological characterization and transcriptome analysis of leaf angle mutant bhlh112 in maize [Zea mays L.]

Leaf angle is an important agronomic trait in maize [Zea mays L.]. The compact plant phenotype, with a smaller leaf angle, is suited for high-density planting and thus for increasing crop yields. Here, we studied the ethyl methane sulfonate (EMS)-induced mutant bhlh112. Leaf angle and plant height were significantly decreased in bhlh112 compared to the wild-type plants. After treatment of seedlings with exogenous IAA and ABA respectively, under the optimal concentration of exogenous hormones, the variation of leaf angle of the mutant was more obvious than that of the wild-type, which indicated that the mutant was more sensitive to exogenous hormones. Transcriptome analysis showed that the ZmbHLH112 gene was related to the biosynthesis of auxin and brassinosteroids, and involved in the activation of genes related to the auxin and brassinosteroid signal pathways as well as cell elongation. Among the GO enrichment terms, we found many differentially expressed genes (DEGs) enriched in the cell membrane and ribosomal biosynthesis, hormone biosynthesis and signaling pathways, and flavonoid biosynthesis, which could influence cell growth and the level of endogenous hormones affecting leaf angle. Therefore, ZmbHLH112 might regulate leaf angle development through the auxin signaling and the brassinosteroid biosynthesis pathways. 12 genes related to the development of leaf were screened by WGCNA; In GO enrichment and KEGG pathways, the genes were mainly enriched in rRNA binding, ribosome biogenesis, Structural constituent of ribosome; Arabidopsis ribosome RNA methyltransferase CMAL is involved in plant development, likely by modulating auxin derived signaling pathways; The free 60s ribosomes and polysomes in the functional defective mutant rice minute-like1 (rml1) were significantly reduced, resulting in plant phenotypic diminution, narrow leaves, and growth retardation; Hence, ribosomal subunits may play an important role in leaf development. These results provide a foundation for further elucidation of the molecular mechanism of the regulation of leaf angle in maize.

GhBOP1 as a Key Factor of Ribosomal Biogenesis: Development of Wrinkled Leaves in Upland Cotton

Block of proliferation 1 (BOP1) is a key protein that helps in the maturation of ribosomes and promotes the progression of the cell cycle. However, its role in the leaf morphogenesis of cotton remains unknown. Herein, we report and study the function of GhBOP1 isolated from Gossypium hirsutum. The sequence alignment revealed that BOP1 protein was highly conserved among different species. The yeast two-hybrid experiments, bimolecular fluorescence complementation, and luciferase complementation techniques revealed that GhBOP1 interact with GhPES and GhWDR12. Subcellular localization experiments revealed that GhBOP1, GhPES and GhWDR12 were localized at the nucleolus. Suppression of GhBOP1 transcripts resulted in the uneven bending of leaf margins and the presence of young wrinkled leaves by virus-induced gene silencing assay. Abnormal palisade arrangements and the presence of large upper epidermal cells were observed in the paraffin sections of the wrinkled leaves. Meanwhile, a jasmonic acid-related gene, GhOPR3, expression was increased. In addition, a negative effect was exerted on the cell cycle and the downregulation of the auxin-related genes was also observed. These results suggest that GhBOP1 plays a critical role in the development of wrinkled cotton leaves, and the process is potentially modulated through phytohormone signaling.

Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development

N6-methyladenosine (m⁶A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m⁶A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m⁶A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m⁶A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways.

Research Progress on the Leaf Morphology, Fruit Development and Plant Architecture of the Cucumber

Cucumber (Cucumis sativus L.) is an annual climbing herb that belongs to the Cucurbitaceae family and is one of the most important economic crops in the world. The breeding of cucumber varieties with excellent agronomic characteristics has gained more attention in recent years. The size and shape of the leaves or fruit and the plant architecture are important agronomic traits that influence crop management and productivity, thus determining the crop yields and consumer preferences. The growth of the plant is precisely regulated by both environmental stimuli and internal signals. Although significant progress has been made in understanding the plant morphological regulation of Arabidopsis, rice, and maize, our understanding of the control mechanisms of the growth and development of cucumber is still limited. This paper reviews the regulation of phytohormones in plant growth and expounds the latest progress in research regarding the genetic regulation pathways in leaf development, fruit size and shape, branching, and plant type in cucumber, so as to provide a theoretical basis for improving cucumber productivity and cultivation efficiency.

Melon shoot organization 1, encoding an AGRONAUTE7 protein, plays a crucial role in plant development

A melon gene MSO1 located on chromosome 10 by map-based cloning strategy, which encodes an ARGONAUTE 7 protein, is responsible for the development of shoot organization. Plant endogenous small RNAs (sRNAs) are involved in various plant developmental processes. In Arabidopsis, sRNAs combined with ARGONAUTE (AGO) proteins are incorporated into the RNA-induced silencing complex (RISC), which functions in RNA silencing or biogenesis of trans-acting siRNAs (ta-siRNAs). However, their roles in melon (Cucumis melo L.) are still unclear. Here, the melon shoot organization 1 (mso1) mutant was identified and shown to exhibit pleiotropic phenotypes in leaf morphology and plant architecture. Positional cloning of MSO1 revealed that it encodes a homologue of Arabidopsis AGO7/ZIPPY, which is required for the production of ta-siRNAs. The AG-to-C mutation in the second exon of MSO1 caused a frameshift mutation and significantly reduced its expression. Ectopic expression of MSO1 rescued the Arabidopsis ago7 phenotype. RNA-seq analysis showed that several genes involved in transcriptional regulation and plant hormones were significantly altered in mso1 compared to WT. A total of 304 and 231 miRNAs were identified in mso1 and WT by sRNA sequencing, respectively, and among them, 42 known and ten novel miRNAs were differentially expressed. cme-miR390a significantly accumulated, and the expression levels of the two ta-siRNAs were almost completely abolished in mso1. Correspondingly, their targets, the ARF3 and ARF4 genes, showed dramatically upregulated expression, indicating that the miR390-TAS3-ARF pathway has conserved roles in melon. These findings will help us better understand the molecular mechanisms of MSO1 in plant development in melon.

Action of Salicylic Acid on Plant Growth

The phytohormone salicylic acid (SA) not only is a well-known signal molecule mediating plant immunity, but also is involved in plant growth regulation. However, while its role in plant immunity has been well elucidated, its action on plant growth has not been clearly described to date. Recently, increasing evidence has shown that SA plays crucial roles in regulating cell division and cell expansion, the key processes that determines the final stature of plant. This review summarizes the current knowledge on the action and molecular mechanisms through which SA regulates plant growth via multiple pathways. It is here highlighted that SA mediates growth regulation by affecting cell division and expansion. In addition, the interactions of SA with other hormones and their role in plant growth determination were also discussed. Further understanding of the mechanism underlying SA-mediated growth will be instrumental for future crop improvement.

An Efficient Marker Gene Excision Strategy Based on CRISPR/Cas9-Mediated Homology-Directed Repair in Rice

In order to separate transformed cells from non-transformed cells, antibiotic selectable marker genes are usually utilized in genetic transformation. After obtaining transgenic plants, it is often necessary to remove the marker gene from the plant genome in order to avoid regulatory issues. However, many marker-free systems are time-consuming and labor-intensive. Homology-directed repair (HDR) is a process of homologous recombination using homologous arms for efficient and precise repair of DNA double-strand breaks (DSBs). The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) system is a powerful genome editing tool that can efficiently cause DSBs. Here, we isolated a rice promoter (Pssi) of a gene that highly expressed in stem, shoot tip and inflorescence, and established a high-efficiency sequence-excision strategy by using this Pssi to drive CRISPR/Cas9-mediated HDR for marker free (PssiCHMF). In our study, PssiCHMF-induced marker gene deletion was detected in 73.3% of T0 plants and 83.2% of T1 plants. A high proportion (55.6%) of homozygous marker-excised plants were obtained in T1 progeny. The recombinant GUS reporter-aided analysis and its sequencing of the recombinant products showed precise deletion and repair mediated by the PssiCHMF method. In conclusion, our CRISPR/Cas9-mediated HDR auto-excision method provides a time-saving and efficient strategy for removing the marker genes from transgenic plants.

Morphological Characterization and Transcriptome Analysis of New Dwarf and Narrow-Leaf (dnl2) Mutant in Maize

Lodging is the primary factor limiting high yield under a high plant density. However, an optimal plant height and leaf shape can effectively decrease the lodging risk. Here we studied an ethyl methanesulfonate (EMS)-induced dwarf and a narrow-leaf mutant, dnl2. Gene mapping indicated that the mutant was controlled by a gene located on chromosome nine. Phenotypic and cytological observations revealed that dnl2 showed inhibited cell growth, altered vascular bundle patterning, and disrupted secondary cell wall structure when compared with the wild-type, which could be the direct cause of the dwarf and narrow-leaf phenotype. The phytohormone levels, especially auxin and gibberellin, were significantly decreased in dnl2 compared to the wild-type plants. Transcriptome profiling of the internodes of the dnl2 mutant and wild-type revealed a large number of differentially expressed genes enriched in the cell wall biosynthesis, remodeling, and hormone biosynthesis and signaling pathways. Therefore, we suggest that crosstalk between hormones (the altered vascular bundle and secondary cell wall structure) may contribute to the dwarf and narrow-leaf phenotype by influencing cell growth. These results provide a foundation for DNL2 gene cloning and further elucidation of the molecular mechanism of the regulation of plant height and leaf shape in maize.

The Diverse Manifestations of Regeneration and Why We Need to Study Them

For hundreds of years, the question of why some organisms can regenerate missing body parts while others cannot has remained poorly understood. This has been due in great part to the inability to genetically, molecularly, and cellularly dissect this problem for most of the history of the field. It has only been in the past 20-30 years that important mechanistic advances have been made in methodologies that introduce loss and gain of gene function in animals that can regenerate. However, we still have a very incomplete understanding of how broadly regenerative abilities may be dispersed across species and whether or not such properties share a common evolutionary origin, which may have emerged independently or both. Understanding regeneration, therefore, will require rigorously practiced fundamental, curiosity-driven, discovery research. Expanding the number of research organisms used to study regeneration allows us to uncover aspects of this problem we may not yet know exist and simultaneously increases our chances of solving this long-standing problem of biology.

RNA Sequencing Reveals Dynamic Carbohydrate Metabolism and Phytohormone Signaling Accompanying Post-mowing Regeneration of Forage Winter Wheat (Triticum aestivum L.)

Winter wheat (Triticum aestivum L.) is used as fresh green winter forage worldwide, and its ability to regenerate after mowing determines whether it can be used for forage production; however, the molecular mechanism of regeneration is poorly understood. This study identified long-chain coding and non-coding RNAs in the wheat cultivar "XN9106," which is cultivated for forage and grain production separately in winter and summer, and analyzed their function during post-mowing regeneration. The results showed that the degradation of carbohydrate plays an important role in regeneration, as demonstrated by decreased carbohydrate content. The increased gene expression of enzymes including β-amylase, β-fructofuranosidase, sucrose synthase, sucrose-6-phosphate synthase, trehalose-6-phosphate synthase, and trehalose-6-phosphate phosphatase in mowed seedlings suggests regeneration is fueled by degraded carbohydrates that provide energy and carbon skeletons for the Krebs cycle and amino acid synthesis. The decreased auxin content relieved the inhibition of cytokinin synthesis, that controls the transition from cell division to cell expansion and stimulates cell expansion and differentiation during the cell expansion phase, and eventually accelerate post-mowing regeneration of seedlings. Additionally, differentially expressed long-chain non-coding RNAs (lncRNAs) might participate in the regulation of gene expression related to carbohydrate metabolism and hormone signal transduction. This study demonstrated the responses of key mRNAs and lncRNAs during post-mowing regeneration of winter wheat and revealed the importance of carbohydrate and hormone during regeneration, providing valuable information for genetic improvement of forage wheat.

Phytochrome regulates cellular response plasticity and the basic molecular machinery of leaf development

Plants are plastic organisms that optimize growth in response to a changing environment. This adaptive capability is regulated by external cues, including light, which provides vital information about the habitat. Phytochrome photoreceptors detect far-red light, indicative of nearby vegetation, and elicit the adaptive shade-avoidance syndrome (SAS), which is critical for plant survival. Plants exhibiting SAS are typically more elongated, with distinctive, small, narrow leaf blades. By applying SAS-inducing end-of-day far-red (EoD FR) treatments at different times during Arabidopsis (Arabidopsis thaliana) leaf 3 development, we have shown that SAS restricts leaf blade size through two distinct cellular strategies. Early SAS induction limits cell division, while later exposure limits cell expansion. This flexible strategy enables phytochromes to maintain control of leaf size through the proliferative and expansion phases of leaf growth. mRNAseq time course data, accessible through a community resource, coupled to a bioinformatics pipeline, identified pathways that underlie these dramatic changes in leaf growth. Phytochrome regulates a suite of major development pathways that control cell division, expansion, and cell fate. Further, phytochromes control cell proliferation through synchronous regulation of the cell cycle, DNA replication, DNA repair, and cytokinesis, and play an important role in sustaining ribosome biogenesis and translation throughout leaf development.

A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis

Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants' features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem's solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells' spatial localization in the initial plant organ-one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.

Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.