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Leaf variegation is a key ornamental trait of (Jianlan); however, the molecular mechanisms underlying leaf color mutations in variegated sectors remain poorly understood. Elucidating the regulatory networks associated with pigment variation is essential for both basic research and ornamental improvement. Wild-type plants and two leaf color mutants-spot variegation type (BanYi) and line variegation type (XianYi)-were analyzed. Samples were divided into five groups based on leaf origin and color: CK (wild type), B (yellow sectors of BanYi), BL (green sectors of BanYi), X (yellow sectors of XianYi), and XL (green sectors of XianYi). Integrated transcriptomic and metabolomic analyses were performed. Differential expression analysis was conducted across four comparison groups (B vs BL, B vs CK, X vs CK, and X vs XL). Co-expression analysis, metabolite profiling, correlation analysis, and weighted gene co-expression network analysis (WGCNA) were used to identify key regulatory genes and modules associated with pigment accumulation. A total of 6,716 differentially expressed genes (DEGs) were identified, with 141 shared among all comparison groups. These DEGs were significantly enriched in phenylpropanoid biosynthesis, zeatin biosynthesis, and flavonoid biosynthesis pathways. Twenty-four DEGs involved in flavonoid biosynthesis, including structural genes such as , , and , showed elevated expression in variegated leaf sectors. In addition, 80 transcription factors from the MYB, bHLH, and WRKY families were co-expressed with 50 pigment-related DEGs, suggesting coordinated transcriptional regulation. Metabolomic analysis identified 3,024 differentially accumulated metabolites (DAMs), of which 56 were shared across all groups. Correlation analysis revealed strong associations between co-DEGs and co-DAMs. WGCNA further identified key modules, including the \"MEtan\" module, which contained 83 genes significantly correlated with pigment-related metabolites such as 1'-Hydroxy-γ-carotene and violaxanthin. These results demonstrate that leaf variegation in is regulated by coordinated transcriptional and metabolic networks, particularly involving flavonoid and carotenoid-related pathways. The identified structural genes, transcription factors, and co-expression modules provide novel insights into the genetic basis of leaf color variation and offer valuable candidate targets for the ornamental improvement of Jianlan.

Air space-type variegation is the most diverse among the species of known variegated leaf plants and is caused by conspicuous intercellular spaces between the epidermal and palisade cells and among the palisade cells at non-green areas. Trifolium pratense, a species in Fabaceae with V-shaped air space-type variegation, was selected to explore the application potential of variegated leaf plants and accumulate basic data on the molecular regulatory mechanism and evolutionary history of leaf variegation. We performed comparative transcriptome analysis on young and adult leaflets of variegated and green plants and identified 43 candidate genes related to air space-type variegation formation. Most of the genes were related to cell-wall structure modification (CESA, CSL, EXP, FLA, PG, PGIP, PLL, PME, RGP, SKS, and XTH family genes), followed by photosynthesis (LHCB subfamily, RBCS, GOX, and AGT family genes), redox (2OG and GSH family genes), and nitrogen metabolism (NodGS family genes). Other genes were related to photooxidation, protein interaction, and protease degradation systems. The downregulated expression of light-responsive LHCB subfamily genes and the upregulated expression of the genes involved in cell-wall structure modification were important conditions for air space-type variegation formation in T. pratense. The upregulated expression of the ubiquitin-protein ligase enzyme (E3)-related genes in the protease degradation systems were conducive to air space-type variegation formation. Because these family genes are necessary for plant growth and development, the mechanism of the leaf variegation formation in T. pratense might be a widely existing regulation in air space-type variegation in nature.

'Zebrinus' is a landscape plant with high ornamental value, whose core ornamental feature is determined by the irregularly distributed yellow variegation on its leaves, supporting its extensive application in landscape design and configuration. 'Zebrinus', as a typical variegated-leaf gramineous plant, possesses a key phenotypic trait of leaf variegation that distinguishes it from ordinary species. However, up to the present moment, we know little about the molecular regulatory mechanism underlying this unique variegation, with relevant research carried out in the exploratory stage. This study was performed with the use of two leaf phenotypes [Yellow area of variegated leaves (YS) and Green area of variegated leaves (GS)] of 'Zebrinus'. Differential metabolites between GS and YS leaf samples was conducted using the metabolomic analysis, with a focus on identifying key metabolites associated with leaf variegation. Furthermore, gene expression profiles of GS and YS leaves were acquired through transcriptome sequencing. With the screening of differentially expressed genes (DEGs), this study also carried out functional annotation and pathway enrichment analysis. Moreover, the expression levels of candidate genes in GS and YS leaves were measured via quantitative real-time polymerase chain reaction (qRT-PCR). In addition, a \"gene-metabolite\" regulatory network was constructed by integrating the metabolomic and transcriptomic data to screen out the key metabolites and core genes responsible for regulating leaf variegation in 'Zebrinus'. Metabolomic analysis identified 4,036 common metabolites in GS and YS samples, with major enrichment in the flavonoid biosynthesis pathway. Secondary classification of this pathway indicated that flavonoids had the highest content. Further comparison of the expression levels of key metabolites revealed that the accumulation patterns of neohesperidin, taxifolin, naringenin, and xanthohumol in YS were all higher than those in GS, with naringenin showing the most significant difference, suggesting that it might be the core metabolite regulating leaf spot formation. According to subsequent transcriptome sequencing, 5,252 DEGs were screened out from the YS and GS samples, which were mainly enriched in flavonoid biosynthesis phenylpropanoid biosynthesis and other pathways. qRT-PCR presented the highest expression level in chalcone synthase ( ). Integration of metabolome and transcriptome demonstrated significant enrichment of differential metabolites and DEGs in the flavonoid biosynthesis pathway. Additionally, correlation network graph analysis suggested the highest correlation of naringenin with . This study identifies the core intrinsic regulatory mechanism underlying leaf variegation in 'Zebrinus' through integrated metabolomic and transcriptomic analysis. has a strong correlation with naringenin, suggesting that the transcriptional regulation of the gene may directly affect the biosynthesis of naringenin. The synergistic effect of the two may be one of the key molecular mechanisms underlying the formation of yellow leaf variegation.

Background In the field of ornamental horticulture, phenotypic mutations, particularly in leaf color, are of great interest due to their potential in developing new plant varieties. The introduction of variegated leaf traits in plants like Heliopsis helianthoides , a perennial herbaceous species with ecological adaptability, provides a rich resource for molecular breeding and research on pigment metabolism and photosynthesis. We aimed to explore the mechanism of leaf variegation of Heliopsis helianthoides (using HY2021F1-0915 variegated mutant named HY, and green-leaf control check named CK in 2020 April, May and June) by analyzing the transcriptome and metabolome. Results Leaf color and physiological parameters were found to be significantly different between HY and CK types. Chlorophyll content of HY was lower than that of CK samples. Combined with the result of Weighted Gene Co-expression Network Analysis (WGCNA), 26 consistently downregulated differentially expressed genes (DEGs) were screened in HY compared to CK subtypes. Among the DEGs, 9 genes were verified to be downregulated in HY than CK by qRT-PCR. The reduction of chlorophyll content in HY might be due to the downregulation of FSD2. Low expression level of PFE2, annotated as ferritin-4, might also contribute to the interveinal chlorosis of HY. Based on metabolome data, differential metabolites (DEMs) between HY and CK samples were significantly enriched on ABC transporters in three months. By integrating DEGs and DEMs, they were enriched on carotenoids pathway. Downregulation of four carotenoid pigments might be one of the reasons for HY’s light color. Conclusion FSD2 and PFE2 (ferritin-4) were identified as key genes which likely contribute to the reduced chlorophyll content and interveinal chlorosis observed in HY. The differential metabolites were significantly enriched in ABC transporters. Carotenoid biosynthesis pathway was highlighted with decreased pigments in HY individuals. These findings not only enhance our understanding of leaf variegation mechanisms but also offer valuable insights for future plant breeding strategies aimed at preserving and enhancing variegated-leaf traits in ornamental plants.

FtsH metalloproteases found in eubacteria, animals, and plants are well-known for their vital role in the maintenance and proteolysis of membrane proteins. Their location is restricted to organelles of endosymbiotic origin, the chloroplasts, and mitochondria. In the model organism Arabidopsis thaliana, there are 17 membrane-bound FtsH proteases containing an AAA+ (ATPase associated with various cellular activities) and a Zn2+ metalloprotease domain. However, in five of those, the zinc-binding motif HEXXH is either mutated (FtsHi1, 2, 4, 5) or completely missing (FtsHi3), rendering these enzymes presumably inactive in proteolysis. Still, homozygous null mutants of the pseudo-proteases FtsHi1, 2, 4, 5 are embryo-lethal. Homozygous ftshi3 or a weak point mutant in FTSHi1 are affected in overall plant growth and development. This review will focus on the findings concerning the FtsHi pseudo-proteases and their involvement in protein import, leading to consequences in embryogenesis, seed growth, chloroplast, and leaf development and oxidative stress management.

Background Leaf variegation is an intriguing phenomenon observed in many plant species. However, questions remain on its mechanisms causing patterns of different colours. In this study, we describe a tomato plant detected in an M 2 population of EMS mutagenised seeds, showing variegated leaves with sectors of dark green (DG), medium green (MG), light green (LG) hues, and white (WH). Cells and tissues of these classes, along with wild-type tomato plants, were studied by light, fluorescence, and transmission electron microscopy. We also measured chlorophyll a/b and carotene and quantified the variegation patterns with a machine-learning image analysis tool. We compared the genomes of pooled plants with wild-type-like and mutant phenotypes in a segregating F 2 population to reveal candidate genes responsible for the variegation. Results A genetic test demonstrated a recessive nuclear mutation caused the variegated phenotype. Cross-sections displayed distinct anatomy of four-leaf phenotypes, suggesting a stepwise mesophyll degradation. DG sectors showed large spongy layers, MG presented intercellular spaces in palisade layers, and LG displayed deformed palisade cells. Electron photomicrographs of those mesophyll cells demonstrated a gradual breakdown of the chloroplasts. Chlorophyll a/b and carotene were proportionally reduced in the sectors with reduced green pigments, whereas white sectors have hardly any of these pigments. The colour segmentation system based on machine-learning image analysis was able to convert leaf variegation patterns into binary images for quantitative measurements. The bulk segregant analysis of pooled wild-type-like and variegated progeny enabled the identification of SNP and InDels via bioinformatic analysis. The mutation mapping bioinformatic pipeline revealed a region with three candidate genes in chromosome 4, of which the FtsH -like protein precursor (LOC100037730) carries an SNP that we consider the causal variegated phenotype mutation. Phylogenetic analysis shows the candidate is evolutionary closest to the Arabidopsis VAR 1. The synonymous mutation created by the SNP generated a miRNA binding site, potentially disrupting the photoprotection mechanism and thylakoid development, resulting in leaf variegation. Conclusion We described the histology, anatomy, physiology, and image analysis of four classes of cell layers and chloroplast degradation in a tomato plant with a variegated phenotype. The genomics and bioinformatics pipeline revealed a VAR 1-related FtsH mutant, the first of its kind in tomato variegation phenotypes. The miRNA binding site of the mutated SNP opens the way to future studies on its epigenetic mechanism underlying the variegation.

The mechanisms underlying leaf variegation in the ornamental Ilex × ‘Solar Flare’ remain poorly understood. To investigate this phenomenon, we conducted a comprehensive characterization of its variegated leaves. Compared to green sectors, yellow sectors exhibited severe chloroplast structural abnormalities, including swollen chloroplasts, damaged thylakoid membranes, and reduced chloroplast numbers. These yellow sectors also showed significantly lower chlorophyll and carotenoid levels, along with a depletion of key chlorophyll precursors—protoporphyrin IX (Proto IX), magnesium protoporphyrin IX (Mg-Proto IX), and protochlorophyllide (Pchlide). Photosynthetic efficiency was significantly impaired. Comparative transcriptome analysis identified 3510 differentially expressed genes (DEGs) between yellow and green sectors. Key disruptions in chlorophyll biosynthesis included upregulated CHLD expression and downregulated CHLH and CHLG expression, leading to impaired chlorophyll synthesis. Additionally, chlorophyll degradation was accelerated by PAO upregulation. Defective chloroplast development in yellow sectors was associated with the downregulation of GLK1, GLK2, and thylakoid membrane-related genes (PsbC, PsbO, PsbR, PsaD, and PsaH). These molecular alterations likely drive the variegated phenotype of I. × ‘Solar Flare’. These observations advance our understanding of the genetic and physiological mechanisms regulating leaf variegation in this cultivar.

Background The ‘Gonggan’ mandarin, an elite local cultivar from Zhaoqing City, Guangdong Province, combines the qualities of mandarin and sweet orange. A leaf-variegated mutant enhances its ornamental and economic value, providing an excellent model for studying chloroplast development and photosynthetic pigment metabolism in citrus. Results We found that, in this variegated mutant, chloroplasts are severely deficient or absent in mesophyll cells. Physiological assessments revealed lower levels of chlorophyll, carotenoids, net photosynthetic rate ( Pn ), and stomatal conductance ( Gs ), alongside significantly higher non-photochemical quenching (NPQ) and the non-photochemical quenching coefficient ( qN ), reflecting increased photoprotective energy dissipation. To uncover the molecular basis of leaf variegation, high-quality genome assemblies and transcriptomes were generated for both the normal and variegated ‘Gonggan’ mandarin, enabling comparative multi-omics analysis. Key genes involved in chloroplast development, such as TOC159 , PDV2 , THA8 , and SIG5 , were downregulated in the variegated leaves. Similarly, structural genes linked to chlorophyll degradation, including CLH2 , SGR , NOL , and NYC1 , exhibited altered expression. Downregulation of transcription factors GLK, GNC, and GNC-LIKE (GNL), known regulators of chloroplast development and chlorophyll biosynthesis, was also observed. Conclusions These findings suggest that disrupted expression of critical genes impacts chloroplast development and pigment metabolism, causing the leaf variegation phenotype. Overall, this study lays a foundation for functional genomics research and potential germplasm improvement of ‘Gonggan’ mandarin, and provides new insights into the mechanisms driving color variation in citrus.

Background Primulina pungentisepala is suitable for use as a potted plant because of its beautiful leaf variegation, which is significantly different in its selfed offspring. However, the mechanism of P. pungentisepala leaf variegation is unclear. In this study, two types of offspring showing the greatest differences were compared in terms of leaf structure, chlorophyll contents, chlorophyll fluorescence parameters and transcriptomes to provide a reference for studying the molecular mechanism of structural leaf variegation. Results Air spaces were found between water storage tissue, and the palisade tissue cells were spherical in the white type. The content of chlorophyll a and total chlorophyll (chlorophyll a + b) was significantly lower in the white type, but there were no significant differences in the content of chlorophyll b, chlorophyll a/b or chlorophyll fluorescence parameters between the white and green types. We performed transcriptomic sequencing to identify differentially expressed genes (DEGs) involved in cell division and differentiation, chlorophyll metabolism and photosynthesis. Among these genes, the expression of the cell division- and differentiation-related leucine-rich repeat receptor-like kinases (LRR-RLKs), xyloglucan endotransglycosylase/hydrolase ( XET/H ), pectinesterase ( PE ), expansin ( EXP ), cellulose synthase-like ( CSL ), VARIEGATED 3 ( VAR3 ), and ZAT10 genes were downregulated in the white type, which might have promoted the development air spaces and variant palisade cells. Chlorophyll biosynthesis-related hydroxymethylbilane synthase ( HEMC ) and the H subunit of magnesium chelatase ( CHLH ) were downregulated, while chlorophyll degradation-related chlorophyllase-2 ( CHL2 ) was upregulated in the white type, which might have led to lower chlorophyll accumulation. Conclusion Leaf variegation in P. pungentisepala was caused by a combination of mechanisms involving structural variegation and low chlorophyll levels. Our research provides significant insights into the molecular mechanisms of structural leaf variegation.

Background Accurate cell cycle progression is essential for plant growth and development. UVI4 ( UV-B-insensitive 4 ) and its homologue OSD1 ( Omission of the Second Division ) function as negative regulators of the anaphase-promoting complex/cyclosome (APC/C) and are critical for cell cycle regulation in plants. In potato, UVI4 and OSD1 have a single homologue, StOSD1/UVI4 , and the role of one copy of this gene in cell cycle regulation is largely unknown. Results We showed that mutation of StOSD1/UVI4 in potato resulted in a shorter plant height and a variegated leaf phenotype characterized by mosaic areas with dark green and light green colours. The mutant plants presented altered chloroplast distribution and decreased fluorescence signal in palisade cells within the light-green sectors, accompanied by a significant reduction in total chlorophyll content. Transcriptome analysis revealed the downregulation of genes associated with chlorophyll biosynthesis in the mutant. Paraffin sectioning revealed increased cell volume in the light green regions. Ploidy analysis via 5S rDNA fluorescence in situ hybridization (FISH) demonstrated that the StOSD1/UVI4 mutation induced endomitosis in the palisade cells in the light green sectors. Further ploidy determination in leaf cells via 26S rDNA and 5S rDNA FISH revealed that the StOSD1/UVI4 mutation led to a replication pattern combining incomplete replication with endomitosis. These findings indicate that the StOSD1/UVI4 mutation impairs chloroplast distribution and function in potato and triggers endomitosis. Additionally, the number of nonglandular trichomes on the leaf epidermis decreased, and the second division at meiosis was skipped in the StOSD1/UVI4 mutant. Conclusion Our findings establish a novel link between endomitosis and chlorophyll accumulation in plants. Additionally, we reveal roles for StOSD1/UVI4 in plant morphology (influencing trichome density) and meiosis (ensuring the second division). Collectively, these findings underscore a new role for StOSD1/UVI4 in regulating mitosis, plant morphology, and leaf development in potato.