Expression Patterns Of Candidate Genes Research Articles

CD4 T cell-secreted IFN-γ in Sjögren's syndrome induces salivary gland epithelial cell ferroptosis

BackgroundSjögren's syndrome (SS) is a chronic autoimmune disease that predominantly affects exocrine glands. Previous studies have demonstrated that upregulated interferon-gamma (IFN-γ) in SS triggers ferroptosis in salivary gland epithelial cells (SGECs), resulting in impaired salivary gland secretion. However, the immune cells responsible for secreting IFN-γ remain unclear. Therefore, this study conducted bioinformatics analysis and molecular validation to identify the origin of IFN-γ in SS salivary gland. MethodsThe ‘limma’ package in R software was utilized to identify differentially expressed genes (DEGs) in the human SS dataset. Subsequently, the identified DEGs were compared with the ferroptosis database and screened through Cytoscape to determine candidate genes. The cellular localization and expression patterns of candidate genes were further confirmed in the salivary gland single-cell RNA sequence (scRNA-seq) data set from healthy control and SS mice. Furthermore, in vitro and in vivo studies were performed to analyze the effect of CD4 T-secreted IFN-γ on SGECs' ferroptosis and functions. ResultsUpregulated TLR4, IFNG, and IL33 were screened as candidates ferroptosis ferroptosis-inducing genes in SS salivary glands. The association of IFNG and IL33 with CD4 T cells was established through immune infiltration analysis. The expression of IFN-γ on CD4 T cells was robustly higher compared with that of IL33 as evidenced by scRNA-seq and immunofluorescence co-localization. Subsequent experiments conducted on candidate genes consistently demonstrated the potent ability of IFN-γ to induce SGECs' ferroptosis and inhibit AQP5 expression. ConclusionsOur findings indicate that CD4 T cell-secreted IFN-γ in SS induces SGECs' ferroptosis and inhibits AQP5 expression.

High-frequency hearing vulnerability associated with the different supporting potential of Hensen's cells: SMART-Seq2 RNA sequencing.

Hearing loss is the third most prevalent physical condition affecting communication, well-being, and healthcare costs. Sensorineural hearing loss often occurs first in the high-frequency region (basal turn), then towards the low-frequency region (apical turn). However, the mechanism is still unclear. Supporting cells play a critical role in the maintenance of normal cochlear function. The function and supporting capacity of these cells may be different from different frequency regions. Hensen's cells are one of the unique supporting cell types characterized by lipid droplets (LDs) in the cytoplasm. Here, we investigated the morphological and gene expression differences of Hensen's cells along the cochlear axis. We observed a gradient change in the morphological characteristics of Hensen's cells along the cochlear tonotopic axis, with larger and more abundant LDs observed in apical Hensen's cells. Smart-seq2 RNA-seq revealed differentially expressed genes (DEGs) between apical and basal Hensen's cells that clustered in several pathways, including unsaturated fatty acid biosynthesis, cholesterol metabolism, and fatty acid catabolism, which are associated with different energy storage capacities and metabolic potential. These findings suggest potential differences in lipid metabolism and oxidative energy supply between apical and basal Hensen's cells, which is consistent with the morphological differences of Hensen's cells. We also found differential expression patterns of candidate genes associated with hereditary hearing loss (HHL), noise-induced hearing loss (NIHL), and age-related hearing loss (ARHL). These findings indicate functional heterogeneity of SCs along the cochlear axis, contribute to our understanding of cochlear physiology and provide molecular basis evidence for future studies of hearing loss.

Expression pattern of candidate genes and their correlation with various metabolites of abscisic acid biosynthetic pathway under drought stress in rice

AbstractDrought hampers global rice production. Abscisic acid (ABA) plays versatile roles under different environmental stresses. While the link between drought and ABA is known, its effect on ABA biosynthesis genes and metabolites is unclear. This study explored the impact of drought on various metabolites, namely beta‐carotene, zeaxanthin, antheraxanthin, violaxanthin, neoxanthin, and candidate genes viz. zeaxanthin epoxidase (ZEP) and 9‐cis epoxycarotenoid dioxygenase (NCED) of ABA biosynthesis pathway in rice cultivars (N22 and IR64) at anthesis {65 DAT (Days after transplanting)} with different stress levels. In stressed plants, zeaxanthin significantly increased (92%), while the concentration of beta‐carotene, antheraxanthin, violaxanthin and neoxanthin decreased as drought stress progressed. The concentration of metabolites in roots was notably lower than in leaves in both genotypes. The ZEP expression was upregulated in roots (8.24‐fold) under drought stress. Among five NCED isoforms, NCED3 showed significant upregulation (7.29‐fold) in leaf and root tissue. NCED1 was significantly downregulated as stress progressed and was negatively correlated with ABA accumulation. NCED2, NCED4 and NCED5 showed no significant change in their expression. Drying and rolling of rice leaves was observed after imparting drought stress. The findings revealed that drought stress significantly influenced the expression of candidate genes and the concentration of metabolites of the ABA biosynthesis pathway. There was a significantly higher accumulation of ABA in N22 leaves (47%) and roots (30%) compared to IR64. The N22, a drought‐tolerant genotype, exhibited significantly higher concentrations of intermediates and demonstrated increased expression of ZEP and NCED3, potentially contributing to its resilience against drought.

Integrated single cell and bulk sequencing analysis identifies tumor reactive CXCR6+ CD8 T cells as a predictor of immune infiltration and immunotherapy outcomes in hepatocellular carcinoma.

Various immune cell types in the tumor microenvironment (TME) of hepatocellular carcinoma (HCC) have been identified as important parameters associated with prognosis and responsiveness to immunotherapy. However, how various factors influence immune cell infiltration remains incompletely understood. Hence, we investigated the single cell multi-omics landscape of immune infiltration in HCC, particularly key gene and cell subsets that influence immune infiltration, thus potentially linking the immunotherapy response and immune cell infiltration. We grouped patients with HCC according to immune cell infiltration scores calculated by single sample gene set enrichment analysis (ssGSEA). Differential expression analysis, functional enrichment, clinical trait association, gene mutation analysis, tumor immune dysfunction and exclusion (TIDE) and prognostic model construction were used to investigate the immune infiltration landscape through multi-omics. Stepwise regression was further used to identify key genes regulating immune infiltration. Single cell analysis was performed to explore expression patterns of candidate genes and investigate associated cellular populations. Correlation analysis, ROC analysis, Immunotherapy cohorts were used to explore and confirm the role of key gene and cellular population in predicting immune infiltration state and immunotherapy response. Immunohistochemistry and multiplexed fluorescence staining were used to further validated our results. Patients with HCC were clustered into high and low immune infiltration groups. Mutations of CTNNB1 and TTN were significantly associated with immune infiltration and altered enrichment of cell populations in the TME. TIDE analysis demonstrated that T cell dysfunction and the T cell exclusion score were elevated in the high and low infiltration groups, respectively. Six risk genes and five risk immune cell types were identified and used to construct risk scores and a nomogram model. CXCR6 and LTA, identified by stepwise regression, were highly associated with immune infiltration. Single cell analysis revealed that LTA was expressed primarily in tumor infiltrating T lymphocytes and partial B lymphocytes, whereas CXCR6 was enriched predominantly in T and NK cells. Notably, CXCR6+ CD8 T cells were characterized as tumor enriched cells that may be potential predictors of high immune infiltration and the immune-checkpoint blockade response, and may serve as therapeutic targets. We constructed a comprehensive single cell and multi-omics landscape of immune infiltration in HCC, and delineated key genes and cellular populations regulating immune infiltration and immunotherapy response, thus providing insights into the mechanisms of immune infiltration and future therapeutic control.

Bioinformatics Identification of ZNFs/LINC00520/miR-181d/BCL2 Axis as a Novel Network in Cisplatin-Resistant Lung Adenocarcinoma Cells

Background: Resistance to cisplatin (DDP) leads to poor prognosis in patients with Lung Adenocarcinoma (LUAD) and limits its clinical application. It has been confirmed that autophagy promotes chemoresistance and, therefore, novel strategies to reverse chemoresistance by regulating autophagy are desperately needed. Methods: The differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) between A549 and A549/DDP cell lines were identified using the limma package in R, after gene expression profiles were obtained from Gene Expression Omnibus (GEO) database. By combining Autophagy-Related Genes (ARGs) from Human Autophagy Database (HADb), the interactions lncRNA-miRNAs and the interactions miRNAs-mRNAs respectively predicted by miRcode and miRDB/Targetscan database, the autophagy-related ceRNA network was constructed. Then, extraction of ceRNA subnetwork and Cox regression analyses were performed. A prognosis-related ceRNA subnetwork was constructed, and the upstream Transcription Factors (TFs) regulating lncRNAs were predicted by the JASPAR database. Finally, the expression patterns of candidate genes were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) experiments. Results: A total of 3179 DEmRNAs, 180 DEmiRNAs, and 160 DElncRNAs were identified, and 35 DEmRNAs were contained in the HADb. Based on the ceRNA hypothesis, we established a ceRNA network, including 10 autophagy-related DEmRNAs, 9 DEmiRNAs, and 14 DElncRNAs. Then, LINC00520, miR-181d, and BCL2 were identified to construct a risk score model, which was confirmed to be a well-predicting prognostic factor. Furthermore, 5 TF ZNF family members were predicted to regulate LINC00520, whereas the RT-PCR results showed that the 5 ZNFs were consistent with the bioinformatics analysis. Finally, a ZNF regulatory LINC00520/miR-181d/BCL2 ceRNA subnetwork was constructed. Conclusions: An ZNFs/LINC00520/miR-181d/BCL2 axis as a novel network in DDP-resistant LUAD has been constructed successfully, which may provide potential therapeutic targets for LUAD.

An integrative approach for identification of smoking-related genes involving bladder cancer.

Tobacco smoking is one of the most important environmental risk factors involving bladder tumorigenesis. However, smoking-related genes in bladder carcinogenesis and corresponding genetic effects on bladder cancer risk remain unclear. Weighted correlation network analysis (WGCNA) underlying transcriptome of bladder cancer tissues was applied to identify smoking-related genes. The logistic regression model was utilized to estimate genetic effects of single nucleotide polymorphisms (SNPs) in smoking-related genes on bladder cancer risk in the Chinese and European populations with a total of 6510 cases and 6569 controls, as well as the interaction with smoking status. Transcriptome of cells and tissues was used to profile the expression pattern of candidate genes and their genetic variants. Our results demonstrated that a total of 24 SNPs in 14 smoking-related genes were associated with the risk of bladder cancer, of which rs9348451 in CDKAL1 exhibited an interaction with smoking status (ORinteraction = 1.38, Pinteraction = 1.08 × 10-2) and tobaccosmoking might combine with CDKAL1 rs9348451 to increase the risk of bladder cancer (Ptrend = 4.27 × 10-4). Moreover, rs9348451 was associated with CDKAL1 expression in bladder cancer, especially in smokers (P < 0.001). Besides, CDKAL1 was upregulated in bladder cancer compared to normal adjacent tissues, as well as upregulated via treatment of cigarette smoke extracts. This study highlights the important role of nurture and nature, as well as their interaction on tumorigenesis, which provides a new way to decipher the etiology of bladder cancer with smoking status.

Transcriptome Analysis of Tryptophan-Induced Resistance against Potato Common Scab.

Potato common scab (CS) is a worldwide soil-borne disease that severely reduces tuber quality and market value. We observed that foliar application of tryptophan (Trp) could induce resistance against CS. However, the mechanism of Trp as an inducer to trigger host immune responses is still unclear. To facilitate dissecting the molecular mechanisms, the transcriptome of foliar application of Trp and water (control, C) was compared under Streptomyces scabies (S) inoculation and uninoculation. Results showed that 4867 differentially expressed genes (DEGs) were identified under S. scabies uninoculation (C-vs-Trp) and 2069 DEGs were identified under S. scabies inoculation (S-vs-S+Trp). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that Trp induced resistance related to the metabolic process, response to stimulus, and biological regulation. As phytohormone metabolic pathways related to inducing resistance, the expression patterns of candidate genes involved in salicylic acid (SA) and jasmonic acid/ethylene (JA/ET) pathways were analyzed using qRT-PCR. Their expression patterns showed that the systemic acquired resistance (SAR) and induced systemic resistance (ISR) pathways could be co-induced by Trp under S. scabies uninoculation. However, the SAR pathway was induced by Trp under S. scabies inoculation. This study will provide insights into Trp-induced resistance mechanisms of potato for controlling CS, and extend the application methods of Trp as a plant resistance inducer in a way that is cheap, safe, and environmentally friendly.

Genetic mapping of sexually dimorphic volatile and non-volatile floral secondary chemistry of a dioecious willow.

Secondary chemistry often differs between sexes in dioecious plant species, a pattern attributed to its possible role in the evolution and/or maintenance of dioecy. We used GC-MS to measure floral volatiles emitted from, and LC-MS to quantitate non-volatile secondary compounds contained in, female and male Salix purpurea willow catkins from an F2 family. Using the abundance of these chemicals, we then performed quantitative trait locus (QTL) mapping to locate them on the genome, identified biosynthetic candidate genes in the QTL intervals, and examined expression patterns of candidate genes using RNA-seq. Male flowers emitted more total terpenoids than females, but females produced more benzenoids. Male tissue contained greater amounts of phenolic glycosides, but females had more chalcones and flavonoids. A flavonoid pigment and a spermidine derivative were found only in males. Male catkins were almost twice the mass of females. Forty-two QTL were mapped for 25 chemical traits and catkin mass across 16 of the 19 S. purpurea chromosomes. Several candidate genes were identified, including a chalcone isomerase associated with seven compounds. A better understanding of the genetic basis of the sexually dimorphic chemistry of a dioecious species may shed light on how chemically mediated ecological interactions may have helped in the evolution and maintenance of dioecy.

Rare Variants in Novel Candidate Genes Associated With Nonsyndromic Patent Ductus Arteriosus Identified With Whole-Exome Sequencing.

Background: Patent ductus arteriosus (PDA) is one of the most common congenital heart defects causing pulmonary hypertension, infective endocarditis, and even death. The important role of genetics in determining spontaneous ductal closure has been well-established. However, as many of the identified variants are rare, thorough identification of the associated genetic factors is necessary to further explore the genetic etiology of PDA. Methods: We performed whole-exome sequencing (WES) on 39 isolated nonsyndromic PDA patients and 100 healthy controls. Rare variants and novel genes were identified through bioinformatic filtering strategies. The expression patterns of candidate genes were explored in human embryo heart samples. Results: Eighteen rare damaging variants of six novel PDA-associated genes (SOX8, NES, CDH2, ANK3, EIF4G1, and HIPK1) were newly identified, which were highly expressed in human embryo hearts. Conclusions: WES is an efficient diagnostic tool for exploring the genetic pathogenesis of PDA. These findings contribute new insights into the molecular basis of PDA and may inform further studies on genetic risk factors for congenital heart defects.

Detection of a major QTL and development of KASP markers for seed weight by combining QTL-seq, QTL-mapping and RNA-seq in peanut.

Combining QTL-seq, QTL-mapping and RNA-seq identified a major QTL and candidate genes, which contributed to the development of KASP markers and understanding of molecularmechanisms associated with seed weight in peanut. Seed weight, as an important component of seed yield, is a significant target of peanut breeding. However, relatively little is known about the quantitative trait loci (QTLs) and candidate genes associated with seed weight in peanut. In this study, three major QTLs on chromosomes A05, B02, and B06 were determined by applying the QTL-seq approach in a recombinant inbred line (RIL) population. Based on conventional QTL-mapping, these three QTL regions were successfully narrowed down through newly developed single nucleotide polymorphism (SNP) and simple sequence repeat markers. Among these three QTL regions, qSWB06.3 exhibited stable expression, contributing mainly to phenotypic variance across environments. Furthermore, differentially expressed genes (DEGs) were identified at the three seed developmental stages between the two parents of the RIL population. It was found that the DEGs were widely distributed in the ubiquitin-proteasome pathway, the serine/threonine-protein pathway, signal transduction of hormones and transcription factors. Notably, DEGs at the early stage were mostly involved in regulating cell division, whereas DEGs at the middle and late stages were primarily involved in cell expansion during seed development. The expression patterns of candidate genes related to seed weight in qSWB06.3 were investigated using quantitative real-time PCR. In addition, the allelic diversity of qSWB06.3 was investigated in peanut germplasm accessions. The marker Ah011475 has higher efficiency for discriminating accessions with different seed weights, and it would be useful as a diagnostic marker in marker-assisted breeding. This study provided insights into the genetic and molecularmechanisms of seed weight in peanut.

Differentially Expressed Genes Related to Flowering Transition between Once- and Continuous-Flowering Roses.

Roses are the most important cut flower crops and widely used woody ornamental plants in gardens throughout the world, and they are model plants for studying the continuous-flowering trait of woody plants. To analyze the molecular regulation mechanism of continuous flowering, comparative transcriptome data of once- and continuous-flowering roses in our previous study were used to conduct weighted gene co-expression network analysis (WGCNA) to obtain the candidate genes related to flowering transitions. The expression patterns of candidate genes at different developmental stages between Rosa chinensis “Old Blush” (continuous-flowering cultivar) and R. “Huan Die” (once-flowering cultivar) were investigated, and the relationship of the key gene with the endogenous hormone was analyzed. The results showed that the expression trends of VIN3-LIKE 1 (VIL1), FRIGIDA- LIKE 3 (FRI3), APETALA 2- LIKE (AP2-like) and CONSTANS-LIKE 2 (CO-like 2) genes were significantly different between “Old Blush” and “Huan Die”, and the expression trends of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and CO-like 2 were consistent in the flowering transition of “Old Blush” under different environments. The changes in cytokinin and gibberellic acid (GA3) content were different in the two rose cultivars. The overall change trend of the abscisic acid and GA3 in the flowering transition of “Old Blush” under different environments was consistent. The promoter sequence of CO-like 2 contained a P-box element associated with gibberellin response, as well as binding sites for transcription factors. In a word, we found CO-like 2 associated with continuous flowering and some factors that may synergistically regulate continuous flowering. The results provided a reference for elucidating the molecular regulatory mechanisms of continuous-flowering traits in roses.

Characterization of embryo and protocorm development of Paphiopedilum spicerianum

Paphiopedilum spicerianum (P. spicerianum) is a rare orchid species with high ornamental value. Asymbiotic germination is the most efficient propagation method for conservation and commercial purposes because clonal propagation is very difficult and the separation of native species of Paphiopedilum through aseptic seeding is uncommon owing to their conservatism. However, a high protocorm developmental arresting rate during the asymbiotic germination is the major obstacle for seedling establishment. The fundamental understanding of embryo and protocorm developmental mechanisms will guide the development of an effective propagation method. The morphological and physiological characterization of the key developmental process of embryos and protocorms shows that the mature seeds of P. spicerianum consist of a spherical embryo without an endosperm. Seed coats become heavily lignified once the embryo is mature. Embryo cell size is relatively uniform, and significant structure polarity and cell size gradients occur at the early protocorm stage. The high level of auxin and cytokinin accumulation at the early stage of embryo development and protocorm stage may help to facilitate cell division. The transcriptome profiles of protocorms at three different developmental stages were compared to explore the regulatory mechanism of protocorm development. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that differentially expressed genes were implicated in secondary metabolite metabolism, plant hormone signal transduction and photosynthesis. The temporal expression patterns of candidate genes related to embryo and shoot development were analyzed to reveal their roles in protocorm development: in the early stage of protocorm development, embryonic development related genes such as SERKs and BBM1 were active, while in the late stage of protocorm, shoot apical meristem related genes such as WOX8, CLAVATA2, CUC2, and SCR were active.

Transcriptome Analysis of Flower Development and Mining of Genes Related to Flowering Time in Tomato (Solanum lycopersicum).

Flowering is a morphogenetic process in which angiosperms shift from vegetative growth to reproductive growth. Flowering time has a strong influence on fruit growth, which is closely related to productivity. Therefore, research on crop flowering time is particularly important. To better understand the flowering period of the tomato, we performed transcriptome sequencing of early flower buds and flowers during the extension period in the later-flowering “Moneymaker” material and the earlier-flowering “20965” homozygous inbred line, and we analyzed the obtained data. At least 43.92 million clean reads were obtained from 12 datasets, and the similarity with the tomato internal reference genome was 92.86–94.57%. Based on gene expression and background annotations, 49 candidate genes related to flowering time and flower development were initially screened, among which the greatest number belong to the photoperiod pathway. According to the expression pattern of candidate genes, the cause of early flowering of “20965” is predicted. The modes of action of the differentially expressed genes were classified, and the results show that they are closely related to hormone regulation and participated in a variety of life activities in crops. The candidate genes we screened and the analysis of their expression patterns provide a basis for future functional verification, helping to explore the molecular mechanism of tomato flowering time more comprehensively.

Maternal Oxycodone Treatment Results in Neurobehavioral Disruptions in Mice Offspring.

Opioid drugs are increasingly being prescribed to pregnant women. Such compounds can also bind and activate opioid receptors in the fetal brain, which could lead to long-term brain and behavioral disruptions. We hypothesized that maternal treatment with oxycodone (OXY), the primary opioid at the center of the current crisis, leads to later neurobehavioral disorders and gene expression changes in the hypothalamus and hippocampus of resulting offspring. Female mice were treated daily with 5 mg OXY/kg or saline solution (control; CTL) for two weeks before breeding and then throughout gestation. Male and female offspring from both groups were tested with a battery of behavioral and metabolic tests to measure cognition, exploratory-like, anxiety-like, voluntary physical activity, and socio-communication behaviors. qPCR analyses were performed for candidate gene expression patterns in the hypothalamus and hippocampus of OXY and CTL derived offspring. Developmental exposure to OXY caused socio-communication changes that persisted from weaning through adulthood. Such offspring also showed cognitive impairments, reduced voluntary physical activity, and weighed more than CTL counterparts. In the hippocampus, prenatal exposure to OXY caused sex-dependent differences in expression of genes encoding opioid receptors and those involved in serotonin signaling. OXY exposure induced changes in neuropeptide hormone expression and the epigenetic modulator, Dnmt3a, in the hypothalamus, which could result in epigenetic changes in this brain region. The findings suggest cause for concern that consumption of OXY by pregnant mothers may result in permanent neurobehavioral changes in their offspring. Further work is needed to determine the potential underpinning epigenetic mechanisms.

Temporal candidate gene expression patterns in the sow placenta during early gestation and the effect of maternal L-arginine supplementation

Temporal candidate gene expression patterns in the sow placenta during early gestation and the effect of maternal L-arginine supplementation

Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.).

Transcriptome analysis of maize embryogenic callus and somatic embryos reveals associated genes reprogramming, hormone signaling pathways and transcriptional regulation involved in somatic embryogenesis in maize. Somatic embryos are widely utilized in propagation and genetic engineering of crop plants. In our laboratory, an elite maize inbred line Y423 that could generate intact somatic embryos was obtained and applied to genetic transformation. To enhance our understanding of regulatory mechanisms during maize somatic embryogenesis, we used RNA-based sequencing (RNA-seq) to characterize the transcriptome of immature embryo (IE), embryogenic callus (EC) and somatic embryo (SE) from maize inbred line Y423. The number of differentially expressed genes (DEGs) in three pairwise comparisons (IE-vs-EC, IE-vs-SE and EC-vs-SE) was 5767, 7084 and 1065, respectively. The expression patterns of DEGs were separated into eight major clusters. Somatic embryogenesis associated genes were mainly grouped into cluster A or B with an expression trend toward up-regulation during dedifferentiation. GO annotation and KEGG pathway analysis revealed that DEGs were implicated in plant hormone signal transduction, stress response and metabolic process. Among the differentially expressed transcription factors, the most frequently represented families were associated with the common stress response or related to cell differentiation, embryogenic patterning and embryonic maturation processes. Genes include hormone response/transduction and stress response, as well as several transcription factors were discussed in this study, which may be potential candidates for further analyses regarding their roles in somatic embryogenesis. Furthermore, the temporal expression patterns of candidate genes were analyzed to reveal their roles in somatic embryogenesis. This transcriptomic data provide insights into future functional studies, which will facilitate further dissections of the molecular mechanisms that control maize somatic embryogenesis.

Methylation-sensitive amplification polymorphism analysis reveals the DNA methylation dynamics during capitulum development in Chrysanthemum lavandulifolium

Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino is a diploid plant belonging to the Asteraceae family, with typical capitula composed of female ray florets and bisexual disc florets. The differentiation and development of these two types of florets have long been important research focuses; however, the potential epigenetic mechanisms governing these processes have not been elucidated. In the present study, methylation-sensitive amplification polymorphism method was used to trace the dynamic changes of DNA methylation during capitulum development in C. lavandulifolium. DNA methylation patterns and levels were detected in the whole capitula during seven developmental stages, and the obtained results revealed that DNA demethylation was dominant during this process. In addition, DNA methylation patterns and levels showed significant differences between ray and disc florets. Moreover, the expression patterns of candidate genes potentially involved in the development processes of two types of florets were analyzed by real-time quantitative reverse transcription polymerase chain reaction, and correlation analysis indicated that the expression levels of ClPI, ClAG2, ClSEP1, ClCYC2c, ClCYC2d, and ClCYC2e were highly correlated with DNA methylation levels. These results indicate that DNA methylation may be involved in the differentiation and development of ray and disc florets. This study provides epigenetic insights into the capitulum development in C. lavandulifolium.

Transcriptome analysis deciphers the mechanisms of exogenous nitric oxide action on the response of melon leaves to chilling stress

Chilling stress is a major abiotic factor that limits the growth and productivity of melon (Cucumis melo L.). The application of nitric oxide (NO) can enhance plant tolerance to chilling stress; however, the underlying molecular mechanisms for this process remain poorly understood. In this study, RNA sequencing was performed on melon seedlings exposed to control conditions, chilling stress, or chilling stress in the presence of NO donor sodium nitroprusside (SNP), to identify NO-mediated transcript changes in response to chilling stress. The results identified 488, 1 012, and 1 589 differentially expressed genes (DEGs) between plants in optimum conditions (CK) and chilling stress (CS) groups, plants in the CS and chilling stress + SNP (CN) groups, and those in CK and CN groups, respectively. Through gene ontology (GO) database and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses, the DEGs were classified as predominantly involved in saccharide metabolism, biosynthesis of other secondary metabolites, lipid metabolism, amino-acid metabolism, and signal transduction pathways. In addition, 39 genes related to sugar metabolism including those encoding UDP-glucuronate-4-epimerase, &#946;-glucosidase, glucuronosyltransferase, &#945;-1,4-galacturonosyl transferase, and hexokinase, were upregulated in the CK vs. CS comparison, and genes encoding fructose-bisphosphate aldolase and glucan-endo-1,3-&#946;-glucosidase were upregulated in the CS vs. CN, and CK vs. CN comparisons. A gene encoding an EREBP-like factor was upregulated in the CK vs. CS, CS vs. CN, and CK vs. CN comparisons. The expression profiles of 10 selected genes were analyzed using real-time quantitative PCR, and the candidate gene expression patterns were consistent with the DEG classification from RNA-seq. Overall, the data provide insight into the transcriptional regulation by exogenous NO in the response of melon seedlings to chilling stress. The data from this study are relevant for further research on the molecular mechanisms that underlie chilling resistance in melon plants.

PbGA20ox2 Regulates Fruit Set and Induces Parthenocarpy by Enhancing GA4 Content.

Fruit set and development occur following successful fertilization. Parthenocarpy, a valuable trait in some self-incompatible species, produces seedless fruit without fertilization. Gibberellin (GA) is a crucial hormone in fruit-set regulation and development. While investigating the development of parthenocarpy in pear (Pyrus bretschneideri Rehd.), we determined that GA 20-oxidases (GA20ox) may play key roles in seedless pear fruit development. Sequence analysis revealed three PbGA20ox genes: PbGA20ox1, PbGA20ox2, and PbGA20ox3. We analyzed the expression patterns of candidate genes and found that PbGA20ox2 levels significantly changed in pollinated fruits. Tissue-specific expression assays revealed that PbGA20ox2 is highly expressed in young fruit and leaves. Subcellular localization assays showed it was located in the cytoplasm, nucleus, and plasma membrane. Overexpressed PbGA20ox2 tomato plants were taller and had longer hypocotyls and internodes, and the emasculated flowers produced parthenocarpic fruit. In pear, the transient overexpression of PbGA20ox2 promoted fruit development and delayed the drop of nonpollinated fruit. Furthermore, the fruit of PbGA20ox2-overexpressing tomato and transient PbGA20ox2-overexpressing pear had increased GA4 (but not GA3 and GA1) contents. This result provided evidence that PbGA20ox2 was necessary for GA4-dependent pear fruit development. Our study revealed that PbGA20ox2 altered the GA biosynthetic pathway and enhanced GA4 synthesis, thereby promoting fruit set and parthenocarpic fruit development.

Genetic mapping of Koi herpesvirus resistance (KHVR) in Mirror carp (Cyprinus carpio) revealed genes and molecular mechanisms of disease resistance

Koi herpesvirus is a double-stranded DNA virus that causes fatal disease and mortality in koi and common carp (Cyprinus carpio) of all ages. Koi herpesvirus disease has been added to the list of notifiable diseases of the World Organisation for Animal Health. The genetic basis of fish resistance to Koi herpesvirus remains little understood, and thus, it cannot be used in genetic breeding programs to produce high-resistance carp strains. Dissection of the molecular mechanism of resistance could help prevent or reduce losses due to Koi herpesvirus disease. Common carp is a widely distributed species cultured all around the world. Its allotetraploidy and high economic and environmental value have attracted a great deal of interest in its genetics and genomics. Here, we use both QTL mapping and GWAS in Mirror carp subjected to Koi herpesvirus infection to detect potential loci and genes related to resistance to this virus. Many immune-related genes were identified around the significant QTLs or SNPs, including tnfa, hif1a, galectin-8, rootletin, and palladin. GO and KEGG analyses were performed based on the union of the candidates. Of particular interest were the Herpes simplex infection pathway and mTOR signaling pathway, which play potential roles in the immune response. Using publicly available transcriptome data from Koi herpesvirus infected carp, the expression patterns of candidate genes were obtained, and the results indicated potential roles of homoeolog functional divergence in immune response in the allotetraploid common carp. Overall, our study of the genetic architecture of carp Koi herpesvirus resistance provides many valuable candidate genes, which could be considered in the marker-assisted selection of common carp strains with high resistance to Koi herpesvirus.