scholarly journals Variation in Cytosine Methylation among Pecan Cultivars at Different Developmental Stages

2018 ◽  
Vol 143 (3) ◽  
pp. 173-183 ◽  
Author(s):  
Zhuang-Zhuang Liu ◽  
Tao Chen ◽  
Fang-Ren Peng ◽  
You-Wang Liang ◽  
Peng-Peng Tan ◽  
...  
Keyword(s):  
Cytosine Methylation ◽  
Developmental Stages ◽  
Agronomic Traits ◽  
Methylation Status ◽  
Fruit Size ◽  
Phenotypic Traits ◽  
Dominant Type ◽  
Principal Coordinates ◽  
Variance Contribution ◽  
New Perspective

Cytosine methylation plays important roles in regulating gene expression and modulating agronomic traits. In this study, the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique was used to study variation in cytosine methylation among seven pecan (Carya illinoinensis) cultivars at four developmental stages. In addition, phenotypic variations in the leaves of these seven cultivars were investigated. Using eight primer sets, 22,796 bands and 950 sites were detected in the pecan cultivars at four stages. Variation in cytosine methylation was observed among the pecan cultivars, with total methylation levels ranging from 51.18% to 56.58% and polymorphism rates of 82.29%, 81.73%, 78.64%, and 79.09% being recorded at the four stages. Sufficiently accompanying the polymorphism data, significant differences in phenotypic traits were also observed among the pecan cultivars, suggesting that cytosine methylation may be an important factor underlying phenotypic variation. Hypermethylation was the dominant type of methylation among the four types observed, and full methylation occurred at higher levels than did hemimethylation in the pecan genomes. Cluster analysis and principal coordinate analysis (PCoA) identified Dice coefficients ranging from 0.698 to 0.778, with an average coefficient of 0.735, and the variance contribution rates of the previous three principal coordinates were 19.6%, 19.0%, and 18.2%, respectively. Among the seven pecan cultivars, four groups were clearly classified based on a Dice coefficient of 0.75 and the previous three principal coordinates. Tracing dynamic changes in methylation status across stages revealed that methylation patterns changed at a larger proportion of CCGG sites from the 30% of final fruit-size (30%-FFS) stage to the 70%-FFS stage, with general decreases in the total methylation level, the rate of polymorphism, and specific sites being observed in each cultivar. These results demonstrated that the F-MSAP technique is a powerful tool for quantitatively detecting cytosine methylation in pecan genomes and provide a new perspective for studying many important life processes in pecan.

scholarly journals Genetic Diversity among Lathyrus ssp. Based on Agronomic Traits and Molecular Markers

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1182 ◽  
Author(s):  
Meriem Miyassa Aci ◽  
Antonio Lupini ◽  
Giuseppe Badagliacca ◽  
Antonio Mauceri ◽  
Emilio Lo Presti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Protein Content ◽  
Structure Analysis ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

Grasspea (Lathyrus sativus L.) and its relatives are considered resilient legumes due to their high ability to cope with different stresses. In this study, the genetic diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was assessed by agronomic traits and molecular markers (Simple Sequence Repeat-SSR) in order to detect accessions useful for future breeding strategies. Phenotypic traits showed a high significant variation in which 1000 seed weight (1000 SW) and protein content appeared the most discriminant, as observed by principal component analysis (PCA). SSR analysis was able to detect forty-eight different alleles with an average of 9.6 allele per locus, and a Polymorphic Information Content (PIC) and a gene diversity of 0.745 and 0.784, respectively. Cluster analysis based on agronomic traits as well as molecular data grouped accessions by species but not by geographical origin. This result was confirmed by Principal Coordinates Analysis (PCoA) and Structure Analysis as well. Moreover, genetic structure analysis revealed a high genetic differentiation between L. ochrus and the other species. Analysis of MOlecular Variance (AMOVA) displayed a greater genetic diversity within species (77%) than among them (23%). Finally, a significant positive correlation was observed between agronomic and genetic distances (Mantel’s test). In conclusion, the variability detected within accessions in each species and the differences among species may be useful to plan next breeding programs, focusing on biomass production as well as protein content.

scholarly journals Arabidopsis Displays Centromeric DNA Hypomethylation and Cytological Alterations of Heterochromatin Upon Attack by Pseudomonas syringae

2006 ◽  
Vol 19 (6) ◽  
pp. 577-587 ◽  
Author(s):  
Valeria Pavet ◽  
Cristián Quintero ◽  
Nicolás M. Cecchini ◽  
Alberto L. Rosa ◽  
María E. Alvarez
Keyword(s):  
Pseudomonas Syringae ◽  
High Performance ◽  
Cytosine Methylation ◽  
Methylation Status ◽  
Nuclear Genome ◽  
Microbial Pathogens ◽  
Polymorphism Analysis ◽  
Dna Hypomethylation ◽  
Plastic Components ◽  
Cytological Alterations

Plant tissues display major alterations upon the perception of microbial pathogens. Changes of cytoplasmic and apo-plastic components that sense and transduce plant defenses have been extensively characterized. In contrast, less information is available about modifications affecting the plant nuclear genome under these circumstances. Here, we investigated whether the Arabidopsis thaliana DNA methylation status is altered in tissues responding to the attack of Pseudomonas syringae pv. tomato DC3000. We applied amplified fragment length polymorphism analysis to monitor cytosine methylation at anonymous 5′-CCGG-3′ and 5′-GATC-3′ sites in naïve and infected samples. Plant genomic fragments reducing methylation upon infection, including peri/centromeric repeats such as the 180-bp unit, Athila retrotansposon, and a portion of the nuclear insertion of mitochondrial DNA, were isolated and characterized. P. syringae pv. tomato-induced hypomethylation was detected by high-performance liquid chromatography assays and at the molecular level it did not seem to equally affect all 5-methyl cytosine (5-mC) residues. Nuclei from challenged tissues displayed structural chromatin alterations, including loosening of chromocenters, which also were stimulated by avirulent P. syringae pv. tomato, but not by the P. syringae pv. tomato hrpL¯ mutant. Finally, P. syringae pv. tomato-induced hypomethylation was found to occur in the absence of DNA replication, suggesting that it involves an active demethylation mechanism. All these responses occurred at 1 day postinfection, largely preceding massive plant cell death generated by pathogen attack.

scholarly journals Genetic control of agronomic traits in an oat population of recombinant lines

2010 ◽  
Vol 10 (4) ◽  
pp. 305-311 ◽  
Author(s):  
Itamar Cristiano Nava ◽  
Ismael Tiago de Lima Duarte ◽  
Marcelo Teixeira Pacheco ◽  
Luiz Carlos Federizzi
Keyword(s):  
Grain Yield ◽  
Genetic Control ◽  
Plant Height ◽  
Agronomic Traits ◽  
Test Weight ◽  
Phenotypic Traits ◽  
Phenotypic Data ◽  
Plant Growth Habit ◽  
Vegetative Cycle ◽  
Efficiency Of Selection

Understanding the genetic control of phenotypic traits is essential to increase the efficiency of selection for adapted, high-yielding genotypes. The purpose of this study was to determine the genetic control of nine traits of hexaploid oat. Phenotypic data were collected from a population of 162 recombinant lines derived from the cross 'UFRGS17 x UFRGS 930598-6'. For the traits plant growth habit, hairs on leaf edges and panicle type, monogenic genetic control was observed. A quantitative and/or polygenic genetic control was stated for the traits panicle weight, panicle length, vegetative cycle, plant height, test weight and grain yield. High heritability was estimated for the traits vegetative cycle (h² = 0.89) and plant height (h² = 0.79), while moderate heritability was determined for test weight (h² = 0.51) and grain yield (h² = 0.48).

scholarly journals DNA Cytosine-Demethylating Agent 5-Aza-2'-Deoxycytidine Targets Leukemia Cells through Reducing DNA N6-Methyladenine

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2513-2513
Author(s):  
Xiaochang Liu ◽  
Jiuxia Pang ◽  
Christopher Seiler ◽  
Ryan Kempen ◽  
Hao Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Proliferation ◽  
Mayo Clinic ◽  
Cell Apoptosis ◽  
Genomic Dna ◽  
Cytosine Methylation ◽  
Methylation Status ◽  
Cell Counting ◽  
Leukemia Cells ◽  
Dna Cytosine Methylation

Introduction: It is known that overexpression of DNA methyltransferases (e.g., DNMT1) is frequent and changes of DNA cytosine methylation (5mC) are a constant feature of cancers. DNA methylation inhibitors, such as 5-aza-2'-deoxycytidine (Dec), have been in clinics for patients with leukemia. It is classically believed that promoter hypomethylation coupled by reexpression of epigenetically-suppressed tumor suppressors is a core mechanism behind Dec-impaired leukemia cell growth. However, the fact that global DNA methylation profiling barely predicts Dec-response suggests a demethylation-independent mechanism of Dec-induced cell death. N6-methyladenine (m6A) has been identified recently as an abundant DNA modification in eukaryotes (Wu, Nature 2016;532:329). Importantly, m6A is extensively present in the human genome, and m6A abundance is associated with tumorigenesis (Xie, Cell 2018;71:306). Furthermore, the DNA m6A is dynamically modulated by the methyltransferases (i.e., METTL3, N6AMT1) and demethylases (i.e., ALKBH1), and changes in m6A predict gene expression (Wu, Nature 2016;532:329). Given a potential crosstalk between m6A and distinct epigenetic mechanisms (Yao, Nat. Commun 2017;8:1122), we hypothesized that the anticancer actions of Dec may partially result from changes in DNA m6A in leukemia cells. Methods: Protein expression of target genes was assessed by Western blotting. The levels of DNA cytosine methylation (5mC) and N6-methyladenine (m6A) were measured by dotblotting or liquid chromatography-mass spectrometry (LC-MS/MS). The cell viability and apoptosis were determined by the Cell Counting Kit 8 (CCK8) assays as well as the Annexin V/Propidium Iodide staining and flow cytometry. The peripheral blood mononuclear cells (PBMCs) of leukemia patients from Mayo Clinic were prepared by Ficoll-Hypaque gradient centrifugation. Results: To test our hypothesis, leukemia cells, Kasumi-1, MV4-11, K562 and KU812, were exposed to 2 µM Dec, a clinical achievable concentration, for 72 hours. As expected, Dec treatment led to a downregulation of DNMT1 and DNMT3a, a reduction of 5mC levels by dotblotting using anti-5mC antibody, a blockage of cell proliferation and a promotion of cell apoptosis. When genomic DNA was subjected to dotblotting using anti-m6A antibody, the results revealed a marked decrease of DNA m6A levels in all Dec-treated cells. Then genomic DNA from K562 and MV4-11 cells was enzymatically digested to 2'-deoxynucleosides. dA was quantified by HPLC-UV, while the amount of m6A was measured by isotope dilution HPLC-ESI-MS/MS using 15N labeled internal standard. The standard curves were generated using pure standards, from which the m6A/A ratio was calculated. In agreement with dotblotting results, Dec treatment significantly decreased DNA m6A abundance in both cell lines. Mechanistically, exposure to Dec led to a consistent increase of demethylase fat mass and obesity-associated protein (FTO), but not METTL3 nor ALKBH1 and ALKBH5. Further, knockdown of FTO increased DNA m6A, which was further confirmed by treatment with FTO inhibitors rhein and meclofenamic acid (MA). These data indicate that FTO may be responsible for Dec-induced m6A changes in leukemia cells. To investigate the clinical implications of DNA m6A, we obtained PBMCs from AML patients (n = 10), who received Dec therapy (20 mg/m2 daily for 5 days every 4 weeks) in Mayo Clinic. These PBMCs were further cultured for 48 hours, frozen and stored in 100% ethanol before DNA extraction. The results from dotblotting using anti-5mC or anti-m6A showed that a trend of decrease in both m6A and 5mC abundance is observed, and the pattern of changes in m6A and 5mC displays a positive correlation. Finally, exposure of leukemia cells to the combination of Dec (2 µM) with FTO inhibitor MA (50 µM) induced more cell apoptosis and greater inhibition on cell proliferation as compared to single agent in vitro, supporting FTO inhibitors as new therapeutic agents in leukemia. Conclusion: Our studies suggest that the FTO-DNA m6A axis may partially mediate the therapeutic outcomes of Dec in leukemia. Our findings provide a new mechanistic paradigm for the anticancer activities of Dec, and define the m6A methylation status in leukemia cells as a new pharmacodynamic marker for their response to Dec-based therapy, pointing to a novel treatment strategy for incorporating m6A modulators to enhance the therapeutic index of Dec. Disclosures Al-Kali: Astex Pharmaceuticals, Inc.: Research Funding.

Genetic diversity among Italian melon inodorus (Cucumis melo L.) germplasm revealed by ISSR analysis and agronomic traits

2011 ◽  
Vol 9 (2) ◽  
pp. 214-217 ◽  
Author(s):  
S. Sestili ◽  
A. Giardini ◽  
N. Ficcadenti
Keyword(s):  
Agronomic Traits ◽  
Genetic Relationships ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Phenotypic Traits ◽  
Phenotypic Data ◽  
Morphological And Molecular Data ◽  
And Cluster Analysis ◽  
Almost All ◽  
Issr Primers

The genetic relationships among 13 melon inodorus populations that were collected in southern Italy were assessed using 100 inter-simple-sequence repeat (ISSR) primers and 15 morphological traits. The dihaploid line Nad-1 and the cultivar Charentais-T, both of which belong to the botanical variety cantalupensis, were used as reference accessions in the molecular analysis. A total of 358 polymorphic bands were obtained from 39 of the 100 ISSR primers used, and 15 phenotypic traits were scored and used for genetic-similarity calculations and cluster analysis. The resulting dendrograms based on the ISSR and phenotypic data allowed almost all of the melon genotypes to be distinguished on the basis of the skin colour of the fruits. Mantel's test revealed a good correlation between the morphological and molecular data in their ability to detect genetic relationships among melon ecotypes (r = 0.50, P = 0.99). The data obtained confirm the effectiveness of this approach, and open new perspectives to reveal possible molecular associations with the phenotypic traits analysed.

Genomic DNA methylation analysis revealed that BLNK is a key potential gene in the regulation of autophagy-related thyroid cancer progression

Genome ◽  
2021 ◽  
Author(s):  
Shengchi Zhang ◽  
Yongzhe Zheng ◽  
Guimin Zhang ◽  
Peng Lin ◽  
Wei Wang
Keyword(s):  
Dna Methylation ◽  
Thyroid Cancer ◽  
Cancer Progression ◽  
Protein Interactions ◽  
Methylation Status ◽  
Expression Change ◽  
Prognostic Analysis ◽  
Key Genes ◽  
New Perspective ◽  
The Relationship

The purpose of this study was to explore the relationship between autophagy and DNA methylation, and to identify key genes for autophagy-regulated thyroid cancer progression. We divided patients with thyroid cancer into high-autophagy score (AS) group and low-AS group based on their AS values. The results found that AS was associated with the distant metastasis of thyroid cancer, and adversely affected prognosis. Then, we screened 359 differently expressed genes (DEGs) with DNA methylation status consistent with gene expression change. Functional classification analysis demonstrated that the 359 DEGs consistent with DNA methylation status were significantly involved in adhesion, migration and differentiation of immune cells. To further screen the key genes in the autophagy-related thyroid cancer progression, we constructed a protein-protein interactions (PPI) network and performed prognostic analysis. B cell linker (BLNK) was identified as the key potential gene affecting autophagy-related thyroid cancer progression. Finally, we verified that BLNK promoted the proliferation of thyroid cancer cells, and BLNK expression was regulated by DNA methylation. Our research provides a new perspective for exploring the relationship between autophagy and DNA methylation during the progression of thyroid cancer, and provides a new target for the treatment of metastatic thyroid cancer.

scholarly journals Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to WaterStressed Environments

Agronomy ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 487 ◽  
Author(s):  
Acuña ◽  
Rivas ◽  
Brambilla ◽  
Cerrillo ◽  
Frusso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Stress Resistance ◽  
Prunus Persica ◽  
Agronomic Traits ◽  
Phenotypic Traits ◽  
Flesh Color ◽  
Japanese Plum ◽  
Prunus Salicina

The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

scholarly journals Safeguarding and using global banana diversity: a holistic approach

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Ines Van den houwe ◽  
Rachel Chase ◽  
Julie Sardos ◽  
Max Ruas ◽  
Els Kempenaers ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Holistic Approach ◽  
Global Strategy ◽  
Ex Situ ◽  
Phenotypic Traits ◽  
Research Activities ◽  
Genebank Management

AbstractThe CGIAR genebank International Musa Germplasm Transit Centre (ITC) currently holds 1617 banana accessions from 38 countries as an in vitro collection, backed-up by a cryopreserved collection to safeguard global Musa diversity in perpetuity. The ITC also serves as a vital safety backup and transit centre for national banana genebanks and ensures that germplasm is clean of pests and diseases and freely available under the International Treaty on Plant Genetic Resources for Food and Agriculture. In more than 35 years of activity, the ITC has distributed over 18,000 banana accession samples to researchers and farmers in 113 countries. Ex situ conservation of vegetatively-propagated crops such as banana poses very particular challenges. Maintaining the ITC genebank is labor intense and costly. Efficiencies are sought through research and development of techniques on detecting viruses, the genetic integrity of accessions, and on innovative means of safeguarding banana diversity, such as conserving populations of wild species by seed banking. Although the conservation of global banana diversity is the main objective of the ITC, significant value comes from its holistic approach to better understand and promote its germplasm through numerous research activities and resources. Techniques for morphological and molecular characterization serve to identify and describe the collection, while also determining what gaps should be filled by collecting missions with national partners. The evaluation of desirable agronomic traits inherent in Musa spp. are investigated by a high-throughput phenotyping platform, which helps breeding programs to select cultivars resistant or tolerant to biotic and abiotic stresses. Genomic and bioinformatic studies of several banana wild relatives greatly enhance our understanding of Musa genetic diversity, links to important phenotypic traits and bring new methods for management of the collection. Collectively, these research activities produce enormous amounts of data that require curation and dissemination to the public. The two information systems at the ITC, Musa Genebank Management System and the Musa Germplasm Information System, serve to manage the genebank activities and to make public germplasm-related data for over 30 banana collections worldwide, respectively. By implementing the 10-year workplan set out in the Global Strategy for the Conservation and Use of Musa Genetic Resources, the network MusaNet supports Musa researchers and stakeholders, including the ITC, and most importantly, links to the world’s banana-producing countries via three regional banana networks.

scholarly journals Reassessment of Viroid RNA Cytosine Methylation Status at the Single Nucleotide Level

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 357
Author(s):  
Francesco Di Serio ◽  
Enza Maria Torchetti ◽  
José-Antonio Daròs ◽  
Beatriz Navarro
Keyword(s):  
Cytosine Methylation ◽  
Methylation Status ◽  
Potato Spindle Tuber Viroid ◽  
Nucleotide Level ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Nucleotide Modification ◽  
Rna Structural Motifs ◽  
Infectious Cycle ◽  
Positive Results

Composed of a few hundreds of nucleotides, viroids are infectious, circular, non-protein coding RNAs able to usurp plant cellular enzymes and molecular machineries to replicate and move in their hosts. Several secondary and tertiary RNA structural motifs have been implicated in the viroid infectious cycle, but whether modified nucleotides, such as 5C-methylcytosine (m5C), also play a role has not been deeply investigated so far. Here, the possible existence of m5C in both RNA polarity strands of potato spindle tuber viroid and avocado sunblotch viroid -which are representative members of the nucleus- and chloroplast-replicating viroids, respectively- has been assessed at single nucleotide level. We show that a standard bisulfite protocol efficiently used for identifying m5C in cellular RNAs may generate false positive results in the case of the highly structured viroid RNAs. Applying a bisulfite conversion protocol specifically adapted to RNAs with high secondary structure, no m5C was identified in both polarity strands of both viroids, indicating that this specific nucleotide modification does not likely play a role in viroid biology.

scholarly journals MBD4-Mediated Glycosylase Activity on a Chromatin Template Is Enhanced by Acetylation

2008 ◽  
Vol 28 (15) ◽  
pp. 4734-4744 ◽  
Author(s):  
Toyotaka Ishibashi ◽  
Kevin So ◽  
Claire G. Cupples ◽  
Juan Ausió
Keyword(s):  
Cytosine Methylation ◽  
Methylation Status ◽  
Histone Hyperacetylation ◽  
Glycolytic Activity ◽  
Chromatin Template ◽  
Axis Of Symmetry ◽  
Dna Substrates ◽  
Dna Substrate

ABSTRACT The ability of the MBD4 glycosylase to excise a mismatched base from DNA has been assessed in vitro using DNA substrates with different extents of cytosine methylation, in the presence or absence of reconstituted nucleosomes. Despite the enhanced ability of MBD4 to bind to methylated cytosines, the efficiency of its glycosylase activity on T/G mismatches was slightly dependent on the extent of methylation of the DNA substrate. The reduction in activity caused by competitor DNA was likewise unaffected by the methylation status of the substrate or the competitor. Our results also show that MBD4 efficiently processed T/G mismatches within the nucleosome. Furthermore, the glycolytic activity of the enzyme was not affected by the positioning of the mismatch within the nucleosome. However, histone hyperacetylation facilitated the efficiency with which the bases were excised from the nucleosome templates, irrespective of the position of the mismatch relative to the pseudodyad axis of symmetry of the nucleosome.

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