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Naderi S, Maali-Amiri R, Sadeghi L, Hamidi A. Physio-biochemical and DNA methylation analysis of the defense response network of wheat to drought stress. Plant Physiol Biochem 2024; 209:108516. [PMID: 38537384 DOI: 10.1016/j.plaphy.2024.108516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 04/06/2024]
Abstract
In the present work, physio-biochemical and DNA methylation analysis were conducted in wheat (Triticum aestivum L.) cultivars "Bolani" (drought-tolerant) and "Sistan" (drought-sensitive) during drought treatments: well-watered (at 90% field capacity (FC)), mild stress (at 50% FC, and severe stress (at 25% FC). During severe stress, O2•- and H2O2 content in cultivar Sistan showed significant increase (by 1.3 and 2.5-fold, respectively) relative to cultivar Bolani. In Bolani, the increased levels of radical scavenging activity (by 32%), glycine betaine (GB) (by 11.44%), proline (4-fold), abscisic acid (by 63.76%), and more stability of relative water content (RWC) (2-fold) were observed against drought-induced oxidative stress. Methylation level significantly decreased from 70.26% to 60.64% in Bolani and from 69.06% to 59.85% in Sistan during stress, and higher decreased tendency was related to CG and CHG in Bolani but CG in Sistan under severe stress. Methylation patterns showed that the highest polymorphism in Bolani was mainly as CG. As the intensity of stress increased, the enhanced physio-biochemical responses of Bolani cultivar were accompanied by a more decrease in the number of unchanged bands. According to heat map analysis, the highest difference (84.38%) in methylation patterns was observed between control and severe stress. Multivariate analysis using principal component analysis (PCA) showed a cultivar-specific methylation during stress and that methylation changes between cultivars are much higher than that of within a cultivar. Higher methylation to demethylation in Bolani (30.06 vs. 22.12%) compared to that of cultivar Sistan (23.21 vs. 30.15%) indicated more demethylation did not induce tolerance responses in Sistan. Sequencing differentially methylated fragments along with qRT-PCR analysis showed the efficient role of various DNA fragments, including demethylated fragments such as phosphoenol pyruvate carboxylase (PEPC), beta-glucosidase (BGlu), glycosyltransferase (GT), glutathione S-transferase (GST) and lysine demethylase (LSD) genes and methylated fragments like ubiquitin E2 enzyme genes in the development of drought tolerance. These results suggested the specific roles of DNA methylation in development of drought tolerance in wheat landrace.
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Affiliation(s)
- Salehe Naderi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran.
| | - Leila Sadeghi
- Seed and Plant Certification and Registration Research Institute, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31368-63111, Karaj, Iran
| | - Aidin Hamidi
- Seed and Plant Certification and Registration Research Institute, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31368-63111, Karaj, Iran
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Jia K, Duan J, Cheng G, Li H, Li S, Hu M. DNA Methylation is Involved in Sex Determination in Spinach. Biochem Genet 2023:10.1007/s10528-023-10524-4. [PMID: 37950843 DOI: 10.1007/s10528-023-10524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 09/07/2023] [Indexed: 11/13/2023]
Abstract
DNA methylation plays a critical role in the modulation of gene expression. The role of DNA methylation in sex determination was investigated in spinach. The differentiated cytosine CpG methylation profiles of CCGG motifs were assessed with methylation sensitivity amplification polymorphism (MSAP) in spinach. Among 442 DNA fragments from four plants, 134 methylated fragments were found. Relative proportions of methylation sites were 28.8% in male plants and 31.8% in female plants. At the same time, cytosine methylation levels were higher in females than in males in CCGG motifs of genomes in the spinach. These findings suggest that methylation of CG islands is involved in sex determination and differentiation in spinach.
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Affiliation(s)
- Keli Jia
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Jiaming Duan
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | | | - Heng Li
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Miao Hu
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China.
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Su Y, Liu L, Deng Q, Lü Z, Wang Z, He Z, Wang T. Epigenetic architecture of Pseudotaxus chienii: Revealing the synergistic effects of climate and soil variables. Ecol Evol 2023; 13:e10511. [PMID: 37701023 PMCID: PMC10493196 DOI: 10.1002/ece3.10511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023] Open
Abstract
Whether conifers can withstand environmental changes especially temperature fluctuations has been controversial. Epigenetic analysis may provide new perspectives for solving the issue. Pseudotaxus chienii is an endangered gymnosperm species endemic to China. In this study, we have examined the genetic and epigenetic variations in its natural populations aiming to disentangle the synergistic effects of climate and soil on its population (epi)genetic differentiation by using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP) techniques. We identified 23 AFLP and 26, 7, and 5 MSAP outliers in P. chienii. Twenty-one of the putative adaptive AFLP loci were found associated with climate and/or soil variables including precipitation, temperature, K, Fe, Zn, and Cu, whereas 21, 7, and 4 MSAP outliers were significantly related to precipitation of wettest month (Bio13), precipitation driest of month (Bio14), percent tree cover (PTC), and soil Fe, Mn, and Cu compositions. Total precipitation and precipitation in the driest seasons were the most influential factors for genetic and epigenetic variation, respectively. In addition, a high full-methylation level and a strong correlation between genetic and epigenetic variation were detected in P. chienii. Climate is found of greater importance than soil in shaping adaptive (epi)genetic differentiation, and the synergistic effects of climate and climate-soil variables were also observed. The identified climate and soil variables should be considered when applying ex situ conservation.
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Affiliation(s)
- Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Li Liu
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Qi Deng
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- School of MedicineGuangxi University of Science and TechnologyLiuzhouChina
| | - Zhuyan Lü
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ziqing He
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Luo D, Lu H, Wang C, Mubeen S, Cao S, Yue J, Pan J, Wu X, Wu Q, Zhang H, Chen C, Rehman M, Li R, Chen P. Physiological and DNA methylation analysis provides epigenetic insights into kenaf cadmium tolerance heterosis. Plant Sci 2023; 331:111663. [PMID: 36841339 DOI: 10.1016/j.plantsci.2023.111663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Soil heavy metal pollution is one of the most challenging problems. Kenaf is an important natural fiber crop with strong heterosis and a higher tolerance to heavy metals. However, little is known about the molecular mechanisms of kenaf heavy metal tolerance, especially the mechanism of genomic DNA methylation regulating heterosis. In this study, kenaf cultivars CP085, CP089, and their hybrid F1 seedlings were subjected to 300 µM cadmium stress and found obvious heterosis of cadmium resistance in morphology and antioxidant enzyme activity of F1 hybrid seedlings. Through methylation-sensitive amplification polymorphism (MSAP) analysis, we highlighted that the total DNA methylation level under cadmium decreased by 16.9 % in F1 and increased by 14.0 % and 3.0 % in parents CP085 and CP089, respectively. The hypomethylation rate was highest (21.84 %), but hypermethylation was lowest (17.24 %) in F1 compared to parent cultivars. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between F1 and its parents under cadmium. Furthermore, 21 differentially methylated DNA fragments (DMFs) were analyzed. Especially, the expression of NPF2.7, NADP-ME, NAC71, TPP-D, LRR-RLKs, and DHX51 genes were changed due to cadmium stress and related to cytosine methylation regulation. Finally, the knocked-down of the differentially methylated gene NPF2.7 by virus-induced gene silencing (VIGS) resulted in increased sensitivity of kenaf seedlings under cadmium stress. It is speculated that low DNA methylation levels can regulate gene expression that led to the heterosis of cadmium tolerance in kenaf.
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Affiliation(s)
- Dengjie Luo
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hai Lu
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Caijin Wang
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Samavia Mubeen
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Shan Cao
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Jiao Yue
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Jiao Pan
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xia Wu
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Qijing Wu
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hui Zhang
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Canni Chen
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Muzammal Rehman
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Peng Chen
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China.
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Xiao Y, Chen X, Yin Y, Zheng J, Yi H, Song L. Comparative genetic and epigenetic of the Sphagneticola trilobata (L.) Pruski from different regions in China. BMC Plant Biol 2023; 23:289. [PMID: 37254044 DOI: 10.1186/s12870-023-04277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/09/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Sphagneticola trilobata (L.) Pruski is a prevalent and widely distributed invasive plant in South China. To investigate the molecular mechanisms underlying its rapid adaptation, we employed DNA methylation-sensitive amplified polymorphism (MSAP) and simple sequence repeat (SSR) analysis to study 60 S. trilobata individuals collected from Fuzhou (FZ), Haikou (HK), Jinghong (JH) and Guangzhou (GZ). RESULTS In this study, we computed the Shannon diversity index (I) of SSR and MSAP as 0.354 and 0.303, respectively. The UPGMA phylogenetic tree and PCoA analyses showed that MSAP had a better discriminatory power to distinguish populations from different regions. Notably, the GZ population was found to be the most distinct from the other three populations. Moreover, Mantel analysis revealed a significantly higher correlation between epigenetic distance and geographic distance as compared to genetic distance and geographic distance. Consequently, the correlation between epigenetic distance and geographic distance observed to be markedly stronger than that between genetic distance and geographical distance on Mantel analysis. CONCLUSIONS The S. trilobata populations in various regions displayed a high of complementary genetic and epigenetic diversity, which was a key feature contributing to their rapid invasion. Interestingly, the correlation between epigenetics and geographical distance was significantly stronger than that observed for genetics and geographical distance. These findings indicated that the epigenetic mechanism of S. trilobar exhibited high plasticity, leading to significant differences in methylation pattern across different populations.
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Affiliation(s)
- Yusha Xiao
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiuqing Chen
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yuhan Yin
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jiening Zheng
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Huixian Yi
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Liying Song
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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Katsidi EC, Avramidou EV, Ganopoulos I, Barbas E, Doulis A, Triantafyllou A, Aravanopoulos FA. Genetics and epigenetics of Pinus nigra populations with differential exposure to air pollution. Front Plant Sci 2023; 14:1139331. [PMID: 37089661 PMCID: PMC10117940 DOI: 10.3389/fpls.2023.1139331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Forest species in the course of their evolution have experienced several environmental challenges, which since historic times include anthropogenic pollution. The effects of pollution on the genetic and epigenetic diversity in black pine (Pinus nigra) forests were investigated in the Amyntaio - Ptolemais - Kozani Basin, which has been for decades the largest lignite mining and burning center of Greece, with a total installed generating capacity of about 4.5 GW, operating for more than 70 years and resulting in large amounts of primary air pollutant emissions, mainly SO2, NOx and PM10. P. nigra, a biomarker for air pollution and a keystone species of affected natural ecosystems, was examined in terms of phenology (cone and seed parameters), genetics (283 AFLP loci) and epigenetics (606 MSAP epiloci), using two populations (exposed to pollution and control) of the current (mature trees) and future (embryos) stand. It was found that cone, seed, as well as genetic diversity parameters, did not show statistically significant differences between the exposed population and the control. Nevertheless, statistically significant differences were detected at the population epigenetic level. Moreover, there was a further differentiation regarding the intergenerational comparison: while the epigenetic diversity does not substantially change in the two generations assessed in the control population, epigenetic diversity is significantly higher in the embryo population compared to the parental stand in the exposed population. This study sheds a light to genome dynamics in a forest tree population exposed to long term atmospheric pollution burden and stresses the importance of assessing both genetics and epigenetics in biomonitoring applications.
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Affiliation(s)
- Elissavet Ch. Katsidi
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelos Barbas
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Doulis
- Laboratory of Plant Biotechnology – Genomic Resources, Hellenic Agricultural Organization DEMETER, Institute of Viticulture, Floriculture and Vegetable Crops, Heraklion, Greece
| | - Athanasios Triantafyllou
- Laboratory of Atmospheric Pollution and Environmental Physics (LALEP), Faculty of Engineering, University of Western Macedonia, Kozani, Greece
| | - Filippos A. Aravanopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
- *Correspondence: Filippos A. Aravanopoulos,
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Uthup TK, Karumamkandathil R, Thuppale M. Estimation of Heterografting Associated DNA Methylation Changes in Tree Crops by MSAP Analysis. Methods Mol Biol 2022; 2484:237-257. [PMID: 35461456 DOI: 10.1007/978-1-0716-2253-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The genetic incompatibility of the seedlings which are used as rootstocks (stock-scion interactions) and the mechanical stress induced by grafting are two major factors responsible for the high intraclonal variations observed in tree crops which are propagated through bud grafting. Since stress-induced DNA methylation changes associated with heterografting is a major contributor of such variations in grafted tree crops, a proper assessment of this epigenetic phenomenon is inevitable to devise strategies for the development of more uniform planting materials with minimal intraclonal variations in the future. In order to evaluate and establish the effects of heterografting on the epigenome of plants, availability of ideal plant materials and a standard procedure for testing is very essential. Development of genetically uniform own-rooted seedlings through induction of cleavage polyembryony by a novel technique of half ovulo embryo culture is the first step. Grafting of buds from these genetically and epigenetically uniform plants to genetically divergent rootstock and identification of DNA methylation polymorphism among them forms the second part of the methodology for detecting epigenetic changes associated with grafting in tree crops. Methylation-sensitive amplification polymorphism technique (MSAP), a modified version of AFLP using a pair of methylation-sensitive and insensitive isoschizomers (such as HpaII and MspI), is an ideal methodology to assess DNA methylation polymorphisms on a genomic scale in such plants. Comparative analysis of two sets of restriction digestion products (EcoRI/HpaII and EcoRI/MspI) allows the identification of DNA methylation polymorphisms induced by grafting and will aid in the detection of differentially methylated regions (DMRs) among grafted plants. This chapter describes a detailed protocol for inducing multiple embryos of single zygotic origin and regeneration of seedlings in rubber tree (Hevea brasiliensis), grafting of buds from these genetically uniform own-rooted seedlings to divergent rootstocks, identification of epigenetic changes induced by grafting or stock-scion interactions through MSAP analysis, and locating the differentially methylated genomic region. The methodology described here could be applied to any tree species commercially propagated through grafting for detecting epigenetic changes putatively associated with intraclonal variability.
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Yang M, Liang S, Wang F. Differential DNA methylation between long-winged and short-winged adults of Nilaparvata lugens. 3 Biotech 2021; 11:476. [PMID: 34777933 DOI: 10.1007/s13205-021-03026-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022] Open
Abstract
Nilaparvata lugens, a catastrophic rice pest in South East Asia, has adults with wing dimorphism. DNA methylation has been proved to play an important role in regulation of phenotype differentiation in insects. In this study, methylation sensitive amplification polymorphism (MSAP) was used to investigate the cytosine methylation state at CCGG sites in macropterous male adults (MMA) and brachypterous male adults (BMA) of brown planthopper. In MMA, the fully methylated ratio was 2.96%, hemi-methylated ratio 3.83% and total methylated ratio 6.79%. In BMA, they were 5.53%, 4.19% and 9.72%, respectively. There were significant differences in the methylation of the target sites (CCGG) between MMA and BMA (ØST = 0.2614, P = 0.0354). Based the PCoA results, a much clear separation were also shown between MMA and BMA along the first coordinate (38.8% of variance explained). We also cloned and got nine satisfactory sequences with different methylation states between MMA and BMA. Two of them have similarity with male-specific sequence in chromosome Y and lipophorin receptor gene in N. lugens, respectively. The result showed that the methylation patterns and levels were different between two wing phenotypes of N. lugens, and will facilitate research on the epigenetic mechanism of insect wing dimorphism.
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Zhang W, Wang Y, Diao S, Zhong S, Wu S, Wang L, Su X, Zhang B. Assessment of Epigenetic and Phenotypic Variation in Populus nigra Regenerated via Sequential Regeneration. Front Plant Sci 2021; 12:632088. [PMID: 34295342 PMCID: PMC8290414 DOI: 10.3389/fpls.2021.632088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Somatic variation has been demonstrated in tissue culture regenerated plants of many species. In the genus Populus, phenotypic variation caused by changes in 5-methylcytosine within the plant genome have been reported. To date, the phenotypic and epigenetic stability of plants regenerated from sequential regeneration has not been tested in trees. In this study, we detected DNA methylation of CCGG sites in regenerated plants of five generations in Populus nigra using methylation-sensitive amplified polymorphisms, and evaluated their growth performance and physiological traits. About 10.86-26.80% of CCGG sites in the regenerated plant genome were demethylated and 5.50-8.45% were methylated, resulting in significantly lower DNA methylation levels among all regenerated plants than among donor plants. We detected a significant difference in methylation levels between first regeneration regenerated plants (G1) and those of the other four generations (G2-G5); there were no significant differences among the four later generations. Therefore, the dramatic decrease in DNA methylation levels occurred only in the first and second poplar regenerations; levels then stabilized later in the regeneration process, indicating that two regeneration events were sufficient to change the methylation statuses of almost all CCGG sites sensitive to regeneration. Differences in growth and physiological traits were observed between regenerated plants and donor plants, but were significant only among plants of certain generations. Significant correlations were detected between methylation level and transpiration rate, net photosynthetic rate, peroxidase activity, and instant water utilization efficiency, indicating the involvement of epigenetic regulation in this unpredictable phenotypic variation.
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Affiliation(s)
- Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yanbo Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Nanchang Institute of Technology, Nanchang, China
| | - Shu Diao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shanchen Zhong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shu Wu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Li Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Cascales J, Acevedo RM, Paiva DI, Gottlieb AM. Differential DNA methylation and gene expression during development of reproductive and vegetative organs in Ilex species. J Plant Res 2021; 134:559-575. [PMID: 33759060 DOI: 10.1007/s10265-021-01279-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Differential epigenetic (DNA cytosine methylation) and gene expression patterns were investigated in reproductive and vegetative organs from Ilex paraguariensis and I. dumosa, at distinct developmental stages. We aimed at contributing towards elucidating major molecular changes underlying the sexual differentiation processes which, in these dioecious species, are completely unknown. Simultaneously, as a first step towards the development of an early sexing system, we searched for promising molecular markers. This was assessed through Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment Length Polymorphism on cDNA (cDNA-AFLP) techniques, applying discriminant multivariate analyses, and bioinformatic characterization of differential fragments. A significant positive correlation was found between epigenetic and indirect 'genetic' information for both species, indicating influence of the genetic background on the epigenetic variation. Higher epigenetic than genetic diversities were estimated. Our outcomes showed up to 1.86 times more representation of mCG subepiloci than mCCG in all organs sampled. Along the maturing stages of floral buds, the frequency of mCG evidenced an incremental trend, whereas mCCG and unmethylated conditions showed opposite tendencies. Reproductive and vegetative samples tended to cluster apart based on epigenetic patterns; at gene expression level, organs exhibited clear-cut distinctive patterns, nonetheless profiles of young leaves and floral primordia resemble. Epigenetic and expression data allowed discrimination of I. dumosa´s samples according to the gender of the donor; more elusive patterns were observed for I. paraguariensis. In total, 102 differentially methylated and expressed fragments were characterized bioinformatically. Forty-three were annotated in various functional categories; four candidate markers were validated through qPCR, finding statistical differences among organs but not among sexes. The methylation condition of epilocus C13m33 appears as indicative of gender in both species. Thirty-three organ-specific and 34 gender-specific methylated markers were discriminated and deserve further research, particularly those expressed in leaves. Our study contributes concrete candidate markers with potential for practical application.
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Affiliation(s)
- Jimena Cascales
- Laboratorio de Citogenética y Evolución, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, CONICET-UBA), Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, Ciudad Universitaria, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Raúl Maximiliano Acevedo
- Laboratorio de Biotecnología Aplicada y Genómica Funcional, Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (IBONE, UNNE-CONICET), Universidad Nacional del Nordeste, Sargento Juan Bautista Cabral 2131, Corrientes, W3402BKG, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Daniela Ivana Paiva
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Montecarlo (INTA EEA Montecarlo), Av. El Libertador 2472, Misiones, N3384, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Alexandra Marina Gottlieb
- Laboratorio de Citogenética y Evolución, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, CONICET-UBA), Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, Ciudad Universitaria, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina.
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11
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Reiser S, Pohlmann DM, Blancke T, Koops U, Trautner J. Environmental enrichment during early rearing provokes epigenetic changes in the brain of a salmonid fish. Comp Biochem Physiol Part D Genomics Proteomics 2021; 39:100838. [PMID: 33930773 DOI: 10.1016/j.cbd.2021.100838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Environmental enrichment is used to increase structural complexity of captive rearing systems and has been shown to provoke a wide range of effects in the kept animals. Here we studied the effects of enrichment on DNA methylation patterns at the whole-genome level in the brain of rainbow trout reared in an aquaculture setting. We investigated the epigenetic effects between different types of enrichment (natural substrate vs. artificial substrate vs. barren) in three developmental stages (egg vs. alevin vs. fry) and as enrichment was discontinued at the fingerling stage by means of the Methylation-Sensitive Amplified Polymorphism (MSAP) technique. While enrichment did not affect growth in body size, we found enrichment to affected global DNA methylation in the brain at the egg and alevin stage, i.e., the period during development where the animals are in close physical contact with the substrate. At these stages, trout reared on the two substrates differed more from the control than the substrates differed from each other. Only minor differences between rearing environments were detected following emergence at the fry stage. When enrichment was discontinued during the rearing of fingerlings, no differences in DNA methylation patterns were observed between the rearing environments. Our results provide further evidence on the effects of enrichment in the captive rearing of fish and show that enrichment can even modulate epigenetic patterns. The effect on the epigenome may be causal for the previously reported effects of enrichment on gene expression, behaviour and brain development.
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Affiliation(s)
- Stefan Reiser
- Thünen Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany.
| | | | - Tina Blancke
- Thünen Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany
| | - Udo Koops
- Thünen Institute of Fisheries Ecology, Wulfsdorfer Weg 204, 22926 Ahrensburg, Germany
| | - Jochen Trautner
- Thünen Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany
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12
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Zhang Y, Zhang T, Si F, Wang X, Liu C, Yuan Y, Feng W, Gai S. Changes of DNA Methylation Patterns Reveal Epigenetic Modification of Dormancy Release-Related Genes Is Induced by Chilling in Tree Peony. DNA Cell Biol 2021; 40:606-617. [PMID: 33493084 DOI: 10.1089/dna.2020.6142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DNA methylation is an important epigenetic regulator of gene expression. Application of 5-azacytidine (a methylation inhibitor) significantly promoted bud sprouting rate and the elongation of branches and leaves in "Luhehong" and "Fengdanbai." In total, 11,166 and 11,443 fragments were obtained by methylation-sensitive amplified polymorphism (MSAP) analysis during chilling-induced dormancy release in the two varieties, respectively. Total methylation levels were high in dormant buds, mainly for hemimethylation, which were slowly increased by short-term chilling (7 days) and decreased by long-term chilling. Compared with 0 day, the ratio of the methylation downregulated group increased during dormancy release, whereas that of the upregulated group declined gradually. These variations were consistent with the dynamic expressions of DNA methyltransferase/demethylase genes and their enzyme activity changes. In total, 13 polymorphic MSAP fragments were similar to known proteins (E-value <1e-5), and their methylation statuses were consistent with their expression patterns. The expression change of PsCWH, encoding cell wall hydrolase, might be due to DNA methylation ratios of CpG sites identified by bisulfite sequencing. These results indicated that chilling accumulation promoted bud dormancy release and sprouting through DNA methylation modification of specific genes. This study would provide new insights into the molecular mechanism underlying dormancy release in tree peony.
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Affiliation(s)
- Yuxi Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Tao Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Fuhui Si
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Xueting Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Chunying Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Yanchao Yuan
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Weirong Feng
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
| | - Shupeng Gai
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,University Key Laboratory of Plant Biotechnology in Shandong Province, Qingdao, China
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13
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Varela A, Ibañez VN, Alonso R, Zavallo D, Asurmendi S, Gomez Talquenca S, Marfil CF, Berli FJ. Vineyard environments influence Malbec grapevine phenotypic traits and DNA methylation patterns in a clone-dependent way. Plant Cell Rep 2021; 40:111-125. [PMID: 33068175 DOI: 10.1007/s00299-020-02617-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/30/2020] [Indexed: 05/14/2023]
Abstract
By studying three cv. Malbec clones cultivated in two vineyards with contrasting environmental conditions, we demonstrated that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent. Clonal selection and vegetative propagation determine low genetic variability in grapevine cultivars, although it is common to observe diverse phenotypes. Environmental signals may induce epigenetic changes altering gene expression and phenotype. The range of phenotypes that a genotype expresses in different environments is known as phenotypic plasticity. DNA methylation is the most studied epigenetic mechanism, but only few works evaluated this novel source of variability in grapevines. In the present study, we analyzed the effects on phenotypic traits and epigenome of three Vitis vinifera cv. Malbec clones cultivated in two contrasting vineyards of Mendoza, Argentina. Anonymous genome regions were analyzed using methylation-sensitive amplified polymorphism (MSAP) markers. Clone-dependent phenotypic and epigenetic variability between vineyards were found. The clone that presented the clearer MSAP differentiation between vineyards was selected and analyzed through reduced representation bisulfite sequencing. Twenty-nine differentially methylated regions between vineyards were identified and associated to genes and/or promoters. We discuss about a group of genes related to hormones homeostasis and sensing that could provide a hint of the epigenetic role in the determination of the different phenotypes observed between vineyards and conclude that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent.
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Affiliation(s)
- Anabella Varela
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Verónica N Ibañez
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Rodrigo Alonso
- Catena Institute of Wine (CIW), Bodega Catena Zapata, Cobos w/n, M5509, Agrelo, Mendoza, Argentina
| | - Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Losos Reseros y N. Repetto w/n, Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Losos Reseros y N. Repetto w/n, Hurlingham B1686IGC, Buenos Aires, Argentina
| | | | - Carlos F Marfil
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
| | - Federico J Berli
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
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14
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Abstract
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
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Affiliation(s)
- Thotten Elampilay Sheeja
- Indian Institute of Spices Research, Kozhikode, Kerala, India.
- Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India.
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15
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Guarino F, Heinze B, Castiglione S, Cicatelli A. Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands. Int J Mol Sci 2020; 21:ijms21197393. [PMID: 33036388 PMCID: PMC7582538 DOI: 10.3390/ijms21197393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
Over the last several decades, several lines of evidence have shown that epigenetic modifications modulate phenotype and mediate an organism’s response to environmental stimuli. Plant DNA is normally highly methylated, although notable differences exist between species. Many biomolecular techniques based on PCR have been developed to analyse DNA methylation status, however a qualitative leap was made with the advent of next-generation sequencing (NGS). In the case of large, repetitive, or not-yet-sequenced genomes characterised by a high level of DNA methylation, the NGS analysis of bisulphite pre-treated DNA is expensive and time consuming, and moreover, in some cases data analysis is a major challenge. Methylation-sensitive amplification polymorphism (MSAP) analysis is a highly effective method to study DNA methylation. The method is based on the comparison of double DNA digestion profiles (EcoRI-HpaII and EcoRI-MspI) to reveal methylation pattern variations. These are often attributable to pedoclimatic and stress conditions which affect all organisms during their lifetime. In our study, five white poplar (Populus alba L.) specimens were collected from different monoclonal stands in the Maltese archipelago, and their DNA was processed by means of an innovative approach where MSAP analysis was followed by NGS. This allowed us to identify genes that were differentially methylated among the different specimens and link them to specific biochemical pathways. Many differentially methylated genes were found to encode transfer RNAs (tRNAs) related to photosynthesis or light reaction pathways. Our results clearly demonstrate that this combinatorial method is suitable for epigenetic studies of unsequenced genomes like P. alba (at the time of study), and to identify epigenetic variations related to stress, probably caused by different and changing pedoclimatic conditions, to which the poplar stands have been exposed.
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Affiliation(s)
- Francesco Guarino
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy; (F.G.); (A.C.)
| | - Berthold Heinze
- Department of Forest Genetics, Austrian Federal Research Centre for Forests, 1131 Vienna, Austria;
| | - Stefano Castiglione
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy; (F.G.); (A.C.)
- Correspondence:
| | - Angela Cicatelli
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy; (F.G.); (A.C.)
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16
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Cara N, Marfil CF, Bertoldi MV, Masuelli RW. Methylation-sensitive Amplified Polymorphism as a Tool to Analyze Wild Potato Hybrids. Bio Protoc 2020; 10:e3671. [PMID: 33659341 DOI: 10.21769/bioprotoc.3671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/24/2020] [Accepted: 03/27/2020] [Indexed: 11/02/2022] Open
Abstract
Methylation-Sensitive Amplification Polymorphism (MSAP) is a versatile marker for analyzing DNA methylation patterns in non-model species. The implementation of this technique does not require a reference genome and makes it possible to determine the methylation status of hundreds of anonymous loci distributed throughout the genome. In addition, the inheritance of specific methylation patterns can be studied. Here, we present a protocol for analyzing DNA methylation patterns through MSAP markers in potato interspecific hybrids and their parental genotypes.
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Affiliation(s)
- Nicolás Cara
- Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza (IBAM). Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Almirante Brown 500. Chacras de Coria. Mendoza. M5528AHB. Argentina
| | - Carlos F Marfil
- Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza (IBAM). Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Almirante Brown 500. Chacras de Coria. Mendoza. M5528AHB. Argentina
| | - María V Bertoldi
- Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza (IBAM). Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Almirante Brown 500. Chacras de Coria. Mendoza. M5528AHB. Argentina
| | - Ricardo W Masuelli
- Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza (IBAM). Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Almirante Brown 500. Chacras de Coria. Mendoza. M5528AHB. Argentina
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17
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Medrano M, Alonso C, Bazaga P, López E, Herrera CM. Comparative genetic and epigenetic diversity in pairs of sympatric, closely related plants with contrasting distribution ranges in south-eastern Iberian mountains. AoB Plants 2020; 12:plaa013. [PMID: 32477484 PMCID: PMC7246305 DOI: 10.1093/aobpla/plaa013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/07/2020] [Indexed: 06/01/2023]
Abstract
Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation. Elucidating the complex interplay between genetic and epigenetic variation in wild populations remains a challenge for evolutionary biologists, and the intriguing possibility that epigenetic diversity could compensate for the loss of genetic diversity is one aspect that remains basically unexplored in wild plants. This hypothesis is addressed in this paper by comparing the extent and patterns of genetic and epigenetic diversity of phylogenetically closely related but ecologically disparate species. Seven pairs of congeneric species from Cazorla mountains in south-eastern Spain were studied, each pair consisting of one endemic, restricted-range species associated to stressful environments, and one widespread species occupying more favourable habitats. The prediction was tested that endemic species should have lower genetic diversity due to population fragmentation, and higher epigenetic diversity induced by environmental stress, than their widespread congeners. Genetic (DNA sequence variants) and epigenetic (DNA cytosine methylation variants) diversities and their possible co-variation were assessed in three populations of each focal species using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP). All species and populations exhibited moderate to high levels of genetic polymorphism irrespective of their ecological characteristics. Epigenetic diversity was greater than genetic diversity in all cases. Only in endemic species were the two variables positively related, but the difference between epigenetic and genetic diversity was greater at populations with low genetic polymorphism. Results revealed that the relationship between genetic and epigenetic diversity can be more complex than envisaged by the simple hypothesis addressed in this study, and highlight the need of additional research on the actual role of epigenetic variation as a source of phenotypic diversity before a realistic understanding of the evolutionary relevance of epigenetic phenomena in plant adaptation can be achieved.
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Affiliation(s)
- Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Isla de La Cartuja, Sevilla, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Isla de La Cartuja, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Isla de La Cartuja, Sevilla, Spain
| | - Esmeralda López
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Isla de La Cartuja, Sevilla, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Isla de La Cartuja, Sevilla, Spain
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18
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Zhang XC, Bao WW, Zhang AL, Pathirana R, Wang QC, Liu ZD. Cryopreservation of shoot tips, evaluations of vegetative growth, and assessments of genetic and epigenetic changes in cryo-derived plants of Actinidia spp. Cryobiology 2020; 94:18-25. [PMID: 32413358 DOI: 10.1016/j.cryobiol.2020.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 01/06/2023]
Abstract
A droplet-vitrification protocol was described for cryopreservation of shoot tips of kiwifruit 'Yuxiang' (Actinidia chinensis var. deliciosa). No significant differences were found in root formation and shoot growth between the in vitro-derived shoots (the control) and cryo-derived ones when cultured in vitro. No significant differences were detected in survival and vegetative growth between the in vitro-derived plants (the control) and cryo-derived ones after re-establishment in greenhouse conditions. Inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) did not detect any polymorphic bands in the cryo-derived shoots when cultured in vitro and the cryo-derived plants after re-establishment in greenhouse conditions. These data indicate rooting ability, vegetative growth and genetic stability are maintained in the cryo-derived kiwifruit plants recovered from the droplet-vitrification cryopreservation. Methylation sensitive amplification polymorphism (MSAP) detected 12.8% and 1.6% DNA methylation in the cryo-derived shoots when cultured in vitro and the cryo-derived plants after re-established in greenhouse conditions, respectively. This droplet-vitrification was applied to five cultivars and three rootstocks belonging to A. chinensis var. deliciosa, A. chinensis var. chinensis, A. macrosperma, A. polygama and A. valvata. The highest (68.3%) and lowest (22.5%) shoot regrowth were obtained in A. macrosperma and A. chinensis var. chinensis 'Jinmi', respectively, with an average of 46.4% shoot regrowth obtained across the eight genotypes. The droplet-vitrification protocol described here can be considered the most applicable cryopreservation method so far reported for the genus Actinidia. Results reported here provide theoretical and technical supports for setting up cryo-banks of genetic resources of Actinidia spp.
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Affiliation(s)
- Xiao-Chen Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Wen-Wu Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - A-Ling Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ranjith Pathirana
- Plant & Food Research Australia Pty Ltd, Waite Institute, SA, 5064, Australia
| | - Qiao-Chun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhan-De Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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19
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Pozzi FI, Green GY, Barbona IG, Rodríguez GR, Felitti SA. CleanBSequences: an efficient curator of biological sequences in R. Mol Genet Genomics 2020; 295:837-841. [PMID: 32300860 DOI: 10.1007/s00438-020-01671-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
This work presents a new method and tool to solve a common problem of molecular biologists and geneticists who use molecular markers in their scientific research and developments: curation of sequences. Omic studies conducted by molecular biologists and geneticists usually involve the use of molecular markers. AFLP, cDNA-AFLP, and MSAP are examples of markers that render information at the genomics, transcriptomics, and epigenomics levels, respectively. These three types of molecular markers use adaptors that are the template for PCR amplification. The sequences of the adaptors have to be eliminated for the analysis of the results. Since a large number of sequences are usually obtained in these studies, this clean-up of the data could demand long time and work. To automate this work, an R package, named CleanBSequences, was created that allows the sequences to be curated massively, quickly, without errors and can be used offline. The curating is performed by aligning the forward and/or reverse primers or ends of cloning vectors with the sequences to be removed. After the alignment, new subsequences are generated without biological fragments not desired by the user, i.e., sequences needed by the techniques. In conclusion, the CleanBSequences tool facilitates the work of researchers, reducing time, effort, and working errors. Therefore, the present tool would respond to the problems related to the curation of sequences obtained from the use of some types of molecular markers. In addition to the above, being an open source, CleanBSequences is a flexible tool that has the potential to be used in future improvements to respond to new problems.
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Affiliation(s)
- Florencia I Pozzi
- Instituto de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km. 3, 2580, Marcos Juárez, Córdoba, Argentina. .,Cátedra de Microbiología, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina.
| | - Gisela Y Green
- Cátedra de Epidemiología, Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, S2170, Casilda, Santa Fe, Argentina
| | - Ivana G Barbona
- Cátedra de Estadística, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Gustavo R Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) (CONICET-UNR), Zavalla, Argentina.,Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Silvina A Felitti
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) (CONICET-UNR), Zavalla, Argentina
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20
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Bulut B, Aydinli Z, Türktaş-Erken M. MSAP analysis reveals diverse epigenetic statuses in opium poppy varieties with different benzyisoquinoline alkaloid content. ACTA ACUST UNITED AC 2020; 44:103-109. [PMID: 32256146 PMCID: PMC7129067 DOI: 10.3906/biy-1911-69] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation is one of the major epigenetic modifications influencing the regulation of gene expression. The opium poppy is an important medicinal plant. Its latex contains opium, which is a rich source of pharmaceutical benzyisoquinoline alkaloids (BIA). Here, the methylation-sensitive amplification polymorphism (MSAP) profiling technique using 21 MSAP molecular markers was applied in order to compare levels of DNA methylation between 6 opium poppy varieties. MSAP profiling reflected the different methylation statuses among opium poppy varieties having divergent BIA content. Moreover, different organ-specific epigenetic profiles were observed between the samples. Differential epigenetic profiles of capsules and shoots from the leaves pointed to the impact of methylation on BIA biosynthesis. The data implied that the different DNA methylation status may have important biological significance, in the case of alkaloid content in opium poppy in particular.
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Affiliation(s)
- Betül Bulut
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
| | - Zehra Aydinli
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
| | - Mine Türktaş-Erken
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
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Jiang Q, Qian L, Gu S, Guo X, Zhang X, Sun L. Investigation of growth retardation in Macrobrachium rosenbergii based on genetic/epigenetic variation and molt performance. Comp Biochem Physiol Part D Genomics Proteomics 2020; 35:100683. [PMID: 32279060 DOI: 10.1016/j.cbd.2020.100683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/18/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
Giant freshwater prawn, Macrobrachium rosenbergii is an important freshwater aquaculture species worldwide, and China contributes the most to its global production. However, in recent years in China, many prawns have shown serious growth retardation, which is referred to as "iron prawn." To explore the mechanism behind this phenomenon, we compared the difference between these "iron prawns" and normal prawns in three aspects-changes in genetic diversity, DNA methylation, and transcriptomes-as well as comparing differences in their molt performance. The results are as follows: first, compared with normal prawns, "iron prawns" showed no significant decrease in genetic diversity, but they did show obvious genetic differentiation, and different DNA methylation levels were observed. The genetic and epigenetic variations that existed between "iron prawn" and normal prawn indicated the influence of germplasm on growth performance. Second, transcriptome analysis revealed 1813 differentially expressed genes (DEGs) between the "iron prawn" and normal prawn, and the DEGs mainly enriched the glucose metabolism- and immune-related pathways, such as in glycolysis/gluconeogenesis metabolism, insulin secretion, glucagon signaling pathway, antigen processing and presentation, as well as in complement and coagulation cascades. Enrichment analysis indicated the importance of the glucose level and pathogen attacks to growth performance in the "iron prawn." Finally, a comparison of the molt performance showed that the length of the molt cycle in the "iron prawn" was comparable to normal prawns with the same size, but the specific growth was much lower in the "iron prawn." This result suggested that lower body weight gain per molt cycle should be responsible for growth retardation in the "iron prawn," but not in the longer molt cycle. The results in this study provided fundamental information about the mechanism behind growth retardation in M. rosenbergii.
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Affiliation(s)
- Qun Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lan Qian
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shuwen Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiang Guo
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms, Fisheries Research Institute of Fujian, Xiamen, Fujian, 361000, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Longsheng Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Al-Himdani S, Din A, Wright TC, Wheble G, Chapman TWL, Khan U. The medial sural artery perforator ( MSAP) flap: A versatile flap for lower extremity reconstruction. Injury 2020; 51:1077-1085. [PMID: 32192717 DOI: 10.1016/j.injury.2020.02.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/02/2020] [Accepted: 02/10/2020] [Indexed: 02/02/2023]
Abstract
BACKGROUND The medial sural artery perforator (MSAP) flap provides a thin, pliable and durable soft tissue reconstruction with adequate pedicle length and low donor morbidity. It is an ideal choice for small-to-moderate defects of the lower extremity, although it does have limitations. We report our experience of the flap in a three-pronged anatomical, clinical and patient reported outcome-based study. METHODS Cadaveric fresh frozen lower limbs (n = 10) were used for anatomical dissections to assess pertinent and clinically relevant findings. Data relating to MSAP flaps was collected from a prospectively maintained database over a 2-year period. Both clinical data and modified Enneking scores were analysed. RESULTS Anatomical study: A mean of 2.1 ± 0.99 perforators arose from the medial sural artery, located 11.9 cm ± 2.07 along the line between the popliteal fossa and medial malleolus. The largest perforator was located 13.58 cm ± 2.01 from the popliteal artery. The distance from the dominant perforator to the first branching point within the gastrocnemius was 7.39 ± 1.50 (range 5-9.2 cm). The short saphenous vein was located on average 3.08 cm ± 0.77 from the dominant perforator. Clinical study: Twenty free and nine pedicled MSAPs were included (n = 29). Open lower limb fractures (n = 18, 62%) and infection (n = 10, 35%) were the most common aetiologies. Defects sites included: foot-and-ankle (n = 12, 55%), knee (n = 9, 31%) and anterior leg (n = 4, 14%). Four patients (14%) required SSG to for donor site coverage. Venous congestion was responsible for partial flap necrosis in 6.9%(n = 2) of patients. All wounds were healed at discharge. At 14 months, the mean Enneking score was 72.5%. All patients were ambulant, 96% returned to work and 87% were using pre-operative footwear. CONCLUSIONS The MSAP provides robust foot-and-ankle reconstruction, whilst permitting glide when over the knee. Patient satisfaction and functional outcomes are excellent with careful patient selection. Care should be taken to avoid compression or kinking of the large, thin walled veins as the most commonly observed complication was venous congestion. We advocate MSAP as a first choice flap for small-to-moderate foot, ankle or knee defects.
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Affiliation(s)
- Sarah Al-Himdani
- Southmead Hospital, North Bristol NHS Trust Westbury-on-Trym, Bristol, BS10 5NB, United Kingdom
| | - Asmat Din
- Southmead Hospital, North Bristol NHS Trust Westbury-on-Trym, Bristol, BS10 5NB, United Kingdom
| | - Thomas C Wright
- Southmead Hospital, North Bristol NHS Trust Westbury-on-Trym, Bristol, BS10 5NB, United Kingdom
| | - George Wheble
- Southmead Hospital, North Bristol NHS Trust Westbury-on-Trym, Bristol, BS10 5NB, United Kingdom
| | - Thomas W L Chapman
- Southmead Hospital, North Bristol NHS Trust Westbury-on-Trym, Bristol, BS10 5NB, United Kingdom
| | - Umraz Khan
- Southmead Hospital, North Bristol NHS Trust Westbury-on-Trym, Bristol, BS10 5NB, United Kingdom.
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Pirredda M, González-Benito ME, Martín C, Mira S. Genetic and Epigenetic Stability in Rye Seeds under Different Storage Conditions: Ageing and Oxygen Effect. Plants (Basel) 2020; 9:plants9030393. [PMID: 32210066 PMCID: PMC7154831 DOI: 10.3390/plants9030393] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 02/01/2023]
Abstract
Seed ageing is a complex process and can be described as the loss of viability or quality with time. It is important to elucidate whether genetic and epigenetic stability is altered in stored seeds and in seedlings produced from them. Non-stored and stored rye seeds at different stages of ageing were compared, as well as the seedlings obtained from them. Seeds were stored at 35 °C and 15% water content, under vacuum or air atmosphere. DNA of seeds and seedlings was isolated at three stages of the deterioration curve: P75 (13 days), P20 (29 days), and P0 (36 days). Genetic stability was assessed by RAPD technique, and epigenetic changes by MSAP markers. While seeds showed genetic stability after storage, the similarity of seedlings obtained from seeds stored for 29 days was lower (95%) when compared to seedlings from control seeds. Epigenetic changes were between 15% and 30% (both de novo methylation and demethylation) in the stored seeds compared to control seeds, with no differences between 13 and 29 days of storage with either air or vacuum atmospheres. In seedlings, epigenetic changes significantly increased with storage time. In conclusion, ageing increased epigenetic instability in both seeds and seedlings, when compared to controls.
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Affiliation(s)
| | | | | | - Sara Mira
- Correspondence: ; Tel.: +34-91-06-70888
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24
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Ibáñez MA, Alvarez-Mari A, Rodríguez-Sanz H, Kremer C, González-Benito ME, Martín C. Genetic and epigenetic stability of recovered mint apices after several steps of a cryopreservation protocol by encapsulation-dehydration. A new approach for epigenetic analysis. Plant Physiol Biochem 2019; 143:299-307. [PMID: 31539759 DOI: 10.1016/j.plaphy.2019.08.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/24/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
The genetic and epigenetic stability (analysis of DNA methylation using MSAP markers) of mint (Mentha x piperita L.) apices was studied after each step of a cryopreservation protocol, by encapsulation-dehydration. The effect of the addition of an antioxidant (ascorbic acid) during one of the protocol steps was also evaluated. Eight-week old in vitro recovered shoots from apices after each step of the protocol were genetically stable when compared to control in vitro shoots, using RAPD and AFLP markers. The addition of ascorbic acid in the medium with the highest sucrose concentration did not improve recovery and did not have any effect on stability. Apices sampled immediately after each step showed increased epigenetic differences as the protocol advanced, compared to in vitro control apices, in particular related to de novo methylation events. However, after one-day in vitro recovery, methylation status was similar to control apices. To improve the quality of methylation data interpretation, a simple and fast method for MSAP markers analysis, based on R programming, has been developed which allows the statistical comparison of treatments to control samples and its graphical representation.
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Affiliation(s)
- Miguel Angel Ibáñez
- Departamento de Economía Agraria, Estadística y Gestión de Empresas, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Ana Alvarez-Mari
- Departamento de Economía Agraria, Estadística y Gestión de Empresas, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Héctor Rodríguez-Sanz
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Carolina Kremer
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - María Elena González-Benito
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Carmen Martín
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
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25
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Xin C, Chi J, Zhao Y, He Y, Guo J. Cadmium stress alters cytosine methylation status and expression of a select set of genes in Nicotiana benthamiana. Plant Sci 2019; 284:16-24. [PMID: 31084868 DOI: 10.1016/j.plantsci.2019.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 05/14/2023]
Abstract
In this paper, we evaluated the genotoxicity of cadmium (Cd) in plants by performing a methylation-sensitive amplification polymorphism (MSAP) on the model plant Nicotiana benthamiana. Among 255 loci examined, 14 genes were found to show altered cytosine methylation patterns in response to Cd stress. Four of those genes (NbMORC3, NbHGSNAT, NbMUT, and NbBG) were selected for further analysis due to their predicted roles in plant development. Cd-induced changes of cytosine methylation status in MSAP fragments of selected genes were confirmed using bisulfite sequencing polymerase chain reaction (BSP). In addition, the expression levels of these genes were found to correlate with cadmium dosage, and a knock-down of these four genes via virus-induced genes silencing (VIGS) led to abnormal development and elevated sensitivity to cadmium stress. Silencing of these four genes resulted in altered cadmium accumulation in different parts of the experimental plants. Our data indicate that cadmium exposure causes dramatic changes in the cytosine methylation status of the plant genome, thus affecting the expression of many genes that are vital for plant growth and are involved in cadmium stress response.
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Affiliation(s)
- Cuihua Xin
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Junling Chi
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yibo Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yindi He
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jiangbo Guo
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
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Amraee L, Rahmani F, Abdollahi Mandoulakani B. 24-Epibrassinolide alters DNA cytosine methylation of Linum usitatissimum L. under salinity stress. Plant Physiol Biochem 2019; 139:478-484. [PMID: 31005823 DOI: 10.1016/j.plaphy.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Salinity is a common environmental challenge limiting worldwide agricultural crop yield. Plants employ epigenetic regulatory strategies, such as DNA methylation which relatively allows rapid adaptation to new conditions in response to environmental stresses. Brassinosteroids (BRs) are a novel group of phytohormones recognized as transcription and translation regulators which are able to mitigate the impact of environmental stresses on the plants. In the current investigation, the influence of salinity and 24-epibrassinolide (24-epiBL) was investigated on the extent and pattern of cytosine DNA methylation using methylation-sensitive amplified polymorphisms (MSAP) technique in flax. Upon NaCl (150 mM) exposure, total methylation of CCGG sequences was decreased in comparison to control plants, while 24-epiBL (10-8 M) induced total methylation under salinity stress. Sequencing and analysis of six randomly selected MSAP fragments detected genes involved in various biological and molecular processes such as vitamine B1 biosynthesis, protein targeting and localization, post-translational modification and gene regulation. In conclusion, 24-epiBL seed priming could play critical role in regulation of cellular and biological processes in response to salt stress by epigenetic modification and induction of methylation.
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Affiliation(s)
- Leila Amraee
- Department of Biology, Faculty and Sciences, Urmia University, Urmia, Iran; Institute of Biotechnology, Urmia University, Urmia, Iran
| | - Fatemeh Rahmani
- Department of Biology, Faculty and Sciences, Urmia University, Urmia, Iran; Institute of Biotechnology, Urmia University, Urmia, Iran.
| | - Babak Abdollahi Mandoulakani
- Institute of Biotechnology, Urmia University, Urmia, Iran; Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
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27
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Marfil C, Ibañez V, Alonso R, Varela A, Bottini R, Masuelli R, Fontana A, Berli F. Changes in grapevine DNA methylation and polyphenols content induced by solar ultraviolet-B radiation, water deficit and abscisic acid spray treatments. Plant Physiol Biochem 2019; 135:287-294. [PMID: 30599305 DOI: 10.1016/j.plaphy.2018.12.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 05/21/2023]
Abstract
Environment and crop management shape plant's phenotype. Argentinean high-altitude vineyards are characterized by elevated solar ultraviolet-B radiation (UVB) and water deficit (D) that enhance enological quality for red winemaking. These signals promote phenolics accumulation in leaves and berries, being the responses mediated by abscisic acid (ABA). DNA methylation is an epigenetic mechanism that regulates gene expression and may affect grapevine growth, development and acclimation, since methylation patterns are mitotically heritable. Berry skins low molecular weight polyphenols (LMWP) were characterized in field grown Vitis vinifera L. cv. Malbec plants exposed to contrasting UV-B, D, and ABA treatments during one season. The next season early fruit shoots were epigenetically (methylation-sensitive amplification polymorphism; MSAP) and biochemically (LMWP) characterized. Unstable epigenetic patterns and/or stochastic stress-induced methylation changes were observed. UV-B and D were the treatments that induced greater number of DNA methylation changes respect to Control; and UV-B promoted global hypermethylation of MSAP epiloci. Sequenced MSAP fragments associated with UV-B and ABA showed similarities with transcriptional regulators and ubiquitin ligases proteins activated by light. UV-B was associated with flavonols accumulation in berries and with hydroxycinnamic acids in the next season fruit shoots, suggesting that DNA methylation could regulate the LMWP accumulation and participate in acclimation mechanisms.
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Affiliation(s)
- Carlos Marfil
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Almte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Verónica Ibañez
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Almte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Rodrigo Alonso
- Catena Institute of Wine (CIW), Bodega Catena Zapata, Cobos S/n, M5509, Agrelo, Mendoza, Argentina
| | - Anabella Varela
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Almte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Rubén Bottini
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Almte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Ricardo Masuelli
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Almte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Ariel Fontana
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Almte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina
| | - Federico Berli
- Instituto de Biología Agrícola de Mendoza, CONICET-Universidad Nacional de Cuyo, Facultad de Ciencias Agrarias, Almte. Brown 500, M5507, Chacras de Coria, Mendoza, Argentina.
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Komivi D, Marie AM, Rong Z, Qi Z, Mei Y, Ndiaga C, Diaga D, Linhai W, Xiurong Z. The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with transcript accumulation in sesame. Plant Sci 2018; 277:207-217. [PMID: 30466587 DOI: 10.1016/j.plantsci.2018.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 05/07/2023]
Abstract
DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, probably because of its origin in Africa or India. Understanding DNA methylation patterns under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying sesame contrasting responses to these abiotic stresses. We combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, transcript accumulation, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes. Drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging stress decreased the level of methylation but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the levels of the differentially accumulated transcripts (DATs) highly correlated with the methylation patterns. We observed that DM was associated with an increase of DAT levels while DNM was correlated with a decrease of DAT levels. Altogether, sesame has divergent epigenetic programs that respond to drought and waterlogging stresses and an interplay among DNA methylation and transcript accumulation may partly modulate the contrasting responses to these stresses.
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Affiliation(s)
- Dossa Komivi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal.
| | - Ali Mmadi Marie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Zhou Rong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhou Qi
- College of Life Science, Hubei University, Wuhan, China
| | - Yang Mei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Cisse Ndiaga
- Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal
| | - Diouf Diaga
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Wang Linhai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhang Xiurong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China.
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Chwialkowska K, Korotko U, Kwasniewski M. DNA Methylation Analysis in Barley and Other Species with Large Genomes. Methods Mol Biol 2019; 1900:253-68. [PMID: 30460570 DOI: 10.1007/978-1-4939-8944-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Detailed DNA methylation analyses in plant species with large and highly repetitive genomes can be challenging as well as costly. Here, we describe a complete protocol for a high-throughput DNA methylation changes analysis using Methylation-Sensitive Amplification Polymorphism Sequencing (MSAP-Seq; Chwialkowska et al., Front Plant Sci. 8: 2056 (2017)). This method allows detailed information about DNA methylation changes in large and complex genomes to be obtained at a relatively low cost. MSAP-Seq is based on conventional MSAP marker analysis and employs all its basic steps such as restriction cleavage with methylation-sensitive restriction enzyme, ligation of universal adapters, and PCR amplification. However, the traditional gel-based amplicon separation is replaced by direct, global sequencing with next-generation sequencing (NGS) methods. Consequently, MSAP-Seq allows for parallel analysis of hundreds of thousands of different CCGG sites and evaluation of their DNA methylation state. This technique especially targets to genic regions, so it is well suited for large genomes with low gene density, such as barley and other plants with large genomes.
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30
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Yang SX, Guo C, Zhao XT, Sun JT, Hong XY. Divergent methylation pattern in adult stage between two forms of Tetranychus urticae (Acari: Tetranychidae). Insect Sci 2018; 25:667-678. [PMID: 28217963 DOI: 10.1111/1744-7917.12444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
The two-spotted spider mite, Tetranychus urticae Koch has two forms: green form and red form. Understanding the molecular basis of how these two forms established without divergent genetic background is an intriguing area. As a well-known epigenetic process, DNA methylation has particularly important roles in gene regulation and developmental variation across diverse organisms that do not alter genetic background. Here, to investigate whether DNA methylation could be associated with different phenotypic consequences in the two forms of T. urticae, we surveyed the genome-wide cytosine methylation status and expression level of DNA methyltransferase 3 (Tudnmt3) throughout their entire life cycle. Methylation-sensitive amplification polymorphism (MSAP) analyses of 585 loci revealed variable methylation patterns in the different developmental stages. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between female adults of the two forms. The gene expression of Tudnmt3 was detected in all examined developmental stages, which was significantly different in the adult stage of the two forms. Together, our results reveal the epigenetic distance between the two forms of T. urticae, suggesting that DNA methylation might be implicated in different developmental demands, and contribute to different phenotypes in the adult stage of these two forms.
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Affiliation(s)
- Si-Xia Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Chao Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiu-Ting Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
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Abstract
We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.
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Affiliation(s)
- Chao Liu
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Mingbo Wang
- b CSIRO Agriculture and Food, Clunies Ross Street, Canberra ACT 2061, Australia
| | - Lingli Wang
- c Technical Advice Station of Economic Crop, Yubei district, Chongqing, P.R. China
| | - Qigao Guo
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Guolu Liang
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
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Lele L, Ning D, Cuiping P, Xiao G, Weihua G. Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub. Ecol Evol 2018; 8:2594-2606. [PMID: 29531679 PMCID: PMC5838075 DOI: 10.1002/ece3.3868] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 12/22/2022] Open
Abstract
Environmentally induced phenotypic plasticity is thought to play an important role in the adaption of plant populations to heterogeneous habitat conditions, and yet the importance of epigenetic variation as a mechanism of adaptive plasticity in natural plant populations still merits further research. In this study, we investigated populations of Vitex negundo var. heterophylla (Chinese chastetree) from adjacent habitat types at seven sampling sites. Using several functional traits, we detected a significant differentiation between habitat types. With amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP (MSAP), we found relatively high levels of genetic and epigenetic diversity but very low genetic and epigenetic differences between habitats within sites. Bayesian clustering showed a remarkable habitat-related differentiation and more genetic loci associated with the habitat type than epigenetic, suggesting that the adaptation to the habitat is genetically based. However, we did not find any significant correlation between genetic or epigenetic variation and habitat using simple and partial Mantel tests. Moreover, we found no correlation between genetic and ecologically relevant phenotypic variation and a significant correlation between epigenetic and phenotypic variation. Although we did not find any direct relationship between epigenetic variation and habitat environment, our findings suggest that epigenetic variation may complement genetic variation as a source of functional phenotypic diversity associated with adaptation to the heterogeneous habitat in natural plant populations.
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Affiliation(s)
- Liu Lele
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Du Ning
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Pei Cuiping
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Guo Xiao
- College of Landscape Architecture and ForestryQingdao Agricultural UniversityQingdaoChina
| | - Guo Weihua
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
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Riyahi S, Vilatersana R, Schrey AW, Ghorbani Node H, Aliabadian M, Senar JC. Natural epigenetic variation within and among six subspecies of the house sparrow, Passer domesticus. ACTA ACUST UNITED AC 2017; 220:4016-4023. [PMID: 28877923 DOI: 10.1242/jeb.169268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/01/2017] [Indexed: 12/30/2022]
Abstract
Epigenetic modifications can respond rapidly to environmental changes and can shape phenotypic variation in accordance with environmental stimuli. One of the most studied epigenetic marks is DNA methylation. In the present study, we used the methylation-sensitive amplified polymorphism (MSAP) technique to investigate the natural variation in DNA methylation within and among subspecies of the house sparrow, Passer domesticus We focused on five subspecies from the Middle East because they show great variation in many ecological traits and because this region is the probable origin for the house sparrow's commensal relationship with humans. We analysed house sparrows from Spain as an outgroup. The level of variation in DNA methylation was similar among the five house sparrow subspecies from the Middle East despite high phenotypic and environmental variation, but the non-commensal subspecies was differentiated from the other four (commensal) Middle Eastern subspecies. Further, the European subspecies was differentiated from all other subspecies in DNA methylation. Our results indicate that variation in DNA methylation does not strictly follow subspecies designations. We detected a correlation between methylation level and some morphological traits, such as standardized bill length, and we suggest that part of the high morphological variation in the native populations of the house sparrow is influenced by differentially methylated regions in specific loci throughout the genome. We also detected 10 differentially methylated loci among subspecies and three loci that differentiated between commensal or non-commensal status. Therefore, the MSAP technique detected larger scale differences among the European and non-commensal subspecies, but did not detect finer scale differences among the other Middle Eastern subspecies.
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Affiliation(s)
- Sepand Riyahi
- Evolutionary and Behavioural Ecology Research Unit, Natural History Museum of Barcelona, Psg. Picasso s/n, 08003 Barcelona, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB-CSIC-ICUB), Passeig de Migdia s/n, 08038 Barcelona, Spain
| | - Aaron W Schrey
- Department of Biology, Armstrong State University, Savannah, GA 31419, USA
| | - Hassan Ghorbani Node
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran.,Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
| | - Mansour Aliabadian
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran.,Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
| | - Juan Carlos Senar
- Evolutionary and Behavioural Ecology Research Unit, Natural History Museum of Barcelona, Psg. Picasso s/n, 08003 Barcelona, Spain
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Ngom B, Sarr I, Kimatu J, Mamati E, Kane NA. Genome-wide analysis of cytosine DNA methylation revealed salicylic acid promotes defense pathways over seedling development in pearl millet. Plant Signal Behav 2017; 12:e1356967. [PMID: 28758879 PMCID: PMC5640191 DOI: 10.1080/15592324.2017.1356967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 05/23/2023]
Abstract
Cytosine DNA methylation is an epigenetic regulatory system used by plants to control gene expression. Methylation pattern always changes after abiotic stresses, pathogens and pest infections or after a treatment with salicylic acid (SA). The latter is a key player in plant development and defense against insect herbivores, pathogens, and abiotic stresses. The roles of SA on the methylation patterns and the plant development were performed in 4 pearl millet (Pennisetum glaucum) varieties. Seedlings of 4 early-flowering photosensitive genotypes (PMS3, PMI8, PMG, and PMT2) were grown on MS medium supplemented with null or different doses of SA. Root growth was used as a parameter to evaluate the effects of SA at early stage development. DNA from these seedlings was extracted and Methylation-Sensitive Amplified Polymorphism (MSAP) was measured to assess the effects of SA on methylome. The methylation analysis revealed that SA treatment decreased the methylation, while inhibiting the root growth for all varieties tested, except in PMG at 0.5 mM, indicating a dose and a genotype response-dependence. The methylation level was positively correlated with the root growth. This suggests that SA influences both the methylome by demethylation activities and the root growth by interfering with the root development-responsive genes. The demethylation process, induced by the REPRESSOR OF SILCENCING 1 (ROS1) may activate R genes, or GH3.5 and downregulate the hormonal pathway under root development. These findings showed the pearl millet metabolism prioritized and promoted the defense pathways over vegetative development during stress.
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Affiliation(s)
- Baba Ngom
- Department of Biotechnology and Molecular Biology, Pan African University Institute of basic Sciences, Technology and Innovation, Nairobi, Kenya
| | - Ibrahima Sarr
- CNRA and LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Rte des hydrocarbures, Dakar, Senegal
| | - Josphert Kimatu
- Department of Biology, South Eastern Kenya University, Directorate of Research, Innovation and Technology, Kitui, Kenya
| | - Edward Mamati
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Ndjido Ardo Kane
- CNRA and LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Rte des hydrocarbures, Dakar, Senegal
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García-Fernández P, García-Souto D, Almansa E, Morán P, Gestal C. Epigenetic DNA Methylation Mediating Octopus vulgaris Early Development: Effect of Essential Fatty Acids Enriched Diet. Front Physiol 2017; 8:292. [PMID: 28559849 PMCID: PMC5432645 DOI: 10.3389/fphys.2017.00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022] Open
Abstract
The common octopus, Octopus vulgaris, is a good candidate for aquaculture but a sustainable production is still unviable due to an almost total mortality during the paralarvae stage. DNA methylation regulates gene expression in the eukaryotic genome, and has been shown to exhibit plasticity throughout O. vulgaris life cycle, changing profiles from paralarvae to adult stages. This pattern of methylation could be sensitive to small alterations in nutritional and environmental conditions during the species early development, thus impacting on its health, growth and survival. In this sense, a full understanding of the epigenetic mechanisms operating during O. vulgaris development would contribute to optimizing the culture conditions for this species. Paralarvae of O. vulgaris were cultured over 28 days post-hatching (dph) using two different Artemia sp. based diets: control and a long chain polyunsaturated fatty acids (LC-PUFA) enriched diet. The effect of the diets on the paralarvae DNA global methylation was analyzed by Methyl-Sensitive Amplification Polymorphism (MSAP) and global 5-methylcytosine enzyme-linked immunosorbent assay (ELISA) approaches. The analysis of different methylation states over the time revealed a global demethylation phenomena occurring along O. vulgaris early development being directly driven by the age of the paralarvae. A gradual decline in methylated loci (hemimethylated, internal cytosine methylated, and hypermethylated) parallel to a progressive gain in non-methylated (NMT) loci toward the later sampling points was verified regardless of the diet provided and demonstrate a pre-established and well-defined demethylation program during its early development, involving a 20% of the MSAP loci. In addition, a differential behavior between diets was also observed at 20 dph, with a LC-PUFA supplementation effect over the methylation profiles. The present results show significant differences on the paralarvae methylation profiles during its development and a diet effect on these changes. It is characterized by a process of demethylation of the genome at the paralarvae stage and the influence of diet to favor this methylation loss.
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Affiliation(s)
- Pablo García-Fernández
- Aquatic Molecular Pathobiology Group, Instituto de Investigaciones Marinas (Consejo Superior de Investigaciones Científicas)Vigo, Spain.,Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Danie García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Eduardo Almansa
- Instituto Español de Oceanografía, Centro Oceanográfico de CanariasTenerife, Spain
| | - Paloma Morán
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Camino Gestal
- Aquatic Molecular Pathobiology Group, Instituto de Investigaciones Marinas (Consejo Superior de Investigaciones Científicas)Vigo, Spain
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Kalinka A, Achrem M, Poter P. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L. PeerJ 2017; 5:e2889. [PMID: 28149679 PMCID: PMC5267573 DOI: 10.7717/peerj.2889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/08/2016] [Indexed: 01/05/2023] Open
Abstract
Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue.
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Affiliation(s)
- Anna Kalinka
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Magdalena Achrem
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Paulina Poter
- Department of Cell Biology, Faculty of Biology, University of Szczecin , Szczecin , Poland
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Guevara MÁ, de María N, Sáez-Laguna E, Vélez MD, Cervera MT, Cabezas JA. Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism ( MSAP). Methods Mol Biol 2017; 1456:99-112. [PMID: 27770361 DOI: 10.1007/978-1-4899-7708-3_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.
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Affiliation(s)
- María Ángeles Guevara
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Nuria de María
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Enrique Sáez-Laguna
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Dolores Vélez
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Teresa Cervera
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
| | - José Antonio Cabezas
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
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Xie H, Konate M, Sai N, Tesfamicael KG, Cavagnaro T, Gilliham M, Breen J, Metcalfe A, Stephen JR, De Bei R, Collins C, Lopez CMR. Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine ( Vitis vinifera cv. Shiraz). Front Plant Sci 2017; 8:1860. [PMID: 29163587 PMCID: PMC5670326 DOI: 10.3389/fpls.2017.01860] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/11/2017] [Indexed: 05/21/2023]
Abstract
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
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Affiliation(s)
- Huahan Xie
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Moumouni Konate
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Na Sai
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - Kiflu G. Tesfamicael
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Timothy Cavagnaro
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Andrew Metcalfe
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - John R. Stephen
- Plant Genomics Centre, Australian Genome Research Facility Ltd., Adelaide, SA, Australia
| | - Roberta De Bei
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Cassandra Collins
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Carlos M. R. Lopez
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Carlos M. R. Lopez,
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Chwialkowska K, Korotko U, Kosinska J, Szarejko I, Kwasniewski M. Methylation Sensitive Amplification Polymorphism Sequencing ( MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes. Front Plant Sci 2017; 8:2056. [PMID: 29250096 PMCID: PMC5714927 DOI: 10.3389/fpls.2017.02056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/16/2017] [Indexed: 05/14/2023]
Abstract
Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.
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Affiliation(s)
- Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Urszula Korotko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Kosinska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Szarejko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
- *Correspondence: Miroslaw Kwasniewski
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40
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Smith TA, Martin MD, Nguyen M, Mendelson TC. Epigenetic divergence as a potential first step in darter speciation. Mol Ecol 2016; 25:1883-94. [PMID: 26837057 DOI: 10.1111/mec.13561] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/28/2015] [Accepted: 01/04/2016] [Indexed: 01/07/2023]
Abstract
Recent studies show that epigenetic variation in the form of DNA methylation may serve as a substrate for selection. Theory suggests that heritable epigenetic marks that increase fitness should increase in frequency in a population, and these changes may result in novel morphology, behaviour, or physiology, and ultimately reproductive isolation. Therefore, epigenetic variation might provide the first substrate for selection during the course of evolutionary divergence. This hypothesis predicts that populations in the earliest stages of divergence will differentiate in their methylome prior to any genetic differentiation. While several studies have investigated natural epigenetic variation, empirical studies that test predictions about its role in speciation are surprisingly scarce. Here, we investigate DNA methylation variation using an isoschizomeric digest method, Methyl-Sensitive Amplified Polymorphism, across multiple stages of evolutionary divergence in natural populations of North American stream fishes. We show that epigenetic differentiation between methylomes is greater than genetic divergence among closely related populations across two river drainages. Additionally, we demonstrate that epigenetic divergence is a stronger predictor of the strength of behavioural reproductive isolation and suggest that changes in the methylome could influence the evolution of reproductive isolation between species. Our findings suggest a role for epigenetics not only in the initiation of divergence, but also in the maintenance of species boundaries over greater evolutionary timescales.
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Affiliation(s)
- Tracy A Smith
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Michael D Martin
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Michael Nguyen
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Tamra C Mendelson
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
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Han PP, Wang HJ, Xiang ZX. [In vitro autotetraploid induction and analysis on DNA methylation diversity of Platycodon grandiflorum]. Zhongguo Zhong Yao Za Zhi 2016; 41:396-402. [PMID: 28868853 DOI: 10.4268/cjcmm20160306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 11/17/2022]
Abstract
In order to investigate the epigenetic variations between diploid and autotetraploid of Platycodon grandiflorus. The diploid buds of P. grandiflorus were soaked in the mixture of different concentration colchicines and 0.002 g•mL ⁻¹ dimethyl sulphoxide (DMSO).The identification of autotetraploid plants were based on morphological characteristics, chromosome number and flow cytometry. And then the level and pattern of DNA methylation explored by using the technology of methylation sensitive amplified polymorphism (MSAP).The result demonstrated that the buds soaked in 0.2% colchicines and 0.002 g•mL ⁻¹ DMSO solution for 12 h was ideal conditions to induce autotetraploid of P. grandiflorus, with induction rate of 32.0%.The diploid and tetraploid plants existed distinctly differences in morphological indexes.Totally,1 586 bands were amplified by 20 pairs of selective primers, of which 764 and 822 bands were detected in diploid and autotetraploid respectively. The total methylation ratio,full methylation ratio and hemimethylated ratio were 91.25%,61.25% and 30.65% in diploid of P. grandiflorus,respectively.However,the total methylation ratio,full methylation ratio and hemimethylated ratio of autotetraploid of P. grandiflorus were 86.13%,54.38% and 31.75%, respectively. Compared with diploid, the genomic DNA total methylate ratio and full methylation ratio of autotetration plants decreased by 6.02% and 7.14%.But the hemimethylated ratio of autotetraploid was higher than that of diploid, which more than 1.6%. All this results indicated that DNA methylation patterns have adjusted during the polyploidy process..
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Rakei A, Maali-Amiri R, Zeinali H, Ranjbar M. DNA methylation and physio-biochemical analysis of chickpea in response to cold stress. Protoplasma 2016; 253:61-76. [PMID: 25820678 DOI: 10.1007/s00709-015-0788-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 02/27/2015] [Indexed: 05/27/2023]
Abstract
Cold stress (CS) signals are translated into physiological changes as products of direct and/or indirect of gene expression regulated by different factors like DNA methylation. In this study, some of these factors were comparatively studied in two chickpea (Cicer arietinum L.) genotypes (Sel96Th11439, cold-tolerant genotype, and ILC533, cold susceptible one) under control (23 °C) and days 1, 3, and 6 after exposing the seedlings to CS (4 °C). Under CS, tolerant genotype prevented H2O2 accumulation which led to a decrease in damage indices (malondialdehyde and electrolyte leakage index) compared to susceptible one. The significant activities of antioxidant enzymes (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, and polyphenol oxidase) along with a significant proportion of change in DNA methylation/demethylation patterns were often effective factors in preserving cell against cold-induced oxidative stress. Chickpea cells in response to CS changed access to their genome as the number of bands without change from day 1 to day 6 of exposure to CS particularly in tolerant genotype was decreased. During CS, the methylation level was higher compared to demethylation (29.05 vs 19.79 %) in tolerant genotype and (27.92 vs 22.09 %) in susceptible one. However, for prolonged periods of CS, changes in demethylated bands in tolerant genotype were higher than that of in susceptible one (9.24 vs 4.13 %), indicating higher potential for activation of CS responsive genes. Such a status along with higher activity of antioxidants and less damage indices could be related to cold tolerance (CT) mechanisms in chickpea. Sequencing analysis confirmed the important role of some specific DNA sequences in creating CT with possible responsive components involved in CS. Thus, dynamic assessment using multi-dimensional approaches allows us to progressively fill in the gaps between physio-biochemical and molecular events in creating CT, to comprehend better the nature of the plant stress response and molecular mechanisms behind.
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Affiliation(s)
- Aida Rakei
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran.
| | - Hassan Zeinali
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, 31587-77871, Karaj, Iran
| | - Mojtaba Ranjbar
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, 46168-49767, Iran
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Bocchini M, Bartucca ML, Ciancaleoni S, Mimmo T, Cesco S, Pii Y, Albertini E, Del Buono D. Iron deficiency in barley plants: phytosiderophore release, iron translocation, and DNA methylation. Front Plant Sci 2015. [PMID: 26217365 PMCID: PMC4496560 DOI: 10.3389/fpls.2015.00514] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
All living organisms require iron (Fe) to carry out many crucial metabolic pathways. Despite its high concentrations in the geosphere, Fe bio-availability to plant roots can be very scarce. To cope with Fe shortage, plants can activate different strategies. For these reasons, we investigated Fe deficient Hordeum vulgare L. plants by monitoring growth, phytosiderophores (PS) release, iron content, and translocation, and DNA methylation, with respect to Fe sufficient ones. Reductions of plant growth, roots to shoots Fe translocation, and increases in PS release were found. Experiments on DNA methylation highlighted significant differences between fully and hemy-methylated sequences in Fe deficient plants, with respect to Fe sufficient plants. Eleven DNA bands differently methylated were found in starved plants. Of these, five sequences showed significant alignment to barley genes encoding for a glucosyltransferase, a putative acyl carrier protein, a peroxidase, a β-glucosidase and a transcription factor containing a Homeodomin. A resupply experiment was carried out on starved barley re-fed at 13 days after sowing (DAS), and it showed that plants did not recover after Fe addition. In fact, Fe absorption and root to shoot translocation capacities were impaired. In addition, resupplied barley showed DNA methylation/demethylation patterns very similar to that of barley grown in Fe deprivation. This last finding is very encouraging because it indicates as these variations/modifications could be transmitted to progenies.
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Affiliation(s)
- Marika Bocchini
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Maria Luce Bartucca
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Simona Ciancaleoni
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Youry Pii
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
- *Correspondence: Emidio Albertini, Department of Agriculture, Food and Environmental Sciences, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Daniele Del Buono
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
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Wang H, Dong B, Jiang J, Fang W, Guan Z, Liao Y, Chen S, Chen F. Characterization of in vitro haploid and doubled haploid Chrysanthemum morifolium plants via unfertilized ovule culture for phenotypical traits and DNA methylation pattern. Front Plant Sci 2014; 5:738. [PMID: 25566305 PMCID: PMC4273617 DOI: 10.3389/fpls.2014.00738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/04/2014] [Indexed: 05/19/2023]
Abstract
Chrysanthemum is one of important ornamental species in the world. Its highly heterozygous state complicates molecular analysis, so it is of interest to derive haploid forms. A total of 2579 non-fertilized chrysanthemum ovules pollinated by Argyranthemum frutescens were cultured in vitro to isolate haploid progeny. One single regenerant emerged from each of three of the 105 calli produced. Chromosome counts and microsatellite fingerprinting showed that only one of the regenerants was a true haploid. Nine doubled haploid derivatives were subsequently generated by colchicine treatment of 80 in vitro cultured haploid nodal segments. Morphological screening showed that the haploid plant was shorter than the doubled haploids, and developed smaller leaves, flowers, and stomata. An in vitro pollen germination test showed that few of the haploid's pollen were able to germinate and those which did so were abnormal. Both the haploid and the doubled haploids produced yellow flowers, whereas those of the maternal parental cultivar were mauve. Methylation-sensitive amplification polymorphism (MSAP) profiling was further used to detect alterations in cytosine methylation caused by the haploidization and/or the chromosome doubling processes. While 52.2% of the resulting amplified fragments were cytosine methylated in the maternal parent's genome, the corresponding proportions for the haploid's and doubled haploids' genomes were, respectively, 47.0 and 51.7%, demonstrating a reduction in global cytosine methylation caused by haploidization and a partial recovery following chromosome doubling.
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Affiliation(s)
- Haibin Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & EquipmentNanjing, China
| | - Bin Dong
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yuan Liao
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & EquipmentNanjing, China
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Yuan JL, Sun HM, Guo GP, Yue JJ, Gu XP. Correlation between DNA methylation and chronological age of Moso bamboo (Phyllostachys heterocycla var. pubescens). Bot Stud 2014; 55:4. [PMID: 28510908 PMCID: PMC5432823 DOI: 10.1186/1999-3110-55-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 08/09/2013] [Indexed: 05/13/2023]
Abstract
BACKGROUND Chronological age is the primary consideration when studying the physiological development, aging, and flowering of bamboo. However, it's difficult to determine bamboo's chronological age if the time of germination is unknown. To investigate the chronological age of bamboo from the genomic DNA methylation profile, methylation-sensitive amplification polymorphism (MSAP) was employed to analyze the genomic DNA methylation of Moso bamboo (Phyllostachys heterocycla var. pubescens) from stands of nine germination-ages, using six primer pairs which have previously been shown to yield methylation rates that reflect the age of Moso bamboo. RESULTS The results showed that the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different, and the increase in genomic DNA methylation rate was consistent with the increase of chronological age. Six primer pairs displayed different genomic DNA methylation rates in Moso bamboo of nine age's group; however, a significantly positive correlation existed among these primer pairs. An integrated index was obtained by performing principal component analysis on the six primer pairs to represent the genomic DNA methylation levels in Moso bamboo of various chronological ages, and a quadratic curve between the chronological age and genomic DNA methylation levels was obtained. CONCLUSIONS Such a relationship between DNA methylation and its chronological age may serve a reference for its aging study in Moso bamboo.
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Affiliation(s)
- Jin-Ling Yuan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang China
| | - Hui-Min Sun
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang China
| | - Guang-Ping Guo
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang China
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang China
| | - Xiao-Ping Gu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang China
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Ba Q, Zhang G, Niu N, Ma S, Wang J. Cytoplasmic effects on DNA methylation between male sterile lines and the maintainer in wheat (Triticum aestivum L.). Gene 2014; 549:192-7. [PMID: 24875418 DOI: 10.1016/j.gene.2014.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 11/24/2013] [Accepted: 01/04/2014] [Indexed: 02/03/2023]
Abstract
Male sterile cytoplasm plays an important role in hybrid wheat, and three-line system including male sterile (A line), its maintainer (B line) and restoring (R line) has played a major role in wheat hybrid production. It is well known that DNA methylation plays an important role in gene expression regulation during biological development in wheat. However, no reports are available on DNA methylation affected by different male sterile cytoplasms in hybrid wheat. We employed a methylation-sensitive amplified polymorphism technique to characterize nuclear DNA methylation in three male sterile cytoplasms. A and B lines share the same nucleus, but have different cytoplasms which is male sterile for the A and fertile for the B. The results revealed a relationship of DNA methylation at these sites specifically with male sterile cytoplasms, as well as male sterility, since the only difference between the A lines and B line was the cytoplasm. The DNA methylation was markedly affected by male sterile cytoplasms. K-type cytoplasm affected the methylation to a much greater degree than T-type and S-type cytoplasms, as indicated by the ratio of methylated sites, ratio of fully methylated sites, and polymorphism between A lines and B line for these cytoplasms. The genetic distance between the cytoplasm and nucleus for the K-type is much greater than for the T- and S-types because the former is between Aegilops genus and Triticum genus and the latter is within Triticum genus between Triticum spelta and Triticum timopheevii species. Thus, this difference in genetic distance may be responsible for the variation in methylation that we observed.
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Affiliation(s)
- Qingsong Ba
- Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, Shaanxi, PR China
| | - Gaisheng Zhang
- Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, Shaanxi, PR China.
| | - Na Niu
- Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, Shaanxi, PR China
| | - Shoucai Ma
- Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, Shaanxi, PR China
| | - Junwei Wang
- Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, Shaanxi, PR China
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Díaz-Freije E, Gestal C, Castellanos-Martínez S, Morán P. The role of DNA methylation on Octopus vulgaris development and their perspectives. Front Physiol 2014; 5:62. [PMID: 24605101 PMCID: PMC3932432 DOI: 10.3389/fphys.2014.00062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 01/31/2014] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is a common regulator of gene expression and development in mammalian and other vertebrate genomes. DNA methylation has been studied so far in a few bivalve mollusk species, finding a wide spectrum of levels. We focused our study in the common octopus, Octopus vulgaris, an important organism for neuroscience, physiology and ethology research as well as for human consumption. We aim to confirm the existence of DNA methylation in O. vulgaris and ultimately, if methylation plays a role in gene regulation during octopus development. We used a genome-wide approach, methylation-sensitive amplified polymorphism (MSAP), firstly in four different tissues from the same specimens from adult benthonic individuals to test whether gene expression is regulated by methylation. Secondly, we tested the hypothesis that methylation underlies development by assessing MSAP patters from paralarvae to adult developmental stages. Our data indicate that octopus genome is widely methylated since clear differences can be observed, and the methylation pattern changes with the development. The statistical analyses showed significant differences in methylation pattern between paralarvae, where higher internal cytosine methylation is observed, and the three other post-hatching stages. This suggests an important role of cytosine methylation during the first step of development, when major morphological changes take place. However, methylation seems to have little effect on gene expression during the benthonic phase, since no significant effect was revealed in the analyses of molecular variance (AMOVA) performed. Our observations highlight the importance of epigenetic mechanisms in the first developmental steps of the common octopus and opens new perspectives to overcome high mortality rate during paralarvae growth. Thus, better understanding the molecular regulation patterns could lead to new approaches that increase the efficiency of husbandry of this emergent species for aquaculture.
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Affiliation(s)
- Eva Díaz-Freije
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo Vigo, Spain
| | - Camino Gestal
- Aquatic Molecular Pathobiology Group, Instituto de Investigaciones Marinas (IIM-CSIC) Vigo, Spain
| | | | - Paloma Morán
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo Vigo, Spain
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Chen X, Hu J, Zhang H, Ding Y. DNA methylation changes in photoperiod-thermo-sensitive male sterile rice PA64S under two different conditions. Gene 2014; 537:143-8. [PMID: 24365594 DOI: 10.1016/j.gene.2013.12.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 12/09/2013] [Accepted: 12/11/2013] [Indexed: 01/03/2023]
Abstract
Epigenetic modification can occur at a high frequency in crop plants and might generate phenotypic variation without changes in DNA sequences. DNA methylation is an important epigenetic modification that may contribute to environmentally-induced phenotypic variations by regulating gene expression. Rice Photoperiod-Thermo-Sensitive Genic Male Sterile (PTGMS) lines can transform from sterility to fertility under lower temperatures and short-day (SD) conditions during anther development. So far, little is known about the DNA methylation variation of PTGMS throughout the genome in rice. In this study, we investigated DNA cytosine methylation alterations in the young panicles of PTGMS line PA64S under two different conditions using methylation sensitive amplified polymorphism (MSAP) method. Compared with the DNA methylation level of PA64S under lower temperatures and SD conditions (fertility), higher methylation was observed in PA64S (sterility). The sequences of 25 differentially amplified fragments were successfully obtained and annotated. Three methylated fragments, which are homologous to D2, NAD7 and psaA, were confirmed by bisulfite sequencing and their expression levels were also evaluated by qPCR. Real time quantitative PCR analysis revealed that five of the six selected methylated genes were downregulated in PA64S (sterility). These results suggested that DNA methylation may be involved in the sterility-fertility transition of PA64S under two different environmental conditions.
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Talukdar R, Nechutova H, Clemens M, Vege SS. Could rising BUN predict the future development of infected pancreatic necrosis? Pancreatology 2013; 13:355-9. [PMID: 23890133 DOI: 10.1016/j.pan.2013.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Infected (peri)pancreatic necrosis (IPN) in acute pancreatitis (AP) is associated with organ failure (OF) and high mortality. There are no established early markers of primary IPN. This study aimed to assess the association of simple parameters with primary IPN in AP. METHODS We retrospectively studied 281 patients with AP admitted to Mayo Clinic hospitals and identified those with microbiologically confirmed infections in (peri)pancreatic necrosis and collections. We defined primary IPN as infection of (peri)pancreatic necrotic tissue that developed before interventions. We recorded admission hematocrit, BMI, BUN, serum creatinine, SIRS score and development of persistent organ failure within 48 h of admission; and performed serial SIRS and BUN calculations for at least 48 h. We used univariate and multivariable analysis to assess associations and expressed results as odds ratio (OR)[95% CI]. RESULTS 27 (9.6%) patients developed IPN, of which 21 (77.7%) had primary IPN. 38.1% had Gram positive, 9.5% Gram negative and 52.3% mixed bacterial infections. Five (23.8%) of the patients with IPN had fungal infection. On univariate analysis, SIRS ≥ 2 at admission, rise in BUN by 5 mg/dL within 48 h of admission, persistence of SIRS for 48 h and development of persistent OF within 48 h of disease had significant association with development of primary IPN with OR (95% CI) of 4.12 (1.53-11.15), 10.25 (3.95-26.61), 1.19 (1.69-10.39) and 7.62 (2.58-21.25) [2-tailed p = 0.004, <0.0001, 0.002 and <0.0001] respectively. On multivariable analysis, only rise in BUN by 5 mg/dL within 48 h of admission was associated with primary IPN (p = 0.007). CONCLUSIONS Rising BUN within 48 h of admission can be used to predict development of primary IPN in AP.
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Affiliation(s)
- Rupjyoti Talukdar
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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Li A, Hu BQ, Xue ZY, Chen L, Wang WX, Song WQ, Chen CB, Wang CG. DNA Methylation in Genomes of Several Annual Herbaceous and Woody Perennial Plants of Varying Ploidy as Detected by MSAP. Plant Mol Biol Report 2011; 29:784-793. [PMID: 24415835 PMCID: PMC3881574 DOI: 10.1007/s11105-010-0280-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Polyploidization is known to accompany altered DNA methylation in higher plants, which plays an important role in gene expression regulation and maintaining genome stability. While the characteristics of DNA methylation in different polyploid plants are still to be elucidated; here, status of genomic DNA methylation in a series of diploid, triploid, and tetraploid annual herbaceous plants (watermelon and Salvia) and woody perennials (pear, Poplar, and loquat) were explored by methylation-specific amplified polymorphism analysis. The results indicated that levels of DNA methylation in triploid watermelon and Salvia were lower than their diploid parents. In triploid Poplar and pear, higher levels of DNA methylation were detected, and no significant difference was observed between triploid and tetraploid in all tested materials. Further data analysis suggested that about half of the total detected sites underwent changes of DNA methylation patterns in triploid watermelons and Salvia, as well as an obvious trend towards demethylation. However, the changes of DNA methylation patterns in three triploid woody perennials were only 17.54-33.40%. This implied that the characteristics of DNA methylation are significantly different during the polyploidization of different plant species. Furthermore, the results suggested that the level of DNA methylation was nonlinearly related to the ploidy level, and triploid plants displayed more interesting DNA methylation status. The characteristics and possible functions of DNA methylation in different ploidy series are further discussed.
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Affiliation(s)
- Ai Li
- College of Life Sciences, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Bao-Quan Hu
- College of Life Sciences, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Zhen-Yi Xue
- College of Life Sciences, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Li Chen
- College of Life Sciences, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Wei-Xing Wang
- College of Horticulture and Landscape, Xi Nan University, Chongqing, 400716 People’s Republic of China
| | - Wen-Qin Song
- College of Life Sciences, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Cheng-Bin Chen
- College of Life Sciences, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Chun-Guo Wang
- College of Life Sciences, Nankai University, Tianjin, 300071 People’s Republic of China
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