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Song B, Yu J, Li X, Li J, Fan J, Liu H, Wei W, Zhang L, Gu K, Liu D, Zhao K, Wu J. Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement. Genome Biol 2024; 25:87. [PMID: 38581061 PMCID: PMC10996114 DOI: 10.1186/s13059-024-03220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. RESULTS Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening. CONCLUSIONS Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jinshan Yu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jing Fan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Hainan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Weilin Wei
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Lingchao Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Dongliang Liu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China.
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2
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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. FRONTIERS IN PLANT SCIENCE 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] [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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3
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Zhang Y, Liu C, Cheng H, Tian S, Liu Y, Wang S, Zhang H, Saqib M, Wei H, Wei Z. DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems. BMC Genomics 2020; 21:498. [PMID: 32689934 PMCID: PMC7372836 DOI: 10.1186/s12864-020-06902-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/10/2020] [Indexed: 12/24/2022] Open
Abstract
Background As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation. Results The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation. Conclusions DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.
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Affiliation(s)
- Yang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Shuang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Muhammad Saqib
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
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4
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Martins AA, da Silva MF, Pinto LR. Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP). 3 Biotech 2020; 10:265. [PMID: 32509498 DOI: 10.1007/s13205-020-02257-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/13/2020] [Indexed: 01/15/2023] Open
Abstract
The epigenetic diversity of six genotype groups (commercial cultivars, S. officinarum, S. spontaneum, S. robustum, S. barberi, and Erianthus sp.) was assessed through methylation-sensitive amplification polymorphism (MSAP). A total of 1341 MSAP loci were analyzed, of which 1117 (83.29%) were susceptible to cytosine methylation and responsible for a higher proportion of overall diversity among genotypes. The MSAP selective primer combinations captured different proportions of internal and external cytosine methylation loci across genotype groups, while the average external cytosine frequency was higher for all genotype groups. The genotypes were divided into two subpopulations with a high differentiation index (φst = 0.086) based on epigenetic loci. The genotypes were clustered in three subgroups for both methylated and unmethylated loci, considering dissimilarity values. Four methylated fragments (MFs) were randomly selected and subsequently sequenced and compared with sugarcane public databases using BLASTN. MF alignments suggest that cytosine methylation occurs in sugarcane near CpG islands and tandem repeats within transcribed regions and putative cis-regulatory sequences, which assigned functions are associated with stress adaptation. These results provide the first insights about the distribution of this epigenetic mark in sugarcane genome, and suggest a biological relevance of methylated loci.
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Affiliation(s)
| | - Marcel F da Silva
- Instituto Agronômico, Centro de Cana, CP 206, Ribeirão Preto, SP CEP 14001‑970 Brazil
| | - Luciana Rossini Pinto
- Instituto Agronômico, Centro de Cana, CP 206, Ribeirão Preto, SP CEP 14001‑970 Brazil
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5
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Vuković R, Liber Z, Ježić M, Sotirovski K, Ćurković-Perica M. Link between epigenetic diversity and invasive status of south-eastern European populations of phytopathogenic fungus Cryphonectria parasitica. Environ Microbiol 2019; 21:4521-4536. [PMID: 31314941 DOI: 10.1111/1462-2920.14742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Epigenetic modifications may play an important role in invasion and adaptation of clonal and invasive populations to different environments. The aim of this study was to analyse epigenetic diversity and structure within and among populations of invasive pathogenic fungus Cryphonectria parasitica from south-eastern Europe, where one haplotype S12 dominates. The highest level of epigenetic diversity was found in haplotype S1, followed by S2, while the lowest level of epigenetic diversity was found in haplotype S12. Similar pattern of epigenetic diversity was detected in the control, genetically diverse Croatian population where S1 haplotype dominates. In four south-eastern European populations, the highest level of epigenetic diversity was observed in the Italian population, the oldest population in the studied area, while the lowest diversity was found in most recently established Bulgarian population. This relationship between epigenetic diversity and population age implies the important role of epigenetic modifications on the process of invasion. Our data suggest that epigenetic differences might affect the success of expansion of certain haplotype into new regions. Understanding the role of epigenetic processes in expansion and (pre)adaptation of fungal plant pathogens, besides fundamental knowledge, can contribute to development of strategies for control of fungal spread and pathogenesis.
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Affiliation(s)
- Rosemary Vuković
- Department of Biology, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Zlatko Liber
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Kiril Sotirovski
- Faculty of Forestry, Ss. Cyril and Methodius University of Skopje, Skopje, North Macedonia
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6
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The use of MSAP reveals epigenetic diversity of the invasive clonal populations of Arundo donax L. PLoS One 2019; 14:e0215096. [PMID: 30964932 PMCID: PMC6456200 DOI: 10.1371/journal.pone.0215096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/26/2019] [Indexed: 12/18/2022] Open
Abstract
Among the most widespread plant species with clonal reproduction Arundo donax L. represents one of most studied one characterized by very low genetic biodiversity. Although it is a perennial rhizomatous tall grass native to eastern and southern Asia, it spreads only asexually in the invaded range all over the world thriving very well in a large array of pedo-climatic conditions. This ability to morphologically or physiologically adapt to a broad array of conditions could be attributed to epigenetic mechanisms. To shade light on this relevant issue, 96 stems of A. donax from spontaneous populations distributed across the Italian invaded range (island of Sardinia, Northern and Southern Italy) were analysed. Leaf DNAs were extracted and processed through AFLPs and MSAPs for defining either genetic and epigenetic profiles. Both analyses clearly showed that the A. donax populations of Sardinia island are genetically distinct from those of Italian mainland; AFLPs showed an extremely low genetic biodiversity due to vegetative reproduction, whilst, epi-biodiversity, estimated through MSAP marker, increased within the analyzed populations. These results suggest that the capability of A. donax to invade and thrive in diverse environmental conditions can be, at least, partially attributed to a higher epigenetic variability. Therefore, the different DNA methylation status may have significant and important biological meaning, in particular, in the case of invasive clonal plants such as A. donax, also for the biodiversity definition, and MSAP marker can be considered an useful and cost effective marker to reveal it.
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7
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Groot MP, Wagemaker N, Ouborg NJ, Verhoeven KJF, Vergeer P. Epigenetic population differentiation in field- and common garden-grown Scabiosa columbaria plants. Ecol Evol 2018; 8:3505-3517. [PMID: 29607042 PMCID: PMC5869358 DOI: 10.1002/ece3.3931] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/27/2017] [Accepted: 12/06/2017] [Indexed: 12/12/2022] Open
Abstract
Populations often differ in phenotype and these differences can be caused by adaptation by natural selection, random neutral processes, and environmental responses. The most straightforward way to divide mechanisms that influence phenotypic variation is heritable variation and environmental‐induced variation (e.g., plasticity). While genetic variation is responsible for most heritable phenotypic variation, part of this is also caused by nongenetic inheritance. Epigenetic processes may be one of the underlying mechanisms of plasticity and nongenetic inheritance and can therefore possibly contribute to heritable differences through drift and selection. Epigenetic variation may be influenced directly by the environment, and part of this variation can be transmitted to next generations. Field screenings combined with common garden experiments will add valuable insights into epigenetic differentiation, epigenetic memory and can help to reveal part of the relative importance of epigenetics in explaining trait variation. We explored both genetic and epigenetic diversity, structure and differentiation in the field and a common garden for five British and five French Scabiosa columbaria populations. Genetic and epigenetic variation was subsequently correlated with trait variation. Populations showed significant epigenetic differentiation between populations and countries in the field, but also when grown in a common garden. By comparing the epigenetic variation between field and common garden‐grown plants, we showed that a considerable part of the epigenetic memory differed from the field‐grown plants and was presumably environmentally induced. The memory component can consist of heritable variation in methylation that is not sensitive to environments and possibly genetically based, or environmentally induced variation that is heritable, or a combination of both. Additionally, random epimutations might be responsible for some differences as well. By comparing epigenetic variation in both the field and common environment, our study provides useful insight into the environmental and genetic components of epigenetic variation.
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Affiliation(s)
- Maartje P Groot
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - Niels Wagemaker
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - N Joop Ouborg
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO-KNAW) Wageningen The Netherlands
| | - Philippine Vergeer
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands.,Plant Ecology and Nature Conservation Group Wageningen The Netherlands
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Ma K, Sun L, Cheng T, Pan H, Wang J, Zhang Q. Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume. FRONTIERS IN PLANT SCIENCE 2018; 9:41. [PMID: 29441078 PMCID: PMC5797549 DOI: 10.3389/fpls.2018.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/09/2018] [Indexed: 05/23/2023]
Abstract
Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I∗ = 0.575, h∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.
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Affiliation(s)
- Kaifeng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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9
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He S, Xu W, Li F, Wang Y, Liu A. Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean. PLANT DIVERSITY 2017; 39:300-307. [PMID: 30159523 PMCID: PMC6112301 DOI: 10.1016/j.pld.2017.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 05/05/2023]
Abstract
Investigation of the relationships of phenotypic and epigenetic variations might be a good way to dissect the genetic or molecular basis of phenotypic variation and plasticity in plants. Castor bean (Ricinus communis L.), an important non-edible oilseed crop, is a mono-species genus plant in the family Euphorbiaceae. Since it displays rich phenotypic variations with low genetic diversity, castor bean is a good model to investigate the molecular basis of phenotypic and epigenetic variations. Cytosine DNA methylation represents a major molecular mechanism of epigenetic occurrence. In this study, epigenetic diversity of sixty landrace accessions collected worldwide was investigated using the methylation-sensitive amplification polymorphism (MSAP) technique. Results showed that the epigenetic diversity (based on the polymorphism of DNA methylated loci) exhibited a medium variation (Ne = 1.395, He = 0.242, I = 0.366) at the population level though the variation was great, ranging from 3.80% to 34.31% among accessions. Both population structure analysis and the phylogenetic construction (using the neighbor-joining criteria) revealed that the two main clades were identified, but they did not display a distinct geographic structure. After inspecting the location of polymorphic methylated loci on genome we identified that the polymorphic methylated loci occur widely in nuclear and organelle genomes. This study provides new data to understand phenotypic and epigenetic variations in castor bean.
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Affiliation(s)
- Shan He
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fei Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yue Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Aizhong Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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10
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Herrera CM, Medrano M, Bazaga P. Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept. Mol Ecol 2016; 25:1653-64. [PMID: 26850938 DOI: 10.1111/mec.13576] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 11/26/2022]
Abstract
Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
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Ci D, Song Y, Du Q, Tian M, Han S, Zhang D. Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:723-37. [PMID: 26552881 DOI: 10.1093/jxb/erv485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA methylation, one of the best-studied types of chromatin modification, suppresses the expression of transposable elements, pseudogenes, repetitive sequences, and individual genes. However, the extent and variation of genome-wide DNA methylation in natural populations of plants remain relatively unknown. To investigate variation in DNA methylation and whether this variation associates with important plant traits, including leaf shape and photosynthesis, 20 413 DNA methylation sites were examined in a poplar association population (505 individuals) using methylation-sensitive amplification polymorphism (MSAP) technology. Calculation of epi-population structure and kinships assigned individuals into subsets (K=3), revealing that the natural population of P. simonii consists of three subpopulations. Population epigenetic distance and geographic distance showed a significant correlation (r=0.4688, P<0.001), suggesting that environmental factors may affect epigenetics. Single-marker approaches were also used to identify significant marker-trait associations, which found 1087 high-confidence DNA methylation markers associated with different phenotypic traits explaining ~5-15% of the phenotypic variance. Among these loci, 147 differentially methylated fragments were obtained by sequencing, representing 130 candidate genes. Expression analysis of six candidate genes indicated that these genes might play important roles in leaf development and regulation of photosynthesis. This study provides association analysis to study the effects of DNA methylation on plant development and these data indicate that epigenetics bridges environmental and genetic factors in affecting plant growth and development.
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Affiliation(s)
- Dong Ci
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Min Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Shuo Han
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
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Guarino F, Cicatelli A, Brundu G, Heinze B, Castiglione S. Epigenetic Diversity of Clonal White Poplar (Populus alba L.) Populations: Could Methylation Support the Success of Vegetative Reproduction Strategy? PLoS One 2015; 10:e0131480. [PMID: 26147352 PMCID: PMC4492942 DOI: 10.1371/journal.pone.0131480] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/01/2015] [Indexed: 12/30/2022] Open
Abstract
The widespread poplar populations of Sardinia are vegetatively propagated and live in different natural environments forming large monoclonal stands. The main goals of the present study were: i) to investigate/measure the epigenetic diversity of the poplar populations by determining their DNA methylation status; ii) to assess if and how methylation status influences population clustering; iii) to shed light on the changes that occur in the epigenome of ramets of the same poplar clone. To these purposes, 83 white poplar trees were sampled at different locations on the island of Sardinia. Methylation sensitive amplified polymorphism analysis was carried out on the genomic DNA extracted from leaves at the same juvenile stage. The study showed that the genetic biodiversity of poplars is quite limited but it is counterbalanced by epigenetic inter-population molecular variability. The comparison between MspI and HpaII DNA fragmentation profiles revealed that environmental conditions strongly influence hemi-methylation of the inner cytosine. The variable epigenetic status of Sardinian white poplars revealed a decreased number of population clusters. Landscape genetics analyses clearly demonstrated that ramets of the same clone were differentially methylated in relation to their geographic position. Therefore, our data support the notion that studies on plant biodiversity should no longer be restricted to genetic aspects, especially in the case of vegetatively propagated plant species.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, Fisciano, Italia
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, Fisciano, Italia
| | - Giuseppe Brundu
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italia
| | - Berthold Heinze
- Department of Forest Genetics, Austrian Federal Research Centre for Forests, Vienna, Austria
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, Fisciano, Italia
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Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L. Gene 2015; 562:180-7. [DOI: 10.1016/j.gene.2015.02.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 02/01/2023]
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