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Yoo MJ, Ma T, Zhu N, Liu L, Harmon AC, Wang Q, Chen S. Genome-wide identification and homeolog-specific expression analysis of the SnRK2 genes in Brassica napus guard cells. PLANT MOLECULAR BIOLOGY 2016; 91:211-27. [PMID: 26898295 DOI: 10.1007/s11103-016-0456-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/15/2016] [Indexed: 05/22/2023]
Abstract
Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) proteins constitute a small plant-specific serine/threonine kinase family involved in abscisic acid (ABA) signaling and plant responses to biotic and abiotic stresses. Although SnRK2s have been well-studied in Arabidopsis thaliana, little is known about SnRK2s in Brassica napus. Here we identified 30 putative sequences encoding 10 SnRK2 proteins in the B. napus genome and the expression profiles of a subset of 14 SnRK2 genes in guard cells of B. napus. In agreement with its polyploid origin, B. napus maintains both homeologs from its diploid parents. The results of quantitative real-time PCR (qRT-PCR) and reanalysis of RNA-Seq data showed that certain BnSnRK2 genes were commonly expressed in leaf tissues in different varieties of B. napus. In particular, qRT-PCR results showed that 12 of the 14 BnSnRK2s responded to drought stress in leaves and in ABA-treated guard cells. Among them, BnSnRK2.4 and BnSnRK2.6 were of interest because of their robust responsiveness to ABA treatment and drought stress. Notably, BnSnRK2 genes exhibited up-regulation of different homeologs, particularly in response to abiotic stress. The homeolog expression bias in BnSnRK2 genes suggests that parental origin of genes might be responsible for efficient regulation of stress responses in polyploids. This work has laid a foundation for future functional characterization of the different BnSnKR2 homeologs in B. napus and its parents, especially their functions in guard cell signaling and stress responses.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Tianyi Ma
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Ning Zhu
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Lihong Liu
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Alice C Harmon
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA.
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA.
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Chwialkowska K, Nowakowska U, Mroziewicz A, Szarejko I, Kwasniewski M. Water-deficiency conditions differently modulate the methylome of roots and leaves in barley (Hordeum vulgare L.). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1109-21. [PMID: 26739862 PMCID: PMC4753852 DOI: 10.1093/jxb/erv552] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
One of the strategies of plant adaptation to stress is the modulation of gene expression, which may result from the regulation of DNA methylation. This study attempted to characterize and compare the barley methylome of leaves and roots under water-deficiency treatment and in the subsequent rewatering phase. Our results, obtained using methylation-sensitive amplification polymorphism sequencing analysis, indicated that the overall DNA methylation level in the barley genome was high and in general stable under water-deficiency conditions. Nevertheless, numerous differentially methylated sites (DMSs) were induced by stress in the leaves and roots. Equal proportions of novel stress-induced methylation and demethylation events were observed within the genes in the leaves, but new methylations dominated in the roots. Repetitive elements preferentially underwent demethylation in the leaves and novel methylations in the roots. Importantly, rewatering and plant recovery resulted in the reversibility of the majority of stress-induced methylation events, but this process was more efficient in the leaves than in the roots. Different biological processes were enriched within the subsets of the DMSs that were identified in the genic regions of leaves and roots. We assume that the organ specificity of the methylome changes in response to water deficiency might be an important regulatory mechanism that leads to multi-level mechanisms of stress tolerance in barley.
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Affiliation(s)
- Karolina Chwialkowska
- Department of Genetics, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Urszula Nowakowska
- Department of Genetics, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Anna Mroziewicz
- Department of Genetics, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Miroslaw Kwasniewski
- Department of Genetics, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
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Alonso C, Pérez R, Bazaga P, Medrano M, Herrera CM. MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild-growing species. Mol Ecol Resour 2015; 16:80-90. [PMID: 25944158 DOI: 10.1111/1755-0998.12426] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 12/28/2022]
Abstract
Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cytosine methylation in genomic DNA obtained by HPLC analysis. A screening of literature revealed that methylation of cytosines at cleavage sites assayed by MSAP was greater than genome-wide estimates obtained by HPLC, and percentages of methylation at different nucleotide contexts varied within and across species. Concurrent HPLC and MSAP analyses of DNA from 200 individuals of the perennial herb Helleborus foetidus confirmed that methyl-cytosine was more frequent in CCGG contexts than in the genome as a whole. In this species, global methylation was unrelated to methylation at the inner CG site. We suggest that global HPLC and context-specific MSAP methylation estimates provide complementary information whose combination can improve our current understanding of methylation-based epigenetic processes in nonmodel plants.
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Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, Sevilla, 41092, Spain
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Ferreira LJ, Azevedo V, Maroco J, Oliveira MM, Santos AP. Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress. PLoS One 2015; 10:e0124060. [PMID: 25932633 PMCID: PMC4416925 DOI: 10.1371/journal.pone.0124060] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/28/2015] [Indexed: 01/20/2023] Open
Abstract
DNA methylation has been referred as an important player in plant genomic responses to environmental stresses but correlations between the methylome plasticity and specific traits of interest are still far from being understood. In this study, we inspected global DNA methylation levels in salt tolerant and sensitive rice varieties upon salt stress imposition. Global DNA methylation was quantified using the 5-methylcytosine (5mC) antibody and an ELISA-based technique, which is an affordable and quite pioneer assay in plants, and in situ imaging of methylation sites in interphase nuclei of tissue sections. Variations of global DNA methylation levels in response to salt stress were tissue- and genotype-dependent. We show a connection between a higher ability of DNA methylation adjustment levels and salt stress tolerance. The salt-tolerant rice variety Pokkali was remarkable in its ability to quickly relax DNA methylation in response to salt stress. In spite of the same tendency for reduction of global methylation under salinity, in the salt-sensitive rice variety IR29 such reduction was not statistically supported. In 'Pokkali', the salt stress-induced demethylation may be linked to active demethylation due to increased expression of DNA demethylases under salt stress. In 'IR29', the induction of both DNA demethylases and methyltransferases may explain the lower plasticity of DNA methylation. We further show that mutations for epigenetic regulators affected specific phenotypic parameters related to salinity tolerance, such as the root length and biomass. This work emphasizes the role of differential methylome flexibility between salt tolerant and salt sensitive rice varieties as an important player in salt stress tolerance, reinforcing the need to better understand the connection between epigenetic networks and plant responses to environmental stresses.
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Affiliation(s)
- Liliana J. Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780–157 Oeiras, Portugal
| | - Vanessa Azevedo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780–157 Oeiras, Portugal
| | - João Maroco
- UIPES, ISPA-Instituto Universitário, Lisbon, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780–157 Oeiras, Portugal
| | - Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780–157 Oeiras, Portugal
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Busconi M, Colli L, Sánchez RA, Santaella M, De-Los-Mozos Pascual M, Santana O, Roldán M, Fernández JA. AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L.) germplasm. PLoS One 2015; 10:e0123434. [PMID: 25885113 PMCID: PMC4401542 DOI: 10.1371/journal.pone.0123434] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/04/2015] [Indexed: 11/22/2022] Open
Abstract
The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP) and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence) and epigenetic (cytosine methylation) level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12) effective different genotypes), the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28) different effective epigenotypes). The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real) and accessions from the East (Cuenca and Teruel) were clearly recognised.
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Affiliation(s)
- Matteo Busconi
- Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
- BioDNA, Centro di Ricerca sulla biodiversità e sul DNA antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (JAF)
| | - Licia Colli
- Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
- BioDNA, Centro di Ricerca sulla biodiversità e sul DNA antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rosa Ana Sánchez
- IDR-Biotechnology, Universidad de Castilla—La Mancha, Albacete, Spain
| | - Marcela Santaella
- IDR-Biotechnology, Universidad de Castilla—La Mancha, Albacete, Spain
- Centro de Investigación Agraria de Albaladejito, Consejería de Agricultura de Castilla–La Mancha, Cuenca, Spain
| | | | - Omar Santana
- Centro de Investigación Agraria de Albaladejito, Consejería de Agricultura de Castilla–La Mancha, Cuenca, Spain
| | - Marta Roldán
- IDR-Biotechnology, Universidad de Castilla—La Mancha, Albacete, Spain
| | - José-Antonio Fernández
- IDR-Biotechnology, Universidad de Castilla—La Mancha, Albacete, Spain
- * E-mail: (MB); (JAF)
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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. FRONTIERS IN PLANT SCIENCE 2015; 6:514. [PMID: 26217365 PMCID: PMC4496560 DOI: 10.3389/fpls.2015.00514] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [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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