Epigenetic mechanisms of salt tolerance and heterosis in Upland cotton (Gossypium hirsutum L.) revealed by methylation-sensitive amplified polymorphism analysis

Wang, Baohua; Zhang, Mi; Fu, Rong; Qian, Xiaowei; Rong, Ping; Zhang, Yan; Jiang, Peng; Wang, Junjuan; Lu, Xuke; Wang, Delong; Ye, Wuwei; Zhu, Xinyu

doi:10.1007/s10681-015-1586-x

Cited by 24 publications

(13 citation statements)

References 49 publications

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“…Besides the important role that DNA demethylases play in plant development, growing evidence has suggested that plant responses to environment stresses is also closely related to the level of DNA demethylation [ 21 , 22 , 23 , 24 ]. In recent years, besides model plants Arabidopsis thaliana [ 25 ] and rice [ 26 , 27 , 28 ], many other plant species have been used to study DNA methylation under abiotic stress, such as cotton [ 29 ], sorghum [ 30 ], soybean [ 31 ], tomato [ 32 ], and Populus. trichocarpa [ 33 ], which suggested that DNA methylation plays an important role in regulating plant adaptation to environmental stress.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus

Liu

Lin

et al. 2018

Genes

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DNA methylation plays important roles in genome protection and the regulation of gene expression and it is associated with plants’ responses to environments. DNA demethylases are very important proteins in DNA methylation regulation. In this study, we performed genome-wide and deep analysis of putative demethylases (DMEs) in pear. Seven DME genes were found in the pear genome and were defined as PbDME1–7 based on their domain organization. Results were supported by the gene structural characteristics and phylogenetic analysis. The gene structure of the DME genes were relatively complex and the DME7 proteins didn’t contain the Perm_CXXC domain. The DME genes experienced a whole genome duplication event (WGD) that occurred in the ancestor genome of pear and apple before their divergence based on the Ks values. Expression results showed that high salinity stress could influence the expression level of DMEs and salt-responsive genes in Pyrus betulaefolia. Furthermore, the methylation levels of salt-responsive genes changed under salt stress treatment. Results suggested important roles of PbDME genes in response to salt stress and are useful for better understanding the complex functions of this DME genes, which will facilitate epigenetic studies in pear trees salt tolerance.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus

Liu

Lin

et al. 2018

Genes

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“…First, any RNA was digested using 20 mg/mL RNase for 30 min at room temperature. MSAP detection with the introduced CE was performed as described by Wang et al (2016). The robustness of the three biological replicates for each sample was identified using multiple primers and identical MSAP bands among all three replicates were detected (data not shown).…”

Section: Dna Isolation and Msap Assaymentioning

confidence: 99%

“…Numerous stress-induced differentially methylated regions associated with differentially expressed genes have been found in plants exposed to abiotic (Zhang et al, 2013;Al-Lawati et al, 2016;Wang et al, 2015Wang et al, , 2016 and biotic stresses (Dowen et al, 2012;Shao et al, 2015). Previous studies have identified different trends of DNA methylation under disease stress conditions.…”

Section: Dna Methylation and Disease Stressmentioning

confidence: 99%

“…In this study, we used a capillary electrophoresis (CE)-based methylation-sensitive amplified polymorphism (MSAP, Xiong et al, 1999;Xu et al, 2000) method. This has been shown to be an effective and reliable method for detecting whole-genome DNA methylation (Wang et al, 2015(Wang et al, , 2016. The DNA methylation levels after disease exposure and in a nodisease control were detected in three cotton accessions; two G. hirsutum near-isogenic lines and one Gossypium mustelinum accession.…”

Section: Introductionmentioning

confidence: 99%

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Methylation-sensitive amplified polymorphism analysis of Verticillium wilt-stressed cotton (Gossypium)

et al. 2016

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In this study, a methylation-sensitive amplification polymorphism analysis system was used to analyze DNA methylation level in three cotton accessions. Two disease-sensitive near-isogenic lines, PD94042 and IL41, and one disease-resistant Gossypium mustelinum accession were exposed to Verticillium wilt, to investigate molecular disease resistance mechanisms in cotton. We observed multiple different DNA methylation types across the three accessions following Verticillium wilt exposure. These included hypomethylation, hypermethylation, and other patterns. In general, the global DNA methylation level was significantly increased in the disease-resistant accession G. mustelinum following disease exposure. In contrast, there was no significant difference in the disease-sensitive accession PD94042, and a significant decrease was observed in IL41. Our results suggest that disease-resistant cotton might employ a mechanism to increase methylation level in response to disease stress. The differing methylation patterns, together with the increase in global DNA methylation level, might play important roles in tolerance to Verticillium wilt in cotton. Through cloning and analysis of differently methylated DNA sequences, we were also able to identify several genes that may contribute to disease resistance in cotton. Our results revealed the effect of DNA methylation on cotton disease resistance, and also identified genes that played important roles, which may shed light on the future cotton disease-resistant molecular breeding.

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“…The MSAP method was established in 1997 (Reyna-Lopez et al, 1997 ) and has been effective in many global analyses of DNA methylation in various plant species (Xiong et al, 1999 ; Peraza-Echeverria et al, 2001 ; Chakrabarty et al, 2003 ; Portis et al, 2004 ; Filek et al, 2006 ; Salmon et al, 2008 ; Tan, 2010 ; Wang et al, 2011 ; Guzy-Wrobelska et al, 2013 ; Marconi et al, 2013 ; Tang et al, 2014 ). This method is still widely used in model and non-model plants ( A. thaliana —Li et al, 2015 ; Xu et al, 2015 ; Allium sativum —Gimenez et al, 2016 ; Brassica napus —Gautam et al, 2016 ; Gossypium hirsutum —Wang et al, 2016 ; Malus × Domestica —Kumar et al, 2016 ; O. sativa —Li et al, 2017 ; Vicia faba —Abid et al, 2017 ). Aside from its simplicity and usefulness, MSAP only provides a general overview of the methylation state and does not provide a specific sequence context.…”

Section: Introductionmentioning

confidence: 99%

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

et al. 2017

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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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Epigenetic mechanisms of salt tolerance and heterosis in Upland cotton (Gossypium hirsutum L.) revealed by methylation-sensitive amplified polymorphism analysis

Cited by 24 publications

References 49 publications

Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus

Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus

Methylation-sensitive amplified polymorphism analysis of Verticillium wilt-stressed cotton (Gossypium)

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

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