Levels of DNA methylation and transcript accumulation in leaves of transgenic maize varieties

Vilperte, Vinicius; Agapito-Tenfen, Sarah Zanon; Wikmark, Odd-Gunnar; Nodari, Rubens Onofre

doi:10.1186/s12302-016-0097-2

Cited by 13 publications

(8 citation statements)

References 87 publications

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“…However, the insertion of the transgene stabilized the massive loss of mC in pOsNAR2.1-OsNAR2.1. The tissue culture process can cause the loss of methylation in both WYJ7 and NP ( Figure 1a) according to both our results and those of Stroud, et al [20], but pOsNAR2.1-OsNAR2.1 in WYJ7 showed stabilization of the loss rather than pUbi-OsNAR2.1 in NP. Therefore, we consider that overexpression of OsNAR2.1 is not the reason behind the stabilization.…”

Section: Discussionsupporting

confidence: 89%

“…Previous research has reported that phenotypes are influenced by both genetic and epigenetic mechanisms [20,55,56]. Epigenetic modifications caused by the tissue culture process occur in an apparently random manner and it is thus difficult to predict phenotypic changes resulting from these modifications [4,5,7,57,58].…”

Section: Discussionmentioning

confidence: 99%

“…However, there is only sporadic research concerning global DNA methylation changes in transgenic plants. Potential global DNA methylation modification occurring in transgenic plants is still largely unexplored [18][19][20][21][22][23]. There have been reports of transgenic plants from different genetic backgrounds having random and undesirable phenotypes [24][25][26].…”

Section: Introductionmentioning

confidence: 99%

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Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?

Fan

Chen

et al. 2020

IJMS

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Transgenic technologies have been applied to a wide range of biological research. However, information on the potential epigenetic effects of transgenic technology is still lacking. Here, we show that the transgenic process can simultaneously induce both genetic and epigenetic changes in rice. We analyzed genetic, epigenetic, and phenotypic changes in plants subjected to tissue culture regeneration, using transgenic lines expressing the same coding sequence from two different promoters in transgenic lines of two rice cultivars: Wuyunjing7 (WYJ7) and Nipponbare (NP). We determined the expression of OsNAR2.1 in two overexpression lines generated from the two cultivars, and in the RNA interference (RNAi) OsNAR2.1 line in NP. DNA methylation analyses were performed on wild-type cultivars (WYJ7 and NP), regenerated lines (CK, T0 plants), segregation-derived wild-type from pOsNAR2.1-OsNAR2.1 (SDWT), pOsNAR2.1-OsNAR2.1, pUbi-OsNAR2.1, and RNAi lines. Interestingly, we observed global methylation decreased in the T0 regenerated line of WYJ7 (CK-WJY7) and pOsNAR2.1-OsNAR2.1 lines but increased in pUbi-OsNAR2.1 and RNAi lines of NP. Furthermore, the methylation pattern in SDWT returned to the WYJ7 level after four generations. Phenotypic changes were detected in all the generated lines except for SDWT. Global methylation was found to decrease by 13% in pOsNAR2.1-OsNAR2.1 with an increase in plant height of 4.69% compared with WYJ7, and increased by 18% in pUbi-OsNAR2.1 with an increase of 17.36% in plant height compared with NP. This suggests an absence of a necessary link between global methylation and the phenotype of transgenic plants with OsNAR2.1 gene over-expression. However, epigenetic changes can influence phenotype during tissue culture, as seen in the massive methylation in CK-WYJ7, T0 regenerated lines, resulting in decreased plant height compared with the wild-type, in the absence of a transformed gene. We conclude that in the transgenic lines the phenotype is mainly determined by the nature and function of the transgene after four generations of transformation, while the global epigenetic modification is dependent on the genetic background. Our research suggests an innovative insight in explaining the reason behind the occurrence of transgenic plants with random and undesirable phenotypes.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?

Fan

Chen

et al. 2020

IJMS

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“…Stable transgene expression and heritability are key factors for the development and application of transgenic crops. Environmental factors, such as soil salinity, water accessibility and temperature all play crucial roles in Bt transgene expression 50 , 51 . Trtikova et al found that the Cry1Ab expression in MON 810 maize under hot/dry stress was significantly lower than that under optimal conditions 52 .…”

Section: Discussionmentioning

confidence: 99%

Elevated CO2 alters transgene methylation not only in promoterregion but also in codingregion of Bt rice under different N-fertilizer levels

Liu

Wang

Chen

et al. 2020

Sci Rep

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The earth has been undergoing climate change, especially in recent years, driven by increasing concentration of atmospheric carbon dioxide (CO2) and rising earth-surface temperature, which could reduce N allocation to Bt toxin for transgenic Bt crops (Bt crops), but the N fertilization is considered to be an effective method to enhance the C–N balance in Bt crops in the case of elevated CO2 in future. DNA methylation not only in promoterregion but also in codingregion of transgene plays a critical role in transgene expression regulation and silencing of transgenic crops. Recent research has emphasized the risks of increased transgene silencing of Bacillus thuringiensis (Bt) rice under elevated CO2. In this study, the effects of elevated CO2 (vs. ambient CO2) on exogenous Bt toxins and transgene expression in promoterregion and codingregion of Bt rice during tillering stage (cv. HH1 expressing fused Cry1Ab/Cry1Ac) were evaluated under three nitrogen (N) fertilizer rate (1/4, 1 and 2 N levels). The aboveground and belowground biomass, and foliar Bt protein content of Bt rice were all significantly increased with the augmentation of N-fertilizer. And elevated CO2 significantly increased belowground biomass, total soluble protein content, transgene methylation levels in promoterregion (P1), and in total of promoterregion(P1) and codingregion (P2 + P3) (i.e., P1 + P2 + P3) at 1 N level, and it also increased transgene methylation levels in codingregion (P2), and in total of promoterregion and codingregion (P1 + P2 + P3) at 2 N level. In addition, elevated CO2 decreased foliar Bt protein content at 1 N level. The transgene methylation levels in promoterregion and codingregion were negatively correlated with Bt-transgene expression level. The methylation level of cytosines located at CG sites was higher than those at CHG and CHH sites in P1, P2 and P3 fragments regardless of the CO2 or N-fertilizer level. The correlation of transgene mehtylation in promoterregion with transgene expression is even stronger than that in codingregion. These data indicate that N fertilization supply will increase the Bt toxin content in transgenic Bt rice, especially under elevated CO2.

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“…In addition to molecular characterization, NGS facilitates transcriptome pro ling [7] and can elucidate the potentially altered expression pro les of genes anking the transgene insert. Recently, highthroughput sequencing combined with "-omics" pro ling technologies, including transcriptomics, proteomics and metabolomics, has been widely used to analyze both target and unexpected effects [8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Genetically Modified Soybean Lines Exhibit Less Transcriptomic Variation Compared to Natural Narieties

Long¹,

Xu²,

Liu³

et al. 2020

Preprint

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BackgroundGenetically modified (GM) soybeans provide a huge amount of food for human consumption and animal feed. However, the possibility of unexpected effects of transgenesis has increased food safety concerns. High-throughput sequencing profiling provides a powerful approach to directly evaluate unintended effects caused by foreign genes.ResultsIn this study, we performed transcriptomic analyses to evaluate differentially expressed genes (DEGs) in individual soybean tissues, including cotyledon (C), germ (G), hypocotyl (H), and radicle (R), instead of using the whole seed, from four GM and three non-GM soybean lines. A total of 3,351 DEGs were identified among the three non-GM soybean lines. When the GM lines were compared with their non-GM parents, 1,836 to 4,551 DEGs were identified. Furthermore, Gene Ontology (GO) analysis of the DEGs showed more abundant categories of GO items (199) among non-GM lines than between GM lines and the non-GM natural varieties (166). Results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most KEGG pathways were the same for the two types of comparisons.ConclusionsThe study successfully employed RNA sequencing to assess the differences in gene expression among four tissues of seven soybean varieties, and the results suggest that transgenes do not induce massive transcriptomic alterations in transgenic soybeans compared with those that exist among natural varieties. This work thus provides important support for safety evaluation of genetically modified soybeans based on seed tissues.

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Levels of DNA methylation and transcript accumulation in leaves of transgenic maize varieties

Cited by 13 publications

References 87 publications

Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?

Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?

Elevated CO2 alters transgene methylation not only in promoterregion but also in codingregion of Bt rice under different N-fertilizer levels

Genetically Modified Soybean Lines Exhibit Less Transcriptomic Variation Compared to Natural Narieties

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