Epigenetic of DNA Methylation Patterns in Lowland and Upland Malaysian Rice Cultivars under Induced Drought and Salinity

Yap, Wai Sum; Yeo, Yang Lin; Lai, Kok Song; Wee, Chien-Yeong

doi:10.1016/j.nbt.2016.06.1299

Cited by 5 publications

(3 citation statements)

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“…Comprehensive studies have showed that plant DNA methylation was predominantly associated with growth and development [ 30 , 31 ], secondary metabolism [ 32 , 33 ] and various stress responses, including salt stress [ 34 , 35 ], drought stress [ 36 , 37 ], and cold stress [ 38 , 39 ]. Since DNA methylation is involved in regulating a wide range of biological processes, DMT genes have been identified and analyzed in several plant species, such as Arabidopsis thaliana [ 40 , 41 ], rice [ 42 , 43 ], maize [ 44 , 45 ], and wheat [ 46 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

Feng

Liu

et al. 2021

BMC Genomics

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Background DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperature-sensitive genic male sterile (P/TGMS) lines play an important role in hybrid seed production of wheat. However, only a few studies have reported on the effect of DMT genes on temperature-sensitive male sterility of wheat. Although DMT genes have been investigated in some plant species, the identification and analysis of DMT genes in wheat (Triticum aestivum L.) based on genome-wide levels have not been reported. Results In this study, a detailed overview of phylogeny of 52 wheat DMT (TaDMT) genes was presented. Homoeolog retention for TaDMT genes was significantly above the average retention rate for whole-wheat genes, indicating the functional importance of many DMT homoeologs. We found that the strikingly high number of TaDMT genes resulted mainly from the significant expansion of the TaDRM subfamily. Intriguingly, all 5 paralogs belonged to the wheat DRM subfamily, and we speculated that tandem duplications might play a crucial role in the TaDRM subfamily expansion. Through the transcriptional analysis of TaDMT genes in a TGMS line BS366 and its hybrids with the other six fertile lines under sterile and fertile conditions, we concluded that TaCMT-D2, TaMET1-B1, and TaDRM-U6 might be involved in male sterility in BS366. Furthermore, a correlation analysis showed that TaMET1-B1 might negatively regulate the expression of TaRAFTIN1A, an important gene for pollen development, so we speculated regarding an epigenetic regulatory mechanism underlying the male sterility of BS366 via the interaction between TaMET1-B1 and TaRAFTIN1A. Conclusions Our findings presented a detailed phylogenic overview of the DMT genes and could provide novel insights into the effects of DMT genes on TGMS wheat.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

Feng

Liu

et al. 2021

BMC Genomics

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“…In addition, the pattern of DNA methylation in different rice cultivars would change under drought stress 30,36 , it was also found that change of methylation pattern in two wheat cultivars was various along with the increase of water deficit, and was especially significant in wheat AK58, furthermore, the change of methylation pattern also exhibited various trends in different potato cultivars under drought stress 37 . Therefore, compared with that of wheat XM13, wheat AK58 might be more rapidly in response to water deficit by the change of DNA methylation.…”

Section: Ck-t1 Ck-t2 Ck-t3 Ck-t4 Ck-t5 Ck-t1 Ck-t2 Ck-t3 Ck-t4 Ck-t5mentioning

confidence: 95%

Responsive changes of DNA methylation in wheat (Triticum aestivum) under water deficit

Duan

Zhu

et al. 2020

Sci Rep

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DnA methylation plays an important role in the growth and development of plant, and would change under different environments. In this study, 5-methyl cytosine (5mC) content and methylation level exhibited tissue specificity in genomic DNA of wheat seedling, and increased significantly in leaf along with the increase of water deficit, which was especially significant in leaf of wheat AK58. Fullmethylation might dominate in genomic DNA of wheat seedling, the increase of full-methylation level under water deficit was significantly higher than that of hemi-methylation level. Under water deficit, DNA methylation of wheat seedling showed significant polymorphism, this polymorphism was always higher in root, especially was higher in root of wheat AK58. Further analysis appeared that changes of DnA methylation in wheat seedling took methylation as principle and demethylation as supplement under water deficit. Therefore, under water deficit, the degree, level and polymorphism of DNA methylation in wheat seedling showed tissue specificity and species specificity, and were higher in wheat AK58 compared with those of wheat XM13, perhaps wheat AK58 could more rapidly respond to water deficit by changes of DNA methylation, which would contribute to reveal molecular mechanism of wheat adapting to water deficit. Growth and development of plant are often influenced by environment, yet some studies indicated that plant could rapidly respond to the change of environment by epigenetic modification 1. As one important mode of epigenetic modifications, DNA methylation could regulate gene expression by changing chromatin structure, DNA conformation, DNA stability, DNA-protein interaction and so on 2. In nuclear genome of plant, about 20-30% cytosines are methylated, and levels of DNA methylation are different in all kinds of tissues, organs or stages 3-5. If DNA methylation is insufficient or increases in plant, growth and phenotype of plant might be aberrant 6-8 , for example, Arabidopsis thaliana would exhibit dwarf plant, smaller leaf, clump growth or maturity decline because of the reduction of DNA methylation, and these aberrant traits may be inherited to filial generation 9. Manning et al. found that DNA hyper-methylation of Cnr point in Tomato would inhibit the maturation of fruit and cause appearance variation of fruit, such as colorless fruit, pericarp absence, etc 6. Furthermore, level and status of DNA methylation might change under stress conditions, such as salt 10-12 , drought 13-15 , low temperature 16 , heavy metal 17 , pathogen 18 , and so on 19. Water deficit could lead to hyper-methylation in Pea and methylation level of second C in CCGG sequence increases by 40% 20 , low temperature would cause methylation and demethylation at some points of CCGG sequence in Oryza sativa 21. Under salt stress, methylation level of cytosine in CCGG sequence would increase by 0.2-17.6% in Rape seed 22 , and methylation level in Manioc would increase significantly 23. Tang et al. also found that drought might cause methylation level d...

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“…Comprehensive studies have showed that plant DNA methylation was predominantly associated with growth and development [30,31], secondary metabolism [32,33] and various stress responses including salt stress [34,35], drought stress [36,37], cold stress [38,39]. Since DNA methylation is involved in regulating a wide range of biological processes, DMT genes have been identi ed and analyzed in several plant species, such as Arabidopsis thaliana [40,41], rice [42,43], maize [44,45], and wheat [46].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Identification and Transcriptional Characterization of Dna Methyltransferases Conferring Temperature-sensitive Male Sterility in Wheat

Feng

Liu

et al. 2020

Preprint

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Background: DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod or/and temperature-sensitive genic male sterile (P/TGMS) lines play an important role in hybrid seed production of wheat. However, only few studies have been reported about the effect of the DMT genes on temperature-sensitive male sterility of wheat. Although DMT genes have been researched in some plant species, the identification and analysis of DMT genes in wheat (Triticum aestivum L.) based on genome-wide levels has not been reported.Results: In this study, a detailed overview of phylogeny of 52 wheat DMT (TaDMT) genes was presented. Homoeolog retention for TaDMT genes was significantly above the average retention rate for whole-wheat genes, indicating the functional importance of many DMT homoeologs. We found that the strikingly high number of TaDMT genes mainly resulted from the significant expansion of TaDRM subfamily. Intriguingly, all 5 paralogs belonged to the wheat DRM subfamily and we speculated tandem duplications might play a crucial role in the TaDRM subfamily expansion. Through the transcriptional analysis of TaDMT genes in a TGMS line BS366 and its hybrids and its hybrids with other six fertile lines under sterile and fertile conditions, we concluded that TaCMT-D2, TaMET1-B1, and TaDRM-U6 might be involved in male sterility in BS366. Furthermore, a correlation analysis showed that TaMET1-B1 might negatively regulate the expression of TaRAFTIN1A, an important gene for pollen development, so we speculated an epigenetic regulatory mechanism underling the male sterility of BS366 by the interaction between TaMET1-B1 and TaRAFTIN1A.Conclusions: Our findings presented a detailed phylogenic overview of the DMT genes and could provide novel insights into the effects of the DMT genes on TGMS wheat.

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Epigenetic of DNA Methylation Patterns in Lowland and Upland Malaysian Rice Cultivars under Induced Drought and Salinity

Cited by 5 publications

References 0 publications

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

Responsive changes of DNA methylation in wheat (Triticum aestivum) under water deficit

Genome-wide Identification and Transcriptional Characterization of Dna Methyltransferases Conferring Temperature-sensitive Male Sterility in Wheat

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