The Role of Plant DNA Methylation in Development, Stress Response, and Crop Breeding

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript entitled „The Role of Plant DNA Methylation in Stress Response and Crop Breeding“ represents a comprehensive review of cytosine methylation dynamics in plants, particularly horticulturally important and its responses to number of both abiotic and biotic stressors. The manuscript is conveniently divided into 7 chapters and a conclusion that describe, perhaps in too many details, the mechanisms of proper maintenance of DNA methylation and the main functions of DNA methylation in plant development and interaction with environment. The final chapter is devoted to the importance and perspectives of DNA methylation in crop breeding. Although several similar review articles have been published in the last two years (the list can be found at the end of the report), the submitted manuscript probably summarizes the issue in the most comprehensive way, often in too many details. Particularly useful are the paragraphs regarding the influence of methylation on flowering and fruit ripening. Regardless, I would have some serious comments about the manuscript

1.      Considerably complex relationships between the components involved in the de novo methylation (section 2.1) could be much better understood using appropriate schemes.

2.      Because this is a review, it should refer to the original sources and not to another review such as: 6. Zhang, M.; Kimatu, J.N.; Xu, K.; Liu, B. DNA cytosine methylation in plant development. J. Genet. Genom. 2010, 37, 1–12. 7. Ashapkin, V.V.; Kutueva, L.I.; Aleksandrushkina, N.I.; Vanyushin, B.F. Epigenetic Mechanisms of Plant Adaptation to Biotic and 792 Abiotic Stresses. Int. J. Mol. Sci. 2020, 21, 7457. 12. Vidalis, A. et al. Methylome evolution in plants. Genome Biol. 17, 264 (2016). 13. Zhu, J. K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 43, 143–166 (2009). 81. Zhang, H. & Zhu, J. K. Active DNA demethylation in plants and animals. Cold Spring Harb. Symp. Quant. Biol. 77, 161–173 921 (2012). 144. Arora H, Singh RK, Sharma S, Sharma N, Panchal A, Das T, Prasad A, Prasad M. DNA methylation dynamics in response to 1043 abiotic and pathogen stress in plants. Plant Cell Rep. 2022 Oct;41(10):1931-1944. 150. Kumar, S., et al. (2020). DNA methylation dynamics under salt stress in crop plants. Plant Physiology and Biochemistry, 157, 1054 192–202. 157. Boyko, A., & Kovalchuk, I. (2010). Transgenerational response to stress in plants and its application for breeding. Journal of 1067 Experimental Botany, 62(3), 633–644. 159. Zhang, H., Lang, Z. & Zhu, J. K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489–506 1071 (2018). And others.

Exceptionally, it is possible to mark "for review citation" in the text.

3.      Figure 1 is almost identical to Figure 1 in the review entitled „DNA methylation dynamics in response to abiotic and pathogen stressin plants“ (Heena Arora 1 · Roshan Kumar Singh1 · Shambhavi Sharma1 · Namisha Sharma1,2 · Anurag Panchal1 · Tuhin Das 1 ·Ashish Prasad 1 · Manoj Prasad1,3). Plant Cell Reports (2022) 41:1931–1944. https://doi.org/10.1007/s00299-022-02901-x). It would be appropriate to sufficiently modify Figure 1 or to include a reference to the relevant publication in the legend.

 

 

Minor comments:

L33. histones-including > histones, including

L34. phosphorylation-which > phosphorylation, which

L46-49. „Within plant genomes, heterochromatic regions, which are rich in transposable elements, are typically highly methylated across all sequence contexts. Conversely, dispersed transposons or repetitive elements in euchromatic arms are predominantly methylated and silenced“. Both sentences say essentially the same thing. Instead of the second sentence, specific differences in the methylation of heterochromatin and euchromatin need to be stated.

L45: This methylation occurs across all three sequence contexts: CG, CHG and CHH (where H represents A, C, or T).,…. >  This methylation occurs across all sequence contexts (CG, CHG and CHH, where H represents A, C, or T).

L61: …are critical for maintaining genomic methylation patterns > are critical for establishing and maintaining genomic methylation patterns

L70: ….a unique mechanism……where?.....perhaps in plants?.......

L77-79: Is that a caption for figure 1?

L142: what means ZMP? - I recommend consistently using the full names of individual factors in brackets after their abbreviations, as is the case for AGO4, IDP…. In contrast, DME is specified in L351 regardless of having been defined previously (L225)

L317-319: „Intriguingly, the pericentromeric regions of A. thaliana and tomato exhibit a context bias in CHH methylation, characterized by low levels of methylated CCG and enrichment in methylated CAA, CTA, or CAT contexts“. This sentence as a whole does not make sense because the pseudosymmetric CCG motif does not belong to the nonsymmetric CHH motifs. It would be appropriate to emphasize somewhere in the text that CG and CWG (a subset of CHG) motifs are symmetrical, whereas CHH motifs are asymmetric. CCG motifs are partially symmetrical, and methylation of the first cytosine is dependent on CG methylation (citation). Therefore, CCG methylation is usually lower than CWG methylation.

L330: …….what means „small RNAs“ ?  genes for small RNAs or small RNAs interact with genomic DNA or chromatin?

L360: „DME-mediated demethylation occurs in androtrophic cells and is accompanied by 359 the downregulation of DDM1“ please insert relevant citation

L362, L529 and L616:  RNA-directed DNA methylation (RdDM). > RdDM the abbreviation that was previously defined is enough. Moreover, it is necessary to unify the meaning of RdDM: either RNA-directed DNA methylation (L362) or RNA-dependent DNA methylation (L529, L616)

L385-387: “Notably, the highest DNA methylation levels are observed in the small columnar cells of the root meristem, potentially due to reduced exposure of peri centromeric chromatin to RdDM factors” (relevant citation)

L455: Tomato (S. lycopersicum) > Tomato

L469: 21st century > 21^st century

L480: CHG and CHH regions > CHG and CHH motifs (sequence contexts)

L489-490: Moreover, it was observed that DNA methylation regulates the activity of plant transit factors under heat stress (relevant citation).

L492: Drought stress typically induces dynamic alterations in DNA methylation across the 492 plant genome, which are negatively correlated with gene expression (relevant citation).

L504: In maize, drought-induced differential methylation was detected via AMP-PCR, with changes predominantly occurring in regions within genes responsible for plant survival functions, such as protein synthesis, DNA repair, and amino acid metabolism (relevant citation).

L510: In alfalfa, a two-stage drought stress regime significantly enhanced drought tolerance compared to a single drought event, a phenomenon associated with methylation remodeling of relevant genes (relevant citation).

L517: This dynamic change usually involves three methylation patterns: CG, CHG, and CHH (C for cytosine and H for non-G bases).> This dynamic change usually involves cytosine methylation in all motifs (CG, CHG, and CHH)

L626: Salicylic acid (SA), a key signaling molecule in plant immunity, exhibits significant changes in the methylation status of genes associated with its biosynthesis and signaling under biotic stress. This sentence needs to be reformulated.

L673: what means „exalleles“? Perhaps epialleles?

Table 1 should list the full names of all organisms

L861: levins>Levins

There are duplicated citations 167 and 168; 82 and 87

The citation 151. (Song, Q., et al. 2019. Role of epigenetics in plant stress responses and adaptation. Plant, Cell & Environment, 42(3), 583–589) cannot be identified anywhere -probably does not exist.

A list of similar review articles published in the last two years:

1.      Epigenetic gene regulation in plants and its potential applications in crop improvement. Heng Zhang & Jian-Kang Zhu  Nature Reviews Molecular Cell Biology (2024)

2.      DNA cytosine methylation dynamics and functional roles in horticultural crops Peipei Liu1,†, Ruie Liu2,†, YapingXu3, Caixi Zhang2, Qingfeng Niu1,* And ZhaoboLang4,*Horticulture Research, 2023, 10: uhad170

https://doi.org/10.1093/hr/uhad170

3.      Recent progress of molecular mechanisms of DNA methylation in plant response to abiotic stress  Xuefang Lu, Yunzhi Liu, Junrong Xu, Xiaojun Liu, Yuzhen Chi, Ruixia Li, Lijuan Mo, Liyu Shi, Shaojing Liang, Wenjin Yu, Changxia Li Environmental and Experimental Botany 218 (2024) 105599

4.      Epigenetic regulations under plant stress: A cereals perspective. Vishal Dinkar a,1, Saurabh Pandey b,1, Amarjeet Kumar c, Aalok Shiv d, Dalpat Lal e, Alka Bharati f, Anjali Joshi g, Sneha Adhikari h, Aparna i, Ashutosh Singh j,*, Pramod Kumar Pandey k, Ajay Kumar Chandra Environmental and Experimental Botany 220 (2024) 105688

5.      Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response. Emanuela Talarico 1,†, Alice Zambelli 2,† , Fabrizio Araniti 2 , Eleonora Greco 1, Adriana Chiappetta 1 and Leonardo Bruno 1,* Epigenomes 2024, 8, 30. https://doi.org/10.3390/epigenomes8030030

6.      Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms. Ming Yin 1,2,†, Shanwen Wang 3,4,†, Yanfang Wang 1,5, Ronghua Wei 6, Yawei Liang 1, Liying Zuo 1, Mingyue Huo 1, Zekai Huang 4, Jie Lang 4, Xiuqin Zhao 1, Fan Zhang 1, Jianlong Xu 1,5 , Binying Fu 1 , Zichao Li 2,*and Wensheng Wang 1,3,5,* Plants 2024, 13, 2700. https://doi.org/10.3390/plants13192700

7.      Insights into the Epigenetic Basis of Plant Salt Tolerance. Dongyu Zhang 1,2,†, Duoqian Zhang 1,2, Yaobin Zhang 1,2,†, Guanlin Li 1,2, Dehao Sun 1,2, Bo Zhou 2,*and Jingrui Li 2,* Int. J. Mol. Sci. 2024, 25, 11698. https://doi.org/10.3390/ijms252111698

8.      Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. Mukhtar Iderawumi Abdulraheem 1,2,3 , Yani Xiong 1,2,3, Abiodun Yusuff Moshood 1,2,3, Gregorio Cadenas-Pliego 4 , Hao Zhang 1 and Jiandong Hu 1,2,3,* Plants 2024, 13, 163. https://doi.org/10.3390/plants13020163

9.      Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops Youfang Fan 1,†, Chao Sun 1,*,†, Kan Yan 2 , Pengcheng Li 1 , Ingo Hein 3, Eleanor M. Gilroy 3, Philip Kear 4 ,Zhenzhen Bi 1, Panfeng Yao 1 , Zhen Liu 1, Yuhui Liu 1 and Jiangping Bai 1,*

10.  DNA Methylation Dynamics in Response to Drought Stress in Crops. Xiaolan Rao, Shengli Yang, Shiyou Lu and Pingfang Yang *Plants 2024, 13, 1977. https://doi.org/10.3390/plants13141977

10.  

Author Response

We appreciate all of the editor’s and the reviewers’ valuable comments and suggestions.

Reviewer comments:

Reviewer #1:

The manuscript entitled “The Role of Plant DNA Methylation in Stress Response and Crop Breeding”represents a comprehensive review of cytosine methylation dynamics in plants, particularly horticulturally important and its responses to number of both abiotic and biotic stressors. The manuscript is conveniently divided into 7 chapters and a conclusion that describe, perhaps in too many details, the mechanisms of proper maintenance of DNA methylation and the main functions of DNA methylation in plant development and interaction with environment. The final chapter is devoted to the importance and perspectives of DNA methylation in crop breeding. Although several similar review articles have been published in the last two years (the list can be found at the end of the report), the submitted manuscript probably summarizes the issue in the most comprehensive way, often in too many details. Particularly useful are the paragraphs regarding the influence of methylation on flowering and fruit ripening. Regardless, I would have some serious comments about the manuscript.

 

Response: Thank you very much for your comments. 

 

 

Major points:

 

1. 1.Considerably complex relationships between the components involved in the de novo methylation (section 2.1) could be much better understood using appropriate schemes.

 

Response: Thank you very much for your comments. We have revised the part of “de novo methylation” as suggested.

 

2. Because this is a review, it should refer to the original sources and not to another review such as: 6. Zhang, M.; Kimatu, J.N.; Xu, K.; Liu, B. DNA cytosine methylation in plant development. J. Genet. Genom. 2010, 37, 1-12. 7. Ashapkin, V.V.; Kutueva, L.I.; Aleksandrushkina, N.I.; Vanyushin, B.F. Epigenetic Mechanisms of Plant Adaptation to Biotic and 792 Abiotic Stresses. Int. J. Mol. Sci. 2020, 21, 7457. 12. Vidalis, A. et al. Methylome evolution in plants. Genome Biol. 17, 264 (2016). 13. Zhu, J. K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 43, 143-66 (2009). 81. Zhang, H. & Zhu, J. K. Active DNA demethylation in plants and animals. Cold Spring Harb. Symp. Quant. Biol. 77, 161-173 921 (2012). 144. Arora H, Singh RK, Sharma S, Sharma N, Panchal A, Das T, Prasad A, Prasad M. DNA methylation dynamics in response to 1043 abiotic and pathogen stress in plants. Plant Cell Rep. 2022 Oct;41(10):1931-1944. 150. Kumar, S., et al. (2020). DNA methylation dynamics under salt stress in crop plants. Plant Physiology and Biochemistry, 157, 1054 192-202. 157. Boyko, A., & Kovalchuk, I. (2010). Transgenerational response to stress in plants and its application for breeding. Journal of 1067 Experimental Botany, 62(3), 633-644. 159. Zhang, H., Lang, Z. & Zhu, J. K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489-506 1071 (2018). And others.

 

Exceptionally, it is possible to mark "for review citation" in the text.

 

Response: Thank you very much for your comments. We have referred the original sources as suggested in current manuscript as suggested.

 

3. Figure 1 is almost identical to Figure 1 in the review entitled “DNA methylation dynamics in response to abiotic and pathogen stressin plants”(Heena Arora 1 Roshan Kumar Singh1  Shambhavi Sharma1 Namisha Sharma1,2 Anurag Panchal1 Tuhin Das 1 Ashish Prasad 1 Manoj Prasad1,3). Plant Cell Reports (2022) 41:1931-1944. https://doi.org/10.1007/s00299-022-02901-x). It would be appropriate to sufficiently modify Figure 1 or to include a reference to the relevant publication in the legend.

 

Response: Thank you very much for your comments. We have included the related reference in the legend.

 

Minor comments:

 

1. L33. histones-including > histones, including

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

2. L34. phosphorylation-which > phosphorylation, which

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

3. L46-49. “Within plant genomes, heterochromatic regions, which are rich in transposable elements, are typically highly methylated across all sequence contexts. Conversely, dispersed transposons or repetitive elements in euchromatic arms are predominantly methylated and silenced”. Both sentences say essentially the same thing. Instead of the second sentence, specific differences in the methylation of heterochromatin and euchromatin need to be stated.

 

Response: Thank you very much for your comments. We have revised the manuscript as suggested as followed: “Euchromatin refers to loosely packed chromatin associated with transcriptionally active genes. DNA methylation within euchromatin predominantly occurs at CpG islands, modulating gene expression by either promoting activation or repressing transcription. Methylation levels are typically low to moderate, serving a dynamic role in the precise regulation of gene activity. This modification is frequently associated with active histone marks, such as H3K4me3, which facilitate transcriptional processes. In contrast, heterochromatin is tightly packed and harbors transcriptionally silent regions, including repetitive DNA and centromeres. DNA methylation in heterochromatin is generally elevated, contributing to gene silencing and the maintenance of genomic stability. This form of methylation is often linked to repressive histone marks, such as H3K9me3, and plays a key role in silencing transposable elements and other repetitive sequences.”

 

4. L45: This methylation occurs across all three sequence contexts: CG, CHG and CHH (where H represents A, C, or T). …> This methylation occurs across all sequence contexts (CG, CHG and CHH, where H represents A, C, or T).

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

5. L61: are critical for maintaining genomic methylation patterns > are critical for establishing and maintaining genomic methylation patterns

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

6. L70: a unique mechanism…. where? perhaps in plants?

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

7. L77-79: Is that a caption for figure 1?

 

Response: Thank you very much for your comments. We have cited the caption for figure 1 in reference 20.

 

8. L142: what means ZMP? - I recommend consistently using the full names of individual factors in brackets after their abbreviations, as is the case for AGO4, IDP. In contrast, DME is specified in L351 regardless of having been defined previously (L225).

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

9. L317-319: “Intriguingly, the pericentromeric regions of A. thaliana and tomato exhibit a context bias in CHH methylation, characterized by low levels of methylated CCG and enrichment in methylated CAA, CTA, or CAT contexts”. This sentence as a whole does not make sense because the pseudosymmetric CCG motif does not belong to the nonsymmetric CHH motifs. It would be appropriate to emphasize somewhere in the text that CG and CWG (a subset of CHG) motifs are symmetrical, whereas CHH motifs are asymmetric. CCG motifs are partially symmetrical, and methylation of the first cytosine is dependent on CG methylation (citation). Therefore, CCG methylation is usually lower than CWG methylation.

Response: Thank you very much for your comments. We have revised it as suggested.

 

10. L330:…what means “small RNAs”?  genes for small RNAs or small RNAs interact with genomic DNA or chromatin?

 

Response: Thank you very much for your comments. We apologize for the mischaracterization here and have removed the “small RNAs”.

 

11. L360: “DME-mediated demethylation occurs in androtrophic cells and is accompanied by 359 the downregulation of DDM1”please insert relevant citation

 

Response: Thank you very much for your comments. We have inserted the relevant citation 105 as suggested.

 

12. L362, L529 and L616:  RNA-directed DNA methylation (RdDM). > RdDM the abbreviation that was previously defined is enough. Moreover, it is necessary to unify the meaning of RdDM: either RNA-directed DNA methylation(L362) or RNA-dependent DNA methylation (L529, L616)

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

13. L385-387: “Notably, the highest DNA methylation levels are observed in the small columnar cells of the root meristem, potentially due to reduced exposure of peri centromeric chromatin to RdDM factors”(relevant citation)

 

Response: Thank you very much for your comments. We have inserted the relevant citation 118 as suggested.

 

14. L455: Tomato (S. lycopersicum)> Tomato

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

15. L469: 21st century > 21st century

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

16. L480: CHG and CHH regions > CHG and CHH motifs (sequence contexts)

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

17. L489-490: Moreover,it was observed that DNA methylation regulates the activity of plant transit factors under heat stress(relevant citation).

 

Response: Thank you very much for your comments. We have inserted the relevant citation 140 as suggested.

 

18. L492: Drought stress typically induces dynamic alterations in DNA methylation across the 492 plant genome, which are negatively correlated with gene expression (relevant citation).

 

Response: Thank you very much for your comments. We have inserted the relevant citation 141 as suggested.

 

19. L504: In maize, drought-induced differential methylation was detected via AMP-PCR, with changes predominantly occurring in regions within genes responsible for plant survival functions, such as protein synthesis, DNA repair, and amino acid metabolism (relevant citation).

 

Response: Thank you very much for your comments. We have inserted the relevant citation 143 as suggested.

 

20. L510: In alfalfa, a two-stage drought stress regime significantly enhanced drought tolerance compared to a single drought event, a phenomenon associated with methylation remodeling of relevant genes (relevant citation).

 

Response: Thank you very much for your comments. We have inserted the relevant citation 144 as suggested.

 

21. L517: This dynamic change usually involves three methylation patterns: CG, CHG, and CHH (C for cytosine and H for non-G bases).> This dynamic change usually involves cytosine methylation in all motifs (CG, CHG, and CHH)

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

22. L626: Salicylic acid (SA), a key signaling molecule in plant immunity, exhibits significant changes in the methylation status of genes associated with its biosynthesis and signaling under biotic stress.This sentence needs to be reformulated.

 

Response: Thank you very much for your comments. We have reformulated it as suggested.

 

23. L673: what means „exalleles“? Perhapsepialleles?

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

24. Table 1 should list the full names of all organisms

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

25. L861: levins>Levins

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

26. There are duplicated citations 167 and 168; 82 and 87

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

27. The citation 151. (Song, Q., et al. 2019. Role of epigenetics in plant stress responses and adaptation. Plant, Cell & Environment, 42(3), 583–589) cannot be identified anywhere -probably does not exist.

 

Response: Thank you very much for your comments. We have cited the correct references.

 

28. A list of similar review articles published in the last two years:

 

[1] Epigenetic gene regulation in plants and its potential applications in crop improvement. Heng Zhang & Jian-Kang Zhu  Nature Reviews Molecular Cell Biology (2024)

 

[2] DNA cytosine methylation dynamics and functional roles in horticultural crops Peipei Liu1,†, Ruie Liu2,†, YapingXu3, Caixi Zhang2, Qingfeng Niu1,* And ZhaoboLang4,*Horticulture Research, 2023, 10: uhad170

 

[3] Recent progress of molecular mechanisms of DNA methylation in plant response to abiotic stress  Xuefang Lu, Yunzhi Liu, Junrong Xu, Xiaojun Liu, Yuzhen Chi, Ruixia Li, Lijuan Mo, Liyu Shi, Shaojing Liang, Wenjin Yu, Changxia Li Environmental and Experimental Botany 218 (2024) 105599

 

[4] Epigenetic regulations under plant stress: A cereals perspective. Vishal Dinkar a,1, Saurabh Pandey b,1, Amarjeet Kumar c, Aalok Shiv d, Dalpat Lal e, Alka Bharati f, Anjali Joshi g, Sneha Adhikari h, Aparna i, Ashutosh Singh j,*, Pramod Kumar Pandey k, Ajay Kumar Chandra Environmental and Experimental Botany 220 (2024) 105688

 

[5] Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response. Emanuela Talarico 1,†, Alice Zambelli 2,† , Fabrizio Araniti 2 , Eleonora Greco 1, Adriana Chiappetta 1 and Leonardo Bruno 1,* Epigenomes 2024, 8, 30. https://doi.org/10.3390/epigenomes8030030

 

[6] Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms. Ming Yin 1,2,†, Shanwen Wang 3,4,†, Yanfang Wang 1,5, Ronghua Wei 6, Yawei Liang 1, Liying Zuo 1, Mingyue Huo 1, Zekai Huang 4, Jie Lang 4, Xiuqin Zhao 1, Fan Zhang 1, Jianlong Xu 1,5 , Binying Fu 1 , Zichao Li 2,*and Wensheng Wang 1,3,5,* Plants 2024, 13, 2700. https://doi.org/10.3390/plants13192700

 

[7] Insights into the Epigenetic Basis of Plant Salt Tolerance. Dongyu Zhang 1,2,†, Duoqian Zhang 1,2, Yaobin Zhang 1,2,†, Guanlin Li 1,2, Dehao Sun 1,2, Bo Zhou 2,*and Jingrui Li 2,* Int. J. Mol. Sci. 2024, 25, 11698. https://doi.org/10.3390/ijms252111698

 

[8] Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. Mukhtar Iderawumi Abdulraheem 1,2,3 , Yani Xiong 1,2,3, Abiodun Yusuff Moshood 1,2,3, Gregorio Cadenas-Pliego 4 , Hao Zhang 1 and Jiandong Hu 1,2,3,* Plants 2024, 13, 163. https://doi.org/10.3390/plants13020163

 

[9] Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops Youfang Fan 1,†, Chao Sun 1,*,†, Kan Yan 2 , Pengcheng Li 1 , Ingo Hein 3, Eleanor M. Gilroy 3, Philip Kear 4 ,Zhenzhen Bi 1, Panfeng Yao 1 , Zhen Liu 1, Yuhui Liu 1 and Jiangping Bai 1,*

 

[10] DNA Methylation Dynamics in Response to Drought Stress in Crops. Xiaolan Rao, Shengli Yang, Shiyou Lu and Pingfang Yang *Plants 2024, 13, 1977. https://doi.org/10.3390/plants13141977

 

Response: Thank you very much for your comments.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

 

The presented review is devoted to the description of the role of DNA methylation in the development of various plant organs and in responses to biotic and abiotic stressors. The review is written clearly and at a high scientific level. Despite the existence of other reviews devoted to the description of the role of plant DNA methylation (for example, https://doi.org/10.3390/plants13101400, doi: 10.3390/ijms23158299, https://doi.org/10.3389/fpls.2021.596236), the presented review includes some additional information and is of interest to the scientific community. Cited references are recent and relevant. Statements and conclusions are supported by the listed citations. At the same time, a serious drawback of the presented manuscript is the lack of figures, which seriously complicates its reading.

Below, specific comments are described.

1. Line 55. Perhaps not mammals but animals?

2. Line 60. DRM1 is missing from Figure 1.

3. Section 2 is a continuous text and needs figures for each subsection.

4. Section 3 needs references in the text to individual sections of Figure 2 (A-E).

5. Figure 2. Its caption contains point D, devoted to chromosome interactions through pericentromeric regions or heterochromatin islands depend on the methylation of these regions. However, Figure 2D is devoted to (E) the biogenesis of circRNAs. At the same time, the text of the review does not have a full section devoted to the role of DNA methylation in the biogenesis of circRNAs, which is shown in Figure 2.

6. Line 601. Aegilops should be written in italics.

7. Table 1. The table caption should be aligned on both sides.

 

 

Author Response

Reviewer #2:

 

The presented review is devoted to the description of the role of DNA methylation in the development of various plant organs and in responses to biotic and abiotic stressors. The review is written clearly and at a high scientific level. Despite the existence of other reviews devoted to the description of the role of plant DNA methylation (for example, https://doi.org/10.3390/plants13101400, doi: 10.3390/ijms23158299, https://doi.org/10.3389/fpls.2021.596236), the presented review includes some additional information and is of interest to the scientific community. Cited references are recent and relevant. Statements and conclusions are supported by the listed citations. At the same time, a serious drawback of the presented manuscript is the lack of figures, which seriously complicates its reading.

Response: Thank you very much for your comments.

 

1. Line 55. Perhaps not mammals but animals?

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

2. Line 60. DRM1 is missing from Figure 1.

 

Response: Thank you very much for your comments. We have added the DRM1 in the figure1.

 

3. Section 2 is a continuous text and needs figures for each subsection.

 

Response: Thank you very much for your comments. We have added the corresponding images and the corresponding references for Section 2.

 

4. Section 3 needs references in the text to individual sections of Figure 2 (A-E).

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

5. Figure 2. Its caption contains point D, devoted to chromosome interactions through pericentromeric regions or heterochromatin islands depend on the methylation of these regions. However, Figure 2D is devoted to (E) the biogenesis of circRNAs. At the same time, the text of the review does not have a full section devoted to the role of DNA methylation in the biogenesis of circRNAs, which is shown in Figure 2.

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

6. 6. Line 601. Aegilops should be written in italics.

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

7. Table 1. The table caption should be aligned on both sides.

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The authors reviewed the mechanism and role of plant DNA methylation for development and adaptation to the environment. They also propose to use DNA methylation for crop production. The review is worth publication.

 Although the review is nicely organized and easy to read, some additional figures will help readers understand complicated methylation mechanisms and regulations (sections 2-1, 2-3, etc.)

Author Response

Reviewer #3:

 

1. The authors reviewed the mechanism and role of plant DNA methylation for development and adaptation to the environment. They also propose to use DNA methylation for crop production. The review is worth publication.

 

Response: Thank you very much for your comments.

 

2. Although the review is nicely organized and easy to read, some additional figures will help readers understand complicated methylation mechanisms and regulations (sections 2-1, 2-3, etc.)

 

Response: Thank you very much for your comments. We have added the corresponding images and the corresponding references for Section 2.

Reviewer 4 Report

Comments and Suggestions for Authors

agronomy-3369405

The Role of Plant DNA Methylation in Stress Response and Crop Breeding

This is an interesting review that is devoted to the role of DNA cytosine methylation in plant stress response and development. This topic is important and interesting because there are still many blank spots about the role of DNA methylation in plant life. Discoveries in this area may help in the future to develop new technologies to improve the properties of agricultural plants. Therefore, the topic of this review is important. This review is in general well-organized and comprehensive. However, there are several issues that should be addressed to improve this manuscript and make it acceptable for publication.

1) This review lacks references to the literature of recent years, starting in 2019. Please pay special attention to the most recent literature and add references from 2021, 2022, 2023, and 2024. Pay special attention to these years, but it is also useful to add 2019 and 2020. I recommend that you exchange some existing references to the most recent ones in order not to magnify the reference list.

2) Section 6. The role of plant DNA methylation in biological stress.

“Biological stress” is not acceptable term. It is not used in this way. I recommend that it should be changed to “biotic stress” throughout the manuscript.

3) This article pays a lot of attention to the role of dna methylation in plant development, but this is not reflected in the title of the article. I recommend reflecting this in some way in the title.

4) In addition to the above issues, this manuscript contains multiple minor issues that prevent this manuscript from publishing. Please carefully proofread the manuscript and correct such issues. See below some examples. Please note that there are much more such mistakes.

- line 60. MET1,  CMT2,  CMT3,  DRM1 are mentioned first time in the manuscript. Provide full names when you mention an abbreviation first time. For example, MET1 should be methyltransferase 1 (MET1), DRM should be the DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE 1 (DRM1), etc. or on line 63 VIM1, VIM2, and VIM3. = VARIANT IN METHYLATION 1 (VIM1). 

- Check all other abbreviations. 

- I recommend to add Abbreviation list at the end of the manuscript.

- line 70, line 102, line 123, line 336, line 617. “ the RNA-directed DNA methylation (RdDM) pathway. “

RdDM is given in full two times. Line 102, 123, 617 should be only RdDM.

- line 570. Plasmodiophora brassicae should be in italics. Line 648 Linaria vulgaris – should be italics. Check the whole manuscript for such issues with species names.

- line 557. “(such as SOD and CAT).” Enzymes should be given in full when mentioned first time.

- line 589. “transposable elements (TEs).” There are also section “3.2 Transposon silence”. Why you do not use TEs here? Do you understand that “transposons” and “transposable elements” is the same thing? Please unify the terminology related to transponsons throughout the manuscript.

Author Response

Reviewer #4:

 

This is an interesting review that is devoted to the role of DNA cytosine methylation in plant stress response and development. This topic is important and interesting because there are still many blank spots about the role of DNA methylation in plant life. Discoveries in this area may help in the future to develop new technologies to improve the properties of agricultural plants. Therefore, the topic of this review is important. This review is in general well-organized and comprehensive. However, there are several issues that should be addressed to improve this manuscript and make it acceptable for publication.

 

Response: Thank you very much for your comments.

 

1. This review lacks references to the literature of recent years, starting in 2019. Please pay special attention to the most recent literature and add references from 2021, 2022, 2023, and 2024. Pay special attention to these years, but it is also useful to add 2019 and 2020. I recommend that you exchange some existing references to the most recent ones in order not to magnify the reference list.

 

Response: Thank you very much for your comments. We have exchanged the existing references to the most recent ones as suggested.

 

2. Section 6. The role of plant DNA methylation in biological stress. “Biological stress”is not acceptable term. It is not used in this way. I recommend that it should be changed to “biotic stress”throughout the manuscript.

 

Response: Thank you very much for your comments. We have revised it as suggested.

 

3. This article pays a lot of attention to the role of dna methylation in plant development, but this is not reflected in the title of the article. I recommend reflecting this in some way in the title.

 

Response: Thank you very much for your comments. We have revised the title as “The Role of Plant DNA Methylation in Development, Stress Response, and Crop Breeding” as suggested.

 

4. In addition to the above issues, this manuscript contains multiple minor issues that prevent this manuscript from publishing. Please carefully proofread the manuscript and correct such issues. See below some examples. Please note that there are much more such mistakes.

 

Response: Thank you very much for your comments. We have revised them as suggested.

 

4a. line 60. MET1, CMT2, CMT3, DRM1 are mentioned first time in the manuscript. Provide full names when you mention an abbreviation first time. For example, MET1 should be methyltransferase 1 (MET1), DRM should be the DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE 1 (DRM1), etc. or on line 63 VIM1, VIM2, and VIM3. = VARIANT IN METHYLATION 1 (VIM1).

 

- Check all other abbreviations.

 

- I recommend to add Abbreviation list at the end of the manuscript.

 

Response: Thank you very much for your comments. We have revised them as suggested.

 

4b. line 70, line 102, line 123, line 336, line 617. ”the RNA-directed DNA methylation (RdDM) pathway. ”

RdDM is given in full two times. Line 102, 123, 617 should be only RdDM.

 

Response: Thank you very much for your comments. We have revised them as suggested.

 

4c. line 570. Plasmodiophora brassicae should be in italics. Line 648 Linaria vulgaris-should be italics. Check the whole manuscript for such issues with species names.

 

Response: Thank you very much for your comments. We have revised them as suggested.

 

4d. line 557. “(such as SOD and CAT).” Enzymes should be given in full when mentioned first time.

 

Response: Thank you very much for your comments. We have revised them as suggested.

 

4e. line 589. “transposable elements (TEs).” There are also section “3.2 Transposon silence”. Why you do not use TEs here? Do you understand that “transposons” and “transposable elements” is the same thing? Please unify the terminology related to transponsons throughout the manuscript.

 

Response: Thank you very much for your comments. We have revised them as suggested.

 

Author Response File: Author Response.pdf

Round 2

Reviewer 4 Report

Comments and Suggestions for Authors

Most my comments have been appropriately addressed. The manuscript has been considerably improved. However, I recommend that the abbreviations on the Figures 1, 2, and 3 should be provided and explained  in full names in the legends to the Figures (e. g. ROS1, DME, RDR6 etc. ) or abbreviation list should be included at the end of the manuscript for all main abbreviations. This can be done at the proofs stage.