Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.)
, Wajya Ajmal 1, Quratulain Mujahid 2, Maryam Murtaza 1, Mansour Almuqbil 3, Shakira Ghazanfar 1, Muhammad Uzair 1,4, Ayesha Wadood 5, Syed Mohammed Basheeruddin Asdaq 6, Rameesha Abid 1, Ghulam Muhammad Ali 7,* and Muhammad Ramzan Khan 1,*
Round 1
Reviewer 1 Report
This work is well designed and related to the journal but there are a lot of error which need to be addressed.
Abstract is too weak do not reflect the actual picture of the work. Specifically, the authors focused on the methods. Results and conclusions are weekly presented.
Very long sentences are used in the abstract section and I also observed repetition of the same words in a single sentence which must be avoid. Short sentences convey clear message and have less chances of mistakes.
Line 31.. P 0.05 should be corrected.
Line 37 name present full gene names.
Aim is also not clear.
Use word gene or genome in key words instead of cell metabolism.
Line 21 must be revised 34% is not absolute.
Line 53. 25.0 and 27.5 percent authors must be consistent use %.
Introduction section must be revised English language and coherence is very weak.
Must discuss about mRNA and genome wide identification techniques. How it can be helpful in agriculture.
Significance of wheat and threat of draught stress should be discussing.
Present aim of the study at the end of introduction.
Section 2.1 write complete methodology.
Line 199-201 is methodology. Not results the authors should be specific to sections.
Section 3.2 discuss result not the methods.
Tables format must be consistent.
Plant names in the whole MS must be italic.
Discussion must be updated with recent studies and make specific comparison.
Line 499-501 how? And use word study or research.
English language is very weak that must be revised.
Author Response
Response to Reviewer 1 Comments
Point 1: I found that sections 2 & 3 should be re‐organized and be shortened. It may be easier for the readers if the authors define properly the mixture of regression model and the class‐ membership equation first before moving to the computation of the GINI and of the Polarization of subgroups. Sections 2.1 and 2.2 are too long and can be significantly reduced. In section 2.1 the authors assume the condition uk > uj, but this does not appear anywhere else in the calculation of the mixture of regression model. After equation (10) all the other equations are not numbered.
Response 1: Please provide your response for Point 1. (in red)
Point 2: The probability for a given country h to be in a class k should be the proportion of observations (households) in country h that belong to the income class k. On page 9, the first equation (it would be easier for the reader if the equation is numbered) is not exactly the proportion of people because the authors take the sum of the probability. The interpretation of the equation in not obvious. Normally, after estimating a mixture of regression model we have for each observation its estimated probabilities to be classified into the different classes identified. What is often done is to classify a given observation into the class where its estimated probability is higher. In many software this is also the method used that gives us the proportion of people in each of the classes. The authors should explain the equation on page 9 and how to interpret it. Alternatively, they may use the proportion approach which will make the interpretation easier.
Response 2: Please provide your response for Point 2. (in red)
Point 1: Abstract is too weak do not reflect the actual picture of the work. Specifically, the authors focused on the methods. Results and conclusions are weekly presented.
Response 1: Its very good point you raised, the abstract part is changed shown as track changes in menuscript. Results and conclusion are elaborated more clearly.
Point 2: Very long sentences are used in the abstract section and I also observed repetition of the same words in a single sentence which must be avoid. Short sentences convey clear message and have less chances of mistakes.
Response 2: Long sentences in abstract part line 35 to 38 and word repetitions are changed to make sense.
Point 3: Line 31.. P 0.05 should be corrected.
Response 3: P 0.05 is corrected to P < 0.05
Point 4: Line 37 name present full gene names.
Response 4: Gene names 31369563, 25245708, 31369545, 25232126, 19959095, 14320, 25550165, 25270582, 20313737, 20334251 and 25231635 are replaced with full their full names
Point 4: Aim is also not clear.
Response 5: Purpose of this study is clarified by adding some clear sentences such as Moreover, the wheat varieties could be identified as drought resistant/sensitive based on the nature of genes expression levels
Point 6: Use word gene or genome in key words instead of cell metabolism.
Response 6: The term “cell metabolism” is replaced with “genome”. Thank you for the good suggestion.
Point 7: Line 21 must be revised 34% is not absolute.
Response 7: The figure is change to “more than 30%” after carefully reviewing the FAO website material again.
Point 8: Line 53. 25.0 and 27.5 percent authors must be consistent use %.
Response 8: Yes the “percent” word was used on some occasions, but they are now replaced with “%” signs everywhere.
Point 9: Introduction section must be revised English language and coherence is very weak.
Response 9: English language is revised and corrected highlighted as track changes. Moreover, links with each paragraph were re-considered carefully.
Point 10: Must discuss about mRNA and genome wide identification techniques. How it can be helpful in agriculture.
Response 10: Material about the role of mRNA and genome wide identification techniques is added in 75 to 77 line numbers.
Point 11: Significance of wheat and threat of draught stress should be discussing.
Response 11: In terms of nutritional values of wheat, the literature is added in 53 to 60 lines
Point 12: Present aim of the study at the end of introduction.
Response 12: Aim is listed at the end of introduction that is to develop adoptable methodology for other crop studies as well apart from wheat
Point 13: Section 2.1 write complete methodology.
Response 13: In that section, more information is added in the form of detailed material such as how expression data was downloaded and, how conditions were applied for gene screening.
Point 14: Line 199-201 is methodology. Not results the authors should be specific to sections.
Response 14: Good point raised by reviewer, the part is shifted and adjusted in method at 4 page of the document.
Point 15: Section 3.2 discuss result not the methods.
Response 15: The material is changed from line 243 to 251. The text not related to results is erased.
Point 16: Tables format must be consistent.
Response 16: Table formates are made consistent such as of table 3.
Point 17: Plant names in the whole MS must be italic.
Response 17: All plant names are italicized
Point 18: Discussion must be updated with recent studies and make specific comparison.
Response 18: Recent articles are referenced as per reviewer kind suggestions. Discussion is updated specially at the end part.
Point 19: Line 499-501 how? And use word study or research.
Response 19: The drought genes are responding to drought at global scale. So based on their fold change we can screen better lines able to grow in less water environements. That is why this study is cruicial for getting insight about how to get better crop production.
Point 20: English language is very weak that must be revised
Response 20: English language is revised on a number of places, word repeatition, sentence structures are corrected
Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments to the authors:
The paper entitled “Genome-Wide Identification of Potential mRNAs in Drought 2 Response in wheat (Triticum aestivum L.)” is an original research article. The rapid identification of stress-responsive genes through RNA-seq technology has some drawbacks, including inconsistent data generation when compared to other regions of the world. The paper will contribute to the science as well. The article has novelty, and the methods are modern.
The topic selection and research methods of this paper are relatively good. The author has also done a lot of research work, the research content is relatively rich, and the relevant data are also relatively detailed. However, the author lacks sufficient logic in the background analysis, problem generation, problem analysis, and discussion of the results, and some sentences have grammatical errors, which lead to a disconnect between the theme and content of this paper.
1. The abstract should highlight the key points and strengthen the logic between the research background, content, results, analysis, and discussion, rather than listing all the results. Moreover, the highlights and key points of this work should be highlighted in the abstract.
2. The keywords need to be different from the words used in the title of the manuscript.
3. The introduction needs to focus on the literature related to the topic. The point lack in this section is connectivity between the paragraphs and sentences. This section needs detailed attention. In this section, some relevant references needed to be cited i.e. 1) doi: 10.3389/fpls.2022.849618 2) https://doi.org/10.1002/jemt.23182
4. Sort out the structure of the paper. The previous discussion is about the importance of the model simulated outcomes that only took drought into account, discarding samples that had also been exposed to stress and the following research discusses its characteristics and demonstrates that, it will be crucial to increase biomass output and economic yield due to the climate and water availability limits. Isn't the to analyze? Therefore, the paper appears to lack content relevance.
5. The methodology overall is well written and organized
6. The comparative discussion needs to be stronger. Needs more evidence from the previous literature to compare with the current results obtained.
7. Since it is an English paper, the sentences should be smooth and reasonable, and it is best to find an English-speaking expert to check.
Author Response
Point 1. The abstract should highlight the key points and strengthen the logic between the research background, content, results, analysis, and discussion, rather than listing all the results. Moreover, the highlights and key points of this work should be highlighted in the abstract.
Response 1: Results are made short, results and conclusion are elaborated more clearly.
Point 2. The keywords need to be different from the words used in the title of the manuscript.
Response 2: The term “cell metabolism” is replaced with “genome”. Thank you for the good suggestion.
Point 3. The introduction needs to focus on the literature related to the topic. The point lack in this section is connectivity between the paragraphs and sentences. This section needs detailed attention. In this section, some relevant references needed to be cited i.e. 1) doi: 10.3389/fpls.2022.849618 2) https://doi.org/10.1002/jemt.23182
Response 3: Links between paragraphs are made and important reference is added in literature review.
Point 4. Sort out the structure of the paper. The previous discussion is about the importance of the model simulated outcomes that only took drought into account, discarding samples that had also been exposed to stress and the following research discusses its characteristics and demonstrates that, it will be crucial to increase biomass output and economic yield due to the climate and water availability limits. Isn't the to analyze? Therefore, the paper appears to lack content relevance.
Response 4: Although simulated models are discussed just to show their role in addressing environemental stresses in crops, because this study is based on purely utilization of insilico techniques. However, our main purpose in this research was to focus on getting worldwide genes involved in drought response in wheat.
Point 5. The methodology overall is well written and organized
Response 5: Thank you for the appreciation dear reviewer
Point 6. The comparative discussion needs to be stronger. Needs more evidence from the previous literature to compare with the current results obtained.
Response 6: Latest research articles are included in discussion as per the reviewer’s good suggestion. In the end part future perspective is made more clear.
Point 7. Since it is an English paper, the sentences should be smooth and reasonable, and it is best to find an English-speaking expert to check.
Response 7: The english is reviewed by expert and sentence structures, grametical mistakes and typoes are corrected. Repetition of words are avoided in revision of the menuscript
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The authors did not respond well to my previous comments and added some new comments (i never suggested). I dont know why authors send me thier responses without checking my comments.
I suggest revising their MS carefully and giving full attention to reviewer comments/recommendations.
The introduction part is weak and can be extended with recent studies.
The discussion part is messy and needs careful revisions.
References are not well organized.
Author Response
Response to Reviewer 1
----------------------------------------------------
Response to Reviewer 1 Comments: Round 1
Point 1: Abstract is too weak do not reflect the actual picture of the work. Specifically, the authors focused on the methods. Results and conclusions are weekly presented.
Response 1: Thankyou for highlighting this issue, the suggestions have been incorporated in the main manuscript. Results and conclusion are elaborated more clearly.
Point 2: Very long sentences are used in the abstract section and I also observed repetition of the same words in a single sentence which must be avoid. Short sentences convey clear message and have less chances of mistakes.
Response 2: Long sentences in abstract part line 35 to 38 and word repetitions has been changed according to the reviewer’s suggestion.
Point 3: Line 31.. P 0.05 should be corrected.
Response 3: P 0.05 is corrected to P < 0.05
Point 4: Line 37 name present full gene names.
Response 4: Gene names 31369563, 25245708, 31369545, 25232126, 19959095, 14320, 25550165, 25270582, 20313737, 20334251 and 25231635 are replaced with full names, as suggested.
Point 5: Aim is also not clear.
Response 5: Purpose of this study is clarified by adding some clear sentences such as Moreover, the wheat varieties could be identified as drought resistant/sensitive based on the nature of genes expression levels.
Point 6: Use word gene or genome in key words instead of cell metabolism.
Response 6: The term “cell metabolism” is replaced with “genome”. Thank you for the good suggestion.
Point 7: Line 21 must be revised 34% is not absolute.
Response 7: The figure is change to “more than 30%” after carefully reviewing the FAO website material again.
Point 8: Line 53. 25.0 and 27.5 percent authors must be consistent use %.
Response 8: Yes the “percent” word was used on some occasions, but they are now replaced with “%” signs everywhere.
Point 9: Introduction section must be revised English language and coherence is very weak.
Response 9: English language is revised and corrected highlighted as track changes. Moreover, links with each paragraph were re-considered carefully.
Point 10: Must discuss about mRNA and genome wide identification techniques. How it can be helpful in agriculture.
Response 10: This issue has been addressed by adding the role of mRNA and genome wide identification techniques in 75 to 77 line numbers.
Point 11: Significance of wheat and threat of draught stress should be discussing.
Response 11: In terms of nutritional values of wheat, the literature is added in 53 to 60 lines
Point 12: Present aim of the study at the end of introduction.
Response 12: Aim is listed at the end of introduction that is to develop adoptable methodology for other crop studies as well apart from wheat.
Point 13: Section 2.1 write complete methodology.
Response 13: In that section, more information is added in the form of detailed material such as how expression data was downloaded and, how conditions were applied for gene screening.
Point 14: Line 199-201 is methodology. Not results the authors should be specific to sections.
Response 14: Thank you for highlighting this issue, Line 199-201 are shifted and adjusted in method at 4 page of the document.
Point 15: Section 3.2 discuss result not the methods.
Response 15: The material is changed from line 243 to 251. The text not related to results is erased.
Point 16: Tables format must be consistent.
Response 16: Table formates are made consistent such as of table 3.
Point 17: Plant names in the whole MS must be italic.
.Response 17: All plant names are has been italicized in the main manuscript/
Point 18: Discussion must be updated with recent studies and make specific comparison.
Response 18: Recent articles are referenced as per reviewer kind suggestions. Discussion is updated specially at the end part.
Point 19: Line 499-501 how? And use word study or research.
Response 19: The drought genes are responding to drought at global scale. So based on their fold change we can screen better lines able to grow in less water environements. That is why this study is cruicial for getting insight about how to get better crop production.
Point 20: English language is very weak that must be revised
Response 20: English language is revised on a number of places moreover, words repeatition and sentence structures has been corrected.
Response to Reviewer 1
----------------------------------------------------
Response to Reviewer 1 Comments: Round 2
Point 1: The authors did not respond well to my previous comments and added some new comments (i never suggested). I dont know why authors send me their responses without checking my comments.
Response 1: We mistakenly added the new comments, please accept our apologies for providing the inconvenience. We have now incorporated all the suggestions into the manuscript carefully.
Point 2: I suggest revising their MS carefully and giving full attention to reviewer comments/recommendations.
Response 2: We have carfully read the MS and provide all attension to reviewer comments/recommendations.
Point 3: The introduction part is weak and can be extended with recent studies.
Response 3: We have strongly update the introduction part with recent studies and latest refernces
- ‘’Mao, H.; Li, S.; Chen, B.; Jian, C.; Mei, F.; Zhang, Y.; Li, F.; Chen, N.; Li, T.; Du, L. Variation in cis-regulation of a NAC transcription factor contributes to drought tolerance in wheat. Molecular Plant 2022, 15, 276-292.
- Ma, J.; Tang, X.; Sun, B.; Wei, J.; Ma, L.; Yuan, M.; Zhang, D.; Shao, Y.; Li, C.; Chen, K.-M. A NAC transcription factor, TaNAC5D-2, acts as a positive regulator of drought tolerance through regulating water loss in wheat (Triticum aestivum L.). Environmental and Experimental Botany 2022, 196, 104805.
- Wu, Z.; Shen, S.; Wang, Y.; Tao, W.; Zhao, Z.; Hu, X.; Yu, P. Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum. Plants 2022, 11, 2511.
- Pan, Y.; Li, M.; Huang, J.; Pan, W.; Shi, T.; Guo, Q.; Yang, G.; Nie, X. Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat. International Journal of Molecular Sciences 2022, 23, 1405’’.
Point 4: The discussion part is messy and needs careful revisions.
Response 4: We have strongly update the discuusion part
Author Response File: Author Response.docx
Reviewer 2 Report
Revised version is good but newly added references are not linked with the texted and needs carefull revision.
Author Response
The newly added references are linked with the texted.
