PONE-D-22-06916First assessment of Iranian pomegranate germplasm using targeted metabolites and morphological traits to develop the core collection and modeling of the current and future spatial distribution under climate change conditionsPLOS ONE

Dear Dr. Zeinalabedini,

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PLOS ONE

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Additional Editor Comments:

Dear Authors

Below, please find the reviewers' comments for your paper. You have carried out the corrections as suggested by the reviewer(s).

with Thanks

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Manuscript titled:

First assessment of Iranian pomegranate germplasm using targeted metabolites and morphological traits to develop the core collection and modeling of the current and future spatial distribution under climate change conditions

There are several linguistic and typographical mistakes in this paper that must be corrected.

1. What is novelty in the abstract? It needs improvement

2. Reference should be according to journal format

3. The manuscript must revise with native English speakers because the manuscript contains a lot of mistakes in grammar and structure, for example, Line 302

“The analysis of Spearman coefficient of correlation between morphological and metabolite traits was showed antioxidant activity correlated positively with total phenol”. Rephrase sentence.

4. Line 312. “also reported there was a negative correlation”. Rephrase the sentence.

5. The discussion section is just descriptive of the results, there are no logical reasoning. Give some recent and comprehensive literature in discussion and support the obtained results. Do not give simple biological inference.

6. Do add the following latest references in discussion part for justification of your results, please.

Zarei A (2017). Biochemical and pomological characterization of pomegranate accessions in fars province of Iran. SABRAO J. Breed. Genet. 49(2): 155–167.

Tarinta T, Chanthai S, Lertrat K, Nawata E, Techawongstien S (2020). Identification of the secondary metabolite capsiate in Capsicum germplasm accessions. SABRAO J. Breed. Genet. 52(2):144–157.

Upadyshev MT (2022). Apple cultivars and rootstocks assay for the identification of diverse viruses and healthy genotypes for breeding. SABRAO J. Breed. Genet. 54(1): 79-87. http://doi.org/10.54910/sabrao2022.54.1.8.

Motyleva SM, Medvedev SM, Morozova NG, Kulikov IM (2021). Leaf micromorphological and biochemical features of scab disease in immune and moderately resistant columnar apple (Malus domestica) cultivars. SABRAO J. Breed. Genet. 53(3): 352-366.

Hong-Qun, L. I., Li-Gang, X. I. N. G., & Xie-Ping, S. U. N. (2022). Predicting the potential distribution of Taxus wallichiana var. Mairei under climate change in China using maxent modeling. Pak. J. Bot. 54(4): 1305-1310.

Ahmad, N., Shakil, A., Shinwari, Z. K., Ahmad, I., & Wahab, A. (2022). Phytochemical study and antimicrobial activities of extracts and its derived fractions obtained from Berberis vulgaris L. and Stellaria media L. leaves. Pak. J. Bot. 54(4): 1517-1521.

Regards

Reviewer #2: - In Materials & Methods, authors explained that 152 genotypes selected from 760 genotypes based on the results of Kazemi alamuti et al. [26]. It is better to explain in brief how and why these genotypes selected and present the genotypes name, source/origin (if applicable) as a supplementary Table. I would appreciate to see official reference numbers for all accessions so that they can be order from reference gene banks and benefit for the entire pomegranate scientists community.

- In Materials & Methods, section “Investigation of morphological characteristics”: explain how many plants per genotypes evaluated? Some information about the field? Are there any statistical design? Or just sampled from a tree in a collection site? Please clarify it.

- Line 124, page 6: “The pH measurement was performed using a digital pH meter (Metrohm model) at 21 °C”, pH of what? Clearly explain.

- Fig 4. Spearman correlation matrix of the traits. This figure is difficult for reader to well understanding the relationship between traits. It is recommended to summarized in a Table.

- I strongly recommended to present a Table about some statistical parameters for all measured traits, like as mean, maximum, minimum, standard deviation and coefficient of variation (CV). This can be better explain the amount of variation in the studied germplasm.

- Are there any ANOVA analysis for traits?

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Reviewer #1: Yes: PROF. DR. NAQIB ULLAH KHAN

Reviewer #2: Yes: Reza Talebi

**********

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PONE-D-22-06916R1First assessment of Iranian pomegranate germplasm using targeted metabolites and morphological traits to develop the core collection and modeling of the current and future spatial distribution under climate change conditionsPLOS ONE

Dear Dr. Zeinalabedini,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Jan 27 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: A Confusion:

Its not clear that the Authors incorporated or not the below suggested References, and 2/3 files of the Article are merged, and it not also clear that which one is revised version, please.

6. Do add the following latest references in discussion part for justification of your results, please.

Zarei A (2017). Biochemical and pomological characterization of pomegranate accessions in fars province of Iran. SABRAO J. Breed. Genet. 49(2): 155–167.

Tarinta T, Chanthai S, Lertrat K, Nawata E, Techawongstien S (2020). Identification of the secondary metabolite capsiate in Capsicum germplasm accessions. SABRAO J. Breed. Genet. 52(2):144–157.

Upadyshev MT (2022). Apple cultivars and rootstocks assay for the identification of diverse viruses and healthy genotypes for breeding. SABRAO J. Breed. Genet. 54(1): 79-87. http://doi.org/10.54910/sabrao2022.54.1.8.

Motyleva SM, Medvedev SM, Morozova NG, Kulikov IM (2021). Leaf micromorphological and biochemical features of scab disease in immune and moderately resistant columnar apple (Malus domestica) cultivars. SABRAO J. Breed. Genet. 53(3): 352-366.

Hong-Qun, L. I., Li-Gang, X. I. N. G., & Xie-Ping, S. U. N. (2022). Predicting the potential distribution of Taxus wallichiana var. Mairei under climate change in China using maxent modeling. Pak. J. Bot. 54(4): 1305-1310.

Ahmad, N., Shakil, A., Shinwari, Z. K., Ahmad, I., & Wahab, A. (2022). Phytochemical study and antimicrobial activities of extracts and its derived fractions obtained from Berberis vulgaris L. and Stellaria media L. leaves. Pak. J. Bot. 54(4): 1517-1521.

Reviewer #2: (No Response)

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: PROF. DR. NAQIB Ullah KHAN

Reviewer #2: Yes: Reza Talebi

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: PONE-22-06916 - Review Report - May 31, 2022.doc

PONE-D-22-06916R2First assessment of Iranian pomegranate germplasm using targeted metabolites and morphological traits to develop the core collection and modeling of the current and future spatial distribution under climate change conditionsPLOS ONE

Dear Dr. Zeinalabedini,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Feb 09 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: (No Response)

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: (No Response)

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: (No Response)

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: PROF. DR. NAQIB ULLAH KHAN

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: SABRAO-J-Breed-Genet-533-352-366-MOTYLEVA.pdf

First assessment of Iranian pomegranate germplasm using targeted metabolites and morphological traits to develop the core collection and modeling of the current and future spatial distribution under climate change conditions

PONE-D-22-06916R3

Dear Dr. Zeinalabedini,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Mehdi Rahimi, Ph.D.

Academic Editor

PLOS ONE

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