Dear Dr. Islam,

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.

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We look forward to receiving your revised submission.

Thanks

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C Anilkumar, Ph.D.

Academic Editor

PLOS ONE

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2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed:

https://doi.org/10.1186/s12284-021-00533-5

https://doi.org/10.1016/j.dib.2024.110176

10.9734/CJAST/2022/v41i333950

In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed.

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Additional Editor Comments:

The manuscript has been reviewed by three expert reviewers. Based on their evaluations, we believe the manuscript may be suitable for publication pending major revisions.

We kindly request that you carefully revise the manuscript in accordance with the reviewers' comments and suggestions. Please submit the revised version along with a detailed point-by-point response outlining how each comment has been addressed.

We look forward to receiving your revised submission.

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?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: The manuscript which looked at identifying of elite rice Lines with better breeding values using genomic prediction and multi-trait Genotype Ideotype Distance Index (MGIDI) for grain yield under irrigation cropping system was well written with good statistical analysis and presentation. However, the tile can be modified to identification of elite rice Lines with better breeding values using genomic prediction and multi-trait Genotype Ideotype Distance Index (MGIDI) for grain yield under irrigation cropping system instead of eco system, because eco system means more than just a field with high level of moisture.

Reviewer #2: Reviewers’ Comments

The manuscript entitled “Identification of Elite Lines of Rice with Better Breeding Values using Genomic Prediction and Multi-trait Genotype Ideotype Distance Index (MGIDI) for grain yield under Irrigated Eco-System” presents breeding strategies to improve rice production under irrigated eco-system. The article is interesting and potentially impactful for researchers worldwide. The content is appropriate, and the authors explain the sections clearly. The study is suitable for publication after the following revisions:

1. In abstract what is DTM? And mention location where this trial was conducted.

2. Use only two data points after decimal in whole MS.

3. All abbreviations explain at least first time like BBS in introduction, follow same pattern in whole MS. Use consistence same abbreviations as GYTH in abstract but fig. 2 used YTH, crossed check all abbreviations in table, figures and MS.

4. For genomic selection use “GS” in whole MS.

5. Many of places have “percent” replace with “%”

6. In introduction mention some earlier study where they use “MGIDI” for genetic gain in other important crops.

7. In material and method: which generation of 200 advanced breeding lines?

8. Need discussion section to improve many sentences of overlapping with results, might be author just give indication of table or figure instead to giving all information again.

9. Discussion section includes why multi season/location is important for estimating breeding value and GS.

10. Overall genotyping related information very less in MS, it should be more emphasis.

11. References are not formatted according to journal special in discussion section.

Reviewer #3: The paper “Identification of Elite Lines of Rice with Better Breeding Values using Genomic Prediction and Multi-trait Genotype Ideotype Distance Index (MGIDI) for grain yield under Irrigated Eco-System‘’ aimed to select elite parental materials and this study evaluated 200 International Rice Research Institute (IRRI) developed advanced breeding lines during 2022 Wet Season (WS-T. Aman) and 2023 Dry Season (DS-Boro) along with two sets of check (10 global and 6 different local for each season) using an alpha lattice design with two replications

The paper is prepared professionally. It includes a well-crafted abstract and an exhaustive introduction that justifies the research undertaken. The introduction points to the deficiencies in the literature on the subject. The aim is clearly defined. Modern analytical methods were used in the research. The discussion of the results is well prepared. The conclusions are well-defined. The illustrative material is appropriate.

In my opinion, the manuscript after minor corrections, will be suitable for publication in a journal.

Detailed comments:

Abstract: Should include some more numeric data obtained from the study

Do not use abbreviations when use first time.

Introduction - The introduction is enough in my opinion. Introduction needs some minor changes

Rice is one of the major cereal grains farmed as a staple diet for more than half of the world's

population. It is a semi-aquatic grass plant that belongs to the Gramineae (Poaceae) family's

genus Oryza. This sentence needs references. I can suggest below ones

Zhang L, Suo L, Shan Y, Wang B (2024). Glutathione alleviates boron toxicity by modulating nitrogen metabolism and boronuptake in rice seedlings. Turkish Journal of Agriculture and Forestry 48 (6): 1011-1022. https://doi.org/10.55730/1300-011X.3237.

Habib, M.A., Azam, M.G., Haque, M.A. et al. Climate-smart rice (Oryza sativa L.) genotypes identification using stability analysis, multi-trait selection index, and genotype-environment interaction at different irrigation regimes with adaptation to universal warming. Sci Rep 14, 13836 (2024). https://doi.org/10.1038/s41598-024-64808-9

The purpose of plant breeding is to assemble more desirable combinations of genes or traits in

new varieties, and parents should have performed as magnificent contributors to one or more

traits that are being targeted in the breeding program [11]. Needs more references. I can suggest below ones

Zafar MM, Razzaq A, Anwar Z, Ijaz A, Zahid M, Iqbal MS, Farid G, Seleiman MF, Zaman RQ, Rauf A, Jiang X(2025). Enhancing salt tolerance and yield potential in cotton: insights from physiological responses, genetic variability, and heterosis. Turkish Journal of Agriculture and Forestry 49 (1): 110-124. https://doi.org/10.55730/1300-011X.3252

Any coordinate of experimental area?????

Tables should be arranged better way?

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what does this mean? ). If published, this will include your full peer review and any attached files.

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Reviewer #1: Yes: Esther Fobi Donkor(PhD)

Reviewer #2: Yes: Gurjeet Singh

Reviewer #3: No

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Identification of Elite Rice Lines with Better Breeding Values using Genomic Prediction and Multi-trait Genotype Ideotype Distance Index (MGIDI) for grain yield under Irrigation Cropping System

PONE-D-25-47900R1

Dear Dr. Islam,

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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Kind regards,

C Anilkumar, Ph.D.

Academic Editor

PLOS One

Additional Editor Comments (optional):

Dear authors,

Thanks for making revisions in the manuscript. I and all three expert reviewers are happy about the revisions made, which improved the manuscript significantly. I recommend for the acceptance of the manuscript for publication.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: The authors have addressed the concerns of the reviewers so the manuscript can be accepted for publication

Reviewer #2: Dear Author,

The authors have carefully addressed all the comments and have no further suggestions.

Reviewer #3: Dear Editor,

The author (s) made all necessary changes and corrections on revised version. I believe that the paper is now ready for publication.

**********

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: Esther Fobi Donkor

Reviewer #2: Yes: Gurjeet Singh

Reviewer #3: No

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