PONE-D-23-12677Developing climate-resilient rice varieties (BRRI dhan97 and BRRI dhan99) suitable for salt stress environments in BangladeshPLOS ONE

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PLOS ONE

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Reviewers' comments:

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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: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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: No

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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: The study on Developing climate-resilient rice varieties (BRRI dhan97 and BRRI dhan99) suitable for salt stress environments in Bangladesh is worthy of investigation and reporting in understanding further this complex abiotic stress affecting rice productivity severely. Study has successfully released two high yielding rice cultivars for salinity prone areas in Bangladesh. However, there are major corrections and supporting data is needed to validate the current study. The comments are appended below:

1- Authors has tested a set of lines in salinity 'hotspot' locations with tolerant and susceptible checks but not provided any yield data of these lines under non stress/ normal conditions. Its very important that line/variety not only perform under stress but also should perform high yielding with acceptable grain quality under non stress conditions.

2- Salinity tolerance in rice is a multifactorial trait highly influenced by environment, correlation with other traits is required to understand how agronomic traits are affecting the yield under salinity.

3- Authors has not provided how breeding values are estimated? It could be explained clearly which lines has shown high breeding value and what basis?

4- Authors has genotyped the lines/ varieties using 20 trait linked SNPs ad mostly these are grain quality traits but what about screening with SNPs linked with seedling stage/ reproductive stage SNPs for salinity? It will be crucial to see the genotyping result for salinity traits also. Is SNPs for salinity traits not available in rice? Include this also in discussion section.

5- What is the year of release of two salinity tolerant rice variety mentioned BRRI dhan97 and BRRI dhan99? Its important to mention in manuscript either it’s a newly released varieties or released long back if so mention the adoption rate in farmers field.

Reviewer #2: The paper is very interesting and good piece of work from shortlisting of elite lines to release varieties for commercial cultivation. However i found certain issues to be improved for its scientific accuracy and recommendations. There is no line number on MS, so difficult to prompt for specific part of MS.

1. There is no clue - how these 12 rice genotypes were selected? What was the basis or past research efforts to choose these 12 genotypes? Arbitrary?

2. Please try to avoid grey sources to cite for big estimates. Do you feel that reference 11 is good enough (working on PGP) to refer as prediction for 2050? Even the reference 12 is a compilation from FAO and other sources. Please doubly check if the narrative is correct. Once satisfied for authenticity of source, then cite. Same issue for reference 4 : "billions of hectares are effected by salinity? Is this correct? How many billion ha?; what percent of total arable area? You mentioned rice is being cultivated in 166 mha globally (not billion), how much of that under salinity?

3. Do you mean salt-responsive as quickly negatively affected by stress? Please clarify.

4. Locations for RYT, ALART and PVT etc could be given in table along with stress ranges to understand the locations easily. (M & M 2.1)

5. Forty to 45 days old seedlings is recommended practice for transplanting in the saline areas? Similarly Zn dose is also lower than usual recommendation (5kg/ha). Is this Bangladesh specific recommendation?

6. ASV doesn't give exact picture. A good breeding program should look for the YSI (Yield stability index which encompass both stability (ASV) and yield ranking). This can be incorporated quickly as it is a derived parameter but improve and strengthen results for inferences. Please calculate and infer based on YSI. This will improve the confusion on yield data vis-a-vis ASV on page 8.

7. In result table 1, 5 and 6; it would be good if authors could add the salinity stress level against the locations to get the inferences from table immediately. This will remove the confusion to say specific site or trial as stressed, for example selected two genotypes yielded 6.24, 6.34 and 6.36 t/ha comparing to tolerant and sensitive checks (6.41 and 6.01 t/ha respectively). [6 t/ha yield under stress is good yield] - page 12. Two of them are having potential to produce >7t/ha under favourable - Page 13. How much BR67 and and BR28 under favourable envt?

8. Page 13 : 2 selected genotypes tolerates 14 dS/m salinity: for how many days comparing to BR67?

9. In fig 3, G10 and G4 are on vertices and on positive side of PC1. But you selected G11 and G4 (table 3). G11 is not shown as winning genotype. Could it be explained please?

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Reviewer #1: Yes: SHAILESH YADAV

Reviewer #2: No

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PONE-D-23-12677R1Developing climate-resilient rice varieties (BRRI dhan97 and BRRI dhan99) suitable for salt stress environments in BangladeshPLOS ONE

Dear Dr. Rahman,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration and based on the reviewers suggestions, I would like to invite you to submit a revised version of the manuscript following minor revision that addresses the points raised during the review process.

Please submit your revised manuscript by Nov 03 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,

Md Ashrafuzzaman, 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: (No Response)

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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

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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

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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: I agree with authors response and changes made in this revised version. Kindly include regional yield trial(RYT) data Table in supplementary section and also include related texts in results section.

Reviewer #2: Authors tried to address the issues raised (reviewer 2) but not addressed in the manuscript. I would like to reiterate that we need redressal of points and their inclusion in the main manuscript.

1. We know the process of varietal release in Bangladesh but it is not known to all the readers. So in the M & M, please include a passing remark in section 2.2 that best performing 12 genotypes are derived from OYT and PYT conducted at XYZ location. If you can, please give the initial numbers of genotypes in OYT and PYT mentioning that: original data on this is not reported, it is acceptable. This way, readers will know that these 12 genotypes are developed through a fixed process (not arbitrary).

2. When i mentioned that please avoid giving grey literature or not use unless very authentic/related reference, authors responded with citation from authorities like Epstein but not included into manuscript. Why? Just to convince me? We need to convince readers. Can a paper on "Plant Growth Promoting" bacteria substantiate it, that too a very low ranking journal? Probably authors could not understand what i wanted to convey. Please do the needful.

3. About my query number 4 on stress status of trail locations. Again Authors tried to respond me through a very vague table. It should be very precise or with range of stress. What is low, medium, high, low to high ? Can authors mention some range atleast and give as supplementary table to strengthen 2.1 section? It should be for all readers (not only for me).

4. About my query 5: there is something wrong with Zn calculation. You mentioned 10-11 kg ZnSO4/ha. But the sentence in section 2.3 says: "Fertilizers were supplied at a rate of 120:19:60: 20:3.6 kg NPKSZn/ha (260-97-120-110-11kg/ha, respectively in the form of urea, TSP, MoP, gypsum, and zinc sulphate)". The minimum Zn is 20% in ZnSO4 and once Zn is heptahydrate or so, the concentration varies. So 3.6 Zn cannot be 11 kg ZnSO4, by any means. So please confirm if 3.6 is correct or 11 kg correct.

5. About query 6 on YSI, i did not find any mention of YSI calculation in M & M. Please include its derivation. When Fig 3 is not able to conclusively select G11; and your selection is based on YSI for G4 and G11; why you donot include the YSI supplementary table 3 as main table in the text. Please do so as this table is the concrete basis of your genotype selection.

6. With reference to my query 7, you did not address what i wanted to do. But if you don't want include the stress level in table 1, 5 and 6 (but it would be better if you do); please respond to my above-mentioned query no.3 with definite range.

7. Few small corrections: under section 2.7 (Chemical property), another abbreviation of ASV used. Please highlight this in section that it is alkali spreading value for grain quality trait. Otherwise, reader may confuse. Another correction in table 3, column 6, 7 and 8 are for grain yield at XYZ location. Please correct it.

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Reviewer #1: Yes: SHAILESH YADAV, Africa Rice Center (AfricaRice), Cote d’Ivoire

Reviewer #2: No

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Developing climate-resilient rice varieties (BRRI dhan97 and BRRI dhan99) suitable for salt stress environments in Bangladesh

PONE-D-23-12677R2

Dear Dr. Akhlasur Rahman,

I am 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,

Md Ashrafuzzaman, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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 #2: All comments have been addressed

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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 #2: Yes

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

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 #2: Yes

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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 #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 #2: Authors have addressed to the queries to my satisfaction, hence it is ready for the publication in PLOS.

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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.

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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 #2: Yes: Rakesh Kumar Singh, Principal Scientist and Program Leader (CDG), ICBA Dubai

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