PONE-D-23-21095Developing adapted wheat lines with broad-spectrum resistance against stem rust: Introgression of Sr59 through backcrossing and selections based on genotyping-by-sequencing dataPLOS ONE

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Additional Editor Comments:

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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: Partly

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

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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 findings reported in this manuscript, along with the material that will be available, is valuable to the wheat research community in providing broad stem rust resistance due to the Sr59 allele that has been transferred into more adapted germplasm. Overall, the science is sound in this manuscript and ready for publication. Throughout, there are a few comments on some grammar mistakes, clarification on figures/tables, and also one little part of the materials and methods. Otherwise, the manuscript is really clear to read, and I congratulate the authors on doing a wonderful job on their research.

Major comments:

The abstract is too long. The limit listed for the journal is 300 words and the current abstract is over 400. I suggest finding a way to only include the most relevant findings for most people who will use these wheat lines. The information on the Ph1 locus could be eliminated from the abstract to reduce word count.

What was the field location used for phenotypic evaluations? Please provide a description, along with coordinates. Part of this research was done in Sweden, Denmark, and the US, which would greatly change the results for this part of the project. Also, please provide a more detailed description of small plots, such as rows, length, type, etc. Also, why was only one replication in the field used?

For all the figures and tables, not enough information is given for each. Please expand with more details for each one. For figure 1: which reference/genome are the physical positions based on, what are the dark red sections, and state that the markers are the three KASP markers. For figure 2: the panel description of a, b, and c doesn’t make what is in the figure so please correct, give a description of the colors used in the figure legend/text section, and more details on this figure. For figure 3, please describe each cluster A-E and make sure it matches what was in the text of the manuscript. For figure 4, please include cluster information. For figure 5, what is the reference used for all the physical positions? For table 1: what is the scale used or the citation for this, please remove the “e” from the end of “note” (I think you meant to say “not available”).

Minor comments:

Line 48: Include scientific name for wheat.

Line 52: Either take out “reached” or “attained”.

Line 54: Random “Wheat.” as its own sentence.

Line 58-59: This sentence doesn’t flow smoothly. It may sound better to rewrite as “…and may cause human health issues and be harmful to the environment [5].”

Line 62: remove “within” and rewrite sentence so has corrected grammar.

Line 71-72: Please fix grammar mistakes in this sentence as well.

Line 73: remove “about” before 35. Otherwise, state “about half”.

Line 115: Please state what type of cultivars these are. The thought behind this suggestion is so readers who are interested in requesting these lines can know what growth type (pretty sure all three are spring) and wheat species (Triticum aestivum).

Line 234: Please state which figure these KASP markers are on (pretty sure it is figure 1). The authors had switched briefly to discussing Figure 2b so it is confusing which one the KASP are on.

Lines 249-251: For figure 3, the clusters are labelled as letters in the figure, which don’t match the numbers in the text. Please change either the text or the figure labelling so they match.

Line 256-258 discusses clusters in Figure 4, but no clusters are labelled in this figure. Please label this figure so it matches the text.

Lines 312-315: Table 3 should be referenced in this section.

Line 334: There is no Figure 3B as stated in the text. Please correct to either figure 3 or the correct figure.

Line 372: Remove “was” after REEDLING#1.

Reviewer #2: TA5094 is the T2DS•2RL translocation line with the stem rust resistance gene Sr59. The present study described the transfer and subsequent evaluation of Sr59 into agronomically better genetic backgrounds using wheat cultivars as backcross parents. This is a necessary step for wheat breeding.

Some suggestions have been placed in the attached file.

A major concern is how to physically map the Sr59 resistance gene on chromosome 2RL (Figure 1). The authors should present a more detailed description.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-23-21095.pdf

Developing adapted wheat lines with broad-spectrum resistance to stem rust: Introgression of Sr59 through backcrossing and selections based on genotyping-by-sequencing data

PONE-D-23-21095R1

Dear Dr. Rahmatov,

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.

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Kind regards,

Pramod Prasad, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

All the revision have been made.

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

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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 #2: (No Response)

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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

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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 #2: The manuscript has been improved largely. The authors have adequately addressed my comments and I feel that this manuscript is now acceptable for publication.

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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.

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 #2: No

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