Dear Dr Gehring,

Thank you for submitting your revised manuscript entitled "RNA Pol IV has antagonistic parent-of-origin effects on Arabidopsis endosperm" for consideration as a Research Article by PLOS Biology along with the Review Commons reports. Thank you also for your patience as we completed our editorial process, and please accept my apologies again for the delay in providing you with our decision due to the Christmas holidays.

Your manuscript has now been evaluated by the PLOS Biology editorial staff as well as by an academic editor with relevant expertise and I am writing to let you know that we would like to send your submission back to the original reviewers. However, we would like to consider it as a Short Report. Please select this article type from the dropdown menu when you complete the metadata.

Before we can send your manuscript to the reviewers, we need you to complete your submission by providing the metadata that is required for full assessment. To this end, please login to Editorial Manager where you will find the paper in the 'Submissions Needing Revisions' folder on your homepage. Please click 'Revise Submission' from the Action Links and complete all additional questions in the submission questionnaire.

Once your full submission is complete, your paper will undergo a series of checks in preparation for peer review. Once your manuscript has passed the checks it will be sent out for review. To provide the metadata for your submission, please Login to Editorial Manager (https://www.editorialmanager.com/pbiology) within two working days, i.e. by Jan 10 2022 11:59PM.

If your manuscript has been previously reviewed at another journal, PLOS Biology is willing to work with those reviews in order to avoid re-starting the process. Submission of the previous reviews is entirely optional and our ability to use them effectively will depend on the willingness of the previous journal to confirm the content of the reports and share the reviewer identities. Please note that we reserve the right to invite additional reviewers if we consider that additional/independent reviewers are needed, although we aim to avoid this as far as possible. In our experience, working with previous reviews does save time.

If you would like to send previous reviewer reports to us, please email me at ialvarez-garcia@plos.org to let me know, including the name of the previous journal and the manuscript ID the study was given, as well as attaching a point-by-point response to reviewers that details how you have or plan to address the reviewers' concerns.

During the process of completing your manuscript submission, you will be invited to opt-in to posting your pre-review manuscript as a bioRxiv preprint. Visit http://journals.plos.org/plosbiology/s/preprints for full details. If you consent to posting your current manuscript as a preprint, please upload a single Preprint PDF.

Given the disruptions resulting from the ongoing COVID-19 pandemic, please expect some delays in the editorial process. We apologise in advance for any inconvenience caused and will do our best to minimize impact as far as possible.

Feel free to email us at plosbiology@plos.org if you have any queries relating to your submission.

Kind regards,

Ines

--

Ines Alvarez-Garcia, PhD

Senior Editor

PLOS Biology

ialvarez-garcia@plos.org

Dear Dr Gehring,

Thank you for submitting your revised Short Report entitled "RNA Pol IV has antagonistic parent-of-origin effects on Arabidopsis endosperm" for publication in PLOS Biology. I have now obtained advice from the original Review Commons reviewers and have discussed their comments with the Academic Editor. 

Based on the reviews (attached below), we will probably accept this manuscript for publication, provided you satisfactorily address the remaining points raised by Reviewer 2. Please also make sure to address the following data and other policy-related requests.

In addition, we would like you to consider a suggestion to improve the title:

"RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm"

As you address these items, please take this last chance to 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 cover letter that accompanies your revised manuscript.

We expect to receive your revised manuscript within two weeks.

To submit your revision, please go to https://www.editorialmanager.com/pbiology/ and log in as an Author. Click the link labelled 'Submissions Needing Revision' to find your submission record. Your revised submission must include the following:

-  a cover letter that should detail your responses to any editorial requests, if applicable, and whether changes have been made to the reference list

-  a Response to Reviewers file that provides a detailed response to the reviewers' comments (if applicable)

-  a track-changes file indicating any changes that you have made to the manuscript. 

NOTE: If Supporting Information files are included with your article, note that these are not copyedited and will be published as they are submitted. Please ensure that these files are legible and of high quality (at least 300 dpi) in an easily accessible file format. For this reason, please be aware that any references listed in an SI file will not be indexed. For more information, see our Supporting Information guidelines:

https://journals.plos.org/plosbiology/s/supporting-information  

*Published Peer Review History*

Please note that you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. Please see here for more details:

https://blogs.plos.org/plos/2019/05/plos-journals-now-open-for-published-peer-review/

*Early Version*

Please note that an uncorrected proof of your manuscript will be published online ahead of the final version, unless you opted out when submitting your manuscript. If, for any reason, you do not want an earlier version of your manuscript published online, uncheck the box. Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us as soon as possible if you or your institution is planning to press release the article.

*Protocols deposition*

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. 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

Please do not hesitate to contact me should you have any questions.

Sincerely,

Ines

--

Ines Alvarez-Garcia, PhD,

Senior Editor,

PLOS Biology

ialvarez-garcia@plos.org

------------------------------------------------------------------------

DATA POLICY: IMPORTANT - PLEASE READ

You may be aware of the PLOS Data Policy, which requires that all data be made available without restriction: http://journals.plos.org/plosbiology/s/data-availability. For more information, please also see this editorial: http://dx.doi.org/10.1371/journal.pbio.1001797 

Note that we do not require all raw data. Rather, we ask that all individual quantitative observations that underlie the data summarized in the figures and results of your paper be made available in one of the following forms:

1) Supplementary files (e.g., excel). Please ensure that all data files are uploaded as 'Supporting Information' and are invariably referred to (in the manuscript, figure legends, and the Description field when uploading your files) using the following format verbatim: S1 Data, S2 Data, etc. Multiple panels of a single or even several figures can be included as multiple sheets in one excel file that is saved using exactly the following convention: S1_Data.xlsx (using an underscore).

2) Deposition in a publicly available repository. Please also provide the accession code or a reviewer link so that we may view your data before publication. 

Regardless of the method selected, please ensure that you provide the individual numerical values that underlie the summary data displayed in the following figure panels as they are essential for readers to assess your analysis and to reproduce it:

Fig. 1A, B, D-F; Fig. 2A-F; Fig. 3B-H; Fig. S1; Fig. S2A-C; Fig. S3B; Fig. S4; Fig. S6A-D; Fig. S7A-D, F; Fig. S8A-F and Fig. S9A, B

NOTE: the numerical data provided should include all replicates AND the way in which the plotted mean and errors were derived (it should not present only the mean/average values).

Please also ensure that figure legends in your manuscript include information on WHERE THE UNDERLYING DATA CAN BE FOUND, and ensure your supplemental data file/s has a legend.

In addition, please provide the accession numbers of the sequencing data submitted to NCBI GEO and make them publicly available at this stay.

Please ensure that your Data Statement in the submission system accurately describes where your data can be found.

-------------------------------------------------------------------------

BLURB

Please also provide a blurb which (if accepted) will be included in our weekly and monthly Electronic Table of Contents, sent out to readers of PLOS Biology, and may be used to promote your article in social media. The blurb should be about 30-40 words long and is subject to editorial changes. It should, without exaggeration, entice people to read your manuscript. It should not be redundant with the title and should not contain acronyms or abbreviations. For examples, view our author guidelines: https://journals.plos.org/plosbiology/s/revising-your-manuscript#loc-blurb

------------------------------------------------------------------

Reviewers' comments

Rev. 1:

I could quibble about how functional significant some of these differences are, but the authors have essentially satisfied my concerns.

Rev. 2: Thomas Städler – note that this reviewer has signed the review

This manuscript is a revised version of a manuscript that I previously reviewed for Review Commons. In my mind, it was a solid piece of work back then, and now has been revised based on the extensive comments by the three original referees. Overall, the Results section has been successfully streamlined, and the Discussion section has been expanded to better reflect the implications of this work. There are, however, some remaining issues that I would like to have addressed before publication.

(1) I am curious as to the omission of parts of all reviewers' comments from the "Response to Referees" part of this submission. For example, in my case, only comments that I listed under the sections "Major Comments" and "Minor Comments" have been replicated and addressed by the authors, whereas the required sections "Evidence, reproducibility and clarity" and "Significance" have been left out. Exactly the same applies to the feedback given by referee 3, and some of the minor comments made by referee 2 are "missing". I can understand that my longish and generally very positive assessment previously made in my "Summary" has gone without specific responses, but I did make specific suggestions in the "Significance" part that I would like to have addressed. I could understand why the authors might feel that including my suggestions would make their paper too speculative, but this should be explicitly stated in the "Responses".

(2) Although I specifically requested that all cited references should include volume and page (or article) numbers, as is the rule for all journals that I am familiar with, Satyaki & Gehring have not delivered, despite their assurances. I count 12 references with such problems, and 2 of those are listed with a single author when in reality there are 4 authors (Grossniklaus et al. 1998) and 6 authors (Köhler et al. 2003), respectively. In addition, in most cases genus and species names are not italicized in the References section, plus a few other formatting issues.

Minor Comments

* Page 3, lines 17-21: the explanation of the rationale underlying the kinship model does not appear to be entirely correct. There might be cases where the inclusive fitness of mothers is not optimal under equal provisioning (e.g. if fathers differ in genetic quality and mothers can somehow sense this); the model's rationale is that relatedness of mothers to all of her offspring is identical, while under a polygamous mating system fathers sire offspring that compete for finite maternal resources with their half-sibs.

* Page 4, 1st paragraph: at first occurrence in the main text, the names of genera should be spelled out (Arabidopsis, Brassica, Capsella).

* Page 16, 1st paragraph of section "Pol IV, conflict, ….": the beginning of this section needs a few citations, as well as more details. I don't think that all viviparous species would qualify; the relationship asymmetry obtains under multiple paternity or, more generally, scales with the degree of relatedness between (multiple) parents.

* Page 18, line 7: technically, Brandvain & Haig (2005) called it "weak inbreeder/strong outbreeder" model.

* Page 18, lines 6-19: this constitutes the new paragraph that the authors inserted in response to my previous comments. There is nothing "wrong" with it but I think it is omitting some recent developments suggesting that the WISO hypothesis needs to be broadened to include differences in levels of parental conflict among obligate outcrossers. In other words, it now appears that differences in the breeding system are not the only factor influencing levels of parental conflict, as recent empirical data in Mimulus (Coughlan et al. 2020, Curr. Biol.) and Solanum (Roth et al. 2019, Genetics; Städler et al. 2021, Curr. Opin. Plant Biol.) suggest that larger differences in effective population size between hybridizing, outbreeding lineages result in greater asymmetry in seed development and levels of seed failure. These aspects are at the core of what I suggested to consider in my previous referee comments (alluded to above under major point 1).

* Page 20, line 9: substitute "were" for "was" at end of line.

* Page 22, line 4: there is a duplicate "that" before "2/3".

* References: the above-mentioned incomplete information concerns Blevins et al. 2015, Gehring et al. 2011, Ji et al. 2014, Kim et al. 2013, Martin 2011, Mi & Thomas 2009, Milbocker & Sink 1969, Panda et al. 2020, Pignatta et al. 2014, 2015.

* Figure S5: the figure legend mentions Schon & Nodine 2017, but the full citation is not given anywhere.

Rev. 3: Steven E. Jacobsen – note that this reviewer has signed the review

The authors have made all of the recommended changes and the paper is ready for publication.

Dear Dr Gehring,

On behalf of my colleagues and the Academic Editor, Xuemei Chen, I am pleased to say that we can in principle accept your Short Reports "RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm" for publication in PLOS Biology, provided you address any remaining formatting and reporting issues. These will be detailed in an email that will follow this letter and that you will usually receive within 2-3 business days, during which time no action is required from you. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have any requested changes.

Please take a minute to log into Editorial Manager at http://www.editorialmanager.com/pbiology/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process.

PRESS

We frequently collaborate with press offices. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximise its impact. If the press office is planning to promote your findings, we would be grateful if they could coordinate with biologypress@plos.org. If you have previously opted in to the early version process, we ask that you notify us immediately of any press plans so that we may opt out on your behalf.

We also ask that you take this opportunity to read our Embargo Policy regarding the discussion, promotion and media coverage of work that is yet to be published by PLOS. As your manuscript is not yet published, it is bound by the conditions of our Embargo Policy. Please be aware that this policy is in place both to ensure that any press coverage of your article is fully substantiated and to provide a direct link between such coverage and the published work. For full details of our Embargo Policy, please visit http://www.plos.org/about/media-inquiries/embargo-policy/.

Thank you again for choosing PLOS Biology for publication and supporting Open Access publishing. We look forward to publishing your study. 

Sincerely, 

Ines

--

Ines Alvarez-Garcia, PhD 

Senior Editor 

PLOS Biology

ialvarez-garcia@plos.org