Dear Dr Hall,

Thank you for submitting your manuscript entitled "Circadian regulation of the transcriptome in a complex polyploid crop" for consideration as a Research Article by PLOS Biology, and apologies again for our delay in sending you an initial decision.

Your manuscript, reviews from Review Commons, and Response to Reviewers have now been evaluated by the PLOS Biology editorial staff. I am writing to let you know that we are, in principle, interested in the study and would therefore like to send your revised manuscript back to the reviewers from Review Commons.

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Lucas

Lucas Smith, Ph.D.

Associate Editor

PLOS Biology

lsmith@plos.org

Dear Dr Hall,

Thank you for your patience while we considered your revised manuscript "Circadian regulation of the transcriptome in a complex polyploid crop" for publication as a Methods and Resources at PLOS Biology. This revised version of your manuscript has been evaluated by the PLOS Biology editors, the Academic Editor and the original reviewers from Review Commons.

You can read the reviewer comments below my signature. As you will see, the reviewers feel the revision has largely addressed their original concerns and they highlight that this is a valuable dataset. However, the reviewers have identified a number of minor issues which we think should be addressed before publication, in a revision that we think will not take very long.

Based on the reviews, we are likely to accept this manuscript for publication, provided you satisfactorily address the remaining points raised by the reviewers.

**IMPORANT: In addition to addressing the reviewer comments please also make sure to address the following data request:

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

Sincerely,

Luke

Lucas Smith, Ph.D.

Associate Editor,

lsmith@plos.org,

PLOS Biology

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Reviewer remarks:

Reviewer #1: I appreciate the work done by Rees et al. to address and respond to my concerns from the first review. This dataset will be a fantastic resource for the community and will hopefully inspire others to perform circadian studies in other crops as well as other cultivars within a species.

I have a few minor comments to improve clarity in the text:

1. In figure 1, panels l-m. It would be helpful to have the color legend directly on the figure to easily identify the subgenomes.

2. This is just a comment, but I love supplemental figure 6 and think this is really cool and a great way to emphasize the importance of time course data and being carefully about assessing subgenome dominance from single time point (or single condition) studies.

3. For Figure 3 and supplemental figure 17, it is difficult to make statements about expression level when there is no statistical support. Given that these are normalized plots without SD showing the variation I would suggest either running a test or de-emphasizing the expression level and focusing more on the period and phase.

4. On line 383 referring to HFR1 expression the Figure reference should be 4e not 4c.

5. The results section on starch metabolism has some redundancies that could be eliminated with a little reorganizing. Currently, starch regulation is explained at the start of the section and then there is a shift to discussing Rubisco and then returning to starch synthases. It would improve flow to bring all the relevant starch metabolism text together.

Reviewer #2: The authors have addressed all of my comments and concerns sufficiently.

In one of the edits a parenthesis needs closing (line 146).

As stated in my first review of this paper on Review Commons I believe that this is a very valuable, and carefully constructed resource to the circadian biology community and beyond, including crop improvement.

Reviewer #3: After revision by the authors, I have no objections to the manuscript.

Dear Dr Hall,

Thank you for the submission of your revised Methods and Resources article, "Circadian regulation of the transcriptome in a complex polyploid crop", for publication in PLOS Biology. On behalf of my colleagues and the Academic Editor, Pamela Ronald, I am pleased to say that we can in principle accept your manuscript for publication, provided you address any remaining formatting and reporting issues. These will be detailed in an email you should receive within 2-3 business days from our colleagues in the journal operations team; no action is required from you until then. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have completed 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, 

Lucas Smith, Ph.D., Ph.D.

Associate Editor

PLOS Biology

lsmith@plos.org