Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia

Kumpei Shiragaki; Shonosuke Seko; Shuji Yokoi; Takahiro Tezuka

doi:10.1371/journal.pone.0271091

Peer Review History

Original SubmissionApril 11, 2022
20 May 2022 Decision Letter - Tzen-Yuh Chiang, Editor PONE-D-22-10615Capsicum annuum with causal allele of hybrid weakness is prevalent in AsiaPLOS ONE Dear Dr. Tezuka, 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. Please submit your revised manuscript by Jul 04 2022 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, Tzen-Yuh Chiang Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf. 2. We note that Figure 1 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: a) You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].” b) If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only. The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/ The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/ Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/ Landsat: http://landsat.visibleearth.nasa.gov/ USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/# Natural Earth (public domain): http://www.naturalearthdata.com/ 3. 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. [Note: HTML markup is below. Please do not edit.] 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: Yes Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ****** 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 Reviewer #3: Yes ****** 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: Yes Reviewer #3: Yes ****** 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 manuscript is well written and I would like to congratulate the authors to the interesting manuscript and would like to recommend it for publication. the findings reported in the manuscript 'Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia' will have great impact in the field of Capsicum sp. breeding. Reviewer #2: In this manuscript, the authors reported their study of the presence of B or b allele for hybrid weakness in Capsicum annuum accessions from different countries. The work also inculded previous results which had been published in Japanese. Crossing between accessions with different genotypes were performed and SSR markers were analyzed. The experiments were nicely performed, and data were convincing. The manuscript is written in a clean and clear manner, and is easy to follow. I have only a few tiny suggestions. 1. Line 133, "tris" should be "Tris". 2. Line 142, "Mega" should be "MEGA". 3. Lines 84-86, I would suggest to revise it as "We used 94 C. annuum accessions (including 16 C. annuum var. glabriusculum accessions, Table S1), one C. chinese accession...". In this way, readers would not try to find information of other species from Table S1. 4. Line 107, ", Tokyo, Japan" can be removed. It has been introduced for Sakata Seed Co. before (line 88). Reviewer #3: Reproductive isolation, including hybrid weakness, plays an important role in the formation of species.In this manuscript, authors surveyed whether 94 C. annuum accessions had B or b alleles by crossing with C. chinense having the A allele. Of the 94 C. annuum accessions, five had the B allele, three of which were native to Latin America and two were native to Asia. When combined with previous studies, the percentage of B carriers was 41% in Japan, 13% in Asia excluding Japan, 6% in Latin America, and 0% in Europe and Africa. In addition, 48 accessions of C. annuum from various countries were subjected to SSR analysis. Clades with high percentages of B -carriers were formed in the phylogenetic trees. In the principal coordinate analysis, most B -carriers were localized in a single group, although the group also included b -carriers. Based on these results, we presumed that the B allele was acquired in some C. annuum lines in Latin America, and B -carriers were introduced to the world during the Age of Discovery, as along with the b -carriers. The manuscript has been well written. A good result about the B allele from C. annuum has been identified. It would be useful for the relative people to know. (1)Line 61- 62: Capsicum migrated to Europe and Africa from Latin America and to Southeast Asia during the 17–18th centuries from Peru. From my view, “pepper was introduced to Southeast Asia during the 16th centuries probably by Portuguese .” For evidence: In 1542, the Portuguese brought pepper to Goa, India, and pepper began to spread in South Asia. Then it spread to Malacca and spread in Southeast Asia. At the same time, the Spanish brought pepper to Luzon, the Philippines, which is another transmission point of pepper in Southeast Asia (watt, 2014). It was first recorded in Japanese literature that chili was introduced in 1552. Balthazar Gago, a Portuguese missionary, gave it as a gift to daiyo Town, which was then known as Toyoda and Toyoda of Kyushu Island, 39 years earlier than China (Yamamoto, 2018). During the compilation of Korean "history of Korea", it was introduced into the Korean "history of Korea" in 1602. The earliest record of pepper in China can be found in Zunsheng eight notes by Gao Lian of the Ming Dynasty (1591): "pepper is born, white flowers, and the fruit looks like bald pen head. It tastes spicy and red, which is very impressive." Reference: Watt G. 2014. A dictionary of the economic products of India. Landon: Cambridge University Press：197 Yoshimoto Yamamoto (translated by Chen Xian-ruo ). 2018. World history of pepper: a journey across Europe, Asia, and Africa, a hot table revolution. Taiwan:Marco Polo Press：256 (2)Line 114-, “DNA extraction” Whose DNA will be extracted should be mentioned. ****** 6. 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 #1: Yes:** Julia Meitz-Hopkins, PhD Reviewer #2: No Reviewer #3: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0271091.r001
Revision 1
10 Jun 2022 Author Response Dear Dr. Tzen-Yuh Chiang, We would like to thank reviewers for their valuable comments. We revised our manuscript according to their comments. Below, we have included point-by-point responses (black text) to your and reviewers’ comments (blue text). 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. We checked the format of the paper. 2. We note that Figure 1 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). The map in Figure 1 was obtained from OpenStreetMap under Open Data Commons Open Database License. Therefore, we can use the map under the Creative Commons Attribution License. We added a sentence and a link of copyright (lines 172-173). Reviewer #1: The manuscript is well written and I would like to congratulate the authors to the interesting manuscript and would like to recommend it for publication. the findings reported in the manuscript 'Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia' will have great impact in the field of Capsicum sp. breeding. Thank you for reviewing and evaluating our paper. Reviewer #2: In this manuscript, the authors reported their study of the presence of B or b allele for hybrid weakness in Capsicum annuum accessions from different countries. The work also inculded previous results which had been published in Japanese. Crossing between accessions with different genotypes were performed and SSR markers were analyzed. The experiments were nicely performed, and data were convincing. The manuscript is written in a clean and clear manner, and is easy to follow. I have only a few tiny suggestions. Thank you for pointing out some mistakes. We revised each point as follows. 1. Line 133, "tris" should be "Tris". We revised that as you pointed out (line 134). 2. Line 142, "Mega" should be "MEGA". We revised that as you pointed out (line 143). 3. Lines 84-86, I would suggest to revise it as "We used 94 C. annuum accessions (including 16 C. annuum var. glabriusculum accessions, Table S1), one C. chinese accession...". In this way, readers would not try to find information of other species from Table S1. Thank you for suggesting a very nice revision. We revised the sentence as you suggested (line 84-86). 4. Line 107, ", Tokyo, Japan" can be removed. It has been introduced for Sakata Seed Co. before (line 88). We revised that as you pointed out (line 107). Reviewer #3: Reproductive isolation, including hybrid weakness, plays an important role in the formation of species.In this manuscript, authors surveyed whether 94 C. annuum accessions had B or b alleles by crossing with C. chinense having the A allele. Of the 94 C. annuum accessions, five had the B allele, three of which were native to Latin America and two were native to Asia. When combined with previous studies, the percentage of B carriers was 41% in Japan, 13% in Asia excluding Japan, 6% in Latin America, and 0% in Europe and Africa. In addition, 48 accessions of C. annuum from various countries were subjected to SSR analysis. Clades with high percentages of B -carriers were formed in the phylogenetic trees. In the principal coordinate analysis, most B -carriers were localized in a single group, although the group also included b -carriers. Based on these results, we presumed that the B allele was acquired in some C. annuum lines in Latin America, and B -carriers were introduced to the world during the Age of Discovery, as along with the b -carriers. The manuscript has been well written. A good result about the B allele from C. annuum has been identified. It would be useful for the relative people to know. Thank you for reviewing our manuscript. According to your advice, we revised the manuscript as mentioned below. (1)Line 61- 62: Capsicum migrated to Europe and Africa from Latin America and to Southeast Asia during the 17–18th centuries from Peru. From my view, “pepper was introduced to Southeast Asia during the 16th centuries probably by Portuguese .” For evidence: In 1542, the Portuguese brought pepper to Goa, India, and pepper began to spread in South Asia. Then it spread to Malacca and spread in Southeast Asia. At the same time, the Spanish brought pepper to Luzon, the Philippines, which is another transmission point of pepper in Southeast Asia (watt, 2014). It was first recorded in Japanese literature that chili was introduced in 1552. Balthazar Gago, a Portuguese missionary, gave it as a gift to daiyo Town, which was then known as Toyoda and Toyoda of Kyushu Island, 39 years earlier than China (Yamamoto, 2018). During the compilation of Korean "history of Korea", it was introduced into the Korean "history of Korea" in 1602. The earliest record of pepper in China can be found in Zunsheng eight notes by Gao Lian of the Ming Dynasty (1591): "pepper is born, white flowers, and the fruit looks like bald pen head. It tastes spicy and red, which is very impressive." Reference: Watt G. 2014. A dictionary of the economic products of India. Landon: Cambridge University Press：197 Yoshimoto Yamamoto (translated by Chen Xian-ruo ). 2018. World history of pepper: a journey across Europe, Asia, and Africa, a hot table revolution. Taiwan:Marco Polo Press：256 Thank you for pointing this out. Andrew (1995) also mentioned that it was introduced to Asia in the 16th century. We corrected the centuries when pepper was introduced to Asia (line 61-62). Andrews J. Peppers: the domesticated Capsicums. University of Texas Press; 1995 (2)Line 114-, “DNA extraction” Whose DNA will be extracted should be mentioned. We added the information on whose DNA (line 115). Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0271091.r002
24 Jun 2022 Decision Letter - Tzen-Yuh Chiang, Editor Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia PONE-D-22-10615R1 Dear Dr. Tezuka, 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Tzen-Yuh Chiang 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 #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? 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: No 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 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 Reviewer #3: Yes ****** 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 Reviewer #3: 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 #1: All comments have been addressed by the author. As mentioned in the initial review, the manuscript is well written and I would like to congratulate the authors to the interesting manuscript and would like to recommend it for publication. the findings reported in the manuscript 'Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia' will have great impact in the field of Capsicum sp. breeding. Reviewer #2: The authors have made revisions according to all comments from the reviewers. I think it is ready to be accepted. Reviewer #3: Hybrid weakness plays an important role in the formation of species. In the manuscript, authors surveyed whether 94 C. annuum accessions had B or b alleles by crossing with C. chinense having the A allele. Of the 94 C. annuum accessions, five had the B allele, three of which were native to Latin America and two were native to Asia. Based on these results, the B allele was acquired in some C. annuum lines in Latin America, and B -carriers were introduced to the world during the Age of Discovery, as along with the b -carriers has beed concluded. The comments from me have been well addressed. I have no more comments and suggestion on the manscript. I agree to accept it for publication. ****** 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 #1: Yes: Julia Meitz-Hopkins Reviewer #2: No Reviewer #3: No ******** https://doi.org/10.1371/journal.pone.0271091.r003
Formally Accepted
28 Jun 2022 Acceptance Letter - Tzen-Yuh Chiang, Editor PONE-D-22-10615R1 Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia Dear Dr. Tezuka: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Tzen-Yuh Chiang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0271091.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .