PONE-D-20-38978

Identifying Suitable Tester for Evaluating Striga Resistant Lines using DArTseq Markers and Agronomic Traits

PLOS ONE

Dear Degife Asefa Zebire,

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.

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We look forward to receiving your revised manuscript.

Kind regards,

Vikas Sharma, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments:

You will see that reviewers suggesting the thorough revision for your manuscript. Therefore, you are requested to revise the manuscript and address the queries raised by reviewers.

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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

Reviewer #3: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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: No

Reviewer #3: 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: Yes

Reviewer #3: 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: This study is useful and novel for evaluating the Striga Resistant Lines using suitable tester. Authors used DArTseq

Markers and agronomic traits to identify the suitable tester. The stud is well supported with both sequence based and field based study clearly demarcating the suitable tester for evaluating the Striga Resistant Lines. I recommend this article to publish in your journal. However I have found few spelling mistakes in the article are as following.

There should be a space after genus name S. hermonthica Line 69 and Line 225, Line 291

Tester spelling misspelled in line 243

Furthermore spelling is misspelled in line 465

Reviewer #2: Comments:

1. Please mention details of T1 in the Abstract.

2. In Table-3 as you have compared agronomic traits, add morphological

pictorial parameter to support your data.

3. Reframe the conclusion section for better understanding of the reader.

4. You should perform in vitro or in vivo studies to see If any

adverse effects of these resistant strains for future commercial use.

5. In line 434-435, you should include relevant data.

6. You need to use some more markers along with SNP marker?

Reviewer #3: The manuscript entitled “Identifying Suitable Tester for Evaluating Striga Resistant Lines using DArTseq Markers and Agronomic Traits”, has been extensively reviewed by me and found that Authors have developed Tester which has resistance to Striga. Manuscript is good but there are major concerns in the study which needs to be addressed. There are more typological errors in the whole document and needs to be improved in the revision. Manuscript needs to be improved rigorously and based on my analysis I recommend major revision. I consider this manuscript only when all the queries will be answered thoroughly.

Minor Comments:

1. Maize (Zea mays L; 2n = 2x = 20) is one of the most important cereal crops worldwide by 60 providing food, feed and bioenergy [1, 2]…..correct the sentences.

2. 69 affected areas [9]. Inbred lines that combine high yield with resistance to S.hermonthica can be…..there should be space.

3. 84 Smith [21] and Hallauer et al. [13] concluded that a homozygous recessive inbred line with a low 85 frequency of desirable dominant genes and favourable alleles would be the most effective tester to 86 identify new inbred lines with high frequency of favourable alleles in testcrosses……lines are not clear improve this.

4. 88 [22, 13]. Mwimali et al. [23] found two Busseola fusca resistant single-crosses as desirable testers…scientific name should be italics.

5. 121 The present studies were, therefore, conducted to characterize Striga resistan…..it should be……The present study is….

6. 138 for DNA extraction. Leaves were collected from 4 to 15 leaves of each line and tester and then 139 bulked. The samples…..my question is that why there is need to bulk the DNA.

7. 179 first standardized in SAS version 9.4 [47]. Correlation among the different traits were analyzed… It should be traits was

8. The principal component analysis was computed in SAS using the correlation

181 matrix of trait means-centered averaged over environments….write the full form of SAS software.

9. 225 level of reactions to S.hermonthica ranged from 0.02 to 0.45 with an average of 0.36….scientific name should be with space.

10. 295 The performances of the three tester for the traits measured across environments are presented in 296 Table 3…language written is very simple inprove the sentence.

11. 164 Population structure analysis was performed from 6081 SNPs and a physical distance of 11 kb. 165 between adjacent markers…sentences is incomplete.

Major Commnets:

12. Why authors have not used SSRs markers as they are also widely distributed in the genome?

13. 133 tolerant and susceptible reactions to the parasite, under Striga infested and Striga noninfested 134 conditions at Abuja and Mokwa in Nigeria for two years. …Authors have used only two …I always see it should be 3 years….I thinks there will be biased results, chances of association of false SNPs are there….explain it?

14. The authors have used only 30 samples ….which I think it’s the only major drawback of the manuscript….at least 96 is required to find the marker trait association….. add more samples,,,,because with 30 samples you will get false results.

15. The samples were sent to 145 the Diversity Array technology company [38]. All protocols including Library construction, 146 sequencing, and SNP calling were performed at the Diversity Arrays facility, Canberra, Australia…..write all the protocols in the methods…

16. 192 genotypes. Gene diversity from 6081 SNP markers used to genotype 30 inbred lines and three 193 testers ranged from 0.10 to 0.50 in which 34% of the loci had values between 0.095-0.295 while 194 66 % of them fell in the range of 0.297-0.500 with an average of 0.35. These results indicate high 195 genetic divergence of the Striga resistant inbred lines and testers..Gene diversity value is very low….which again due to less number of samples.

17. The level of heterozygosity found in about 92% of the inbred lines

200 varied from 0.00 to 0.25 with only 8% of the lines having heterozygosity values ranging from 0.25 201 to 1.00. Further analyses revealed that nearly 33% of the markers had observed heterozygosity 202 (Ho) values of 0.00 to 0.05 with only one locus having a heterozygosity value of 1.00, signifying 203 that most of the loci were fixed. The He value also ranged from 0.012 to 0.50 with a mean of 0.35. 204 The fixation index (F) varied significantly from -1.00 to 1.00 with a mean of 0.66, suggesting that205 the presence of higher levels of homozygosity within the lines that were studied….value of heterozygosity is also very low….which showed your samples are rich in homozygosity.

18. Legend to figures come in the end,,,,improve it.

19. There are lots of typological errors in the whole manuscript, correct them?

20. Discussion and conclusion needs to be strengthened?

21. In reference section scientific names needs to be italics, authors have to be serious while submit revise manuscript?

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Reviewer #1: Yes: Dr Vikrant Jaryan

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.]

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PONE-D-20-38978R1

Identifying Suitable Tester for Evaluating Striga Resistant Lines using DArTseq Markers and Agronomic Traits

PLOS ONE

Dear Dr. Abebe Menkir

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 08/06/2021. 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: http://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,

Vikas Sharma, 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.

Additional Editor Comments (if provided):

Although, manuscript is complete now but due to some doubts and language errors it require one more revision. Please check the below mentioned points carefully:

Line 28-30 revise the sentence to make it clearer it is confusing or beak it into two.

Line 31: "marker-based distance estimates (r= 0.389, P= 0.01) was observed for when T2 has paired" remove grammatical errors.

Key Words: "mantel test" should be " Mantel test".

Lines 62-65: which 81 lines please clear, also revise sentence.

Lines 116-118:  "generate 90 test crosses, which were evaluated along with two checks" are these 90  samples were evaluated???  

line 163: "from the 30 yellow Striga maize inbred lines and three testers" only 30 maize imbred lines and three testers were evaluated?????

both these statements in lines 116-118 and line 163 are conflicting please check where is the error and make a correlation in study.

you are using the term "DArT-seq" however, standard term is "DArT"  check care and use appropriate term.

Language require careful revision throughout manuscript, therefore, revise the manuscript  thoroughly.

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

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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: Partly

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: Although authors have addressed all the comments but still I find some spelling and punctuation mistakes in the manuscript. The manuscript is improved by incorporating all the comments by various reviewer. I like to point these mistakes which is yet to be correct in the manuscript.

Line 21 Striga should be in italics.

Line 52 & Line 210 S.hermonthica there should be space after genus name

Line 71 Busseola fusca the name of species should be in italics

Line 123 -80°c here symbol of celcius in capital (°C)

Reviewer #2: The author have addressed all the raised issues and incorporated changes wherever suggested in previous review. So article can be accepted for publication, however, it is advised to proofread article to remove linguistic errors. Further advised to add more markers along with SNP markers for future studies.

Reviewer #3: The manuscript entitled Identifying Suitable Tester for Evaluating Striga Resistant Lines using DArTseq Markers and Agronomic Traits has been satisfactorily revised by the authors and can be accepted for publication. There are still minor mistakes and typological errors which can be corrected at the time of proofreading.

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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 #1: No

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.

Identifying Suitable Tester for Evaluating Striga Resistant Lines using DArTseq Markers and Agronomic Traits

PONE-D-20-38978R2

Dear Dr. Degife Zebire,

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.

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Kind regards,

Vikas Sharma, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors have addressed all the raised issues. Manuscript can be accepted now in its present form.

Reviewers' comments: