PONE-D-22-21858Influence of relay intercropping of barley with chickpea on biochemical characteristics and yield under water stressPLOS ONE

Dear Dr. Bijanzadeh,

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.

 See the additional editor comments section for further explanation.

Please submit your revised manuscript by Dec 23 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,

Sergio Saia, Ph.D.

Academic Editor

PLOS ONE

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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. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability.

"Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

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We will update your Data Availability statement to reflect the information you provide in your cover letter

Additional Editor Comments:

Dear authors,

I agree with both reviewers that the ms is interesting but badly handled by the statistical point of view. In particular, the statistical analysis is not replicable and application of a LSD post hoc to such a complex design will bring you to high chances of false positive results. 

I thus suggest you to carefully take into account the revierwers' comment and make one again a protected statistical analysis. Since you can use SAS, I can also provide you a suggestion, as follows:

BEFORE RUNNING IT, DELETE THE EXPLANATION WITHIN 2 ASTERISKS, ALSO, PLEASE MIND THAT i CALLED THE IRRIGATION AS 'IR' AND THE CROPPING SYSTEM AS 'CS', REPL IS FOR REPLICATES

proc glimmix data=work.NAME_OF_FILE;

title ‘NAME OF YOUR EXPERIMENT’; *you can delete this line if you want*

class IR CS Repl Year;

model YOUR_VARIABLE = IR|CS/ DDFM=KR; *The the symbol | is not an i, and will also produce the interactions terms, you can also split it in 3 treatments, e.g. taking into account the time of intercropping, but it will make your analysis definitely more complex and hard to discuss. KR will correct the estimate of the variances and of the standard errors*

random Year Rep(Year); *year must be a random statement and replication within year too. Replication per se is not a random statement since the experiment is not replicated in the same plots of the previous year. This will make your analysis simpler, providing a rebuilt least squared means across years. In figs and tabs, you will thus report the year and replicate means, not the results by year, which is not correct nd was used at the time of McIntosh 1983, but not now after Littel et al 1992 with mixed models*

LSMEANS  IR|CS / adjdfe=row adjust=tukey pdiff lines; *this will adjust for multiple comparison and provide you the classical "letter statements. Please note that LSmeans may differ from your means depending on the probability density distribution of your data and presence of unbalancing in the dataset. LSmeans are "predicted population margins; that is, they estimate the marginal means over a balanced population." [from the SAS guidelines. Adjust=Tukey does not adjust multiple comparisons for the post-hoc tukey, but for the post-hoc of tukey-kramer. This is more advisable when the total comparisons are more than 6, as in your experiment"*

run;

quit;

In addition to the suggestion above, I suggest you to change the sentence "Means sharing the same letter do not differ significantly based on LSD (p≤0.05) test." to "Means with a letter in common should not be considered different according to the post-hoc test at p≤0.05".

Lastly, I mind you that Plos requires for the row data to be published. You should upload at least the means and standard deviations or errors (to be specified along the number of replicates) in the supplementary materials or other repository and indicate it in the ms.

Regards

Sergio.

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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: Partly

Reviewer #2: No

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

Reviewer #1: I Don't Know

Reviewer #2: No

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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: No

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: While the research carried out might bring some valuable insights into the intercropping (and relay cropping) performance under water stress conditions, the manuscript presents several weaknesses that must be addressed. I provide some general comments for each part of the manuscript in this section:

General: the English level of the manuscript is not adequate for a scientific manuscript. There are several grammar mistakes, misspellings, word choices and sentence constructions that make the text unintelligible at some points.

Introduction: the ideas expressed are not well connected.

I lacked some references and explanations relating to the relationship between pigment contents and crop performance and how intercropping affects these variables.

M&M: please, consider the size of plots in future research, 3x2 m is quite a small size for intercrop trials. Plots of this size tend to overestimate the yield that a farmer would get in a commercial field.

You do not state the application field of your research: horticultural, field crops, etc. If field cropping is the target of your research, the use of sowing machines should be considered rather than hand sowing, as the latter does not represent the conditions a farmer might face in a field.

The statistical analyses are not described in sufficient detail to be replicated by other researchers or to correctly interpret the results.

Results: The result display is quite poor. The significative triple interaction in all the variables led to several Figures and Tables that are quite difficult to comprehend from an external reviewer. In addition, the result section does not provide clear and key results of this research.

Discussion: the English level in which the discussion is written does not allow an objective evaluation of it, as some mistakes (grammar or word choice) can lead to incorrect judgement.

Conclusions: some results are summarized in this section, but no clear conclusions are stated.

Reviewer #2: The manuscript “Influence of relay intercropping of barley with chickpea on biochemical characteristics and yield under water stress” aimed to investigate the effects of water stress on barley-chickpea relay intercropping. The evaluation focused both on agronomic performance and biochemical parameters of crops.

On the whole, the topic of this paper is very interesting. Despite the effects of the co-cultivation between cereals and grain legumes on biochemical aspects of crops have been rarely investigated in previous study on intercropping, they are fundamental for better understand the interactions between crops in a more diversified cropping system. Therefore, I appreciate the novelty of this manuscript.

The introduction provides sufficient background, even if the number of relevant references can be increased. The research is design appropriately and methods are adequately described (except for the statistics section). I’m convinced that authors of this manuscript have extremely interesting data however they failed to valorize them in this manuscript. In fact, the results are not clearly presented, a lot of details are missing, and the manuscript is very difficult to read. Moreover, results can be misinterpreted due to the inappropriate statistical analysis.

General comments:

English language and style: The manuscript is not easy to read, an extensive editing of English language and style is required.

Statistical analysis: statistical analysis needs to be revised. I have several concerns related with the data presented in table 5, 6, 7, 8 and figures. Standard errors are missing everywhere, and unit of measures are often wrong. Please see specific comments below.

Data presentation: Tables and figure needs to be deeply revised according to the revised statistical analysis.

Specific comments:

Line 47: Please add a reference “…another crop (cit).

Line 53: Please add a reference “…of the world (cit).

Line 53: Please add a reference “…final yield (cit).

Line 84: “At the best of our knowledge” instead of “Until now”

Line 98: Please add reference defining the soil type e.g “Jahn R, Blume H, Asio V, Spaargaren O, Schad P (2006) Guidelines for soil description, 4th edn. FAO, Rome”

Line 126: Please, define the plowing depth.

Line 129: Define inter-rows space.

Line 144: for barley and chickpea the effective root zone is around 20 -25 cm, why did you consider 90 cm?

Table 3 and 4: In order to improve the tables readability, please define the meaning of I and C in the caption.

Lin 147: Is it a common practice irrigating barley in Iran? Or it is just ax experimental practice?

Line 311: “mg. mg. g-1 “ is not the correct annotation for the unit of measure. The correct annotation is “mg · g-1”. Please check all the unit of measure in the text and SE should be also included.

Everywhere in the text: please, you should include standard error (SE) when you report data in the text.

TABLES

Table 1:

• “Soil organic matter (SOM)” instead of “Organic content”

• I would express N as g/kg

• P, is it total P or Olsen P? Same for the nitrogen, which kind of protocol did you follow for the Nitrogen determination? Kjeldahl method? Please add this information in table caption.

Table 5: You mentioned that “year” and “irrigation regime” are significant factors. In this case you should perform the statistical analysis separately for each year and for each irrigation regime. In the table you have assigned letters of significance in the wrong way. Please perform a post hoc separately for year and irrigation regime and eventually assign capital letter for indicating differences between years. You should include standard error (SE).

Table 6: see comments above

Table 7: see comments above

Table 8: see comments above

Line 362: “Unit. mg-1 protein” “Unit· mg-1 protein”

FIGURE

Figure 1: You should perform post-hoc of your model separately for 2017 and 2018. Use lowercase letter for 2017 and uppercase letter for 2018. SE are missing, please provide them. In case that year is not a significant factor you could present data as average between 2017 and 2018 for each of the treatments. Another option can be present data on 2017 and 2018 in two separate graphs.

Same for figure 2, 3, 4, 5, 6, 7.

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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: No

Reviewer #2: No

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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.

PONE-D-22-21858R1Influence of relay intercropping of barley with chickpea on biochemical characteristics and yield under water stressPLOS ONE

Dear Dr. Bijanzadeh,

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. in particular, see my opinion in the "additional editor's comments".

Please submit your revised manuscript by May 04 2023 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,

Sergio Saia, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

Deal authors, one of the 2 former reviewers accepted to re-review your ms. I frankly have to say that I almost agree with the reviewer. In particular, the english language can be improved by yourself trying to use simpler sentences and making a general polishing of the work. So far, my greatest worry is about the statistical analysis and the reviewer pointed to the need of ensuring its reliability, by suggesting the GLMM (which, by the way, can also handle non normal distributed data o residues and few replications). I please exhort you to carefully take into account that the statistical analysis should be done reducing the false positive and false negative results, with a certain degree of protection of the results given by proper statistics (e.g. Benjamini and Hochberg or Tukey-Kramer, etc.)

Regarding the statistics, please pass over to the indication of the rev. regarding "Values with different letters are not significantly different at 0.05 confidence level." The correct statement is "Values with a letter in common should not be considered different at 0.05 probability.", which poses an additional degree of protection of the results.

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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: (No Response)

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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: Partly

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

Reviewer #2: No

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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: Yes

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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: No

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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 authors mentioned that the English has been revised in the manuscript but it is seems not: the paper is difficult to read, especially for the results section. Moreover, there are too many tables and figures. I would suggest removing some tables or move them in supplementary material and to add relevant information in the main text. Figures 3, 4 and 5 for instance can be merged in 1 graph. I still have some concerns about statistical analysis (see specific comments below). I’m convinced that your data and research topic is interesting however, I would suggest the authors for an extensive English check otherwise the MS could be not considered for the publication.

See specific comments below.

Abstract:

Line 25: “as split plot based on a randomized complete block design” I would remove this information from the abstract.

Line 37-30: I would suggest removing this detailed sentence from the abstract, it is more appropriate for materials and methods section. It is enough informative if you mention that the second factor was the sowing time (December vs January).

Line 31: “Chlorophyll a content of barley increased in b1c2, by consuming less water compared to sole cropping.” Better if you explain it in terms of…In case of relay intercropping, the early establishment of barley determined an higher chlorophyll content in biomass compared to… due to the… Please try to be more precise in your statement, why b1c1 consumed less water? Less competition from chickpea? Early establishment ensured a growth advantage and therefore a better use of water?

Line 33: What do you mean with “(b1c1 and b1c2) created a suitable canopy to pigment contents improvement”.

Line 34 “carotenoid content of chickpea” please specify if you are referring to chickpea biomass or grains.

Line 35-36 “Barley-chickpea intercropping reacted to water deficit through enzymes activity, water use efficiency and land equivalent enhancement compared to sole cropping”. The WUE and LER are not “reactions”. It is better saying that intercropping enhanced the WUE and guaranteed a more efficient use of space (LER>1) compared with sole crops.

Line 36-38 “Under water stress, in b1c2, by increasing total chlorophyll and water use efficiency, grain yield of barley enhanced compared to b1”. This sentence is not clear at all.

Line 38: “It seems”. Not appropriate for abstract

Introduction:

My impression is that sentences are not linked to each other. The introduction needs to be rephased in order to improve the readability of the paper. Moreover, make clear your objectives and hypothesis. I strongly suggest submitting the manuscript for an extensive English revision by experts.

Line 104: carried out instead of “laid out”

Line 127: Is it Darab cv a registered cultivar of chickpea or an ecotype?

Line 132: “which is suitable for hot and dry areas” better say suitable for arid/semi-arid conditions.

Line 183: “hand harvested manually” remove manually.

Material and methods:

Line 268-271: Please provide models that have been used, including fix and random parts. Moreover, did you check if 1) the responses for each factor level have a normal distribution, 2) If these distributions have the same variance and 3) if the data are independent? Otherwise, you should opt for gl(m)m assuming other data distributions. You just have 3 replications, were they enough for studying the interactions of your experiment? Were the residuals of your models normally distributed? You should add more information for this section. In particular I would suggest the author to include the structure of model that has been used (factor that you used in the analysis and if some factors were nested in others) and the procedure for model selection.

Results:

Line 300-314: I would move this part in MM section.

Line 323: here and throughout the text use the same number of decimals for mean and SE

Line 459-461: please, specify better that you are referring to the early established barley.

Line 461-463: This result is not clearly presented. Please rephase.

Line 468: Express yield as t ha-1 instead of kg ha-1

Line 472-474: This is discussion and not results.

Line 478: what is the biological yield. Add information on the procedure that you used for the determination of biological yield in MM section

Line 478-493: Appropriate annotation should be used. t/ha instead of kg/ha. This section is almost impossible to read. The English should be significantly improved.

Tables:

Table 1: “(mg/kg-1)” this is not the correct annotation. Please use mg/kg or mg kg-1. Moreover, you recorded N tot 0.75 mg/kg and it looks like very low. Check the measure unit, 0.75 g/kg seems more reasonable.

Table 3: what is the difference between “Year” and “replication (year)”

Table 5 and 6: I would remove the capital letters. You mentioned that Year x Irrigation was significant so why did you perform the post-hoc test within years?.

Figures:

I would suggest using some colors for increasing the readability of figures.

Reduce the number of figures. Information included in figures 3,4 and 5 can be presented in just one figure using colors and multiple bars.

Figure 1,2,3,4,5 and 6:

• Bars represent mean±SE instead of “Vertical bars represent ±SE”.

• “In each irrigation regime, means with a letter in common should not be considered different according to the Tukey's test at p≤0.05” this is not clear. I suggest to rephase as: Values with different letters are not significantly different at 0.05 confidence level.

Figure 3 and 4: Use t/ha instead of kg/ha

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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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[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.

Influence of relay intercropping of barley with chickpea on biochemical characteristics and yield under water stress

PONE-D-22-21858R2

Dear Dr. Bijanzadeh,

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,

Sergio Saia, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

in the galley proof, please correct the word "Shapori" to "Shapiro"

Reviewers' comments: