PONE-D-23-28150Haitian Coffee agroforestry systems harbor considerable, dynamic and under-reported variety mixtures and genetic diversityPLOS ONE

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"C.P.M. was funded by PhD grants from the French Embassy in Haiti and the ARTS program (IRD).This work was supported by the Agricultural and Agroforestry Technological Innovation Program (HA-L1107, HA-G1038) funded by the IDB, GAFSP, IFAD and Haitian government. L.V. was supported by Research Foundation-Flanders (FWO; G090719N)." 

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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: Yes

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

Reviewer #1: Yes

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: No

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: Yes

Reviewer #2: Yes

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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: The authors studied the genetic diversity of Coffee arabica plants found at two discreet locations with historical importance found in Northern and Southern Haiti. This study revealed higher than expected genetic diversity and the presence of clades (e.g., Typica, Burbon, and Catimor) at the farm level; suggesting the crops of individual growers represent diverse coffee. Although additional work will need to be done to identify if these results are representative. The authors link “local knowledge” with clades and identify a -relatively-robust degree of concurrence, particularly for discriminating from monoculture. The authors identify coffee farms as repositories of varietals and sources of genetic materials, an important first step to cataloging plants that may benefit Haitian Coffee Agroforestry Systems in face of global climate changes and variable growing conditions.

While I acknowledge there are regulations that may limit the sharing of data, I would encourage uploading of data to public repositories (where permissible), the identification of accession# for genetic/genomic information available from reference materials (when available), and/or use public repositories like GitHub or protocols.io. This would greatly improve reproducibility and reanalysis of sequencing data in future studies.

Lines 125-128 – SNPs are an effective, validated method to characterize diversity and used to discriminate across several systems (prokaryotes and eukaryotes). When combined with other data sources can be used to reveal structural variation. However, they usually cannot, de novo, reveal structure (e.g., indels and CNVs) in most systems. Please clarify if the intent was structural genomic variation for C. arabica. Please also include additional references as Bawin was not accessible to me (login required) and Zhang does not provide sufficient detail.

A table or additional accounting in M&M as to the number of specimens from each farm/locality as well as the number of specimens from each reference set (CATIE, HARC, IRD) would aid a reader with a wholistic understanding of the total number (representants) and source of the diversity for both the HiPlex and KASP data e.g., is the only C. congensis from IRD.

It appears the figure legends and figure numbers do not match for Figure 3 and Figure 4.

Minor – In general, the manuscript is well written however, I encourage the authors to review the grammar/spelling to ensure it is of high quality and conveys the impact of their work clearly. For example, line 32, “as well as”, line 91 spacing before bracket, line 160 is missing a period, line 231 “amplicon”, line 254 “R” is a statistical software and should be capitalized, to identify century both Roman numerals and numbers are used, etc.

In line 113 can the definition (e.g., rust tolerance) of “elite” be provided as it seems to be used for various intents in the literature? Also, is the possessive form (apostrophe) intended?

In line 141 can the authors expand on what, “high-potential” refers to?

In line 200 can the number of specimens sequenced from HARC be identified?

Reviewer #2: The study is well organized

Title: needs clarification Suggest adding remove under-reported with other sentence

There is no need to use keywords that are already present in the title.

in line 172 Selection of study sites not clear please suggst screening the location for study

Deep discussions and related recent studies must be included in the result and discussion part.

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Reviewer #1: No

Reviewer #2: No

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Haitian coffee agroforestry systems harbor complex Arabica variety mixtures and under-recognized genetic diversity

PONE-D-23-28150R1

Dear Dr. Claude Patrick Millet,

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.

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Kind regards,

Awatif Abid Al-Judaibi, PhD

Academic Editor

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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 #1: 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

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

Reviewer #1: 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

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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 #1: 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: (No Response)

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If you choose “no”, your identity will remain anonymous but your review may still be made public.

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Reviewer #1: No

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