PONE-D-20-17403

Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion

PLOS ONE

Dear Dr. Guan,

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Tzong-Yueh Chen, Ph.D.

Academic Editor

PLOS ONE

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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

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

Reviewer #1: N/A

Reviewer #2: I Don't Know

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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

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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 author wants to use the transcriptomic analysis to compare the differences in the molecular mechanism between individuals with different growth performance after domestication (food conversion), and to identify SNPs that may be related to this as a benchmark for subsequent selection. But the experimental design has many doubts as follows: First, the author should emphasize the selection criteria of the broodstock, otherwise the differences between the broodstock individuals may affect the representative meaning of the offspring. Second, in the process of domestication, the cannibalism might be occurred due to size selection of fish was not performed. Thus, the better growth performance might be due to eat more. Just like the author said the behavior might have a genetic basis, but the results are focused on growth performance instead of behavior. If the author wants to emphasize the growth performance, it is recommended that the experimental design should be rearrangement. For example, size sorting should be carried out during the domestication process, or the fish fry that has been domesticated with the same size should be selected for another growth experiment. In my opinion, the result will be more representative. There are, however a few inconsistencies that require further explanations or changes prior to publication in PLOS ONE.

Results:

Figure 1A and C: The result of 1A is not represented survival rate. The initial length of fish in Fig. 1C is between 5.69-5.92 cm, which is inconsistent of that mentioned in materials and methods.

Figure 6: The calculation method of fold change in RNA-seq and qRT-PCR is different. It is suggested that the FC results of two analyses should be separated. By the way, the FC results of CDC20 are different in these two analyses. In addition, “RNA-sep” should be changed to “RNA-seq”.

Furthermore, there are some typos in the indicated lines as follows:

Line 107, “De novo” should be italicized.

Line 132, There is an extra space between control and mainly.

Line 141, “Date” should be changed to “Data”.

Reviewer #2: The manuscript (PONE-D-20-17403) entitled "Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion" which submitted to PLOS ONE by Guan WZ et al. has been reviewed.

The author used artificial feed to raise hybrid mandarin fish for 3 months, and measured the food conversion rate, survival rate, total length, and body weight of the hybrid fish, absolute length and weight gain rate. Then use RNA-Seq to identify potential genes involved in the pathways activated growth performance. For example: fatty acid biosynthesis (FASN and ACACB), collection of duct acid secretion (ATP6E and KCC4), cell cycle (CDC20 and CCNB) and insulin-like growth factor (insulin) -like growth factor, IGF) system (IGFBP1) and other pathways may be related to the growth of mandarin fish. Finally, it was also found in fast-growth fish, more potential single nucleotide polymorphisms (SNPs) were detected than in slow-growing fish. However, there are still some problems with the experimental design and content of this manuscript, which need to be supplemented and further explained and clarified by the author.

Q1-

What is the breeding pattern and origin of “the fifth generation hybrid fish” mentioned in this manuscript material and method? Regarding the source and definition of breeding biological materials, it is necessary to ask the author to add more details in the manuscript.

Q2-

What is the control group for the measurement of food conversion rate, survival rate, total length, body weight, absolute length, and weight gain rate of hybrid fish? In theory, there should be non-hybrid pure breeds or hybrids of different generations for comparison. To use this to emphasize the advantages of hybrids, the author should add Siniperca chuatsi and Siniperca scherzeri two uncrossed pure breeds. It is the control group (triple group) and compares various growth and survival values.

Q3-

P156, Group1-3 in Figure 1(A) refers to the number of deaths at 0, 30, and 90 days in the triple-repeat population of the hybrid population. Why is there no 60-day data? It is impossible to understand why the author presented the triple-duplicate data of a hybrid species alone. What is the significance?

Q4-

Figure 1(C) and Figure 1(D) are the growth data of how many months old? It is suggested that the author should make up and give details.

Q5-

In order to make it easier for readers to understand, basically the author should provide the growth data or growth curve of the F and S groups at each month of age?

Q6-

Although the author mentioned in the manuscript that more potential single nucleotide polymorphisms (SNPs) are detected in fast-growth fish than in slow-growing fish. However, the author did not actually provide such comparative figures or tables in the manuscript.

Q7-

There are more potential single nucleotide polymorphisms (SNPs) found in fast-growing fish. These nucleotide variation site markers are mainly located on those important growth genes. The authors also found in this result. No relevant research diagrams or tables are provided in this manuscript.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: Reviewer comments.docx

Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion

PONE-D-20-17403R1

Dear Dr. Guan,

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,

Tzong-Yueh Chen, Ph.D.

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

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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: Yes

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

Reviewer #1: Yes

Reviewer #2: 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

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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

Reviewer #2: 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: The authors have satisfactorily responded to my question and made the necessary changes to the manuscript. Thus, the revised version of the manuscript appears to be good for publishing in PLOS ONE.

Reviewer #2: The author has responded to related questions in the manuscript and actually provided supplementary information such as figures or tables.

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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