Variation in Platycladus orientalis (Cupressaceae) Reproductive Output and Its Effect on Seed Orchard Crops’ Genetic Diversity
, Shi-Ping Cheng 6, Yue Li 1 and Jian-Feng Mao 1,*
Round 1
Reviewer 1 Report
Variation in Platycladus orientalis (Cupressaceae) reproductive output and its effect on seed orchard crops’ genetic diversity
The paper touches on seed orchards’ genetic efficiency of Platycladus orientalis. The reproductive output (fertility) variation for 166 clones in a first-generation P. orientalis seed orchard over five years and across three years for each gender was assessed. The fertility variation and genetic diversity parameters were estimated for each gender-year combination. The reproductive strobili production variation (CV), fertility variation (Ψ), and the effective number of parents (Np) as tools to determine the genetic diversity and quality of a P. orientus seed orchard crops were presented.
The abstract of the paper, as well as the conclusions, are very general and could be improved to make the scientific soundness to the audience more communicative in the field of the obtained results.
In the abstract, the line, 25 - 30 statement does not conclude from the obtained results.
Line 294 - 312 of the paper seems to be part of an introduction section.
The references of the paper were carefully prepared to represent relevant data, which support the discussion of obtained results. The historical review papers as well newly published data were utilised.
Addidtional comments
Supplementary Table 2, and Supplementary Table 3 were not possible to access by the reviewer. Probably, they were not attached by the Authors (?) during the submission process. It would be good to get this data to be verified by the reviewer. So, because of this reason and some other conclude remarks additional review turn in my opinion is needed.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The paper is well well written, although on some parts difficult to follow the text due to the large amount of material studied. Unfortunately, I could not see the Supplementary material and judge its quality and correctness.
The authors did not follow the Instructions for Authors and thus in the manuscripts there are numerous formatting and typos to be improved. Their list is attached.
Ln 115 replace “square hectometer” by “hectare” (square hectometer). Hectare is more common unit.
Ln 116, 117 Spacing 2 x 2 m means rectangular spacing 2 m between rows and 2 m within row. What does it mean 6 m between rows. Explain the spacing excactly. In this form it is difficult to understand.
Ln 259–267 remove Bold in Tables and Figures
Ln 342 replace ”black pine” by “Pinus nigra”
Ln 343-344 replace ”loblolly pine” by “Pinus contorta”
Ln 371, 408 replace P. orientus by P. orientalis
Ln 484 remove spaces 21–25. At the end of the line there is 21–25. Is it mistake (dobled date) or is it range of pages?
Ln 485, 319 Bruchánik instead of Bruchanik
Ln 497 Master thesis
Ln 513 crops. Doctoral
Ln 493, 526 replace journal name “International Journal of Forest Genetics” by “Forest Genetics”
General comments in entire manuscript:
Latin names should be in Italics both in manuscript and References
Minus, from–to (range of pages) and hyphen (inserted sentence) should be written with N-dash (e.g. Ln 190, 208, 215, 219, Table 1, 2, 3 and others)
According to the Instructions to Authors after authors´initials in Authors Contributions should be dot.
Format of References does not correspond to the format given in the Instructions to Authors or papers published in the Forests.
Remove “and” between authors.
Separate authors by semicolon (e.g. Allendorf, F.W.; Luikart, G.).
Abbreviate journal names.
N-dash instead of hyphen in range of pages.
Abbreviated journal name and volume in Italics.
Year in Bold.
Format for journal papers is as follows (in some references it is correct, in others not):
Van Beek, T.A.; Montoro, P. Chemical analysis and quality control of Ginkgo biloba leaves, extracts, and phytopharmaceuticals. J. Chromatogr. A 2009, 1216, 2002–2032.
Author Response
Dear Reviewer 2
RE: Manuscript-ID: forests-1388896: Variation in Platycladus orientalis (Cupressaceae) reproductive output and its effect on seed orchard crops’ genetic diversity.
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Manuscript Number: forests-1388896
Title: Variation in Platycladus orientalis (Cupressaceae) reproductive output and its effect on seed orchard crops’ genetic diversity
Authors: Si-Qian Jiao, et al.
Remarks:
This submitted paper investigated variations in male and female reproductive fertilities among clones in the seed orchard of Platycladus orientalis over multiple years, and the effects on the reproductive contributions to the seed pools and their genetic diversity. The authors found that the relative reproductive allocation to the male and female functions differed among clones and the resultant skewed parental contributions affect the genetic diversity of seed pools. I consider that the insights obtained from the study should be useful for the genetic management of seed crops, the utilization of the improved seedlings and the construction of next-generation breeding populations. So, I consider that the concept of this paper itself is potentially acceptable for the publication in this journal.
However, the present version of the paper has some major problems, particularly regarding with the unclearness in novelty; throughout the manuscript, it is unclear what is already known results and what is the new insight obtained by the present study. This leads to the misunderstandings by the readers and the difficulties in catching the main theme of the study. There are also unclear explanations and presentations of methodology, and the verbose and unnecessary sentences throughout the paper. The paper also has inconsistency of the results and the discussions, some results were not appeared in the discussion section. In addition, the paper has many unclear and incorrect word uses and phrases throughout the manuscript, and for many sentences, I did not understand what the authors really mean.
As a result, I recommend the authors to reconsider again the entire manuscript with a sufficient effort, based on the major and minor suggestions commented as below.
Major Comments:
- As commented in the Remarks, I felt little novelty in the present version of the paper, particularly in Introduction. There are only the reviews of the related previous papers, but not the statement what is still unknown or insufficient for the further understandings of the research field. The authors should explain the main theme (including new questions and difference with the previous papers) more clearly.
- There are results which is not explained in the Methods section. For example, the explanation of analysis procedures regarding with the increase in GD with an increasing numbers of Np (Fig. 3) should be necessary. Also, there are no discussions regarding with the results of Fig. 3 and Table 5. Genetic diversity and parent diversity should be important in the present paper, so the authors should provide any important discussions about the results obtained from the Figure and the Table.
- Concerning with the Major comment #1, some parts in the Introduction and Discussion sections are verbose and redundant, which may lead to the difficulties in catching the main theme of the study clearly. For example, the paragraph of lines 73-96 is verbose and I do not understand what the authors want to say by here. In Discussion also, the first paragraph (lines 294-312) is not necessarily related directly with the results of the present study, most of which should be cut or deleted entirely. Sentences of lines 354-358 and lines 367-376 say almost similar things, which should be integrated and slimmed. There could be similar points where sentences should be refined and reconstructed, so the authors should check and reconsider again throughout the manuscript to make the paper more easily readable.
- There are many incorrect and unclear word uses throughout the manuscript. Particularly, strictly speaking, words like “xxx’s xxx” such as “seed orchard crops’ genetic diversity” (in title), “parental population genetic superiority” (in lines 35-36), “seed crops’ effective population size” (in line 39) seems unclear and incorrect (for example, “effective population size of seed crops” should be better). Such phrasings are found rather frequently, so the authors should reconsider throughout the manuscript and I recommend to correct these points.
Specific comments:
Introduction
- Lines 97-. “P. orientalis” should be italicized.
Materials and Methods
- Lines 121- and 131-. Should “10 grades” be 11 (from 0 to 10)?
- Lines 125- and 130-. The grading of the male and female reproductive fertilities is key important information of the methodology in the present paper, so the concrete 基準 should be represented in the paper, not only by the citation of the previous paper.
- Lines 137-. There is no information on the ANOVA model. Also, if the authors include the factor of clone, it should be nested within provenances.
- Lines 197-. There is no explanation on “the relative proportion of the parental significant number (NP)”. What is this statistics? Also, “NP” seems to be confusing with “Np” (the effective number of parents). Please reconsider.
- Lines 204-, 285-, and so on. “genetic diversity (GD)” seems to be confusing with “gene diversity” in Table 5. If they are the same, please uniform the word uses.
Results
- Lines 225-: “…, with male reproductive output always higher than that of female …”. I wonder how the authors can compare male and female reproductive outputs only based on the data of the grading score, not the count data. To begin with, the efforts (resources) for producing one male strobili and one female flower cannot be comparable. Please reconsider.
- Lines 238-. I think that “maleness index” (Fig. 1) merely indicate clone variation of male-to-female ratio and therefore variation in this statistics do not necessarily mean the negative correlation between male and female production amounts (grade scores).
- Table 4. I think that the presentation of correlations is enough by either of the Pearson’s coefficient or the Spearman’s one.
- Lines 262-265: “These results indicated … pollen-cones (Table 4).”. These two sentences had better be moved into the front of the former sentence “The cumulative curves …” (lines 261-).
- Lines 266-. It is unclear what the words “Similar trends” indicates. “Similar trends” regarding with what?
- Lines 271-. “slightly” -> “significantly”?
- Lines 288-. The sentence “Thus, the management of … of parents.” should be moved into the Discussion section.
Discussion
- Lines 314-316. I do not understand the sentence “Generally, and … reproductive output symmetry.” by the results of Table 4.
- Lines 328-330. The sentence “(However,) the presence of … (Burczyk and Chalupka 1997).” Should be moved into the next of the first sentence of the same paragraph “Sexual asymmetry is … (Ross 1990).”.
- Lines 333-338. The two sentences “While we did not … seed crop management.” is not necessary for the discussion of the main theme, so they had better be deleted or moved into the Conclusion section as a statement of future research needs (seeds).
- Lines 344-345. I think that the separation of the paragraphs here is not necessary.
- Lines 377-. As pointed in the Specific comment #11 also, please reconsider whether the male and female reproductive amounts can be compared by only the data of the present study. Also, should “Table 3” be “Table 2”?
- Lines 388-. I think that the “orchards’ final seed yields” is affected by also the genetic variation of clones.
- Lines 391-. I do not understand the clause “however, in the present study … in a missing opportunity.”; is this unnecessary?
Conclusion
- Lines 406-408: “Here, we used … seed orchard crops.” As pointed in the Major comment #2 also, the authors should provide any discussions about the important results regarding with the reproductive variations and the (genetic) diversity of the seed crops (Fig. 3 and Table 5).
Author Response
Dear Reviewer 3:
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Variation in Platycladus orientalis (Cupressaceae) reproductive output and its effect on seed orchard crops’ genetic diversity
As the reviewer, I am still not satisfied with the informative structure of the abstract and the conclusions sections. The abstract of the paper, as well as the conclusions, are very general and could be improved to make the scientific soundness to the audience more communicative in the field of the obtained results. These sections are essential to the readers to guarantee the citation of the paper in the future. I should be pointed to the most important obtained data of the results to make the paper more interesting for readers.
Due to new data regarding reproductive output and its effect on seed orchard crops’ genetic diversity of Platycladus orientalis, which is a conifer tree of important ecological meaning in China the paper is valuable to be published. I would expect in the conclusions of the paper some recommendations regarding the establishment of future seed orchards.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Manuscript Number: forests-1388896-v2
Title: Variation in Platycladus orientalis (Cupressaceae) reproductive output and its effect on seed orchard crops’ genetic diversity
Authors: Si-Qian Jiao, et al.
Remarks:
This revised paper has improved substantially; the Introduction section, regarding with the presentation of the new questions and the difference with the previous studies, has become clearer and has been rewritten concisely. In the Discussion section also, necessary discussions have been followed and the discussions were concentrated more on the main theme of the study with an appropriate volume.
There are still some unclear explanations and word uses which should be reconsidered. Please revise once again based on the major and minor comments provided as below.
Major and minor comments:
Materials and Methods
- In the cover letter (Response 3.11), the authors replied that the direct comparison of male and female reproductive grading scores is allowable because grading score is just in proportion to (like a logarithm of a big value) the quantities of both male and female strobili production. If so really, such an explanation, in order to make this comparison relevant, should be added in the corresponding place in Methods (in Lines 351-367 in Subsection 2.1).
- In the cover letter (Response 3.8), the authors replied that they added a factor of clones nested within provenances in the ANOVA and updated Table 1. However, such revisions are unclear to be reflected in the manuscript.
For example, if the authors have updated really the ANOVA model by including the factor of clones nested within provenances, the factor of “Provenance*Clone” is not necessary in the model. Please check or reanalyze again.
Regarding with this, in the presentations regarding with the nested-ANOVA, the word use such as “ANOVA” (Line 371, and so on) should be corrected into “nested-ANOVA”, and “clones” (Line 372, and so on) should be corrected into “clones nested within provenances”, throughout the M&M, Results and Discussion sections. Also, in Results in Table 3, the factor name “Clone”, “Year*Clone”, and so on, should be corrected into like “Provenance (Clone)”, “Year*Provenance (Clone)”, and so on.
Results
- Lines 536-, and so on. If the authors’ response 3.11 (as in Comment #1) is really OK, the word uses such as “the male reproductive output” should be revised into like “the scores of the male reproductive output” throughout the manuscript. Please reconsider.
- Lines 566-. “… that the paternal was greater than the maternal contribution” -> “… that the paternal contribution was greater than the maternal one”.
Discussion
- Lines 656-658. I do not understand “… affects gene exchange among the orchard’s parental population”; I think that “parental population” does not change but “the genetic composition of the resultant seed crops” does. So the sentence should be rewritten as like “The variation of gender and reproductive outputs in the parental populations of the seed orchards is expected to influence the genetic composition of the (resultant) seed crops.”.
- Lines 776: “… indicating that mixing seeds from several years”. I think that mixing seeds from both several clones and several years could increase the genetic diversity. Please reconsider.
- Lines 787-925. In this revised paragraph, the authors’ discussion, like that it is important to make the optimal choice to balance genetic diversity and genetic gain, is very good. However, the fact that genetic diversity of the parental population could be covered and saturated by collecting seeds from more than about 30 mother trees, just as well as the result of the present study, has been already reported and suggested in many previous studies of gene preservation or sampling strategy (see the example references below). It is better to explain such a fact, citing these previous studies, in order to assure that the genetic diversity assessment of seed crops in the present study is based on insights of such previous studies.
References:
Hoban S, Schlarbaum S (2014) Optimal sampling of seeds from plant populations for ex-situ conservation of genetic biodiversity, considering realistic population structure. Biol Cons 177: 90-99
Hale ML, Burg TM, Steeves TE (2012) Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PLoS ONE 7: e45170
Volk GM, Richards CM, Reilley AA, Henk AD, Forsline PL, Aldwinckle HS (2005) Ex-situ conservation of vegetatively propagated species: development of seed-based core collection for Malus sieversii. J Am Soc Hort Sci 130: 203-210
Author Response
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Author Response File: Author Response.pdf
