Fertility Variation and Gene Diversity in Forest Populations

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Please, my opinion about the manuscript is attached.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Author Response

Authors greatly thank for your valuable comments and suggestions.

As you commented, we take some terminology, for example, coancstry, group coancestry, gene diversity, status number and effective parent number. So, we improved the introduction as follows,

We introduce several key concepts such as coancstry, group coancestry, gene diversity, status number and effective parent number. We defined that coancestry between pair of individuals is the probability that genes taken at random from each of the concerned individuals are identical by descent (Cockerham, 1967). The group coancestry is the probability that the two gene are identical by descent in a large gene pool, and equals the average of all coancestry values among any combination of the individuals in a population [42]. Gene diversity indicates that genes are different, and equals the expected heterozygosity. 

Also, we add a paragraph as,

Status number was defined as the half of inverse of group coancestry by Lindgren and Mullin [5], which has the same meaning as the half of inverse of the probability that two gene are drawn at random are identical by descent in a population. The status number is an intuitively appealing way of presenting group coancestry, as it connects to the familiar concept of number (i.e., population size). The ratio of the status number and the census number will be useful, so that it calls the relative status number.

Concerning the heritability parts, authors fully agree with your comments, so we deleted the paragraph on page 6.

Authors insert the discussion as “Unlike crop plants, forest trees have a large difference in fertility. Additionally, the reproductive capacity of trees varies greatly depending on their age classes. In years of good seed production, the fertility variation is smaller among individuals, and the variation is larger in poor years.”

On behalf of the coauthors, I'd appreciated very much for you reviewing and concerns.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The review summarizes very relevant information on fertility variation that is very useful for the management of forest populations. However, here are some things to consider.

• Reviewing the title, the part “genetic diversity of forest populations” causes confusion, giving the impression that the review will address all aspects of the genetic diversity of forest populations. It could be more specific, perhaps: “Variation in the fertility of forest populations.”

• The section must include information on the molecular markers (ISSR, SSR, AFLP, RFLP, others) that have been used to evaluate fertility variation. In addition, the genetic parameters used (H, He, Ho??) and the values determined in some Pinus species must be included.

• Include information about the evaluation of floral synchrony, how it influences fertility, the parameters used to evaluate. This is very relevant in the management of seed orchards, a topic that is addressed in the document.

• At the end of the document (before conclusions) you must integrate information on how the variation in fertility and fecundity influences reproductive indicators (e.g. seed potential, seed efficiency, germination capacity, ...).

Author Response

Dear reviewer;

Authors are very grateful for your valuable comments and suggestions. 

Reviewer's comments) The review summarizes very relevant information on fertility variation that is very useful for the management of forest populations. However, here are some things to consider.

• Reviewing the title, the part “genetic diversity of forest populations” causes confusion, giving the impression that the review will address all aspects of the genetic diversity of forest populations. It could be more specific, perhaps: “Variation in the fertility of forest populations.
  --> Author's response: Authors discussed on this comments, and concluded that it would be more informative as the original form.
• The section must include information on the molecular markers (ISSR, SSR, AFLP, RFLP, others) that have been used to evaluate fertility variation. In addition, the genetic parameters used (H, He, Ho??) and the values determined in some Pinus species must be included.
  --> Author's response: Authors include some molecular study in the introduction.
• Include information about the evaluation of floral synchrony, how it influences fertility, the parameters used to evaluate. This is very relevant in the management of seed orchards, a topic that is addressed in the document.
  --> Author's response: Authors include some studies on flower synchrony in the last part of the result.
• At the end of the document (before conclusions) you must integrate information on how the variation in fertility and fecundity influences reproductive indicators (e.g. seed potential, seed efficiency, germination capacity, ...).
  --> Author's response: Authors include some studies on reproductive success (seed, germination, etc) in the last part of the result.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Thank you for considering me to revise the manuscript titled “Fertility Variation and Gene Diversity in Forest Populations". The manuscript provides fairly robust information.

The manuscript needs English editing, spelling (as provoked in line 28) as well as grammatical errors, and long sentences should be revised throughout the manuscript.

The available analyses to explore fertility variation and gene diversity in forest populations should be highlighted in the abstract and the introduction.

The citation distribution should be considered The first sentences in lines 27-31 are presented without citation while the following sentence has nine citations.

The structure of the review article is not the same as the research article including material and methods and results. the structure should be revised and improved.

The role of natural accession and artificially produced mutants in enhancing fertility variation and gene diversity in forest populations should be explored.

Exploring gene diversity using novel molecular approaches as next-generation sequencing should be presented.
The assessed characteristics for exploring fertility variation should be clarified.

The presented information needs to be discussed better and associated.

 

Some journals are not abbreviated as “Silvae Genetica” should be “Silvae Genet.”; “Tree Genetics and Genomes” should be abbreviated as “Tree Genet. Genomes” and the other journals throughout the reference list.

Comments on the Quality of English Language

Moderate editing of English language is required

Author Response

Dear reviewer;

Authors are very grateful for your valuable comments and suggestions. 

The manuscript needs English editing, spelling (as provoked in line 28) as well as grammatical errors, and long sentences should be revised throughout the manuscript.
-> Author's response) We checked by English check program and native speakers.

The available analyses to explore fertility variation and gene diversity in forest populations should be highlighted in the abstract and the introduction.
-> Author's response) It is already done, but we updated again.

The citation distribution should be considered the first sentences in lines 27-31 are presented without citation while the following sentence has nine citations.
-> Author's response) Authors cite separately with different distribution.

The structure of the review article is not the same as the research article including material and methods and results. the structure should be revised and improved.
-> Author's response) We think the present form would be more understandable, and the editor accepted the format.

The role of natural accession and artificially produced mutants in enhancing fertility variation and gene diversity in forest populations should be explored.
-> Author's response) Author feel that this is somewhat outside the scope of the review.

Exploring gene diversity using novel molecular approaches as next-generation sequencing should be presented.
-> Author's response) Authors include some molecular study in the introduction.

The assessed characteristics for exploring fertility variation should be clarified.
-> Author's response) We just followed the original papers that used the characteristics (e.g., flower, seed, cone fruit, etc)

The presented information needs to be discussed better and associated.
-> Author's response) Authors improve and modify the discussion. For example, we discuss on some molecular marker study, flower synchrony and seed germination that associated with the fertility variation.

 Some journals are not abbreviated as “Silvae Genetica” should be “Silvae Genet.”; “Tree Genetics and Genomes” should be abbreviated as “Tree Genet. Genomes” and the other journals throughout the reference list.
-> Author's response) Authors agree and all references are modified as the comments.

Author Response File: Author Response.pdf

Reviewer 4 Report

Comments and Suggestions for Authors

The topic is very important. But, there are following problems in this paper: 

1) Most equations and figures discribed in the paper are from literatures (mainly from Kang and Lindgren)，and lack new ideas.

2) There are no "unpublished knowledge" and “unpublished experiece” in the whole manuscript.

3) A lot of discriptios in the conclusions (such as " we have created a comprehensive guide for future research in this field." , " Additionally, environmental monitoring using GPS and GIS software could help track factors that significantly influence individual fertility. ", et al. ) are devoid of substance and too empty.

3) The full and abbreviations of the Latin names of trees are irregularity.

 

Author Response

Dear Reviewer;

Authors greatly thank for your valuable comments. This is the author's responses as below, 

1) Most equations and figures described in the paper are from literatures (mainly from Kang and Lindgren) and lack new ideas.
-> Author's response) This is a review paper, so authors try to compile related papers with fertility and interpret comprehensive understand and implementation on population genetics.

2) There are no "unpublished knowledge" and “unpublished experience” in the whole manuscript.
-> Author's response) The original expression was ambiguous, so authors rephrase as ‘various knowledge and experience’.

3) A lot of descriptions in the conclusions (such as " we have created a comprehensive guide for future research in this field." , " Additionally, environmental monitoring using GPS and GIS software could help track factors that significantly influence individual fertility. ", et al.) are devoid of substance and too empty.
-> Author's response) The original expression was also ambiguous and not necessary. Authors rephrase the first sentences as “Through an extensive analysis of existing literature and knowledge, we have created a comprehensive guide for future research on fertility variation and gene diversity.”
Authors delete the later part because of the devoid.

4) The full and abbreviations of the Latin names of trees are irregularity.
-> Author's response) We just followed the original papers that used the full name or the abbreviation. Authors check again and use it consistently.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Attached is my opinion on the revised manuscript.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Author Response

Response to Reviewer 1 Comments

Thank you very much for taking the time to review this manuscript (ID: forests-2578229) again. Please find the detailed responses below and the corresponding revisions highlighted in track changes in the re-submitted files.

Point-by-point response to Comments and Suggestions for Authors

Comments 1: l. 42-43 "Gene diversity to monitor fertility variation was discussed to achieve higher diversity in seed crops" Regarding the sentence on lines 42-43, the intended meaning is: One aspect of the discussion involved considering gene diversity is to monitor and achieve higher fertility variation in seed crops. Is this correct?
Response 1: Thank you for pointing this out. We agree with this comment. Therefore, we have changed as commented. (line 42-43)

Comments 2: l. 80-81. Gene diversity and expected heterozygosity are not synonymous, although both terms reflect genetic variability in a population. Expected heterozygosity is one of the measures of genetic diversity, while gene diversity encompasses the broader concept of genetic variability. Therefore, 'Gene diversity indicates that genes are different and equals the expected heterozygosity' is inaccurate.
Response 2: Authors thank you for this comment. We fully agree with this comment, and revised as “The gene diversity indicates that genes are different, and could be considered as the synonym of expected heterozygosity in this review.”(line 81-83)-

Comments 3: l. 79 "The group coancestry is the probability that the two gene are identical by descent in a large gene pool, and equals the average of all coancestry values among any combination of the individuals in a population [42]". Regardless of the grammar error in this sentence, the probability that two genes are identical by descent (IBD) is not limited to a large gene pool. The IBD concept pertains to the ancestry of genes within a population or subgroup of individuals, and it is irrelevant whether the gene pool is large or small. The cited study does not define group coancestry in the manner presented in this manuscript. Please consider referencing Cockerham, Genetics (1967), who introduced this concept, and Kang, Lindgren, Mullin Theor Appl Genet (2001) 103:1099–1107 for a more accurate understanding. In the context of group coancestry, please explain why you consider a large gene pool.
Response 3: Many thanks for your pointing out. We agree with the comments and there was wrong citation. Thus, we have cited correctly as commented and the sentences is changed as “The group coancestry is the average of all coancestries among population members in a coancestry matrix, including self coancestry. It is also the probability that two genes taken at random (with replacement) from a population are identical by descent [43, 44]”. (line 78-81)
43. Cockerham, C.C. Group inbreeding and coancestry. Genetics1967, 56(1), 89-104. DOI: 10.1093/genetics/56.1.89
44. Kang, K.S.; Lindgren, D; Mullin, T. Prediction of genetic gain and gene diversity in seed orchard crops under alternative management strategies. Theor. Appl. Genet. 2001, 103, 1099–1107. DOI: 10.1007/s001220100700

Comments 4: L. 84-87 "The status number is an intuitively appealing way of presenting group coancestry, as it connects to the familiar concept of number (i.e., population size). The ratio of the status number and the census number will be useful, so that it calls the relative status number". Unclear: Is the status number associated with the effective population size or census size?
Response 4: Thank you for pointing this out. We want to say (i.e., effective population size). The status number is an effective population size, which describes the census number of unrelated individuals corresponding to the gene diversity of the resulting seed crops (line 88-91).

Comments 5: l. 152-153 Unclear: "pi is the probability that both gametophytes from the same parent contribute to the offspring summed a whole parent of ith individual"
Response 5: p_i is the total fertility as the whole parent of the i^th individual, which is the average of female and male gametophytes contribution to the offspring. (line 156-158).

Comments 6: l. 190 “with no disruptive circumstances” – what does it mean?

Response 6: Thank you for pointing this out. We mean “without any disruptive circumstances (i.e., under conditions that rule out mutation, migration, genetic drift and natural selection)”. (line 194)
Comments 7: l. 201-204 lack of references
Response 7: Thank you for pointing this out. We agree with this comment. Therefore, we cited some references as [15, 23, 30]. (line 209)

Thank you very much in advance for your kind consideration.

Sincerely yours,

Author Response File: Author Response.pdf

Reviewer 4 Report

Comments and Suggestions for Authors

The paper has not been modified according to the revision suggestions put forward by the reviewers.

Author Response

Response to Reviewer 4 Comments

Thank you very much for taking the time to review this manuscript (ID: forests-2578229) again. Please find the detailed responses below and the corresponding revisions highlighted in track changes in the re-submitted files.

Point-by-point response to Comments and Suggestions for Authors

Comments 1:  Most equations and figures described in the paper are from literatures (mainly from Kang and Lindgren) and lack new ideas.
Response 1: Authors agree with the comments. There are a total of 23 equations given in revised version of the paper. However, only five equations (1, 2, 3, 6 and 15) are from Kang and Lindgren (1998 & 1999). Also, an equation of (12 and 13) is delivered as a theoretical framework. There are 5 figures in revised version of the paper, but only Figure 1 is from Kang and Lindgren (1999).
Authors also include flowering synchronization and reproductive success in the end of Discussion. Information of recent molecular study is given in Introduction (marker assisted selection, DNA markers, etc.).

Comments 2: There are no "unpublished knowledge" and “unpublished experience” in the whole manuscript.
Response 2: They had been separated to the text by limited sentences. Instead, authors give the several key concepts such as coancestry, group coancestry, gene diversity, status number and effective number of parents in Introduction, and we try to discuss the methods how to interconnect the key concepts and interpret the linked variables. Authors also develop the link between the sibling coefficient (Y) and H-W equilibrium in the Equation (10).
Authors add some more references to supplement the new concept.

Comments 3:  A lot of descriptions in the conclusions (such as "we have created a comprehensive guide for future research in this field”, " Additionally, environmental monitoring using GPS and GIS software could help track factors that significantly influence individual fertility”) are devoid of substance and too empty.
Response 3: Authors greatly thanks for the comments. The original expression was ambiguous and not necessary. So, authors rephrase the first sentences as “Through an extensive analysis of existing literature and knowledge, we have created a comprehensive guide for future research on fertility variation and gene diversity.” Authors delete the later part because of the devoid. 

Comments 4:  The full and abbreviations of the Latin names of trees are irregularity.
Response 4: Latin names of trees are given irregularly in Introduction and sub-titles 3.1.1 and 3.2.5

Many thanks for your valuable comments.

Author Response File: Author Response.pdf