Identification of Sugarcane S. spontaneum (Poaceae) Germplasm: Evidence from rDNA-ITS and rDNA Locus Analyses
, Zuhu Deng 1,2,* and Fan Yu 1,*Round 1
Reviewer 1 Report
The present study aimed to identify S. spontaneum germplasm using rDNA-ITS and rDNA with various methods. Sequences of rDNA ITS, ARMS PCR, and FISH. The findings of this study proved that rDNA could be a valuable marker for further identification and the relationship and ploidy of S. spontaneum in sugarcane breeding. This work would interest the readers, but some parts should be revised:
1. Title should be revised as "Identification of sugarcane, S. spontaneum (Poaceae) germplasm: evidence from rDNA-ITS and rDNA locus analyses"
2. Species names are not written in italics only a few times throughout the text.
Line 31: Family name should not be written in italics.
Line 35: Family name should not be written in italics since the genera name is given in the previous sentence.
Lins 57-57: rDNAs are also valuable in determining the phylogenetics of plants, although it is relatively evolved at a lower rate. Each marker's value depends on the evolutionary relatedness of the taxa under study. ITS may be more useful in determining relatively closely related plant taxa. As you have cited from reference 17, ITS sequences were useful in determining Saccharum and its related genera. Therefore, please do not use the general term "phylogenetic relationships of plants " and would better state the plant taxa.
Lines 63-73: The aim of the study needs to be stated clearly. The study's objective should not present the finding and conclusion of the study. Please clarify the study's objective at the end of the introduction and accordingly make it consistent in the other parts of the manuscript.
Line 75: Write Saccharum in italics.
Line 84: "Mg2+" + must be superscript.
Line 85: "Taq polymerase" Taq must be in italics.
Lines 80-123; Equipment and consumables providers should be written as "(Carl Zeiss, Gottingen, Germany)". Pls provide for all others.
Line 95: "Solanum" write in italics.
Line 96: "out-group" Write as outgroup.
Line 96: "Saccharum" Write in italics.
Line 99-100: "the maximum likelihood (ML) method to calculate genetic distances" ML does not use to calculate the genetic distances. It is a method of construction a phylogenetic tree.
Line 100: "Saccharum" Write in italics.
Line 129: Yang et al.
Line 155 Figure legend: "Saccharum" Win italics.
Line 242: S. spontaneum write in italics
References: Make sure that all genera and species names are in italics. Pls check the format of the references. The Journal names should be abbreviated.
Author Response
Dear Editor and reviewers:
Thank you for your kind letter. We revised the manuscript in accordance with the reviewers’ comments, and carefully proof-read the manuscript to minimize typographical, grammatical, and bibliographical errors. According to the reviewers’ comments, we have corrected the sentence. Special thanks to you for your warmly work and good comments. Point-by-point Responses to the reviewers are listed below this letter.
Responds to the reviewer1’s comments:
- Title should be revised as "Identification of sugarcane, S. spontaneum (Poaceae) germplasm: evidence from rDNA-ITS and rDNA locus analyses".
Response: Thanks for your suggestion. We have edited it accordingly in the revised manuscript (page 1, line 1).
- Species names are not written in italics only a few times throughout the text.
Line 31: Family name should not be written in italics.
Line 35: Family name should not be written in italics since the genera name is given in the previous sentence.
Line 75: Write Saccharum in italics.
Line 84: "Mg2+" + must be superscript.
Line 85: "Taq polymerase" Taq must be in italics.
Lines 80-123; Equipment and consumables providers should be written as "(Carl Zeiss, Gottingen, Germany)". Pls provide for all others.
Line 95: "Solanum" write in italics.
Line 96: "out-group" Write as outgroup.
Line 96: "Saccharum" Write in italics.
Line 99-100: "the maximum likelihood (ML) method to calculate genetic distances" ML does not use to calculate the genetic distances. It is a method of construction a phylogenetic tree.
Line 100: "Saccharum" Write in italics.
Line 129: Yang et al.
Line 155 Figure legend: "Saccharum" Win italics.
Line 242: S. spontaneum write in italics
References: Make sure that all genera and species names are in italics. Pls check the format of the references. The Journal names should be abbreviated.
Response: Thank you very much for your suggestions. We've modified the format where appropriate (line 31、35、75、85、86、96、101、155、244).
- Lins 57-57: rDNAs are also valuable in determining the phylogenetics of plants, although it is relatively evolved at a lower rate. Each marker's value depends on the evolutionary relatedness of the taxa under study. ITS may be more useful in determining relatively closely related plant taxa. As you have cited from reference 17, ITS sequences were useful in determining Saccharum and its related genera. Therefore, please do not use the general term "phylogenetic relationships of plants " and would better state the plant taxa.
Response: Thanks for your suggestion. We had revised this expression in the paper (line 57).
- Lines 63-73: The aim of the study needs to be stated clearly. The study's objective should not present the finding and conclusion of the study. Please clarify the study's objective at the end of the introduction and accordingly make it consistent in the other parts of the manuscript.
Response: Thanks so much for your suggestions. We have carefully clarified the study's objective at the end of the introduction (line 65-73).
Author Response File: 
Author Response.docx
Reviewer 2 Report
Here authors have discussed tetra-primer ARMS-based on rDNA-ITS to identify novel S. spontaneum linkage based on the chromosome numbers. The findings are important for sugarcane research and contribute to research on evolution of the Saccharum genus. The study is well organized and presented. I recommend few improvements:
1. Authors need to include some significant studies on molecular markers for introduction and discussion, as marker-based analysis is widely used in conjunction with rDNA, ITS and PCR. For example, Upadhyay, A., et al., 2010a. Microsatellite and RAPD Analysis of Grape (Vitis spp.) Accessions and Identification of Duplicates/misnomers in Germplasm Collection, vol. 67 (1). Indian J Horticulture, pp. 8–15 and Upadhyay, A., et al., 2010b. Microsatellite analysis to differentiate clones of Thompson seedless grapevine. Indian J Horticulture 67 (2), 260–263; Hinge, V.R., Shaikh, I.M., Chavhan, R.L., et al., 2022. Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars. Sci. Rep. 12, 7979. https://doi.org/10.1038/s41598-022-11992-1.
2. Figure 3. Caption is too short and brief. Please elaborate and explain the content of the figure, so that readers can assimilate information thoroughly.
3. Table 3. What is purpose each plant material used needs to be added in a separate column? Please distinguish how each line differs from other.
4. Please provide statement about availability of each plant material, if possible provide link each germplasm line and reference library or germplasms centers. Novel insights and take away message are missing.
5. Authors could add the significance and key results into the conclusions sections. Need to elaborate conclusions and provide future directions of the study.
Author Response
Dear Editor and reviewers:
Thank you for your kind letter. We revised the manuscript in accordance with the reviewers’ comments, and carefully proof-read the manuscript to minimize typographical, grammatical, and bibliographical errors. According to the reviewers’ comments, we have corrected the sentence. Special thanks to you for your warmly work and good comments. Point-by-point Responses to the reviewers are listed below this letter.
Responds to the reviewer2’s comments:
- Authors need to include some significant studies on molecular markers for introduction and discussion, as marker-based analysis is widely used in conjunction with rDNA, ITS and PCR. For example, Upadhyay, A., et al., 2010a. Microsatellite and RAPD Analysis of Grape (Vitis spp.) Accessions and Identification of Duplicates/misnomers in Germplasm Collection, vol. 67 (1). Indian J Horticulture, pp. 8–15 and Upadhyay, A., et al., 2010b. Microsatellite analysis to differentiate clones of Thompson seedless grapevine. Indian J Horticulture 67 (2), 260–263; Hinge, V.R., Shaikh, I.M., Chavhan, R.L., et al., 2022. Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars. Sci. Rep. 12, 7979. https://doi.org/10.1038/s41598-022-11992-1.
Response: Thanks for your suggestion. We had revised this expression in the ms (line 210).
- Figure 3. Caption is too short and brief. Please elaborate and explain the content of the figure, so that readers can assimilate information thoroughly.
Response: Thanks for your suggestion. We had revised this expression in the ms (line 156).
- Table 3. What is purpose each plant material used needs to be added in a separate column? Please distinguish how each line differs from other.
Response: Thanks for your suggestion. We had added the purpose of each plant material in Table 1 (line 80).
- Please provide statement about availability of each plant material, if possible provide link each germplasm line and reference library or germplasms centers. Novel insights and take away message are missing.
Response: Thanks for your suggestion. We had revised the expression and added the material origin in Table2 (line 193).
- Authors could add the significance and key results into the conclusions sections. Need to elaborate conclusions and provide future directions of the study.
Response: Thanks for your suggestion. We had revised this expression in the revised ms (line 246-256).
Author Response File: Author Response.docx
Round 2
Reviewer 2 Report
Authors have addressed comments.
