Analysis of Genetic Diversity and Population Structure in Yam (Dioscorea Species) Germplasm Using Start Codon Targeted (SCoT) Molecular Markers
Round 1
Reviewer 1 Report
Dear authors,
it was a pleasure to review such a good manuscript. A lot of applied statistical methods have been applied in this work that confirms the hypotheses that have been set.
Comments for author File: 
Comments.pdf
Author Response
The authors appreciate the time and effort by the reviewer for reviewing this manuscript and for providing insightful comments and suggestions to improve its quality. We have revised the manuscript as per the reviewer's suggestions and comments. We have incorporated the following reviewer’s specific comments in the revised version of manuscript. The point-by-point responses are provided below.
Response to Comments from Reviewer
Manuscript: “Analysis of Genetic Diversity and Population Structure in Yam 2 (Dioscorea species) Germplasm Using Start Codon Targeted 3 (SCoT) Molecular Markers”
Comments: Dear authors, it was a pleasure to review such a good manuscript. A lot of applied statistical methods have been applied in this work that confirms the hypotheses that have been set.
Response: Thank you the positive contents. We appreciate.
Abstract
General comment: The abstract is written in a structured way and provides all necessary information about the manuscript.
Line 27 the variance->a variance
Response: Thank you for the observation. We have replaced “the variance” with “a variance”.
Introduction
General comments: The introduction is written in a structured way. You could consider explaining some examples which combine SCoT with breeding programs.
Response: Thank you for the comment. We have explained some examples combining SCoT with breeding programs.
Line 52 climate resilient -> climate-resilient; is need-> is a need
Response: Thank you for the observation. We have replaced “climate resilient” with “climate-resilient” and “is need” to “is a need”.
Line 53 high yielding -> high-yielding
Response: Thank you for the observation. We have replaced “high yielding” with “high-yielding”.
Line 55... of genetic.. -> on genetic
Response: Thank you for the observation. We have replaced “of genetic” with “on genetic”.
Line 56 pre-requisite -> prerequisite
Response: Thank you for the observation. We have replaced “pre-requisite” with “prerequisite”.
Line 62 priotized -> prioritized
Response: Thank you for the observation. We have replaced “priotized” with “prioritized”.
Line 71 without the
Response: Thank you for the observation. We have deleted “the”.
Material and methods
General comments: This chapter is very clearly written and there is no confusion whatsoever. What is certainly not clear is why you should not state which yam species were used in the research.
Line 102 with respect to -> concerning
Response: Thank you for the observation. We have replaced “with respect to” with “concerning”.
Line 103 cool-box -> cool box
Response: Thank you for the observation. We have replaced “cool-box” with “cool box”.
Line 105 Table. I will put in one column species name of accession; the second column needs to centre (alignment)
Response: Thank you for the observation. We have inserted a column on the species of the yam accession and also aligned the second column.
Line 111 nuclease free -> nuclease-free
Response: Thank you for the observation. We have replaced “nuclease free” with “nuclease-free”.
Subtitle 2.3. COMMENT: it should state what PCR-related modifications have been made.
Response: Thank you for the observation. We have indicated the modifications on annealing temperature and duration of PCR thermal cycling conditions.
Line 133 5 minute -> 5-minute
Response: Thank you for the observation. We have replaced “5 minute” with “5-minute”.
Line 158 was -> were
Response: Thank you for the observation. We have replaced “was” with “were”.
Line 161 groups -> group
Response: Thank you for the observation. We have replaced “groups” with “group”.
Line 164 without the Evanno’s
Response: Thank you for the observation. We have deleted “the”.
Line 165 online based -> online-based
Response: Thank you for the observation. We have replaced “online based” with “online-based”.
Results
General comments: The results chapter is very concisely written. The statistical analyses used to confirm the hypotheses of the manuscript
Figure 1. maybe put in supplementary material.
Response: Thank you for the observation. We have transferred Figure 1 to the supplementary material section.
Line 206 are divided 2
Response: Thank you for the observation. We have replaced “grouped” with “divided”.
Line 207 sub-lusters -> sub-clusters
Response: Thank you for the observation. We have revised.
Line 218 of yam
Response: Thank you for the observation. We have added “of”.
Table 3 line 227 without grey line
Response: Thank you for the observation. We have removed the grey line.
Line 262 were -> was
Response: Thank you for the observation. We have replaced “were” with “was”.
Discussion
General comments: The discussion was properly discussed according to the results. Perhaps it would be necessary to create a sub-chapter on the practical application of the results of this research. for example. Which individual should be used for future breeding programs or conservation programmes?
Also, some sentence need to explain more deeply, you could find a reference in the paper: „Genetic diversity and differentiation of pedunculate oak (Quercus robur L.) populations at the Southern Margin of its distribution range—Implications for conservation“
Response: Thank you for the comment. We have provided the information in the discussion section.
Line 275 ... to determine population structure of many plant species [36]. you quote only one reference, put more references in this brackets to confirm “many“
Response: Thank you for the observation. We have put more relevant references to confirm “many”.
Line 275-276 sentence „Several gene-based markers have been developed to aid in the investigation of genetic diversity and population structure analyses and one of such molecular marker is SCoT.“ Not clear
Response: Thank you for the comment. We have revised the sentence.
Line 278 their -> its
Response: Thank you for the observation. We have changed “their” to “its”.
Line 286 is -> are
Response: Thank you for the observation. We have replaced “is” with “are”.
Line 306 in -> of this study; the use
Response: Thank you for the observation. We have revised the sentence accordingly.
Line 307 of sampling
Response: Thank you for the observation. We have added the word “of”.
Line 310-311 the genetic->without the
Response: Thank you for the observation. We have deleted “the”.
Line 311 indicates -> indicate; a low
Response: Thank you for the observation. We have revised the sentence accordingly.
Line 318 sentence „In addition, these results indicated that the SCoT markers used in this study are very informative and efficient and can be used in genetic diversity studies, DNA fingerprinting, construction of genetic linkage maps, quantitative traits (QTL) mapping and marker-assisted breeding in yam.“ Please explain!
Line 324 an average
Response: Thank you for the observation. We have added “an”.
Line 327 high -> highly ....... check!!!!
Response: Thank you for the observation. We have revised the sentence accordingly.
Line 337 without the germplasm
Response: Thank you for the observation. We have deleted “germplasm”.
Line 341 STRUTURE -> STRUCTURE; without The bayesian
Response: Thank you for the observation. We have revised the sentence accordingly.
Line 351 background -> backgrounds
Response: Thank you for the observation. We have replaced “background” with “backgrunds”.
Line 352-353 Sentence „ The presence of high genetic variability within the population signifies the divergence of yam accessions within a single population, indicating that any region holds a particular important genetic diversity.“ Why? Please explain.
Response: Thank you for the comment. We have clarified the information.
Conclusions
General comments: Great conclusion
Line 387 a high
Response: Thank you for the observation. We have revised accordingly.
Line 394 In addition, (need comma)
Response: Thank you for the observation. We have added a comma.
Line 395 a wide
Response: Thank you for the observation. We have revised accordingly.
Line 397 a need
Response: Thank you for the observation. We have revised accordingly.
Supplementary material: 3
Need more information about SCoT markers. Refill the table with additional marker information.
Response: Thank you for the comment. We have provided additional marker information including the annealing temperatures and size ranges of the amplified products.
Reviewer 2 Report
Article submitted for revision (ijpb-2242093) presents an interesting research for the yam (Dioscorea species) breeding. This species is very important food security crop with nutritional and medicinal values. Hence , there is a need to breed new excellent recombinant varietes. Genetic analysis conducted in this examinations with the use of start codon targeted (SCoT) molecular markers revealed the genetic diversity and population structure in 20 yam accessions grown in Kenya. The obtained results may be the guide for the selection of appropriate parents for yam breeding. I have noticed some minor factual and technical errors in the text. In the Abstract (line 24)
I suggest to replace the word "Averages" with the word "Means" most commonly used for the explanation of UPGMA (see line 156 in the text). In the Introduction : line 39 - a space should be put between 2019 and [2]; line 42- square bracket should be added after [2. In the Results: line 193- instead of E10 should be E11 (Figure 1); line 200 - instead of E6 and C as well as E4 and C should be E6 and B as well as E4 and B (see supplementary Table S2). Line 204 - instead of the value of Jaccard's similarity coefficients 0.61 between two major clusters should be 0.59 (see dendrogram); line 207 - the letter "c" sholud be added to "sub-lusters" (in the beginning of this line), next - sub-cluster II(a) with 6 yam (not 12) accessions and sub-cluster II(b) with 12 (not 6 ) yam accessions (see dendrogram). Line 209 - sholud be sub-cluster II(b) (not a); line 211- instead of sub-cluster II(b) should be II(a) (see dendrogram). The header of the Figure 2. should be on the same page with Dendrogram as well as the Table 4. In the Discussion: line 328 - instead of C shloud be B (see comments above). Line 331- instead of the value 0.2 sholud be the value of similarity coefficient between two major clusters 0.59 (see comments above). I recommend to publish this article in IJPB journal after minor revision.
Author Response
The authors appreciate the time and effort by the editor and reviewers for reviewing this manuscript and for providing insightful comments and suggestions to improve its quality. We have revised the manuscript as per the reviewer’s suggestions and comments. We have incorporated the following reviewer’s specific comments in the revised version of manuscript. The point-by-point responses are provided below.
Response to Comments from Reviewer
Article submitted for revision (ijpb-2242093) presents an interesting research for the yam (Dioscorea species) breeding. This species is very important food security crop with nutritional and medicinal values. Hence, there is a need to breed new excellent recombinant varieties. Genetic analysis conducted in this examinations with the use of start codon targeted (SCoT) molecular markers revealed the genetic diversity and population structure in 20 yam accessions grown in Kenya. The obtained results may be the guide for the selection of appropriate parents for yam breeding. I have noticed some minor factual and technical errors in the text.
In the Abstract (line 24)
I suggest to replace the word "Averages" with the word "Means" most commonly used for the explanation of UPGMA (see line 156 in the text).
Response: Thank you for the observation. We have replaced averages with means.
In the Introduction:
Line 39 - a space should be put between 2019 and [2];
Response: Thank you for the observation. We have inserted a space between 2019 and [2].
Line 42- square bracket should be added after [2.
Response: Thank you for the observation. We have added square bracket after [2].
In the Results:
Line 193- instead of E10 should be E11 (Figure 1);
Response: Thank you for the observation. We have revised E10 to E11.
Line 200 - instead of E6 and C as well as E4 and C should be E6 and B as well as E4 and B (see supplementary Table S2).
Response: Thank you for the observation. We have revised appropriately.
Line 204 - instead of the value of Jaccard's similarity coefficients 0.61 between two major clusters should be 0.59 (see dendrogram);
Response: Thank you for the observation. We have revised the anomaly and used 0.59 instead of 0.61.
Line 207 - the letter "c" sholud be added to "sub-lusters" (in the beginning of this line), next - sub-cluster II(a) with 6 yam (not 12) accessions and sub-cluster II(b) with 12 (not 6 ) yam accessions (see dendrogram).
Response: Thank you for the observation. We have revised the anomaly in the manuscript text.
Line 209 - should be sub-cluster II(b) (not a);
Response: Thank you for the observation. We have revised the section accordingly.
Line 211- instead of sub-cluster II(b) should be II(a) (see dendrogram). The header of the Figure 2. should be on the same page with Dendrogram as well as the Table 4.
Response: Thank you for the observation. We have revised accordingly.
In the Discussion:
Line 328 - instead of C should be B (see comments above).
Response: Thank you for the observation. We have revised accordingly.
Line 331- instead of the value 0.2 should be the value of similarity coefficient between two major clusters 0.59 (see comments above).
Response: Thank you for the observation. We have revised accordingly.
