Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)
Round 1
Reviewer 1 Report
Construction of a Draft Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)
Generally, the paper reads very well and embodies 19 years of hard work and is technically sound. I do have some minor concerns about the paper which I have addressed below.
Title: I would not use the word ‘Draft’ in the Title- either remove or perhaps use the word Preliminary instead. It gives more of an unfinished title to the body of work that has been carried out.
Introduction:
Line 29- change ‘was’ to ‘is’
Line 34- change ‘caused by’ to ‘due to’
Line 39- add and in the human diet too
Line 47-Remove ‘joined’ and perhaps add ‘been included in’
Line 48- Paragraph starting ‘So far …’ perhaps give some more background information on why these cultivars were used to construct the initial genetic maps- had one higher protein content and/or fungal resistant for example.
Line 67- Again some more information on the cultivars Tanjil and Unicrop- why were they used?
Line 97- plant high? should this be plant height?
You have selected on these phenotypic traits outlined in line 97- any seed quality traits?
Results:
A common feature of these papers is use of countless acronyms which for someone a non-expert who picks up the paper their use can be baffling- e.g. what are ISSR primers- after looking it up I learnt they are inter-simple sequence repeats- perhaps a supplementary glossary of such terms might help? What is also confusing is that the authors do define in the Materials and Method section what the primers are but this after the Results section!! I have checked other ‘Agronomy’ articles and the Materials and Method section comes after the ‘Introduction’- could the authors please amend this as it is makes the reading of the paper very frustrating.
Figure 2 and 3 need to be redrawn or enlarged- I cannot read them!
For Figure 4 and 5 what are the labels on the outer section of the circle?
For Figure 6 and 7 – again very small and not sure it adds anything to paper as it too small to read and understand- can this be re-drawn or a rethinking on how these results could be presented in a more informative and precise way please?
Discussion:
Line 213- References please after ‘wheat’.
Could more text be added on the significance of the new map in terms of identifying important chromosomal regions with important agronomic traits- higher protein content and/or fungal resistance. The Discussion finishes abruptly for me with no outstanding finds and take-home messages from what has been a lot of work carried out over 19 years. The Conclusion of the paper needs to be moves too. Only when these issues have been addressed can I recommend for publication.
Author Response
We would like to thank the reviewer of valuable comments and usefulness suggestions. We address all yours comments. Please find more details bellow.
According to suggestion we update manuscript title - "Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin L.)".
In the section introduction redaction suggestion in line 29 to 47 and 97 were corrected.
The notice about line 48 and 67.
Needed information about mapping population background were added in line actual line 69 and the new version of this paragraph is: “The second mapping population has been obtained by crossing the 'Tanjil' (highly resistant to the anthracnose, the phomopsis stem blight, grey leaf spot disease, CMV virus transmission, aphid colonization) and 'Unicrop' (not resistance) varieties. Based on that, a single genetic map has been created for this population using the NGS-based RAD-sequencing technology. The 8246 markers (including SNP 7563) were grouped in 20 linkage groups. The total length of the linkage map was 1629.9 cM.”.
Section Material and methods as suggested was move after introduction section.
Figure 2 and 3 were updated and now should be more clear now.
Labels for Figure 4 and 5 was made bigger and should be easy to read now.
Figure 6 and 7 were move as supplementary data in height resolution and should be easy to read now.
The discussion section was improve. We add more information about the significant of a new map. The new paragraph with this information was added in line 316-336. The bibliography was supplemented.
The conclusion section was slightly corrected. New information were added in line 380-382.
Reviewer 2 Report
There is no doubt that authors have done significant work, but have not presented their research findings in a better way so that readers are not distracted. I feel that some sentences do not convey what authors intend to say. The results are good but lack cohesiveness. Authors need to highlight how their outcome will help genome assembly and research community that use their genomic resources. These genomic resources could be very useful for other researchers in calling SNPs while working on the same crop. I feel that manuscript needs improvement in presenting their outcomes.
Author Response
We would like to thank the reviewer of valuable comments and usefulness suggestions. We address all yours comments. Please find more details bellow.
According to suggestion of others reviewers we update manuscript title - "Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin L.)".
Section Material and methods as suggested was move after introduction section.
Figure 2 and 3 were updated and now should be more clear now.
Labels for Figure 4 and 5 was made bigger and should be easy to read now.
Figure 6 and 7 were move as supplementary data in height resolution and should be easy to read now.
The discussion section was improve. We add more information about the significant of a new map. The new paragraph with this information was added in line 316-336. The bibliography was supplemented. We hope that this will be enough to present possibilities usefulness of our data for other researchers.
The conclusion section was slightly corrected. New information were added in line 380-382.
Reviewer 3 Report
1). Manuscript ID: agronomy-591802
2). Manuscript Title: Construction of a Draft Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)
3). Suggestions for improvement:
The experiments are thoughtfully conceived and conducted. However, the following changes needs to be done before acceptance.
A). Please improve the resolution of Figs. 2 & 3.
B). Include full forms of all the acronyms, when they are mentioned for the first time in the text.
C). This relevant reference can be included in the introduction:
----Muhammad Munir Iqbal, Mark Huynh, Joshua A. Udall, Andrzej Kilian, Kedar N. Adhikari, Jens D. Berger, William Erskine & Matthew N. Nelson (2019). The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop. BMC Genetics volume 20, Article number: 68
D). Please read the reviewed manuscript for further comments.
Comments for author File: 
Comments.pdf
Author Response
We would like to thank the reviewer of valuable comments and usefulness suggestions. We address all yours comments. Please find more details bellow.
According to suggestion of others reviewers we update manuscript title - "Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin L.)".
Section Material and methods as suggested was move after introduction section.
Figure 2 and 3 were updated and now should be more clear now.
Labels for Figure 4 and 5 was made bigger and should be easy to read now.
Figure 6 and 7 were move as supplementary data in height resolution and should be easy to read now.
All acronyms were included in text.
All the comments marked in text was addressed.
The work by Iqbal et al was added to our paper in Introduction and Discussion section.
Round 2
Reviewer 1 Report
I am pleased that the authors took my suggestions on board. I still do have concerns about Figures 2 and 3 as they are too small and do not add anything to the paper. Perhaps a table format would be better?
Author Response
We are greate once again for your time in reviewing our work. We are aware of imperfections of both Fig2 and Fig3. However, we think that it's almost impossible to produce much better quality figures of genetic in the format of the standard page (A4) with over 1000 unique locus. We also saw many similar quality pictures in recently published papers with a high number of unique markers. We strongly believe that resulted genetic map is essential for our publication and would like to keep both this figure in the manuscript. We agree with your suggestion that the tabular format could be better for reading data provided by our map. The map in tabular format has been already included in our paper (as supplementary Table S6: Genetic linkage map for ExL population). Hoverer, this table contains over 4000 rows and we don't think putting this table directly to manuscript would be a good idea. What is more, even if we select only unique locus from genetic map and put only this information into a table would produce tables with over 1000 rows. We believe that this table still would be too big to include into the manuscript. In conclusion, despite of imperfections of Fig2 and Fig3 we would like to leave them not modified in manuscript. We believe that both Fig2 and Fig3 in current forms are readable (maybe not easy). If readers would like to find more precise information about the location of specified markers on created a genetic map he could find this information in supplementary Table S6.
