Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breedsâ€
, Arsen V. Dotsev 1, Nikolay V. Bardukov 1, Margaret S. Fornara 1, Gottfried Brem 1,2 and Natalia A. Zinovieva 1
Round 1
Reviewer 1 Report
This is a well written manuscript, although its audience will be perhaps small. I do think that the inclusion of some of the graphics (eg the picture with cows in it) from your conference presentation would add to the readability of this manuscript and increase your readership.
Author Response
Dear Reviewer,
We would like to thank you for your valuable comments, which helped us to improve our manuscript.
The picture with cows presented on conference has been revised and updated: breeds were clearly divided by stature and the productivity type of the each breed was provided. We included the revised figure in graphical abstract to increase the readership.
We used the English editing services for our manuscript to revisions for grammar, punctuation, terminology, word choice and native English tone by native English editors.
We rewrote some paragraphs in the Results and Conclusion sections to concordance them and make the results clearer.
Reviewer 2 Report
Reviewed paper deals with GWAS oriented on stature traits. namely body weight and height on withers. Selected breeds were divided into contrast groups based on their average body weight and height on wisthers resp. Additionaly authors compared breeds goruped to two contrast production type (dairy vs. beef) + local/ primitive as mentioned in the results. Design of the study is appropriate, size of the sample sufficient and standard quality control protocol used for genotyping data. Association study was concerned on signals collected at BTA4 and BTA14.
Within this section, I would like to ask authors to use standard terminology when describing prodfuction type (dairy/ beef instead of milk, meat) as accepted in academic as well in the cattle industry. It could benefit for the reader.
On the other hand there are several mean values used in the statistic, in case authors calculated mean based on "normal" statistics, please consider use of term "average" to be sure, which mean value you mean:)
L.94 - 99 calculating "mean of means" is not well accepted in statistics but in this case it is acceptable for the purpose of use by authors. I would recommend to omit details of calculations on which distribution of breeds was made.
L.101-108 regarding the previous I would rewrite this paragraph accordingly.
Fig. 1 - regarding the previous I would recommend to rewrite accordingly the description.
Discussion however is very general.
L. 148-158 I appreciate that authors choose Wagyu as breed for comparison as this is ideal. They mentioned some controversies but without any deeper analysis. This would be really giving added value to the work especially in connection to the European (cosmopolitan) breeds´ pool. However, some of papers cited are exotic (can understand in global context and Euroasian origin of majority of breeds used in study), or outdated [42], even valid. In total authors discused their results with "only" 17 references. In case of conference papers is this, however acceptable.
Maybe the last limited authors to provide more precise conclusions and therefore I would ask authors to provide some added value to their research and add some more meaning to the conclusions, othervise general and saying nothing new about purpose of such research.
Language is of minor revisions as probably authors used AI tools for checking of grammar as visible by some not-common wording. But scientific language does´nt need to look for new constructions when describing already defined and accepted things. Therefore, I would recommend authors to read carefully the entire article and revert some changes made.
Author Response
Dear Reviewer,
We would like to thank you for careful reading our manuscript. We agree with all the comments and made the appropriate corrections in the article (they are highlighted in red). Please, find below the point-by-point response to the comments.
Reviewer: L.94 - 99 calculating "mean of means" is not well accepted in statistics but in this case it is acceptable for the purpose of use by authors. I would recommend to omit details of calculations on which distribution of breeds was made.
L.101-108 regarding the previous I would rewrite this paragraph accordingly.
Fig. 1 - regarding the previous I would recommend to rewrite accordingly the description.
Reply: We rewrote these paragraphs according to your comments, omitting the details, and trying do not distort the meaning.
Reviewer: Discussion however is very general.
L. 148-158 I appreciate that authors choose Wagyu as breed for comparison as this is ideal. They mentioned some controversies but without any deeper analysis. This would be really giving added value to the work especially in connection to the European (cosmopolitan) breeds´ pool. However, some of papers cited are exotic (can understand in global context and Euroasian origin of majority of breeds used in study), or outdated [42], even valid. In total authors discused their results with "only" 17 references. In case of conference papers is this, however acceptable.
Maybe the last limited authors to provide more precise conclusions and therefore I would ask authors to provide some added value to their research and add some more meaning to the conclusions, othervise general and saying nothing new about purpose of such research.
Reply: We corrected few paragraphs in Discussion and Conclusion sections, considering your comments.
Reviewer: Language is of minor revisions as probably authors used AI tools for checking of grammar as visible by some not-common wording. But scientific language does´nt need to look for new constructions when describing already defined and accepted things. Therefore, I would recommend authors to read carefully the entire article and revert some changes made.
Reply: We used the English editing services for our manuscript to revisions for grammar, punctuation, terminology, word choice and native English tone by native English editors.
Reviewer 3 Report
The manuscript “Genome-wide screening for SNPs associated with stature in diverse cattle breeds” present results that potentially can increase the knowledge regarding complex traits.
My main concerns related with this study are three:
1.- Description of the GWAS analysis is not described properly. Authors just refed as “To identify SNPs that were significantly associated with withers height and weight, 89 we performed across-breed genome-wide association studies using a multivariate linear-90 mixed model implemented in PLINK 1.9.
2.- Authors mention in the introduction several genes related with the stature. A gen network analysis must be realize in order to contribute to increase the knowledge regarding complex traits.
3.- Authors mention they use Bos taurus genome assembly UMD 3.1.1 instead to use the newest one. Please justify this issue.
Authors must answers these issues in order to proceed with the proper reviews of the manuscript.
Author Response
Dear Reviewer,
We would like to thank you for your valuable comments, which helped us to improve our manuscript. Please, find below the point-by-point response to the comments.
Reviewer 3: My main concerns related with this study are three:
Description of the GWAS analysis is not described properly. Authors just refed as “To identify SNPs that were significantly associated with withers height and weight, 89 we performed across-breed genome-wide association studies using a multivariate linear-90 mixed model implemented in PLINK 1.9.
Reply: We clarified the description of the analysis.
Reviewer 3: Authors mention in the introduction several genes related with the stature. A gen network analysis must be realize in order to contribute to increase the knowledge regarding complex traits.
Reply: The analysis of the gene networks was not the main purpose of our research. We agree that it could increase knowledge of the genetics of complex traits. We will consider your recommendation in our future studies.
Reviewer 3: Authors mention they use Bos taurus genome assembly UMD 3.1.1 instead to use the newest one. Please justify this issue.
Reply: To define the positions of SNPs genotyped using Bovine GGP HD BeadChip and BovineHD BeadChip (Illumina, Inc., San Diego, CA, USA, we used the Manifest file from Illumina, which was designed using UMD 3.1.1 assembly. The most of GWAS concerning body size traits mentioned in our manuscript (in introduction and discussion sections) were conducted using UMD 3.1.1 assembly. We have made choices in favor the same assembly to perform the correct comparing our results with previous studies.
Round 2
Reviewer 2 Report
I have no further comments.
Reviewer 3 Report
no more comments
