Positive Selection and Adaptive Introgression of Haplotypes from Bos indicus Improve the Modern Bos taurus Cattle
Round 1
Reviewer 1 Report
The paper is very interesting and well prepared. The analysis is devoted to specialist but using such method it is possible to know the history of breeding and selection. Below please find few notice for better reading.
- Figure 1 - in sections A there is proportion of ROH in genome (question the proportion of numbers or of sum of lenght), if number - by what was the number divided? If percentage of sum of lengt why Jersey has such low number. Generally it could be good to explain more detail relations between all five pictures in Figure 1.
- Figure 4. - there is lack of unit on the picture (lenght of ROH)
- The right taxonomy of Bison and Wisent is Bison bison and Bison bonasus
- in lines 305-306 there is mistake - should be introgression from Bos indicus to Bos taurus
- line 330 effect of favored genotype is 0,692 but in table 1. is 0,629
- this part of results (3.4) could be rejected because this is the only example in Holstein. The comparison of genotype within selected genes could be a subject of another paper.
- Names of other species - they should be in the same style - all in latin or all in English (in lines 87 and 468 is Bos indicus and other names in English)
Author Response
Reviewer 1
Comments and Suggestions for Authors
The paper is very interesting and well prepared. The analysis is devoted to specialist but using such method it is possible to know the history of breeding and selection. Below please find few notice for better reading.
Figure 1 - in sections A there is proportion of ROH in genome (question the proportion of numbers or of sum of lenght), if number - by what was the number divided? If percentage of sum of lengt why Jersey has such low number. Generally it could be good to explain more detail relations between all five pictures in Figure 1.
AU: Thank you very much for your comments. We have redefined and clarified the concept of proportion of ROH and how to calculate it in figure 1 section A in the revised manuscript (Lines 214-217). The proportion of ROH reflects the degree of inbreeding using a genomic character and is calculated as the length of ROH divided by the total length of cattle genome (~3G). From Figure 1, we could see that the proportion of ROH in Jersey is relatively medium compared with the highest and lowest, which was added in the lines 214-217 in revised manuscript.
Figure 4. - there is lack of unit on the picture (lenght of ROH)
The right taxonomy of Bison and Wisent is Bison bison and Bison bonasus
in lines 305-306 there is mistake - should be introgression from Bos indicus to Bos taurus
line 330 effect of favored genotype is 0,692 but in table 1. is 0,629
AU: Thank you very much for spotting these typing errors. We have modified these errors correspondingly. The taxonomy of Bison and Wisent have been rewritten on line 278 The introgression should be from Bos indicus to Bos taurus on line 292. The number should be 0.629, which has been modified on line 300.
this part of results (3.4) could be rejected because this is the only example in Holstein. The comparison of genotype within selected genes could be a subject of another paper.
Names of other species - they should be in the same style - all in latin or all in English (in lines 87 and 468 is Bos indicus and other names in English)
AU: Thank you very much for the great suggestion. We would very much like to examine further more in more populations and identify more haplotypes that are selected in the next paper. We have checked all the species name in order to make them in the same style.
Reviewer 2 Report
Abstract: In line 23, dramatic event may not be a scientific comment.
Introduction: In line 55, "These important haplotypes largely con-55 contributed to the improvement of the modern taurine cattle breeds", what about Bos indicus?
Materials and methods: no comment, they look okay to me but again I am not an expert to evaluate them through and through.
Results: In fig 1, graphs resolution can be better. Something in different language popping up when cursor moved to graph. Same goes with other graphs and figures. In Fig. 1B and C texts are not visible.
In fig 5 and 6, the breed names are coming on the figure. They can be moved.
Discussion: no comments
Author Response
Reviewer 2
Comments and Suggestions for Authors
Abstract: In line 23, dramatic event may not be a scientific comment.
AU: Thanks for your suggestion. We have replaced this words instead with more professional ones.
Introduction: In line 55, "These important haplotypes largely con-55 contributed to the improvement of the modern taurine cattle breeds", what about Bos indicus?
AU: Thank you for the comment. We would very much to put more effort on the study of Bos indicus when we have more samples from Bos indicus, which would be our future direction of study.
Materials and methods: no comment, they look okay to me but again I am not an expert to evaluate them through and through.
Results: In fig 1, graphs resolution can be better. Something in different language popping up when cursor moved to graph. Same goes with other graphs and figures. In Fig. 1B and C texts are not visible.
AU: Thank you very much for the reminder. We have replaced fig 1 with a new fig 1 with higher resolution. We add a full texts of figures in the beginning of the figures and tables.
In fig 5 and 6, the breed names are coming on the figure. They can be moved.
AU: We have changed fig 5 and 6 according to the comment.
Discussion: no comments
