Biodiversity of Russian Local Sheep Breeds Based on Pattern of Runs of Homozygosity†
, Arsen Dotsev 1, Marina Selionova 2, Gottfried Brem 1,3 and Natalia Zinovieva 1Round 1
Reviewer 1 Report
I am missing clear presentation of the interest of the breeders in the evaluation of genomic inbreeding in form of observed inbreeding depression or fixation of deleterious alleles. More attention shall be given to the fact why those breeds are important, what is the level of their diversity and economic importance of the sheep industry. Othervise is the study only average giving just use of state-of-the art methodology to the new dataset, with repeated observations and comments to the results. Authors shall explain in detail why recent autozygosity event are dangerous for the local/ autochtonous breeds, especially if of limited size. I am missing diversity status of populations evaluated, even from supplementary material seems that population sizes are OK, only unevenly distributed between the different regions under study. This shall be somehow discussed as well.
More attention shall be given to the fact why those breeds are important, what is the level of their diversity and economic importance of the sheep industry.
Author Response
Dear Reviewer, thank you very much for valuable comments!
We added parts on the economic importance of the sheep industry and significance of local breeds (L 77-104). The effects of autozygosity on local breeds were described more fully (L 430-449).
Author Response File: 
Author Response.docx
Reviewer 2 Report
I found the work very interesting and I just would like to suggest you some arrangement as a minor revision.
Introduction
Line 58: Please explain the FROH acronym.
Line 77: please change “aboriginal” with “local” or “autochthonous”.
Line 82: I did not understand if this study was performed on samples from a previous study and from on-line database or if it was performed on new data. Please specify.
Materials and methods
Line 88: please change in “2.1 Samples and genotyping”
Line 90: please clarify samples as above.
Line 91 to 98: I suggest adding a summary table, as supplementary, with details of breeds and reference (if there are).
Line 99: were Buubei samples divided based on a previous PCA results? Please specify.
Results
All the figures are too small please enlarge it.
Line 225: please modify in “Estimation of genomic inbreeding coefficient based on runs of homozygosity in Russian local sheep breeds”
Line 227 to 233: please modify in “Thus, the FROH values varied from 0.033 (MONG) to 0.072 (ANDB) in coarse wool group (Figure 4a), and from 0.033 (ALTM) to 0.069 (NCSN) in semi-fine wool group (Figure 4b), and from 0.035 (BKFF) to 0.066 (VOLG) in fine wool group (Figure 4c).”
Line 240: the legend is incomplete, please correct.
Line 265: please modify “…..not established in semi-fine wool breeds….”
Author Response
Dear Reviewer, thank you very much for valuable comments!
Introduction
Point 1: Line 58: Please explain the FROH acronym.
Response 1: Corrected
Point 2: Line 77: please change “aboriginal” with “local” or “autochthonous”.
Response 2: Changed
Point 3: Line 82: I did not understand if this study was performed on samples from a previous study and from on-line database or if it was performed on new data. Please specify.
Response 3: We used 50k genotypes which were generated in our previous study (Deniskova et al 2018, https://gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0399-5). To enlarge the sample number, we additionally collected samples from local breeds which were genotyped using 600k chip. Both datasets are our own. The on-line link was corresponded to our published study based on 50k genotypes to provide additional information on Russian breeds to potential readers.
We agreed that the description of used dataset was vague. In this regard, we added Table 1 which showed the details on the genotypes, sampling regions, and productivity types.
Materials and methods
Point 4: Line 88: please change in “2.1 Samples and genotyping”
Response 4: Changed
Point 5: Line 90: please clarify samples as above.
Response 5: Clarified
Point 6: Line 91 to 98: I suggest adding a summary table, as supplementary, with details of breeds and reference (if there are).
Response 6: We added Table 1 in the main text which showed the details on the genotypes, sampling regions, and productivity types.
Point 7: Line 99: were Buubei samples divided based on a previous PCA results? Please specify.
Response 7: Specified
Results
Point 8: All the figures are too small please enlarge it.
Response 8: We enlarged all the figures.
Point 9: Line 225: please modify in “Estimation of genomic inbreeding coefficient based on runs of homozygosity in Russian local sheep breeds”
Response 9: Modified
Point 10: Line 227 to 233: please modify in “Thus, the FROH values varied from 0.033 (MONG) to 0.072 (ANDB) in coarse wool group (Figure 4a), and from 0.033 (ALTM) to 0.069 (NCSN) in semi-fine wool group (Figure 4b), and from 0.035 (BKFF) to 0.066 (VOLG) in fine wool group (Figure 4c).”
Response 10: Modified
Point 11: Line 240: the legend is incomplete, please correct.
Response 11: Corrected
Point 12: Line 265: please modify “…..not estab lished in semi-fine wool breeds….”
Response 12: Modified
Author Response File: Author Response.docx
