A Search for Eurasian Sheep Relationships: Genomic Assessment of the Autochthonous Sheep Breeds in Russia and the Persian Plateau

Round 1

Reviewer 1 Report

Although it is not the main aim of the manuscript, I miss an explanation regarding the significant differences you have described for the Romanov and Kermani breeds. Is there any explanation for their notably high genomic differences with regard their respective, or expected, clusters? If so, or if you have any hypothesis, you should state them.

 

Author Response

Dear Reviewer, thank you very much for your consideration!

We agree with the comment and have provided hypotheses, which may explain such a pattern of differentiation of Kermani and Romanov sheep breeds (L234-281).

Please find it as follows.

«Besides PCA and Admixture results provided a pattern of moderate differentiation of Iranian Kermani breed from majority of other investigated sheep populations. Kermani breed is a dual-purpose fat-tailed sheep, which was originated in southeastern parts of Iran, and well fits to the dry and harsh climatic conditions, which are predominant in the Kerman province. The samples of Kermani breed used in this study were obtained from population isolated for long time. The relatively low values of heterozygosity and other diversity indicators, which were calculated earlier, implicitly pointed on the isolation of Kermani sheep group. This population probably has some private alleles that leads to its separate clustering showed by PCA and Admixture as well as explains to the long branch in the Treemix tree and on Neighbor Net graph. However, Iranian native ancestry is clearly present in Kermani breed because it joined Baluchi in the the Treemix tree and on Neighbor Net graph, which corresponded to the results obtained with using microsatellites.

Furthermore, we found a strong separation of the Russian Romanov breed from other studied breeds from both countries. This genomic pattern might be caused by several major factors and was corresponded to the previous results based on 50k and 600k data. The Romanov sheep is a highly prolific breed originated in the Central Russia (Yaroslavl region, Volga Valley) and gained world fame for its remarkable reproductive traits. The presence of specific genetic variants, which underlie such a reproductive performance of the Romanov breed, is being discussed. However, we can hypothesize that accumulation of the specific genomic components might contribute to the observed separation pattern. Nevertheless, more convincing reason is probably the Romanov breed belonging to North European short-tailed sheep, which originally inhabit the area from Russia to Iceland. Based on high-density SNP profiles, Rochus, C. M. et al (2020) studied population structure of five Swedish native sheep breeds and demonstrated the clear differentiation between North European short-tailed group and other sheep populations including transboundary and local breeds. These findings are well agreed with our results because the Romanov breed is a single representative of North European short-tailed group in our sample».

Thank you very much for your valuable comments, which helped us to improve the manuscript and makes it more interesting for potential readers.

Author Response File: Author Response.pdf

Reviewer 2 Report

The paper is relevant to the scope and aim of the journal and SI. From my point of view, I would expect from authors provide something new - methodology, discovery of unknown history of sheep breed  development but this was probably not the ambition.

Pleenty of such a papers are in presence appearing from various countries in Africa or Asia - similar methodology, similoar art of description results as well conclusions. 

Therefore, either the paper is scientifically sound, I would expect more analysis of data, new methodologies - i.e. new pipelines to increase not only the value of paper but also interest of the readers.

In this stage, I am sorry I can not evaluate the paper higher.

 

 

Author Response

Dear Reviewer, thank you very much for your valuable comments!

We agree with your comments and understand your evaluation of the paper. Actually, we did not aim to develop new methodology or pipeline. Our aim was to fill the gap in the genetic relationships in Eurasia sheep breeds, that fit very well to the scope of the Diversity journal.

Following your recommendations, we made attempts to calculate f3 and D statistics. The f3 statistics revealed low negative values of f3 estimates and Zscore indicating on possible admixture events in Iranian sheep breeds. In our opinion, these results did not provide something new that would extent or deepen our work. Please find the results below.

A	B	C	f3	stderr	Zscore
Baluchi	Shal	Siah_Kabod	-0,000249	0,000298	-0,835
Shal	Baluchi	Siah_Kabod	-0,000249	0,000298	-0,835

The results based on D-statistical estimations corresponded to the patterns, which were obtained in our initial submission.

In our future research, we will make attempts to develop new methodology to provide deeper insight into origin of the Eurasian sheep breeds.

We would like to express our gratitude for the valuable recommendations will navigate our future research to be more comprehensive.

Author Response File: Author Response.pdf

Reviewer 3 Report

Manuscript ID:  diversity-1727371

Title: A search for Eurasian sheep relationships: genomic assessment of the Autochthonous Sheep Breeds in Russia and the Persian Plateau

 

General comments and judgment

The Authors aimed to characterize genomic features of local sheep breeds in Russia and the Persian Plateau (Iran) to unlock possible genetic relationships between these populations. The manuscript is well written, in fluent English language: clear, precise, and easy to understand. Also, it offers interesting insight on the sheep history, contributing to better understand the pattern of admixture, which is present genomes of many Eurasian sheep breeds.

I don’t have any particular request or concern to be addressed, so I suggest to accept the manuscript in its current form.

Author Response

Dear Reviewer,

thank you very much for your consideration! We are greatly appreciate you positive feedback on our manuscript.

Round 2

Reviewer 2 Report

no further comments