Whole Genome Resequencing Reveals Genetic Diversity and Selection Signatures of Ethiopian Indigenous Cattle Adapted to Local Environments

Round 1

Reviewer 1 Report

Terefe et al. carried out the whole genome sequences of 151 samples from 14 Ethiopian indigenous cattle populations, they assessed population genome diversity, differentiation, and signatures of positive selection (using Hp, iHS, FST, and XP-CLR) in comparison to Sudanese zebu, Asian zebu, Ankole, and African and European taurine cattle. This study found high genomic differentiation between Ethiopian and non-Ethiopian cattle populations, while low genomic differentiation and inbreeding between and within Ethiopian cattle populations. They also identified a list of candidate genes using multiple genome scan methods, and detected high frequencies of missense SNPs in GNAS, STING1, and KIT genes with high haplotype differentiations in Ethiopian cattle. Their results may provide important insights into the adaptation of the Ethiopian indigenous cattle. The study is well designed and I only have several minor points.

 

1.        Figure 2 and figure 3 need to be regenerated with high resolution.

2.        Page 4, “Ethiopian cattle genomes” > “Ethiopian cattle sequences”.

3.        Page 5, the analysis of ROH is closely related to the read coverage for sequencing samples, how many coverages of these samples used for ROH analysis for each sample, 10X or 15X? That will directly affect the calling of ROH. Also, I noted “ROHs were estimated from ped and map plink files using detectRUN package”, why not used the method for ROH detection based vcf instead of covert to ped and map?

4.        Page 6, “and integrated haplotype homozygosity (iHS) and among population”, there are three “and” in this sentence.

5.        Page 6, “VCF file” > “vcf file”.

6.        Page 6, “that 1 cM is equal to 1 Mb.” Any reference can be used to support this assumption.

7.        Page 8, “Distribution of the coefficients of error variance”, The admixture analysis of the first dataset captured the maximum ancestry proportion at K = 4, which was supported by the lowest coefficient of error variance (Figure 3a). what is result indicated based on population history?

8.        As previous study has explored Genomic Adaptation of Ethiopian Indigenous Cattle, 26. Terefe, E.; Belay, G.; Han, J.; Hanotte, O.; Tijjani, A. Genomic Adaptation of Ethiopian Indigenous Cattle to High Altitude. Frontiers in Genetics 2022, 13, 1–17, doi:10.3389/fgene.2022.960234. thus, it is better to highlight what’s new of current study comprared to Teefe et al. Frontiers in Genetics 2022.

 

Author Response

Thank you for your comments. For the details of our response please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

Authors of this interesting paper described in detail the genomic diversity and selection signatures pertinent to adaptation to the different environments in Ethiopian indigenous cattle based on whole genome sequencing data.

The title of the paper is descriptive and the abstract corresponds to the main text of the manuscript. The Introduction is well written and gives to the readers an understanding of the main idea and the aim of the study.

The results are well described, but I would like to clarify some points:

1.     Page 5, section 2.4.2. Runs of homozygosity-based genomic inbreeding coefficient (Froh)

Sentence “The number of ROHs, ROH length, and genomic inbreeding coefficient (Froh) per individual chromosomes were summarized using the summaryRUN R-package”. Was it function summaryRUNs in detectRUNS R-package, but not separate R-package? Could you explain what maximum number of missing genotypes and maximum number of opposite genotypes in the runs were used for analysis by detectRUNS?

2.     Page 7, section 3.1. Population genetic structure in Ethiopian cattle populations.

Description of admixture analysis. Sentence “In the second dataset, Bale and Boran…”. As I understand, the first dataset included AFT, ANK, ASZ, ETZ, EUT and SUZ (Figure 2a). Figure 3b corresponds to these groups. What is second dataset? Is it only Ethiopian cattle populations?  

3.     Tables 3 and 5 are very wide and some words and digits in the last columns is not visible. Would it be better to transfer these tables to Supplementary materials?

The study of local cattle, usually well adapted to the different climate and environments condition, is an interesting and important task. I would like to recommend this article for publication in Diversity.

Author Response

Thank you for your comments. For a detailed response, please see the attachment.

Author Response File: Author Response.docx