The Genetic Assessment of South African Nguni Sheep Breeds Using the Ovine 50K Chip

Round 1

Reviewer 1 Report

The manuscript "The genetic assessment of South African Nguni sheep breeds using the Ovine 50K chip" aimed to determine the genetic relationships between native sheep South African  and other sheep breeds using SNP-type markers. The results indicate that disordered crosses pose a threat to the maintenance of two genetic materials and recommend the establishment of a conservation nucleus to minimize the loss of local genetic resources.
The results found are extremely important for the region and for breeders, as it establishes the current situation of local breeds, which can serve as a basis for actions to avoid genetic loss and provide conditions for the elaboration of future programs for the genetic improvement of local breeds.
In this way, I understand that the research has generated an important contribution to the local breeds and to the breeders who depend on them for their subsistence.

Author Response

Thank you for the comments and review, the authors appreciate your inputs into our manuscript

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript entitled: The genetic assessment of South African Nguni sheep breeds using the Ovine 50K chip, addresses an interesting research point in breeding of sheep, highlighting the genetic distance and admixtures among these breeds.

The manuscript idea is novel with great interest and it is well written as well. The authors have used the standard journal format in manuscript writing.

The evaluation is based on that overall value of data presented and novelty of the idea. In addition, it is on the scope of this outstanding journal.

 

Comments for author File: Comments.pdf

Author Response

Thank you for the comments and review, the authors appreciate your inputs into our manuscript

Author Response File: Author Response.docx

Reviewer 3 Report

In this manuscript investigated the genetic relationship between Nguni sheep ecotypes and the relationship to other selected South African breeds, using SNP markers. The subject of this study is suitable for Agriculture journal. The authors showed that SNP markers could be successfully used to assess genetic variation amongst South African Nguni sheep ecotypes. This is an interesting study but I have a number of concerns (bellow indicated) about the manuscript in its current form that needs to be addressed by the authors prior to consideration.  These concerns should be addressed by the authors.

 

1. The aim of the study should be clearly stated in the abstract section.
2. The authors informed that Nguni sheep is subdivided into four ecotypes namely, Zulu, Swazi, Landim and Pedi, but the Landim type was not evaluated in the study, and the reason should be explained.
3. The authors should not be so categorical in mentioning that there is no published evidence (line 57) on Nguni sheep genetic diversity that has been conducted using SNP markers when the literature exists. The objectives must be specified for the Nguni sheep in South African conditions.
4. Agarose gel (1%) electrophoresis band image of total extracted genomic DNA should be added as a figure in the MM section.
5. In the MM section, information should be given about how the sample genotyping is done.
6. The results have been well presented and the results have been supported by the discussion. However, the sentences given below in the conclusion section cannot be understood. Please rewrite it more clearly.

-“The latter (what is the latter) could include populations from the Makhathini and Zululand Research Stations in South Africa.”

-“………the Swazi ecotype despite their close relationship with the Zulu ecotype fosters a lot of perspectives (what is a lot of perspectives), future investigation within this population………..”

-“Crossbreeding poses a threat to the genetic integrity of the Zulu and Swazi ecotypes as both types were highly admixed with Damara sheep and analysis indicated a possible contribution directed from these two to Damara indicating genetic fusion across these populations.” This sentence should be transferred to the discussion section and may be discussed further.

Author Response

Dear Editor/reviewers

Thank you for the constructive comments and suggestions regarding our manuscript (title: "The genetic assessment of South African Nguni sheep breeds using the Ovine 50K chip". Authors of the manuscript have critically discussed about all the comments and suggestions made by the reviewers.

Reviewer #3,

In this manuscript investigated the genetic relationship between Nguni sheep ecotypes and the relationship to other selected South African breeds, using SNP markers. The subject of this study is suitable for Agriculture journal. The authors showed that SNP markers could be successfully used to assess genetic variation amongst South African Nguni sheep ecotypes. This is an interesting study but I have a number of concerns (bellow indicated) about the manuscript in its current form that needs to be addressed by the authors prior to consideration.  These concerns should be addressed by the authors.

Comment 1 - The aim of the study should be clearly stated in the abstract section

Answer: The aim of the study is stated in the abstract between line 13 and 15 as suggested by the reviewer.

Comment 2 - The authors informed that Nguni sheep is subdivided into four ecotypes namely, Zulu, Swazi, Landim and Pedi, but the Landim type was not evaluated in the study, and the reason should be explained.

Answer: In the case of Landim, awareness of the significance of conservation and sustainable use of animal genetic resources is often limited at the policy level. This plays a major role in the representation of the breed in genetic studies as compared to the other three ecotypes. Lines 33 to 36

Comment 3 - The authors should not be so categorical in mentioning that there is no published evidence (line 57) on Nguni sheep genetic diversity that has been conducted using SNP markers when the literature exists. The objectives must be specified for the Nguni sheep in South African conditions.

Answer: The statement has since been removed following the reviewer’s suggestion. The objective is mentioned in lines 61 to 63 following the reviewer’s suggestion

Comment 4 - Agarose gel (1%) electrophoresis band image of total extracted genomic DNA should be added as a figure in the MM section.

Answer: Your suggestion is highly noted and appreciated; however, we hope you will give us a chance to explain our decision to omit the image. The agarose gel was used to confirm DNA quality visually by checking for sharp bands indicating non-degraded DNA, since we relied on a Nanodrop spectrophotometer, the image was not kept.  

Comment 5 - In the MM section, information should be given about how the sample genotyping is done.

Answer: The information on how the sample genotyping was done is given in lines 110 to 115 following the reviewer’s suggestion.

Comment 6 - The results have been well presented and the results have been supported by the discussion. However, the sentences given below in the conclusion section cannot be understood. Please rewrite it more clearly.

-“The latter (what is the latter) could include populations from the Makhathini and Zululand Research Stations in South Africa.”

Answer: Future analysis of Zulu ecotype should include population from the Makhathini and Zululand Research Stations in South Africa, Reported in lines 359 to 362

-“………the Swazi ecotype despite their close relationship with the Zulu ecotype fosters a lot of perspectives (what is a lot of perspectives), future investigation within this population………..”

Answer: suggest a lot of uncontrolled breeding and the influx of exotic genetic material, reported in line 350 to 351

-“Crossbreeding poses a threat to the genetic integrity of the Zulu and Swazi ecotypes as both types were highly admixed with Damara sheep and analysis indicated a possible contribution directed from these two to Damara indicating genetic fusion across these populations.” This sentence should be transferred to the discussion section and may be discussed further.

Answer: This was moved from the conclusion to lines 312 to 315 in the discussion following the reviewer’s comment

Author Response File: Author Response.docx