Analysis of Genetic Diversity and Population Structure of Liangshan Black Pigs, a New Indigenous Pig Breed in Shandong Province

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

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The study "Analysis of Genetic Diversity and Population Structure of Liangshan Black Pigs, a New Indigenous Pig Breed in Shandong Province, China” by Li et al. aims to evaluate the genetic diversity and population structure of Liangshan black pigs, a newly discovered indigenous breed in Shandong Province, China.  A total of 191 individuals were genotyped using the Zhongxin-I SNP chip to assess genetic diversity, relatedness and possible introgression from five introduced breeds.

The results indicate that the Liangshan Black pig exhibits moderate levels of genetic diversity, as reflected in the observed (HO) and expected (HE) heterozygosity values and the proportions of identity by lineage and identity by state distances. While these values suggest some genetic variability, the study also identifies variability in kinship relationships within the population, highlighting the need for improved breeding management to maintain genetic diversity and avoid excessive inbreeding or introgression from external breeds.

The study also identified introgression from foreign breeds, particularly Duroc, which could threaten the genetic identity of the Liangshan Black pig. To address this, the authors suggest the selective removal of highly introgressed individuals and the implementation of rotational mating schemes to maintain genetic integrity.

This research contributes to the genetic understanding of the breed and provides valuable data for conservation programmes.

 

 

General concept comments

 

The manuscript focuses on the genetic diversity and population structure of Liangshan Black pigs using genome-wide SNP analysis. While studies of genetic diversity in pig breeds are not new, the focus on this particular breed provides valuable insights. The study fits well within the scope of the journal as it contributes to the fields of animal genetics, breeding and conservation. It provides data relevant to livestock management and genetic diversity. The article is generally well structured, with appropriate figures and tables to support the findings. The manuscript is relevant to researchers in the fields of animal genetics, conservation and breeding. While its findings may be of primary interest to a niche audience focused on Chinese pig breeds, the broader implications for genetic diversity and breeding strategies make it valuable to a wider animal science readership.

The objectives and rationale of the study are clearly presented, and the methodology provides a sound basis for assessing genetic diversity and introgression in Liangshan black pigs. To further strengthen the manuscript, the following improvements would be desirable:

-Clarify the criteria for sample selection: The sampling strategy should be more clearly explained. How were the 191 individuals selected? Were they chosen randomly across farms, or was there a specific selection criterion? The term 'lineages' is unclear. Do the authors refer to genealogical lineages (e.g., family pedigrees), previously identified genetic clusters, or historical/geographical subgroups of the Liangshan Black pig? Please clarify how these lineages were defined.

-In the section "Phylogenetic analysis of Liangshan Black pigs," the authors mention that Liangshan Black pigs were divided into nine families based on phylogenetic clades and the distribution of boars (lines 203-204). Clarifying whether sows were considered in the family assignments and, if not, justifying this exclusion.

­- The study confirms Duroc introgression in Liangshan Black pigs, but there is a lack of information to quantify this introgression. It also does not provide specific recommendations for individual removal to maintain genetic integrity. What criteria should be used? It is recommended to explicitly define which individuals should be excluded. This would facilitate more targeted conservation management.

--In Figure 5A (PCA scatterplot of Liangshan Black pigs), the axes are labelled Principal Component 1 (PC1) and Principal Component 2 (PC2), but the percentage of total genetic variability explained by each component is not given. Authors should include this information in the figure or text.

Correct minor grammatical issues

• These results highlight the need for improving the breeding management to maintain genetic diversity and reduce the risk of inbreeding.

to improve

• The study also identifies variability in kinship relationships within the population, highlighting the necessity and need for improved breeding management to maintain genetic diversity.

Necessity and need mean the same thing, so it's redundant.

• The averages of the proportion of IBD and IBS distance are 0.152 and 0.713 respectively, and their medians are 0.142 and 0.712, respectively.

 “averages of the proportion“ is an unusual English construction

• This thus raises the possibility that Liangshan Black pigs may have genetic components introgressed from Western introduced breeds. Excessive use of connectors

 

 

 

Comments for author File: Comments.pdf

Author Response

1. Clarify the criteria for sample selection: The sampling strategy should be more clearly explained. How were the 191 individuals selected? Were they chosen randomly across farms, or was there a specific selection criterion? The term 'lineages' is unclear. Do the authors refer to genealogical lineages (e.g., family pedigrees), previously identified genetic clusters, or historical/geographical subgroups of the Liangshan Black pig? Please clarify how these lineages were defined.

Response: Thank you for your comment. We have clarified the criteria for sample selection. Specifically, the samples encompassed all 48 boars in the farm, and 143 sows randomly chosen across the farm. Please refer to line 81-83 in the revised manuscript for details.. 

2. In the section "Phylogenetic analysis of Liangshan Black pigs," the authors mention that Liangshan Black pigs were divided into nine families based on phylogenetic clades and the distribution of boars (lines 203-204). Clarifying whether sows were considered in the family assignments and, if not, justifying this exclusion.

Response: In the process of family assignments, both sows and boars were considered. Due to their large number, sows are not the limiting factor for family assignment, so we did not clarify. We have clarified in the revised manuscript.

3. The study confirms Duroc introgression in Liangshan Black pigs, but there is a lack of information to quantify this introgression. It also does not provide specific recommendations for individual removal to maintain genetic integrity. What criteria should be used? It is recommended to explicitly define which individuals should be excluded. This would facilitate more targeted conservation management.

Response: We carefully examined the analysis results of Structure, and found that there was indeed quantitative information regarding introgression.We have clarified this in the revised manuscript. Moreover, we provided a criterion to explicitly define which individuals should be excluded. Please refer to line 235-237 and 347-348 in the revised manuscript for details.

4. In Figure 5A (PCA scatterplot of Liangshan Black pigs), the axes are labelled Principal Component 1 (PC1) and Principal Component 2 (PC2), but the percentage of total genetic variability explained by each component is not given. Authors should include this information in the figure or text.

Response: We have described the percentage of variability explained by each component in the manuscript. “PC1 and PC2 accounted for 62.01% and 27.32% of the variation, respectively.”, which can be found at line 216-217 in the revised manuscript for details.

5. The study also identifies variability in kinship relationships within the population, highlighting the necessity and need for improved breeding management to maintain genetic diversity. Necessity and need mean the same thing, so it's redundant.

Response: Thanks! We have revised it.

6. The averages of the proportion of IBD and IBS distance are 0.152 and 0.713 respectively, and their medians are 0.142 and 0.712, respectively.  “averages of the proportion“ is an unusual English construction.

Response: We have revised it to “the average proportion ”.

7. This thusraises the possibility that Liangshan Black pigs may have genetic components introgressed from Western introduced breeds. Excessive use of connectors.

Response: We have removed “thus”.

Reviewer 2 Report

Comments and Suggestions for Authors

Dear authors, 

The paper is well wrtitten and has all necessary elements to be accepted in present form. However, I would suggest small improvements: 

• can you provide more informaton about breed (phenotype, producivity...) in the indroduction chapter?
• my suggestion, if possible, try to compare obtained results with results from breeds from other countries and continets. In that way readers from all over the world might get a better context and state of the breed and make research more relevamt in global academic population. 

Author Response

1.can you provide more information about breed (phenotype, productivity...) in the introduction chapter?

Response: We sincerely appreciate the reviewer's insightful suggestion. We added one reference document in the revised manuscript, and in the reference the body conformation and production performance of Liangshan black pigs were detailed described. 

2. my suggestion, if possible, try to compare obtained results with results from breeds from other countries and continents. In that way readers from all over the world might get a better context and state of the breed and make research more relevant in global academic population.

Response: Thank you for the comment, which is a valuable perspective that enhances the broader relevance of our study. In the current manuscript, we have already conducted a preliminary comparison with other Chinese local breeds and the introduced pig breeds. For example, in Section 4.1 (line 282-286), we conducted comparison between the obtained results with results from other breeds to show the high genetic diversity of Liangshan Black pigs; in in Section 4.3 (line 335-349), we expounded the relationship between Liangshan Black pigs and the introduced breeds based on PCA, ancestry composition and evolutionary distance analyses. While we recognize the value of deeper international comparisons, our study is designed to characterize the genetic architecture of a newly described local breed within its specific ecological and cultural context. Expanding this aspect to include a broader range of global breeds would require significant additional data and analytical resources, potentially diverting attention from our core objective. Sorry we did not add further in - depth comparison.

Reviewer 3 Report

Comments and Suggestions for Authors

„Analysis of Genetic Diversity and Population Structure of  Liangshan Black Pigs, a New Indigenous Pig Breed in Shanong Province, China“ is interesting and well-written, clearly structured, paper on novel pig breed and its genetic diversity and structure. I have few comments and questions to improve it and make suitable for publication in Agriculture journal.

I would like to suggest to the Authors to delete „Chine“ from the title of manuscript.

Abstract

This section is too long. It must be corrected and adjusted to the Instruction for authors (no more the 200 words).

Introduction

L47-L48- correct the reference

L45: L39-45: Can the Authors enhance and briefly explaining the economic and ecological importance of conserving Liangshan Black Pigs?

L79-L80: Enhance the sentence and the aim of obtained study.

Materials and Methods

This section is well written and described.

Results

Results are clearly presented.

L141: Please, briefly explain the significance of observed SNP distributions.

L183: Can Authors describe the practical implications of kinship coefficient findings for breeding management.

Discussion

L276: Enhance discussion by linking the genetic diversity results to practical breeding outcomes and adaptability,

L328: Can the Authors recommend future research, including detailed genetic mapping studies or genomic selection programs

L314: Discuss on practical conservation measures to mitigate observed introgression effects.

Conclusion

Conclusion is well written, however I suggest to add future research directions and suggestions.

References

References is not written in accordance to Template and Instruction for authors and must be corrected.

I really enjoyed reading this manuscript. Clearly presented results about a new pig breed. I would like to know if there is any genealogical information about Liangshan Black pigs? It would be interesting to see a comparison of the SNP results and the pedigrees.

 

Author Response

1. I would like to suggest to the Authors to delete Chinafrom the title of manuscript.

Response: Thank you for your comment, and we have taken your suggestion.

2. Abstract: This section is too long. It must be corrected and adjusted to the Instruction for authors (no more the 200 words).

Response: Thanks! We have revised Abstract according to the instruction.

3. Introduction

3.1 L47-L48- correct the reference

Response:Thanks! We have replaced the reference with a more authoritative one in the revised manuscript.

3.2 L45: L39-45: Can the Authors enhance and briefly explaining the economic and ecological importance of conserving Liangshan Black Pigs?

Response: Thanks! We have added sentence to enhance and briefly explaining the economic and ecological importance of conserving Liangshan Black Pigs. Please refer to line 53-55 of the revised manuscript.

3.3 L79-L80: Enhance the sentence and the aim of obtained study.

Response: We have revised the sentence to better reflect the research objectives and its scientific contribution aims to generate integrative scientific evidence. Please refer to line 75-77 of the revised manuscript.

4. Results

4.1 L141: Please, briefly explain the significance of observed SNP distributions.

Response: Thanks! The significance of observed SNP distributions was explained at the end of the next paragraph. Please refer to line 154-156 of the revised manuscript.

4.2 L183: Can Authors describe the practical implications of kinship coefficient findings for breeding management.

Response: Thanks! We have added the sentence to describe the practical implications of kinship coefficient findings for breeding management in the revised manuscript. Please refer to line 313-315 of the revised manuscript.

5. Discussion

5.1 L276: Enhance discussion by linking the genetic diversity results to practical breeding outcomes and adaptability,

Response: We sincerely appreciate your suggestion to enhance discussion. We have added sentences to enhance discussion. Please refer to line 290-294 of the revised manuscript.

5.2 L328: Can the Authors recommend future research, including detailed genetic mapping studies or genomic selection programs.

Response: Done, thanks! We have added recommendation at the end of conclusion in the revised manuscript. Please refer to line 349-353 of the revised manuscript.

5.3 L314: Discuss on practical conservation measures to mitigate observed introgression effects.

Response: Done, thanks! We have added. Please refer to line 364-368 of the revised manuscript.

6. Conclusion is well written, however I suggest to add future research directions and suggestions.

Response: Done, thanks! We have added recommendation at the end of conclusion in the revised manuscript. Please refer to line # on page #.

7. References is not written in accordance to Template and Instruction for authors and must be corrected.

Response: Thank for your reminding. We have corrected the references in accordance to Template and Instruction for authors.  

8. I would like to know if there is any genealogical information about Liangshan Black pigs? It would be interesting to see a comparison of the SNP results and the pedigrees.

Response: Regrettably, there is currently no comprehensive genealogical information available for Liangshan Black pigs. Historically, the breeding of Liangshan Black pigs in their native regions has been largely unstructured, with a lack of formal record - keeping systems.