Identification of Genomic Regions Associated with Fat Deposition in Some Asian and African Sheep Breeds Based on Selection Signature

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Animal science and Food Technology, Agricultural Science and Natural Resources University of Khuzestan, Mollasani, Iran.

2 Department of Animal Science, Faculty of Animal science and Food Technology, Agricultural Science and Natural Resources University of Khuzestan, Mollasani, Iran

3 Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran

4 Department of Animal Science, Faculty of Agriculture and Natural Resources, Shahid Bahonar University of Kerman, Kerman, Iran

Abstract

The selection of novel mutations beneficial only in some subpopulations leads to the retention of signatures across the genome. This study aimed to identify genomic regions, candidate genes, and biological pathways associated with fat deposition in some Asian and African sheep breeds based on selection signatures method and gene set enrichment analysis. A total of 49,034 SNP markers data obtained from 404 animal samples, including 13 fat-tailed and 7 thin-tailed sheep breeds with relatively similar tail and fat-tail dimensions distributed across different regions of Asia and Africa, were used. Principal component analysis (PCA) was utilized for assessing the clustering of animals into their true population, and FST (Theta) statistics was employed for detecting of positive selection signatures. Subsequently, genes reported in the selected regions were identified, and gene set enrichment analysis was performed to identify biological pathways (and candidate genes) associated with fat deposition. PCA analysis showed that all animals clustered into their respective breed groups, and thin and fat tailed sheep breeds could be separated based on different components. In this study, 19 genomic regions were identified to be under selection between thin and fat tailed sheep breeds. Investigation of reported genes in these regions led to the identification of several biological pathways (and candidate genes) directly or indirectly associated with tail morphology (NDUFB, ANO4, ASXL2, ABHD2, and NID2), fat-tail size (ACADL), skeletal or body size (PDGFD, ACAN, HOXC, HOXB, BMP2, and BMP4), immune response (ATG5, IL4, IL5, and IL13), and melanocyte regulation (KITLG). Overall, the findings of this study could play an important role for identifying the genomic regions associated with distinctive phenotypic traits of these breeds, especially fat deposition traits in tails, immunity, and adaptability, which could be of great economic importance in the future considering the observable climatic changes in recent years in various countries.

Keywords

Main Subjects

Extended Abstract

Introduction and Objective

 Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. Such selections are likely to have imposed distinctive selection signatures on the sheep genome. Therefore, detecting selection signatures across the genome may help elucidate mechanisms of selection and pinpoint candidate genes of interest for further investigation. This study aimed to identify genomic regions, candidate genes, and biological pathways associated with fat deposition in some Asian and African sheep breeds based on selection signatures method and gene set enrichment analysis.

 

Materials and Methods

A total of 49,034 SNP markers data obtained from 404 animal samples, including 13 fat-tailed and 7 thin-tailed sheep breeds with relatively similar tail and fat-tail dimensions distributed across different regions of Asia and Africa, were used. Quality control of genotypes was performed based on the minor allele frequency (MAF ≤ 0.02), missing genotype (MIND > 10%), and genotyping rate (GENO > 0.05), using PLINK software. Principal component analysis (PCA) was utilized for assessing the clustering of animals into their true population, and FST (Theta) statistics was employed for detecting positive selection signatures. Subsequently, genes reported in the selected regions were identified with the Genome Data Viewer database, and gene set enrichment analysis was performed to identify biological pathways (and candidate genes) associated with fat deposition.

 

Results

      After quality control, 44913 markers and 400 animals (281 fat-tailed and 119 thin-tailed sheep breeds) were remained for the further analysis. PCA analysis showed that all animals clustered into their respective breed groups, and thin and fat tailed sheep breeds could be separated based on different components. In this study, 19 genomic regions were identified to be under selection between thin and fat tailed sheep breeds. Genes associated with selected markers were subsequently identified. Investigation of reported genes in these regions led to the identification of several biological pathways (and candidate genes) directly or indirectly associated with tail morphology (NDUFB, ANO4, ASXL2, ABHD2, and NID2), fat-tail size (ACADL), skeletal or body size (PDGFD, ACAN, HOXC, HOXB, BMP2, and BMP4), immune response (ATG5, IL4, IL5, and IL13), and melanocyte regulation (KITLG).

 

Conclusion

      The results of the present study and identified genomic regions suggest that the selection during the evolution and adaptation to the different environments and geographical conditions led to population differentiation in Asian and African breeds. Overall, the findings of this study could play an important role for identifying the genomic regions associated with distinctive phenotypic traits of these breeds, especially fat deposition traits in tails, immunity, and adaptability, which could be of great economic importance in the future considering the observable climatic changes in recent years in various countries.

 

Author Contributions

Conceptualization, S.R, and M.H.M; methodology, S.R, and M.H.M; software, S.R, and M.H.M; validation, M.H.M, and M.T.B.; formal analysis, S.R; investigation, M.H.M, A.E; resources, M.H.M, A.E; data curation, M.H.M; writing—original draft preparation, S.R; writing—review and editing, M.H.M, M.T.B, A.E; visualization, M.H.M, M.T.B; supervision, M.T.B, M.H.M; project administration, M.H.M, A.E; funding acquisition, M.T.B. All authors have read and agreed to the published version of the manuscript.”

Data Availability Statement

“Not applicable”

 

Acknowledgements

The authors gratefully acknowledge the International Sheep Genomics Consortium for access to the Ovine HapMap genotypes and the Animal Breeding Center of Iran (ABCI) for access to the data of the Iranian breeds. We sincerely thank all authors who made their data available for the present research. The authors also acknowledge the supports and contributions of INSF (Project No. 40232205), Animal Science Research Institute of Iran, Mobarakandish Institute and AgResearch, New Zealand.

Ethical considerations

The study was approved by the Ethics Committee of the Agricultural Science and Natural Resources University of Khuzestan, Iran (Code: 1402.3918). The authors avoided data fabrication, falsification, plagiarism, and misconduct.

References

منابع

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Iranian Journal of animal Science
Volume 56, Issue 1
March 2025
Pages 19-34

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History

  • Receive Date: 17 April 2024
  • Revise Date: 01 June 2024
  • Accept Date: 16 June 2024

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