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Exploring evidence of positive selection signatures in cattle breeds selected for different traits

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Abstract

Since domestication, the genome landscape of cattle has been changing due to natural and artificial selection forces resulting in several general and specialized cattle breeds of the world. Identifying genomic regions affected due to these forces in livestock gives an insight into the history of selection for economically important traits and genetic adaptation to specific environments of the populations under consideration. This study explores the genes/genomic regions under selection in relation to the phenotypes of Holstein, Hanwoo, and N’Dama cattle breeds using Tajima’s D, XP-CLR, and XP-EHH population statistical methods. The whole genomes of 10 Holstein (South Korea), 11 Hanwoo (South Korea), and 10 N’Dama (West Africa—Guinea) cattle breeds re-sequenced to ~11x coverage and retained 37 million SNPs were used for the study. Selection signature analysis revealed 441, 512, and 461 genes under selection from Holstein, Hanwoo, and N’Dama cattle breeds, respectively. Among all these, seven genes including ARFGAP3, SNORA70, and other RNA genes were common between the breeds. From each of the gene lists, significant functional annotation cluster terms including milk protein and thyroid hormone signaling pathway (Holstein), histone acetyltransferase activity (Hanwoo), and renin secretion (N’Dama) were enriched. Genes that are related to the phenotypes of the respective breeds were also identified. Moreover, significant breed-specific missense variants were identified in CSN3, PAPPA2 (Holstein), C1orf116 (Hanwoo), and COMMD1 (N’Dama) genes. The genes identified from this study provide an insight into the biological mechanisms and pathways that are important in cattle breeds selected for different traits of economic significance.

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Acknowledgements

This work was supported by a grant from the Next-Generation BioGreen 21 Program (Project No. PJ01134905), Rural Development Administration (RDA), Republic of Korea.

Author information

Authors and Affiliations

  1. Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Mengistie Taye, Wonseok Lee, Soomin Jeon & Heebal Kim

  2. College of Agriculture and Environmental Sciences, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia

    Mengistie Taye

  3. Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea

    Joon Yoon & Heebal Kim

  4. International Livestock Research Institute (ILRI), P. O. Box 5689, Addis Ababa, Ethiopia

    Tadelle Dessie & Olivier Hanotte

  5. School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK

    Olivier Hanotte

  6. International Livestock Research Institute (ILRI), P. O. Box 30709-00100, Nairobi, Kenya

    Okeyo Ally Mwai & Stephen Kemp

  7. The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK

    Stephen Kemp

  8. C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea

    Seoae Cho & Heebal Kim

  9. National Institute of Animal Science, RDA, Wanju, Republic of Korea

    Sung Jong Oh

  10. Department of Animal Biotechnology, The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju, 561-756, Republic of Korea

    Hak-Kyo Lee

  11. Institute for Biomedical Sciences, Shinshu University, Nagano, Japan

    Heebal Kim

Authors
  1. Mengistie Taye
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  2. Wonseok Lee
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  3. Soomin Jeon
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  4. Joon Yoon
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  5. Tadelle Dessie
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  6. Olivier Hanotte
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  7. Okeyo Ally Mwai
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  8. Stephen Kemp
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  9. Seoae Cho
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  10. Sung Jong Oh
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  11. Hak-Kyo Lee
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  12. Heebal Kim
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Contributions

MT conceived and designed the study, analyzed the data, and wrote the paper; WL, SJ, and JY helped analyzing the data; OH, TD, SK, OAM, SC, SJO, HKL, and HK designed the project; HK organized and supervised the project.

Corresponding author

Correspondence to Heebal Kim.

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Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

335_2017_9715_MOESM1_ESM.xls

Additional file 1: Summary of positively selected genes: Table S1. Holstein Tajima’s D detected genes; Table S2. Holstein XP-EHH detected genes; Table S3. Holstein XP-CLR detected genes; Table S4. Common genes between statistical methods used for Holstein breed; Table S5. Hanwoo Tajima’s D detected genes; Table S6. Hanwoo XP-EHH detected genes, Table S7. Hanwoo XP-CLR detected genes; Table S8. Common genes between statistical methods used for Hanwoo breed; Table S9. N’Dama Tajima’s D detected genes; Table S10. N’Dama XP-EHH detected genes; Table S11. N’Dama XP-CLR detected genes. Table S12. Common genes between statistical methods used for N’Dama breed; Table S13. Common genes between Holstein, Hanwoo, and N’Dama breeds. (XLS 338 KB)

335_2017_9715_MOESM2_ESM.xlsx

Additional file 2: Overlapping genes with previous studies. Table S14. Genes detected from Holstein cattle in this study that overlapped with previous studies; Table S15. Genes detected from Hanwoo cattle in this study that overlapped with previous studies; Table S16. Genes detected from N’Dama cattle in this study that overlapped with previous studies (XLSX 52 KB)

335_2017_9715_MOESM3_ESM.xls

Additional file 3: Summary of QTL overlapped genes: Table S17. XP-EHH detected genes overlapped with QTL regions in Holstein cattle; Table S18. XP-CLR detected genes overlapped with QTL regions in Holstein cattle; Table S19. Tajima’s D detected genes overlapped with QTL regions in Holstein cattle; Table S20. XP-EHH detected genes overlapped with QTL regions in Hanwoo cattle; Table S21. XP-CLR detected genes overlapped with QTL regions in Hanwoo cattle; Table S22. Tajima’s D detected genes overlapped with QTL regions in Hanwoo cattle; Table S23. XP-EHH detected genes overlapped with QTL regions in N’Dama cattle; Table S24. XP-CLR detected genes overlapped with QTL regions in N’Dama cattle; Table S25. Tajima’s D detected genes overlapped with QTL regions in N’Dama cattle. (XLS 299 KB)

Additional file 4: SNP association: Table S26. Association of SNPs. (XLS 78 KB)

335_2017_9715_MOESM5_ESM.pptx

Additional file 5: Figure S1. Manhattan plot of the –log10 transformed Tajima’s D p values of a) Holstein, b) Hanwoo and 3) N’Dama cattle breeds. Figure S2. The structure of non-synonymous variants on a) ADIPOQ - 1:81006985, b) CPQ - rs109886870, c) PAPPA2 - rs210049354, and d) ATP10B - rs209490227 gene regions. Exons are indicated by vertical brown bars. Alleles are indicated by colored bars, the major allele (green bars) and the minor allele (orange bars). Breed specific significant non-synonymous SNPs are highlighted in yellow, the amino acid changes are indicated under the allele. The frequency of each haplotype is indicated on the right side of the figure. (PPTX 1051 KB)

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Taye, M., Lee, W., Jeon, S. et al. Exploring evidence of positive selection signatures in cattle breeds selected for different traits. Mamm Genome 28, 528–541 (2017). https://doi.org/10.1007/s00335-017-9715-6

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