Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance |
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| Authors: | Mengistie Taye Wonseok Lee Kelsey Caetano‐Anolles Tadelle Dessie Olivier Hanotte Okeyo Ally Mwai Stephen Kemp Seoae Cho Sung Jong Oh Hak‐Kyo Lee Heebal Kim |
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| Affiliation: | 1. Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea;2. College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia;3. International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia;4. The University of Nottingham, School of Life Sciences, Nottingham, UK;5. International Livestock Research Institute (ILRI), Nairobi, Kenya;6. The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Midlothian, UK;7. C&K genomics, Seoul National University, Seoul, Korea;8. National Institute of Animal Science, RDA, Wanju, Korea;9. Department of Animal Biotechnology, The Animal Molecular Genetics & Breeding Center, Chonbuk National University, Jeonju, Korea;10. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea;11. Institute for Biomedical Sciences, Shinshu University, Nagano, Japan |
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| Abstract: | As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light‐colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross‐population composite likelihood ratio (XP‐CLR) and cross‐population extended haplotype homozygosity (XP‐EHH) statistical methods. We identified 296 (XP‐EHH) and 327 (XP‐CLR) positively selected genes. Gene ontology analysis resulted in 41 biological process terms and six Kyoto Encyclopedia of Genes and Genomes pathways. Several genes and pathways were found to be involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland development and sweating, feed intake and metabolism, and reproduction functions. The genes and pathways identified directly or indirectly contribute to the superior heat tolerance mechanisms in African cattle populations. The result will improve our understanding of the biological mechanisms of heat tolerance in African cattle breeds and opens an avenue for further study. |
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| Keywords: | African cattle positive selection signature thermotolerance XP‐CLR XP‐EHH |
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