Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama

BMC Genomics

Research Article

Jaemin Kim¹  Seoae Cho¹  Kwondo Kim²  DongAhn Yoo²  Jung-Woo Ha³  Sojeong Ka⁴  Soo-Jin Kim⁵  Heebal Kim⁶  Hak-Kyo Lee⁷  Dajeong Lim⁸  Tadelle Dessie⁹  Okeyo Ally Mwai^1,10  Stephen Kemp^1,11  Sung Jong Oh^1,12  Olivier Hanotte^1,13 

[1] C&K Genomics, Seoul National University Research Park, 151-919, Seoul, Republic of Korea;C&K Genomics, Seoul National University Research Park, 151-919, Seoul, Republic of Korea;Interdisciplinary Program in Bioinformatics, Seoul National University, 08826, Seoul, Republic of Korea;Clova, NAVER Corp., 13561, Seongnam, Republic of Korea;Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, Republic of Korea;Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, Republic of Korea;C&K Genomics, Seoul National University Research Park, 151-919, Seoul, Republic of Korea;Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, Republic of Korea;C&K Genomics, Seoul National University Research Park, 151-919, Seoul, Republic of Korea;Interdisciplinary Program in Bioinformatics, Seoul National University, 08826, Seoul, Republic of Korea;Department of Animal Biotechnology, Chonbuk National University, 66414, Jeonju, Republic of Korea;Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, 55365, Jeonju, Republic of Korea;International Livestock Research Institute, Addis Ababa, Ethiopia;International Livestock Research Institute, Box 30709-00100, Nairobi, Kenya;International Livestock Research Institute, Box 30709-00100, Nairobi, Kenya;The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, UK;National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea;University of Nottingham, School of Life Sciences, NG7 2RD, Nottingham, UK;International Livestock Research Institute, Addis Ababa, Ethiopia;

关键词: Cattle genome;    Trypanotolerant N’Dama;    SNPs;    Genetic signatures;    Comparative genome-wide analysis;   

DOI  :  10.1186/s12864-017-3742-2

 received in 2016-12-12, accepted in 2017-04-27,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundIndigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied.ResultsWe performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N’Dama cattle. We analysed genetic variation patterns in N’Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N’Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N’Dama may engage in skeletal growth as well as immune systems.ConclusionsOur results imply that N’Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.

【 授权许可】

CC BY   
© The Author(s). 2017

【 图 表 】

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