The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

Kwondo Kim,Heesu Jeong,Tadelle Dessie,Jaemin Kim,Abdulfatai Tijjani,Olivier Hanotte,Getinet Mekuriaw Tarekegn,Heebal Kim,Dajeong Lim,Bashir Salim,Sung Jong Oh,Samsun Sung,Okeyo Ally Mwai,Choongwon Jeong,Seoae Cho,Hak Kyo Lee ,Dong Ahn Yoo ,Tae-Hyung Kwon ,Jung Eun Jang ,Stephen J Kemp ,Jae‐Hoon Jung ,Saet Byeol Lee

doi:10.1038/s41588-020-0694-2

Abstract

Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750-1,050 yr ago, which has shaped the genome of today's cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism.

Highlights

Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism
A total of 45 cattle breeds or populations including 331 samples were classified according to their phenotypes as follows: African Taurine (AFT)[3], African Humped cattle (AFH)
We first highlighted the taurine x indicine admixture characteristics of 16 indigenous African cattle populations, 14 of them living in the Horn of Africa, the main entry point of Asian zebu on the African continent

Summary

Introduction

Cattle pastoralism plays a central role in human livelihood in Africa. Through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine x indicine cattle admixture event dated to c. 750-1,050 years ago, which has shaped the genome of today’s cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune, heat tolerance and reproduction-related genes. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism

Methods

Results

Conclusion