Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep.

Abulgasim Ahbara,Adebabay Kebede,Mohammed Al Abri,Hassan Hussein Musa,Ayelle Abeba,Joram M Mwacharo,Faisal Almathen,Olivier Hanotte,Mukhtar Omar Agoub,Hussain Bahbahani,Elena Ciani,Fabio Pilla,Salvatore Mastrangelo

doi:10.3389/fgene.2018.00699

Abstract

Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.

Highlights

African indigenous sheep originated in the Near East
In this study, using the Ovine 50 K SNP BeadChip genotypes, we investigated the (i) genetic relationships and structure within and between Ethiopian indigenous sheep of different fat-tail morphotypes alongside other sheep populations and breeds from the Caribbean, European, Middle East, China and Africa, and (ii) candidate genome regions and genes associated with tail morphology, fat deposition and possible eco-climatic adaptation in African indigenous sheep
Our findings showed that the Ethiopian indigenous sheep are genetically differentiated from the other populations including other African fat-tail sheep (Figures 2, 3)

Summary

Introduction

African indigenous sheep originated in the Near East They arrived, in the first instance, in North Africa via the Isthmus of Suez by the seventh millennium before present (BP) (Marshall, 2000). These sheep were of thin-tail type and their dispersion southwards into East Africa followed possibly the Nile river valley and the Red Sea coastline (Blench and MacDonald, 2006; GiffordGonzalez and Hanotte, 2011). The second wave brought fat-tail sheep into North and Northeast Africa via two entry points, the Isthmus of Suez and the Horn of Africa across the straits of Bab-el-Mandeb, respectively. Based on structure analysis, Edea et al (2017) showed that the five Ethiopian indigenous sheep populations they analyzed clustered together based on their geographic distribution and tail phenotypes

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Discussion

Conclusion