Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle.

Akil Alshawi,Abdulameer Essa,Sahar Al-Bayatti,Olivier Hanotte

doi:10.3389/fgene.2019.00609

Abstract

The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats, and humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently, four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq, while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at the genome level. Here, we report at a genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho), and admixture. Signatures of selection were studied using extended haplotype homozygosity (EHH) (iHS and Rsb) and inter-population Wright’s Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine, and taurine indicate that the two breeds are crossbreed zebu × taurine, with more zebu background in Jenoubi cattle compared with Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signatures of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g., tick resistance and heat stress), and genes of commercial interest (e.g., marbling score).

Highlights

Archeological and genetic studies support two centers of cattle domestication, the Fertile Crescent and the Northern part of the Indian subcontinent including the Indus Valley (Loftus et al, 1994; Bradley et al, 1998; Troy et al, 2001; Helmer et al, 2005; Bradley and Magee, 2006; Zeder, 2008; Chen et al, 2010; Magee et al, 2014)
We report for the first time at the autosomal genome-wide level, the genome diversity and candidate signatures of positive selection in two Iraqi cattle breeds (Jenoubi and Rustaqi), providing new insights on the past and present breeding dynamics and evolutionary forces that shaped the genome of the cattle population in the region
Our findings indicate that Iraqi breeds possess significant diversity compared to Asian (e.g., Korean Hanwoo), African (e.g., N’Dama), and European breeds (e.g., Holstein-Friesian) (Supplementary Tables S3, S4, and S5)

Summary

Introduction

Archeological and genetic studies support two centers of cattle domestication, the Fertile Crescent and the Northern part of the Indian subcontinent including the Indus Valley (Loftus et al, 1994; Bradley et al, 1998; Troy et al, 2001; Helmer et al, 2005; Bradley and Magee, 2006; Zeder, 2008; Chen et al, 2010; Magee et al, 2014). There are many archeological evidence of the antiquity and importance of cattle husbandry in central Mesopotamia, including cylinder seals (Read, 2015). These animals were of the humpless taurine type. Closer to the Indus Valley center of cattle domestication, archeological evidence of domestic cattle in Mesopotamia is much fewer It includes artistic depictions from the royal tombs of Ur (South of Iraq) including domestic animals (Supplementary Figure S1A, B), with most of the ancient agricultural settlements along the Tigris and Euphrates buried under flooded plains (Read, 2015)

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