Data from: Genome analysis reveals genetic admixture and signature of selection for productivity and environmental traits in Iraqi cattle

The Near East cattle are adapted to different agro-ecological zones
including desert areas, mountains habitats as well as 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 genome level. Here, we report
at 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 x taurine, with more zebu
background in Jenoubi cattle compared to Rustaqi. The Rustaqi has the
greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb
signature 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, heat stress) and genes of commercial interest (e.g. marbling
score).

近东牛（Near East cattle）可适应包括荒漠地带、山地生境以及底格里斯-幼发拉底河水系沿岸湿润区域在内的多种农业生态区。该区域是全球最早且最具影响力的养牛业起源与发展区域之一。目前学界已确认伊拉克牛共有四个主要培育品种，其中杰努比（Jenoubi）牛分布于伊拉克南部湿润区域，鲁斯塔基（Rustaqi）牛则栖息于该国中部干旱区域。尽管这两个品种具有重要的经济与科研价值，但截至目前，伊拉克牛的基因组特征仍未得到充分解析。本研究从全基因组层面解析了这两个伊拉克牛品种的遗传多样性与正选择特征：本研究采集了采自迈桑省（Maysan）与巴士拉省（Basra）的35头无亲缘关系杰努比牛，以及采自巴格达及巴比伦周边区域的60头鲁斯塔基牛，采用Illumina牛高密度SNP芯片（700K，Illumina Bovine HD BeadChip）完成基因分型；本研究通过主成分分析（PCA）、期望杂合度（He）、观测杂合度（Ho）以及群体混合分析，对其群体遗传结构与遗传多样性水平展开研究；选择特征分析则依托扩展单倍型纯合性（EHH）相关的iHS与Rsb统计量，以及群体间Wright's F统计量（Fst）开展。结合欧洲普通牛（European taurine）、亚洲瘤牛（Asian indicine）、非洲瘤牛（African indicine）与非洲普通牛的参照群体进行PCA与群体混合分析后，结果显示这两个伊拉克牛品种均为瘤牛与普通牛的杂交品种，且杰努比牛的瘤牛血统占比高于鲁斯塔基牛。鲁斯塔基牛的平均期望杂合度（He=0.37）在所有供试品种中最高。基于iHS与Rsb统计量的选择特征分析，在两个伊拉克牛品种中鉴定出68个受正选择的候选基因；而Fst分析则鉴定出220个候选基因，这些基因涉及先天与适应性免疫应答、多种环境选择压力（如蜱虫抗性、热应激）以及商业化育种相关性状（如大理石纹评分）。