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Accueil du site → Doctorat → Royaume-Uni → 2019 → Genomic characterisation of Iraqi indigenous taurine x zebu crossbred cattle.

University of Nottingham (2019)

Genomic characterisation of Iraqi indigenous taurine x zebu crossbred cattle.

Alshawi, Akil

Titre : Genomic characterisation of Iraqi indigenous taurine x zebu crossbred cattle.

Auteur : Alshawi, Akil

Université de soutenance : University of Nottingham

Grade : Doctor of Philosophy (PhD) 2019

Résumé partiel
Iraqi cattle breeds are found at the crossroad of the two main cattle regions of domestication ; the Near East and the Northern part of the Indian subcontinent. There are currently four native breeds : Rustaqi (Central Iraq), Jenoubi (Southern Iraq), Sharabi (Northern Iraq - the Tigris Valley, north of Mosul), and Karradi (Northern Iraq in the Kurdistan region). In the harsh environments of Iraq (e.g. high tick prevalence and high temperatures), these native breeds have evolved to overcome these tough conditions. The genomic aspects of these adaptations here not yet been characterised. The main purpose of this thesis is to document at the genome-wide level the genetic diversity (autosomal and mtDNA) and significant candidate gene regions for adaptation (e.g. infectious disease tolerance and thermotolerance) in two of the native Iraqi cattle breeds. We studied Rustaqi and Jenoubi. Rustaqi is found in central Iraq (e.g. around Baghdad and Babylon) in a dry and hot environment. Jenoubi is found in southern Iraq (e.g. Maysan and Basra) in an environment characterised by high temperature and high humidity (Maysan and Basra). The other two cattle breeds (Sharabi and Karradi) could not be sampled because of the political situation at the time of the sampling. The genomes of Jenoubi and Rustaqi breeds were analysed using two genotyping tools : Bovine high-density SNPs BeadChip (700K) and Whole Genome Sequencing (Illumina® HiSeq platform). The study started by exploring genome diversity in Chapter 2. Data from the high-density Bovine SNP BeadChip (HD) were analysed for 35 unrelated Jenoubi and 60 unrelated Rustaqi individuals. Several analyses were performed on the autosomal HD data, such as principle component analysis (PCA), genetic admixture, heterozygosity and homozygosity. We also investigated the mitochondrial DNA origin of these breeds using Whole Genome Sequencing (WGS) for 20 samples (10 Jenoubi and 10 Rustaqi cattle). The results at the autosomal genome level indicate that the Jenoubi breed is more zebu and the Rustaqi breed more taurine. Analysis of the mtDNA sequences shows these two breeds to carry predominantly taurine mtDNA lineages (T2 and T3), with just two individuals of the 20 analysed with the indicine (I2) haplogroups. In Chapter 3, we conducted signature selection analysis on the HD data from the same individuals genotyped in Chapter 2. The aim here was to identify candidate genomic regions for adaptive immunity genes. To this end, we performed Integrated Haplotype Score within populations (iHS), Relative integrated EHH of a site between populations (Rsb), and Inter-population Wright’s (Fst) analysis. The results uncovered 19 genes related to the innate and/or acquired immune response in cattle, including the PRKG1 gene known to be related to tick resistance (in both Iraqi breeds), and the ABCC2 gene linked to gastrointestinal nematode resistance (in Rustaqi cattle). Other identified candidate genes included genes associated with different environmental selection pressures (e.g. the heat stress response), and genes of commercial interest (e.g. marbling score), also in both Jenoubi and Rustaqi cattle.

Mots clés  : Iraqi cattle, Near East region, Diversity and immunity adaptive genes

Présentation

Page publiée le 20 novembre 2019