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Alshawi, Akil (2019) Genomic characterisation of Iraqi indigenous taurine x zebu crossbred cattle. PhD thesis, University of Nottingham.

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Abstract

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.

In Chapter 4, using WGS, we investigated comprehensively candidate-gene regions associated with immunity and adaptive traits for Jenoubi (n = 10 samples) and Rustaqi (n = 10 samples) cattle. Analyses of the selective sweeps within (Hp, Tajima’s D), and among populations (XP-EHH and Fst) disclose several tens of genes linked to adaptive immunity traits. In particular, we detected candidate genes playing an important role in tick resistance. These genes are CD3E, CD3D and CD3G in Jenoubi, and LIPH and B2M in Rustaqi cattle. These genes act against ectoparasites such as ticks through maintaining T- and B-cell activation and facilitating the cellular activity of skin to resist tick infestation at the sites of tick attack. Furthermore, we found genes for defensive responses to Gram-positive bacteria in Jenoubi cattle, an antibacterial humoral response cluster in Rustaqi cattle, and evidence of adaptive genes for heat tolerance (DNAJB1 and DNAJC4 in Jenoubi and Rustaqi, respectively), and thermoregulation (e.g. HOXC11 and HOXC12 in both breeds).

In Chapter 5, we discovered the unique and overlapping gene regions between the Iraqi breeds and reference breeds from Asia, Africa and Europe. This was done using two kinds of genotypic data, HD and WGS. Using HD analysis, we identified: (i) overlaps between candidate genes within and between Iraqi cattle, and between Iraqi breeds and the reference zebu Nellore, taurine N’Dama Guinea and Holstein-Friesian (iHS and Rsb analysis) cattle; and (ii) further overlaps with two African zebu populations, Butana and Kenana (Rsb analysis only). Using WGS analysis, we compared: (i) Hp results within Iraqi breeds and within Kenyan East African Shorthorn Zebu (KEASZ); and (ii) XP-EHH results between Iraqi breeds and African breeds (N’Dama, Ankole, Boran, Ogaden and Kenana).

HD data indicate a greater overlap for Jenoubi than for the Rustaqi in all comparisons. Furthermore, it appears most of the overlaps are present on BTA5 is involved. In particular, several significant overlapped genes were identified, for instance, PRKG1 (tick resistance), PCDH15 (maintenance of the intestinal membrane), PARM1 (anti-apoptosis) and FOCAD (tumour-suppression). We then completed these results with Rsb analysis of African cattle (Butana and Kenana). The results showed common regions on BTA5 also, including six common candidate genes between Iraqi and Butana and five (TRABD, GRIP1, HELB, MOV10L1, SLC6A3, ZC3H7B) between Iraqi and Kenana. These genes are involved in fertility and productivity traits.

Using WGS, we conducted an analysis of overlapping genes comparing the pooled heterozygosity (Hp) of Iraqi and the East African Shorthorn Zebu cattle from Kenya (EASZ). We discovered six candidate genes that are common to both Iraqi and EASZ cattle (e.g. 5S_rRNA gene (associated with marbling score) and CDH10 (associated with fertility)). Thirty-six candidate genes were found in common between Jenoubi and EASZ (e.g. IRAK3 (inflammatory response), DNAJB1 (thermotolerance) and SNORA73 (coat colour)). Ten candidate genes were found in common between Rustaqi and EASZ breeds. Most of these genes are present on BTA2, BTA5 and BTA7. Likewise, the intersection of candidate genes from cross-population analysis (XP-EHH) was conducted using Iraqi and African taurine and zebu breeds (e.g. N’Dama, Ankole and Boran). Our findings uncovered just one gene in common between Iraqi (Jenoubi) and N’Dama - the MSC gene associated with skeletal muscle generation and B-cell differentiation.

To sum up, our project identified a number of important candidate adaptive genes to be under selection in Iraqi cattle, especially in relation to tick resistance and thermotolerance traits. The presence of more adaptive immunity genes detected in this study indicates Iraqi breeds’ ability to face the challenges of the harsh Iraqi agro-ecological environments. Furthermore, our study illustrate for the first time the predominantly maternal taurine origin of Jenoubi and Rustaqi breeds The results of this study offer valuable insight into the genetic diversity and structure of Iraqi cattle that will assist in the preservation and improvement of Iraqi native breeds by designing specific breeding programs to enhance disease resistance and productive performance.

We hope this study will introduce genetic data of Iraqi cattle to the world, and support projects related to cattle conservation and genetic improvement in the Near East region.

Item Type:	Thesis (University of Nottingham only) (PhD)
Supervisors:	Hanotte, Olivier Gilbert, Francis
Keywords:	Iraqi cattle, Near East region, Diversity and immunity adaptive genes
Subjects:	S Agriculture > SF Animal culture
Faculties/Schools:	UK Campuses > Faculty of Medicine and Health Sciences > School of Life Sciences
Item ID:	56927
Depositing User:	Alshawi, Akil
Date Deposited:	21 Oct 2019 10:36
Last Modified:	19 Jul 2021 04:30
URI:	https://eprints.nottingham.ac.uk/id/eprint/56927

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