Gurja BelayTsadkan Zegeye2025-08-182025-08-182024-01https://etd.aau.edu.et/handle/123456789/6979Ethiopia is the home of the largest cattle population in Africa and the fifth in the world. Cattle in Ethiopia are the primary agricultural entity serving fully or partially the livelihood of around 70% of the population. They are the most important generators of the agricultural GDP, contributing around 80% of the annual production of milk and meat. However, despite providing the majority of the livestock products in the country, Ethiopia's indigenous cattle genetic resource has yet to receive much attention. Breed identification and characterization still need to be completed, and an institutional framework for conservation and wise management of their genetic diversity needs to be established. The Tigray National Regional State, in the North of Ethiopia, is the fourth cattle-populated region, with about 8% of Ethiopia's cattle genetic resources. However, Tigray is one of the regions of Ethiopia where its animal genetic resources still need to be fully identified and characterized. This study aimed to undertake a comprehensive characterization of indigenous cattle populations in Tigray (Abergelle, Arado, Begait, Erob and Raya) involving their morphology, ecological niche suitability, genome-wide genetic diversity, and the genomic response of selection to the environmental challenges. Sampling sites were selected purposively to include a comprehensive representation of the indigenous cattle populations from their respective natural breeding areas. A total of 1650 matured cattle from the five populations were included to investigate the phenotypic description based on qualitative and quantitative traits. Data analysis was performed using chi-square involving crosstabs for the qualitative variability and multivariate discriminant analysis involving GLM, STEPDISC, CANDISC, DISCRIM, and Canonical discriminate function procedures of SAS for the quantitative variability. The stepwise discriminant analysis screened eighteen variables with a discriminant power for characterizing the female and thirteen for the male populations. High correct assignments to source populations were obtained for all populations except Abergelle and Erob, where around 30% of each shared morphologic similarity. The five populations were also clustered into four populations, with Abergele and Erob cattle overlapping. The environmental niche of each cattle population was characterized by the new approach applied to livestock, Environmental Niche Modeling (ENM). From the sampling locations, thirty coordinates (4 to 7 per population) were collected using the Geographic Positioning System (GPS) and nine coordinates surrounding 1 kilometer of the initial sampling location were extracted using Google Earth Pro 7.3.1.4507. Finally, 300 coordinates were used to extract data (from thirty-three environmental predictors) for habitat suitability mapping and screening out of the main environmental variables. Four distinct habitat suitability maps were detected, except for the Arado and Erob cattle, with around 66% niche similarity. Six main environmental variables, temperature seasonality, soil bulk density, cultivated land, and annual, wettest and warmest quarter precipitations that could have a potential driving factor for morphological and genetic variability across the indigenous cattle in Tigray were sorted out. Next, the whole genome sequence data was followed to characterize the genome-wide genetic diversity, relatedness, and admixture of the same five cattle populations. A high number of genetic variants were detected, where around seven and thirty-four per cent of SNPs and indels were novel, respectively. The genome-wide average nucleotide diversity ranged from 0.0035 to 0.0036. The number of heterozygous SNPs was about 0.6 to 0.7 higher than homozygous SNPs. There was high variability in ROH records among and within animals of each population, with the lowest record in Arado (777.82) and the highest in Raya (1000.45). Similarly, the analysis of inbreeding revealed differences within and among populations, ranging up to 10% in some individuals of Begait and Raya populations. Only a fraction (0.01% SNPs and 0.22% to 0.27% indels) of the identified variants annotated for functional variability overlapped coding regions. The enrichment analysis of genes overlapped missense private SNPs screened 20 significant GO terms and KEGG pathways common or specific to each population. Out of the gens overlapped missense private SNPs, the genes SCN4A, TAS1R2 and KCNG4 related to body size and length were specifically detected in Begait cattle and genes MMRN2 and VWC2 related to meat quality were detected in Erob cattle supporting the morphological finding. The population structure revealed the ancestry background of the indigenous cattle in Tigray from Asian indicine (85.6% to 88.7%) and African taurine (11.3% to 14.1%) cattle, with very small European taurine introgression in some individuals. Finally, the positive signatures of adaptation of the cattle populations to the main environmental stressors were analyzed following two genomic scans (Hp) and (FST). Selective sweeps of the overlapped regions were analyzed using Hp and FST to retrieve the candidate protein-coding genes. Around 60% of the annotated selective sweeps regions overlapped with protein-coding genes, while the rest lacked genes. GO and KEGG pathways of the protein-coding genes overlapped selective sweep regions revealed enriched (P < 0.05) genes involved in adaptation to moisture-stressed lowlands (HELB, HMGA2, IRAK3, LLPH, UCN2, LOC101902172, ADAMTS16, DDB1, ASIP, IL17B, SNAP29) and moisture-stressed highlands (NQO1, NEK6, LHX2, UCP2, UCP3 and LCMT2). This study shared detailed findings on the morphology, genetic and adaptive diversity of the indigenous cattle in Tigray. Diverse morphological and genomic diversity was observed in the Indigenous cattle in Tigray, indicating their importance as a genetic reservoir at regional and country levels. Moreover, the production type of the indigenous cattle in Tigray screened through the interlinking of morphological description and specific genes selected for production values provide insight into their breeding management.en-USBody MeasurementsDiscriminant Function AnalysisHabitat SuitabilityMultivariate AnalysisPrivate Missense VariantsSelected Environmental VariablesSelective Sweep RegionsIndigenous Cattle in TigrayThesis