The identification of genomic regions associated with tick count, growth traits, and skin thickness in F2 angus x Nguni cattle using genome-wide association analysis

dc.contributor.advisorDzama, Kennedyen_ZA
dc.contributor.advisorMapholi, Ntanganedzenien_ZA
dc.contributor.advisorDube, Bekezelaen_ZA
dc.contributor.advisorMaiwashe, Azwihangwisien_ZA
dc.contributor.authorMkize, Nelisiween_ZA
dc.contributor.otherStellenbosch University. Faculty of AgriSciences. Dept. of Animal Science.en_ZA
dc.descriptionThesis (PhDAgric)--Stellenbosch University, 2023. en_ZA
dc.description.abstractENGLISH ABSTRACT: The aim of the study was to identify genetic determinants associated with tick count, growth traits, and skin thickness in F2 Angus x Nguni crossbred cattle. Two hundred and sixty-six animals were used in the study. Genetic parameters were estimated by fitting a sire model using pedigree records and by fitting an animal model using a kinship matrix in the ASReml software. Hair samples from the animals were genotyped using Illumina BovineSNP150 assay and there were 115 143 SNPs after quality control. A single SNP approach was used for the association tests, using the mixed model function of the mmscore, while adjusting for population stratification and relatedness in GenABEL. A nominal threshold of Pnominal = 5 x 10-5 was applied to the data. Post-GWAS functional annotation, pathway, and cluster analyses were performed using DAVID and ShinyGo bioinformatics resources with the Bos taurus genome used as a background. Fisher's exact test with false discovery rate (FDR) adjustment was used at p (FDR) < 0.05. The heritability estimates from the sire model for tick count, birth, weaning and yearling weights, and skin thickness were 0.21±0.22, 0.36±0.26, 0.32±0.14, 0.32±0.19, and 0.40±0.15, respectively. The respective heritability estimates obtained from an animal model fitting kinship matrix were 0.12±0.15, 0.26±0.16, 0.70±0.18, 0.38±0.18 and 0.58±0.21. These heritability estimates showed the presence of genetic variation for these traits. Thus, improvement of these traits can be expected from selection. Single nucleotide polymorphisms (SNP) for tick count were observed on chromosomes 2 and 4, while those associated with birth weight were on chromosomes 3 and 12. Chromosomes 2 and 18 contained SNPs for weaning weight and chromosome 8 had a SNP for yearling weight. The SNPs for skin thickness were observed on chromosomes 2, 7, 8, 9, and 12. For tick count, functional annotation uncovered enriched gene ontology (GO) terms and pathways related to cellular processes, regulation of biological processes, and response to stimulus. These were relevant for immune system response necessary for understanding host-tick interaction. Candidate genes such as ZNF746, GIMAP8, and RARRES2 could be potential biomarkers for tick control in cattle. The enriched GO terms and pathways for growth traits were related to ubiquinol- cytochrome-c reductase activity, plasma membrane raft, DNA ligase, ATP dependent among others. These categories were relatable to cell differentiation, skeletal muscle development, and metabolism regulation. The uncovered potential candidate genes for growth traits were TRPM8, SPP2, UQCRFS1, MB, TMEFF1, CAVIN4, and MSANTD3. For skin thickness, the enriched GO terms and pathways were related to immune response, cell differentiation, and transmembrane receptor tyrosine-protein kinase among others. The categories were enriched through FER and NTRK2 genes, which could be regarded as potential candidate genes for skin thickness in this population. The study uncovered some novel and previously identified genes as well as biological mechanisms related to tick count, growth traits, and skin thickness in the F2 Angus x Nguni population. These genes could be used to facilitate genetic improvement of tick count, growth traits, and skin thickness in this population.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.af_ZA
dc.format.extentxviii, 150 pages : illustrations (some color)en_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshTick count -- Growthen_ZA
dc.subject.lcshCattle -- Functional genomicsen_ZA
dc.subject.lcshF2 Angus x Nguni cattle -- Breedingen_ZA
dc.subject.lcshTick-borne diseases in animalsen_ZA
dc.subject.lcshGenotype-environment interaction -- Data processingen_ZA
dc.subject.lcshCattle -- Disease resistance -- Genetic aspectsen_ZA
dc.titleThe identification of genomic regions associated with tick count, growth traits, and skin thickness in F2 angus x Nguni cattle using genome-wide association analysisen_ZA
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