Browsing by Author "Wang, Magretha Diane"

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    Copy number variations in South African Nguni cattle : prevalence, characterization and genetic diversity
    (Stellenbosch : Stellenbosch University, 2016-12) Wang, Magretha Diane; Dzama, Kennedy; Muchadey, Farai Catherine; Rees, Jasper; Stellenbosch University. Faculty of Agrisciences. Dept. of Animal Sciences.
    ENGLISH ABSTRACT: Copy Number Variations (CNVs) comprise of deletions, duplications and insertions larger than 1kb that occur within genomes. The identification of CNVs within regions of the bovine genome important for adaptation renders them a potential role in breed formation and adaptation. South African Nguni cattle are adapted and demonstrate an enhanced ability to endure the harsh environmental conditions of Southern Africa. This study investigated the prevalence of CNVs in the genome of South African Nguni cattle. CNV occurrence and distribution within Nguni subpopulations was assessed and comparisons with other South African cattle breeds were performed. The dynamics between CNVs and haplotype blocks (HPBs), correlations amongst CNVs and the genic locality of CNVs were investigated with the objective of determining CNV prevalence in adaptation. The Illumina BovineSNP50 beadchip was used in the first experiment to genotype 492 South African Nguni cattle sampled nationwide. PennCNV software identified 334 CNV regions (CNVRs) of between 30kb and 1Mb in length. Population structure analyses was performed and HPBs identified using ADMIXTURE and PLINK software respectively. Five subpopulations were evident with some degree of CNV segregation amongst populations. CNVRs covered or lay within 10Mb of 289 genes of which 149, 28, 44, 2 and 14 genes exclusive to the five sub-populations were identified. Some degree of overlap between CNVRs and the 541 HPBs was evident. In the second experiment, 59 Nguni genotypes were analyzed using the Bovine 50K Beadchip in conjunction with six other South African breeds. PennCNV software identified 356 unique CNVRs. One hundred and sixty three CNVRs identified in more than 1 animal were utilized as genetic markers to assess within and between breed genetic diversity (GD). Between breed group GD scores were 2.510, 6.115 and 4.233 for the Sanga, Taurine and composite breeds respectively. One hundred and two (Taurine) and seven (Sanga and composite) of the CNVRs demonstrated a significant (p≤0.05) association with one another. PANTHER overrepresentation analyses demonstrated significant representation of a number of processes, functions, components and proteins by correlated CNVR genes. CNVR based phylogenetic clustered animals of the same breed group together. In the third experiment 24 Nguni animals were sequenced at 7X coverage using illumina next generation sequencing technologies. Reads were mapped to the UMD3.1 reference genome and RAPTR-SV software was utilized to identify CNVs. CNVs identifed were filtered according to the number of reads that support the event with low (F10), medium (F45) and high stringencies (F75). Adjacent and overlapping CNVs were merged to form 399, 55 and 23 unique CNVRs that covered or lay within 1Mb of 358, 51 and 23 genes at F10, F45 and F75 stringencies respectively. NGS tools identified smaller CNVs compared to those reported from SNP data. Despite discrepancies between array and NGS methods, CNVR genes represented the same specific ontologies. The study demonstrated CNVRs to be prevalent in South African Nguni cattle, with potential role in breed formation and adaptation. CNVR GD scores, population structure, distribution and incidence dynamics were thus ascertained for the South African Nguni.
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    Genomic population structure and prevalence of copy number variations in South African Nguni cattle
    (BioMed Central, 2015-11) Wang, Magretha Diane; Dzama, Kennedy; Hefer, Charles A.; Muchadeyi, Farai C.
    Background: Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications, insertions and complex multi-site variants. Although CNVs are proven to be involved in a variety of phenotypic discrepancies, the full extent and consequence of CNVs is yet to be understood. To date, no such genomic characterization has been performed in indigenous South African Nguni cattle. Nguni cattle are recognized for their ability to sustain harsh environmental conditions while exhibiting enhanced resistance to disease and parasites and are thought to comprise of up to nine different ecotypes. Methods: Illumina BovineSNP50 Beadchip data was utilized to investigate genomic population structure and the prevalence of CNVs in 492 South African Nguni cattle. PLINK, ADMIXTURE, R, gPLINK and Haploview software was utilized for quality control, population structure and haplotype block determination. PennCNV hidden Markov model identified CNVs and genes contained within and 10 Mb downstream from reported CNVs. PANTHER and Ensembl databases were subsequently utilized for gene annotation analyses. Results: Population structure analyses on Nguni cattle revealed 5 sub-populations with a possible sub-structure evident at K equal to 8. Four hundred and thirty three CNVs that formed 334 CNVRs ranging from 30 kb to 1 Mb in size are reported. Only 231 of the 492 animals demonstrated CNVRs. Two hundred and eighty nine genes were observed within CNVRs identified. Of these 149, 28, 44, 2 and 14 genes were unique to sub-populations A, B, C, D and E respectively. Gene ontology analyses demonstrated a number of pathways to be represented by respective genes, including immune response, response to abiotic stress and biological regulation processess. Conclusions: CNVs may explain part of the phenotypic diversity and the enhanced adaptation evident in Nguni cattle. Genes involved in a number of cellular components, biological processes and molecular functions are reported within CNVRs identified. The significance of such CNVRs and the possible effect thereof needs to be ascertained and may hold interesting insight into the functional and adaptive consequence of CNVs in cattle.
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    Ostrich (Struthio camelus) chick survival to 6 months post hatch : estimation of environmental and genetic parameters and the effect of imprinting, foster parenting and deliberate care
    (Stellenbosch : Stellenbosch University, 2012-03) Wang, Magretha Diane; Cloete, Schalk W. P.; Dzama, Kennedy; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.
    ENGLISH ABSTRACT: The South African Ostrich industry was established more than 100 years ago. Despite appreciable fluctuations and modifications in demand, the industry perseveres, with meat and leather as the current primary driving force. Low and variable early chick survival is globally considered as a major constraint in the industry. In spite of obvious welfare and production implications, research findings concerning ostrich chick survival are scant. Four studies involving chick survival to 24 weeks post hatch were thus performed. South African Black ostrich (Struthio camelus var. domesticus) data obtained from a commercial pair-bred ostrich flock maintained at the Oudtshoorn Experimental Farm, South Africa comprising 10418 records were utilized to run a series of single- and multiple-trait binomial analyses using either linear models (ASREML) or threshold models (Monte Carlo Markov Chain methods, employing Gibbs sampling software) respectively. Suitable fixed and random effect models together with variance and (co)variance components were derived from these analyses. Ostrich chick survival to 24 weeks post hatch was low (28%) with a large environmental component. Preincubation storage time only affected 0 to 3 week survival, while incubator had a significant effect on cumulative survival traits to 24 weeks as well as on 13 to 24 week survival. Female chicks outperformed males at 0 to 12 weeks, 0 to 24 weeks, 4 to 12 weeks and 13 to 24 weeks with regard to survival. Hen age was significant for all traits except survival during the first week as well as for survival from 13 to 24 weeks post hatch. All analyses exhibited comparable low heritability estimates for all survival traits except for 0 to 1 week survival and 13 to 24 week survival (h2 = 0.12 and 0.10; m2 = 0.08 and 0.07 respectively) which demonstrated higher additive genetic and maternal components when threshold models, using Gibbs sampling algorithms, were employed. Neither moisture loss nor day of external pipping exhibited notable additive genetic correlations with any of the estimated survival traits. Day-old chick weight demonstrated a low correlation with early chick survival (rg = 0.24 ± 0.19) with heavier chicks tending to have a higher survival probability. The effects of rearing method on early chick survival and growth were also investigated. Comparisons between chicks reared and fostered by adult ostriches in a semiextensive environment and chicks imprinted onto humans under an intensive system and between regular human handling in an intensive rearing system and the standard farm protocol of an intensive rearing system were made. No difference in the early chick survival to 3 weeks post hatch of chicks reared by foster parents and those chicks imprinted onto humans was demonstrated. At later ages, those chicks reared by foster parents outperformed human imprinted chicks. Human imprinted chicks exposed to regular handling demonstrate an enhanced early survival when compared to chicks exposed to conventional rearing protocol in intensive systems. The study is seen to provide guidance for further research on this topic.