Population Structure and Prevalence of Copy Number Variations within the Genome of South African Nguni Cattle

Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications and insertions. Although CNVs are proven to be involved in a variety of phenotypic discrepancies, the full extent and consequence of these structural variants is yet to be fully understood. No such genomic characterization has been performed in 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. Illumina BovineSNP50 Beadchip data was thus utilized to investigate CNVs in 226 unrelated South African Nguni cattle. Population structure was determined by ADMIXTURE software and animals were grouped into 7 subpopulations. PennCNV hidden Markov model identified 167 CNVs and 192 genes enriched within a 1Mb downstream from CNVs are reported. CNVs ranging from 512 bp to 914 055 bp in size are reported across the seven distinct ecotypes. Only 113 of the 226 animals demonstrated variations in copy number within their genome. 20, 9, 21, 65,19, 16 and 8 genes were unique to specific ecotypes A, B, C, D, E, F and G respectively. Gene ontology analyses demonstrated a number of pathways to be influenced by respective genes, including immune response, metabolic processess and biological regulation processess. Seven Nguni ecotypes exhibiting distinct ecotype and breed specific CNVs are thus presented in this study.