Genomic population structure and prevalence of copy number variations in South African Nguni cattle
Date
2015-11
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
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.
Description
CITATION: Wang, M. D., Dzama, K., Hefer, C. A. & Muchadeyi, F. C. 2015. Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics, 16:894, doi:10.1186/s12864-015-2122-z.
The original publication is available at http://bmcgenomics.biomedcentral.com
The original publication is available at http://bmcgenomics.biomedcentral.com
Keywords
Cattle breeding, Nguni cattle -- Genetic variation, Adaptation and environment
Citation
Wang, M. D., Dzama, K., Hefer, C. A. & Muchadeyi, F. C. 2015. Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics, 16:894, doi:10.1186/s12864-015-2122-z.