Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations.

Magretha D Pierce,Kennedy Dzama,Farai C Muchadeyi

doi:10.3389/fgene.2018.00163

Magretha D Pierce, Kennedy Dzama + Show 1 more

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https://doi.org/10.3389/fgene.2018.00163

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Abstract

Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs.

Highlights

Copy number variations are deletions, duplications, and insertions larger than 50 bp in size that modify the DNA structure and play a significant role in the genomic variability and diversity evident within and among breeds (Letaief et al, 2017)
The largest CNV regions (CNVRs) was present on chromosome 11, while the smallest occurred on chromosome 1
Three hundred and fifty-six Unique CNVRs were identified in 287 animals from 2 Taurine, 2 Composite, 2 Sanga, and 1 Sanga Taurine cross Cattle breeds using the Bovine 50 K Beadchip

Summary

Introduction

Copy number variations are deletions, duplications, and insertions larger than 50 bp in size that modify the DNA structure and play a significant role in the genomic variability and diversity evident within and among breeds (Letaief et al, 2017). They have been observed to affect a greater percentage of genomic sequences relative to other forms of genomic variations like single nucleotide polymorphisms (SNPs) (Zhang et al, 2009; Hou et al, 2012; Liu and Bickhart, 2012). CNVs may be a suitable genomic marker for ascertaining cattle origins and history as well as divergence amongst breeds

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