Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds

A.A Zwane,J.F Taylor,E Van Marle-Köster,A Choudhury,M.L Makgahlela,A Maiwashe

doi:10.4314/sajas.v46i3.10

Abstract

Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The objective of this study was to identify breed informative markers to discriminate between three South African indigenous cattle breeds. Data from BovineSNP50 and GeneSeek Genomic Profiler (GGP-80K) assays were generated for Afrikaner, Drakensberger and Nguni, and were analysed for their genetic differentiation. Hereford and Angus were included as outgroups. Breeds were differentiated using principal component analysis (PCA). Single-nucleotide polymorphisms (SNPs) within the breeds were determined when minor allele frequency (MAF) was ≥ 0.05. Breed-specific SNPs were identified using Reynolds Fst and extended Lewontin and Krakauer's (FLK) statistics. These SNPs were validated using three African breeds, namely N’Dama, Kuri and Zebu from Madagascar. PCA discriminated among the breeds. A larger number of polymorphic SNPs was detected in Drakensberger (73%) than in Afrikaner (56%) and Nguni (65%). No substantial numbers of informative SNPs (Fst ≥ 0.6) were identified among indigenous breeds. Eleven SNPs were validated as discriminating the indigenous breeds from other African breeds. This is because the SNPs on BovineSNP50 and GGP-80K assays were ascertained as being common in European taurine breeds. Lower MAF and SNP informativeness observed in this study limits the application of these assays in breed assignment, and could have other implications for genome-wide studies in South African indigenous breeds. Sequencing should therefore be considered to discover new SNPs that are common among indigenous South African breeds and also SNPs that discriminate among these indigenous breeds.

Highlights

Introduction In southernAfrica, livestock has always played a vital role in the agricultural economies of countries such as South Africa, Namibia and Botswana, where commercial livestock enterprises, smallholder and communal farming contribute to food production, social needs and the general wellbeing of rural households (Bettencourt et al, 2013)
The BovineSNP50 and GGP-80K assays were designed to contain variants that were common to taurine breeds, the authors decided to test their usefulness in identifying informative Single-nucleotide polymorphisms (SNPs) to discriminate between South African indigenous cattle breeds
The levels of genetic variation for SNPs on the BovineSNP50 and GGP-80K assays identified in this study indicate that these assays have utility for genetic studies in South African populations

Summary

Introduction

Introduction In southernAfrica, livestock has always played a vital role in the agricultural economies of countries such as South Africa, Namibia and Botswana, where commercial livestock enterprises, smallholder and communal farming contribute to food production, social needs and the general wellbeing of rural households (Bettencourt et al, 2013). South African indigenous cattle have unique morphological features that distinguish them from other cattle breeds (Makina et al, 2014). These breeds include Nguni, Afrikaner and Drakensberger, known as Sanga cattle, which belong to the subspecies Bos taurus africanus. Sanga are possibly crossbreds between the indigenous humpless cattle (Bos taurus) and Zebu (Bos indicus), whereas Zenga are crossbreds between Zebu and Sanga (Rege, 1999).

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