Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel.

Sithembile O Makina,Michael D Macneil,Este Van Marle-Kã¶Ster,Farai C Muchadeyi,Azwihangwisi Maiwashe

doi:10.3389/fgene.2014.00333

Abstract

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds.

Highlights

African cattle breeds can be divided into two major categories, namely Taurine cattle (Bos taurus) and Indicine cattle (Bos indicus)
Parameter for single nucleotide polymorphism (SNP) validation that included the level of polymorphism, minor allele frequency (MAF) and deviation from Hardy Weinberg equilibrium (HWE) for all six cattle breeds in this study were previously reported (Makina et al, submitted)
Examination across breeds revealed that about 56% of SNPs were polymorphic in all breeds and the distribution of MAF showed that nearly half of the SNPs (41%) showed a higher degree of polymorphism (MAF ≥ 0.05) across the breeds

Summary

Introduction

African cattle breeds can be divided into two major categories, namely Taurine cattle (Bos taurus) and Indicine cattle (Bos indicus). Bos indicus is subdivided into zebu proper and zebu crossbred-types and is phenotypically identifiable by the presence of a substantial cerciothoracic hump (Rege, 1999). The position of the hump on the animal’s back is used to classify the zebu proper and zebu crossbred types into cervico thoracic-humped and thoracic-humped stocks (Epstein, 1971). In crossbreds of humped and thoracic-humped Zebu cattle, the hump is usually cervico-thoracic and these cattle are referred to as Sanga. The Sanga is nowadays considered a separate group of cattle. African cattle can be classified into four different groups distinguished namely B. taurus, B. indicus, Sanga, and Sanga’ zebu types (Rege, 1999). Afrikaner and Nguni cattle are classified under the Sanga group and indigenous to South Africa. Drakensberger and Bonsmara cattle are classified under Sanga types, the origin of the Drakensberger cattle is unclear with a history dating back to the early settlers in the late

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Conclusion