Lashmar, Simon FrederickVisser, CarinaVan Marle-Koster, Este2016-07-042016-03Lashmar, SF, Visser, C & Van Marle-Koster, E 2016, 'SNP-based genetic diversity of South African commercial dairy and fiber goat breeds', Small Ruminant Research, vol. 136, pp. 65-710921-4488 (print)1879-0941 (online)10.1016/j.smallrumres.2016.01.006http://hdl.handle.net/2263/53599Goats (Capra aegagrus hircus) have not been a prioritized livestock species with regards to molecular research. The genetic characterization of commercial South African (SA) goat breeds should contribute to improving the management of available animal genetic resources. The aim of this study was to investigate genetic diversity within and among SA commercial goat breeds utilizing the 50k goat beadchip. 88 goats originating from four breeds (dairy: British Alpine, Saanen, Toggenburg; fibre: Angora) were genotyped with the goat SNP50 beadchip. Average MAF values ranged from 0.25 for the Angora to 0.29 for the Saanen, with 46 983 and 50 368 polymorphic SNPs obtained for the respective breeds. Observed heterozygosity values ranged from 0.365 for the Angora to 0.431 for the Toggenburg breed. Linkage disequilibrium (LD) estimation revealed average r2 values of 0.12 and 0.15 for dairy and fibre breeds, respectively. LD decay was shown to occur after a distance interval of 20-40kb and 40-60kb for dairy and Angora breeds, respectively. Principal component analysis (PCA) produced clusters corresponding to the different production types (dairy and fibre). The Angora, British Alpine and Saanen breeds showed high proportions of membership to respective inferred ancestral populations with ADMIXTURE (97%, 84% and 92%, respectively). The results obtained in this study indicated genetic uniformity within dairy and fibre goats due to productionspecific trait selection. Sufficient levels of genetic variation was, however, observed to allow genetic progress for SA commercial goat breeds pending the improved management of these goat genetic resources.en© 2016 Elsevier B.V. All rights reserved. Notice : this is the author’s version of a work that was accepted for publication in Small Ruminant Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Small Ruminant Research, vol. 136, pp. 65-71, 2016. doi : 10.1016/j.smallrumres.2016.01.006.Call rateCluster analysesHardy-Weinberg equilibriumLinkage disequilibriumMinor allele frequencySouth Africa (SA)Goats (Capra hircus)Postprint Article