Genetic diversity and population structure of South African dairy goats

Abstract

In this study 240 commercial dairy goats (130 Saanen, 51 Toggenburg and 59 British Alpine) were genotyped with a panel of 25 microsatellite markers, 16 of which were on the FAO/ISAG recommended list for genetic diversity studies in Capra hircus. A moderate MNA of 8 was observed for all markers across all three breeds (ranging from 3 to 12 alleles per locus), and the mean PIC of the panel was 0.60. None of the loci investigated in this study were discarded due to HWE deviation, although some did deviate significantly from HWE within the breeds (5 in the Saanen, and 6 each in the Toggenburg and British Alpine). The overall diversity observed for the Saanen, Toggenburg and British Alpine were 62.6%, 63.4% and 63.4% respectively, indicating moderate diversity. Wright’s FIS values for the three breeds ranged between -0.063 to -0.005. Population structure analysis revealed six distinct populations, where the British Alpine and Toggenburg each formed individual clusters, and the Saanen formed three clusters. A crossbred population was also identified. Pedigree analysis found that most of the does contained in the herd book were culled before their third lactation. Ne ranges were estimated based on the available pedigree data of the Saanen (36–341), Toggenburg (18–63) and British Alpine (13–53). Average inbreeding values were 0.0632, 0.1335 and 0.0993 respectively. This study presents an insight to the genetic diversity of dairy goats in South Africa, and can be applied in the genetic management of the existing populations.