A comparison of genetic diversity between South African conserved and field chicken populations using microsatellite markers

Abstract

The objective of the study was to determine genetic diversity within South African indigenous chicken populations and the effectiveness of the current conservation flocks in capturing the available diversity in the founder populations. Two chicken populations, Venda (VD_C) and Ovambo (OV_C) conservation flocks (n = 56) from the Animal Production Institute in Irene and two founder population from which these conservation flocks were sampled; Venda (VD_F) and Ovambo (OV_F) field populations (n = 72) were genotyped for 29 autosomal microsatellite markers. All microsatellites typed were found to be polymorphic. A total of 213 alleles were observed for all four populations. The mean number of alleles per population ranged from 3.52 } 1.09 (VD_C) to 6.62 } 3.38 (OV_F). Mean observed (HO) and expected (HE) heterozygosity in the conservation flocks were 0.55 and 0.57 respectively. The corresponding values for the founder population were 0.62 and 0.68. The observed within population diversity measures indicated that field populations are more diverse than conservation flocks. The Reynolds genetic distance (DReynolds) between conservation flocks and field population observed was 0.22 between VD_C and VD_F and 0.09 between OV_C and OV_F. STRUCTURE was used to cluster individuals to 2 . K . 5. The most probable clustering was found in K = 3, in which the populations were grouped into three clusters. VD_C and OV_C conservation flocks separated as independent clusters, while VD_F and OV_F field populations formed one cluster for any K value. Clustering analysis indicated a clear subdivision of the conservation flocks and field population into genetically distinct populations. The present study suggests that conservation flocks are less diverse compared to field populations.

Keywords: SA chickens, genetic diversity, microsatellites, conservation strategies