Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis

The objective of this study was to investigate the population structure of village chickens found in the five agro-ecological zones of Zimbabwe. Twenty-nine microsatellites were genotyped for chickens randomly selected from 13 populations, including the five eco-zones of Zimbabwe (n = 238), Malawi (n = 60), Sudan (n = 48) and six purebred lines (n = 180). A total of 280 alleles were observed in the 13 populations. Forty-eight of these alleles were unique to the Zimbabwe chicken ecotypes. The average number (+/- SD) of alleles/locus was 9.7 +/- 5.10. The overall heterozygote deficiency in the Zimbabwe chickens (F-IT +/- SE) was 0.08 +/- 0.01, over 90% of which was due to within-ecotype deficit (F-IS). Small Nei's standard genetic distances ranging from 0.02 to 0.05 were observed between Zimbabwe ecotypes compared with an average of 0.6 between purebred lines. The structure software program was used to cluster individuals to 2 <= K <= 7 assumed clusters. The most probable clustering was found at K = 6. Ninety-seven of 100 structure runs were identical, in which Malawi, Sudan and purebred lines split out as independent clusters and the five Zimbabwe ecotypes clustered into one population. The within-ecotype marker-estimated kinships (mean = 0.13) differed only slightly from the between-ecotype estimates. Results from this study lead to a rejection of the hypothesis that village chickens are substructured across agro-ecological zones but indicated high genetic diversity within the Zimbabwe chicken population.