Using microsatellite markers, the genetic structure of 9 domestic duck (Anas platyrhynchos) populations in east china, including Weishan sheldrake, Chaohu sheldrake, Shaoxing, Gaoyou, Dayu, Jinding, Liancheng white, Putian black and San sheldrake, was analyzed. The results showed that the average heterozygosity was higher in 9 populations,which ranged from 0.5137~0.6055. The average heterozygosity of 9 duck populations was 0.5523, which reflected the rich diversity. Considerable breed differentiation was observed and 25.65% of the total genetic variation came from breed differences, this result affirmed that each breed was of own genetic diversity. The DA genetic distances suggested the longer differentiation existed between populations. The domestic duck populations in East China were clustered into four groups based on the NJ clustering, the clustering results had some relationship with the distributions and economic utilizations of these duck breeds.
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