Genetic diversity and population  structure  of Chinese pony breeds using microsatellite markers.
China  is one of the principal origins of ponies in the world. We made a comprehensive  analysis of genetic diversity and population structure of Chinese ponies based  on 174 animals of five indigenous Chinese pony breeds from five provinces using  13 microsatellite markers. One hundred and forty-four alleles were detected;  the mean number of effective alleles among the pony breeds ranged from 5.38  (Guizhou) to 6.78 (Sichuan); the expected heterozygosity ranged from 0.82  (Guizhou) to 0.85 (Debao, Sichuan). Although abundant genetic variation was  found, the genetic differentiation was low between the ponies, with 6% total  genetic variance among the different breeds. All the pairwise F(ST) values  were significant; they varied from 0.0424 for the Sichuan-Yunnan pair to 0.0833  for the Guizhou-Sichuan pair. All five pony breeds deviated from Hardy-Weinberg  equilibrium, except the Yunnan pony. Phylogenetic trees of the five pony breeds  based on genetic distances were constructed using a neighbor-joining method.  The Sichuan and Yunnan ponies were grouped into the same branch, with a high  bootstrap support value (97%). Guizhou and Ningqiang ponies were clustered into  the same branch with a bootstrap value of 56%, whereas the Debao pony was  placed in a separate group, with a bootstrap value of 56%. This grouping  pattern was supported by genetic structure analysis.
Key Laboratory of Animal Genetics, Breeding and Reproduction for Mountainous Areas, Chinese Educational Ministry, Guizhou University, Guiyang, China.
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Xu
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Yang
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Lin
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Yang
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Li
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Wan
D000818:Animals; D001947:Breeding; D002681:China; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population; D005843:Geography; D006736:Horses / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny