Genetic diversity and population structure of Chinese pony breeds using microsatellite markers

Abstract

ABSTRACT. 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 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 11 (3): 2629-2640 (2012) L.X. Xu et al. 2630 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.

Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers

“…Most horse populations in the world have been subjected to intensive artificial selection and genetic introgression over the past several centuries (Hendricks, 2007). However, certain Chinese indigenous horse populations have largely preserved their genetic diversity because they have not been subjected to intensive selection (Lei et al, 2009;Chang, 2011;Jiang et al, 2011;Ling et al, 2011;Xu et al, 2012;Yue et al, 2012), and they have now become valuable and ideal extant horse populations for studying ECAY diversity. There are over 3 million horses in China (Chang, 2011), and the majority of them are indigenous, making them among the largest gene pools of indigenous horses in the world.…”

The origin of Chinese domestic horses revealed with novel mtDNA variants

“…There are over 5 million horses in China (Chang ), and the majority of them are indigenous breeds, which are distributed widely in most provinces of China, while the largest populations inhabit south‐western provinces (south of Yangzi River including Guangxi, Yunnan, Guizhou and Sichuan) and Inner‐Mongolia and Xinjiang province. The Chinese indigenous horses were formed under different ecological conditions and exhibit high levels of morphological and genetic diversity (Lei et al ; Ling et al ; Jiang et al ; Xu et al ; Yue et al ). Literary sources describe that China has a history of horse husbandry over 3000 years, but the origin of domestic horses remains unknown.…”

Genetic distances between horse breeds in Poland estimated according to blood protein polymorphism

“…Nowadays, analyses are more often conducted on non-coding sequences of nuclear DNA, e.g. microsatellites (Cañon et al, 2000;Silva et al, 2012;Xu et al, 2012) as well as on mitochondrial DNA (Vilà et al, 2001;Mirol et al, 2002;Kavar and Dovč, 2008).…”