Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse

Han, Haoyuan; Zhang, Qin; Gao, Kun; Yue, Xiumei; Zhang, Tao; Dang, Ruihua; Lan, Xianyong; Chen, Hong; Lei, Chuzhao

doi:10.5713/ajas.14.0784

Cited by 15 publications

(21 citation statements)

References 34 publications

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“…The low MSY diversity cannot be explained by a low mutation rate; the Y chromosome lineages of modern horses are clearly distinct from those of the Przewalski's horse (E. przewalskii) [7], and prehistoric horses have much more diversity [8][9][10]. Rather, the presence of only six Y chromosome haplotypes (HTs) in modern European horse breeds [2] and the limited microsatellite variability [11][12][13] suggest an extremely low effective population size of males. The decline of Y chromosome diversity in horses likely started about 5,500 years ago with genetic bottlenecks during the domestication process [14,15] and was further enhanced by multiple prehistoric and historic waves of migration [16][17][18].…”

Section: Resultsmentioning

confidence: 99%

Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

et al. 2017

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The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses.

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Section: Resultsmentioning

confidence: 99%

Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

et al. 2017

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“…In horses, however, the assembly for the whole NRY region is not available yet, as the reference genome was characterized from a single mare individual (Wade et al 2009). Studies targeting specific NRY regions have shown limited variation, with haplotypes differing by one mutational step at best, which indicates that only a handful of paternal lines survived until present-day in domestic horses (Lindgren et al 2004;Brandariz-Fontes et al 2013;Wallner et al 2013;Kreutzmann et al 2014;Han et al 2015). By contrast, analyses initially based on the mtDNA control region (D-loop) (Lister et al 1998;Vilà et al 2001;Jansen et al 2002;Cieslak et al 2010), and more recently on complete mitochondrial genomes (Lippold et al 2011a;Achilli et al 2012), revealed horses as the domestic animal showing one of the largest pools of mitochondrial genetic diversity.…”

Section: Gender-biased Contributions To Domesticationmentioning

confidence: 99%

The Evolutionary Origin and Genetic Makeup of Domestic Horses

et al. 2016

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The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.

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“…The Chinese breeds could be divided into five major groups by genotyping these animals for 27 microsatellite loci [13]. Previous study had also shown that there were two haplotypes of Y chromosome discovered in the domestic horse breeds in China [16], which develop into an important tool for horse population genetics [17].…”

Section: Characters Of Jianchang Horse's Mitochondrial Genomementioning

confidence: 99%

The Complete Mitochondrial Genome and Phylogenetic Analysis of Chinese Jianchang Horse (Equus caballus)

Xiao¹,

Yang²

2015

Clon Transgen

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The Jianchang horse is a small horse breed that is popular in China, particularly in the southwest regions of China. The Jianchang horse breed is from the mountainous regions of Liangshan in the Sichuan Province, and has excellent mountainous adaptation when compared to other horses. It was domesticated to fulfill local people's needs for riding and transport across mountainous regions over 1000 years ago.Jianchang horses are well known to be quiet, hardy, powerful, and not vulnerable to environmental stress, these attribute to work effortlessly in the mountainous regions of China. As shown in Figure 1, it is typically small with an average height of 110 cm to 120 cm and a weight of 180 kg to 250 kg. It has small ears and head, long and dense bristle, and caudal seta and mane. It has a sloped croup, slender but well-developed legs, and hard hooves. Its hair is mainly in the bay color, but other colors like black appear occasionally [1].The sequence diversity of the mtDNA control region has been used for analyzing the origin and diversification of domestic horses [2][3][4]. It is widely believed that horses were domesticated from one or several ancestral horse populations [5][6][7]. However, information on its origin and evolution is still limited. In this study, we generate complete mitochondrial genome sequence of Jianchang horse and the complete mtDNA mitochondrial genome was used for phylogenetical analysis. The diversity and origin of the domestic horses in China by mtDNA D-loop have been reported [8]. However, the mtDNA D-loop sequence was not fully show the diversity and origin of the Jianchang horse breeds in the southwest regions of China. It is the first time that molecular evidences were provided for the origin of the Jianchang horse population. AbstractThe Jianchang horse (Equus caballus), a famous breed in the southwest regions of China, has excellent mountainous adaptation. The domestic Jianchang horse is popular in China, but information on its origin and evolution is still limited. In this study, we generate complete mitochondrial genome sequences of Jianchang horse. It is 16,614 bp in length, containing 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and and a noncoding control region (D-loop region). And it was found to be similar to other horse mitochondrial genomes. However, there were 105 nucleotide substitutions in the 13 protein-coding genes. The phylogenetic tree analysis was shown that Jianchang horse was significantly clustered as the clade with Debao and Yunnan horse. This genomic data provides useful information for further studies on the genetic diversity and origin of the Jianchang horse population.

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Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse

Cited by 15 publications

References 34 publications

Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

The Evolutionary Origin and Genetic Makeup of Domestic Horses

The Complete Mitochondrial Genome and Phylogenetic Analysis of Chinese Jianchang Horse (Equus caballus)

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