Y-Chromosome Analysis in Retuertas Horses

Brandariz-Fontes, Claudia; Leonard, Jennifer A.; Vega-Pla, J.L.; Backström, Niclas; Lindgren, Gabriella; Lippold, Sebastian; Rico, Ciro

doi:10.1371/journal.pone.0064985

Cited by 12 publications

(16 citation statements)

References 30 publications

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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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Section: Gender-biased Contributions To Domesticationmentioning

confidence: 99%

The Evolutionary Origin and Genetic Makeup of Domestic Horses

et al. 2016

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“…In contrast to the plenty of mutations in the mitochondrial genome and on the Y chromosome http: //www.openveterinaryjournal.com A.D. Khaudov et al Open Veterinary Journal, (2018), Vol. 8(1): 40-46 ________________________________________________________________________________________________________ variation of pre-domestic horses (Lippold et al, 2011), no diversity was detected in the Y chromosome of domestic horses awhile (Brandariz-Fontes et al, 2013;Lindgren et al, 2004). In the last years, a few polymorphic sites were found in modern horses leading to a small number of haplotypes in contemporary domestic stallions (Ling et al, 2010;Wallner et al, 2013Wallner et al, , 2017Kreutzmann et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers

Khaudov¹,

Duduev²,

Kokov³

et al. 2018

Open Vet J.

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Studies of mitochondrial DNA (mtDNA) as well as the non-recombining part of the Y chromosome help to understand the origin and distribution of maternal and paternal lineages. The Kabardian horse from Northern Caucasia which is well-known for strength, stamina and endurance in distance riding has a large gap in its breeding documentation especially in the recent past. A 309 bp fragment of the mitochondrial D-loop (156 Kabardian horses) and six mutations in Y chromosome (49 Kabardian stallions), respectively, were analyzed to get a better insight into breeding history, phylogenetic relationship to related breeds, maternal and paternal diversity and genetic structure. We found a high mitochondrial diversity represented by 64 D-loop haplotypes out of 14 haplogroups. The most frequent haplogroups were G (19.5%), L (12.3%), Q (11.7%), and B (11.0%). Although these four haplogroups are also frequently found in Asian riding horses (e.g. Buryat, Kirghiz, Mongolian, Transbaikalian, Tuvinian) the percentage of the particular haplogroups varies sometimes remarkable. In contrast, the obtained haplogroup pattern from Kabardian horse was more similar to that of breeds reared in the Middle East. No specific haplotype cluster was observed in the phylogenetic tree for Kabardian horses. On Kabardian Y chromosome, two mutations were found leading to three haplotypes with a percentage of 36.7% (haplotype HT1), 38.8% (haplotype HT2) and 24.5% (haplotype HT3), respectively. The high mitochondrial and also remarkable paternal diversity of the Kabardian horse is caused by its long history with a widely spread maternal origin and the introduction of Arabian as well as Thoroughbred influenced stallions for improvement. This high genetic diversity provides a good situation for the ongoing breed development and performance selection as well as avoiding inbreeding.

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“…The Y chromosome, because of its male specific feature in the mammalian genome, unpairing with X chromosome during the meiosis, provides a powerful tool to trace the paternal origin of mammals ( Skaletsky et al, 2003 ). Despite most of the studies on Y chromosome in domestic horse revealed no genetic variation ( Lindgren et al, 2004 ; Wallner et al, 2004 ; Lau et al, 2009 ; Brandariz-Fontes et al, 2013 ), a recent study on equine Y chromosome short tandem repeats (Y-STR) detected two Y chromosome haplotypes in Chinese domestic horses ( Ling et al, 2010 ), though, no Y-STR polymorphism was found in horses from Portugal, Spain and France ( Brandariz-Fontes et al, 2013 ), indicating horse Y chromosome is not homogeneous and Chinese horse might display more abundant Y chromosome diversity. In addition, Chinese indigenous horse revealed a higher diversity level in comparison with Spanish horses, German draught horses, Swiss horses, Norwegian horses, Portuguese Sorraia and Friesian horse and Japanese native horse breeds using 27 microsatellite markers ( Ling et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse

Han

Zhang

Gao

et al. 2015

Asian Australas. J. Anim. Sci

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In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10−4) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.

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Y-Chromosome Analysis in Retuertas Horses

Cited by 12 publications

References 30 publications

The Evolutionary Origin and Genetic Makeup of Domestic Horses

The Evolutionary Origin and Genetic Makeup of Domestic Horses

Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers

Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse

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