Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

Han, Haitang; Bryan, Kenneth; Shiraigol, Wunierfu; Bai, Ding; Zhao, Yiping; Bao, Wuyingga; Si-qin, Yang; Zhang, Wengang; MacHugh, David E.; Dugarjaviin, Manglai; Hill, Emmeline W.

doi:10.1093/jhered/esz032

Cited by 7 publications

(16 citation statements)

References 28 publications

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“…The F ROH statistic proposed by McQuillan et al 83 was then calculated, whereby the total length of ROH covering an individual animal's genome (L ROH ) is divided by the length of the autosomal genome (L AUTO ); F ROH = L ROH / L AUTO . Here, consistent with other equine studies 84,85 we used the length of the equine autosomal genome (assembly EquCab 2) 86 as 2,242,960 kb (www.ncbi.nlm.nih.gov/genome/145?genome_assembly_id=22878).…”

Section: Methodsmentioning

confidence: 99%

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

McGivney

Han

Corduff

et al. 2020

Sci Rep

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The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (F iS R 2 = 0.942, P = 2.19 × 10 −13 ; F RoH R 2 = 0.88, P = 1.81 × 10 −10 ) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomicsbased methods will be beneficial to actively monitor the population to address the marked inbreeding trend.The Thoroughbred is among the fastest animals selected by humans for sport, originating from "the commingled blood of Arabs, Turks and Barbs" 1 crossed with local British and Irish mares 2 "but selection and training have together made him a very different animal from his parent-stocks" 1 . The Thoroughbred is now a large (N ~ 500,000) global breed but, in the context of modern horse breeds, it has very low genetic diversity 3,4 due to the limited foundation alleles at the establishment of the stud book and restriction of external gene flow subsequent to the closing of the population 5-7 . In Thoroughbred horse breeding selection of potential champion racehorses is a global multi-billion-dollar business, but there is no systematic industry-mediated genomic selection or genetic population management. We hypothesised that the market-driven emphasis on highly valuable pedigrees and the common practice of inbreeding to successful ancestors in attempts to reinforce...

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Section: Methodsmentioning

confidence: 99%

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

McGivney

Han

Corduff

et al. 2020

Sci Rep

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“…As an important breed in northern China, Mongolian horses have rich genomic diversity ( 21 ) and have a variety of excellent traits, such as adaptability, cold resistance, roughage resistance, disease resistance, and good stamina ( 22 , 23 ). Thoroughbred horses, a horse species bred in 17th-century Britain, were manually selected to meet the desired conditions of speed, temperament, and body size ( 24 ).…”

Section: Introductionmentioning

confidence: 99%

Variations in the fecal microbiota and their functions of Thoroughbred, Mongolian, and Hybrid horses

Luo

et al. 2022

Front. Vet. Sci.

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The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional prediction analysis. The alpha diversity analysis showed that Thoroughbred horses had a more abundant and diverse gut microbiota, while the diversity of gut microbiota in Hybrid horses was intermediate between Thoroughbred and Mongolian horses. Subsequent cluster analysis showed that Hybrid horses have a microbiota composition more similar to Mongolian horses. LEfSe analysis revealed that the bacterial biomarkers for Thoroughbred horses at the family level were Prevotellaceae, Rikenellaceae, Fibrobacteraceae, p_251_o5, Lactobacillaceae, and uncultured_bacterium_o_WCHB1_41; the bacterial biomarker for Mongolian horses was Planococcaceae; and the bacterial biomarkers for Hybrid horses were Moraxellaceae, Enterobacteriaceae, and Ruminococcaceae. The functional prediction results indicated that the metabolic pathways differ significantly between the breeds. Regarding metabolism, the Hybrid horses had the lowest proportion of the carbohydrate metabolic pathways, while the energy metabolic pathway had the highest proportion. The abundance ratios of the remaining eight metabolic pathways in Hybrid horses were between Thoroughbred and Mongolian horses. In conclusion, the results of this study showed an association between horse breeds and gut microbiota.

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“…gaitedness, strong hooves and black coat colour) may have contributed to the observed genomic diversity among the Chinese Mongolian populations. Furthermore, these ve Chinese Mongolian as well as two other Asian populations (the Mongolian horse populations in Mongolia and Tuva) were genetically similar to each other but distinct from other global horse populations and were positioned between two large regional groups (European and American/Iberian/Middle Eastern) in the PCA analysis [5]. These results therefore lead to the hypothesis that natural and arti cial selection will have left signatures in the Chinese Mongolian populations for long-term environmental adaptation when compared to other global horse populations.…”

Section: Introductionmentioning

confidence: 84%

“…We recently suggested that Mongolian horse populations may preserve ancient genomic variants that do not exist in other global horse breeds [5] as their paternal lineages can be dated to the early domesticates, at least 1400 YBP [40] . Therefore, a second possible explanation is that DOM2 horses did not replace all locally domesticated horse populations and Chinese Mongolian (and Mongolian and Tuva) horses may be the result of an entirely separate domestication event not linked to the Volga-Don origins.…”

Section: Selection Signals Relating To Geographic Originmentioning

confidence: 99%

“…The phenotypes for the ve Chinese Mongolian horse populations were documented and photographs of each horse taken at the time of sample collection. The detailed information has been previously described [5]. Contrasting cohorts selected from additional global breeds were de ned to identify signatures of selection.…”

Section: Composite Selection Signature (Css) Cohorts Of Contrasting P...mentioning

confidence: 99%

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Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health

Han

Randhawa

MacHugh

et al. 2022

Preprint

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Background: Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genes within genomic regions under selection for traits specific to Wushen (gait), Abaga Black (black coat colour) and Baicha Iron Hoof (hoof quality) horse, as well as other global breeds to identify regional-specific signatures of selection.Results: We first validated the use of the composite selection signals approach by identifying the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade.Conclusions: Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified.

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Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

Cited by 7 publications

References 28 publications

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

Variations in the fecal microbiota and their functions of Thoroughbred, Mongolian, and Hybrid horses

Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health

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