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KMID : 0381120190410060621
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Genes and Genomics
2019 Volume.41 No. 6 p.621 ~ p.628
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Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski’s horse
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Seong Ha-Seung
Kim Nam-Young
Kim Dae-Cheol
Hwang Nam-Hyun
Son Da-Hye
Shin Jong-Suh
Lee Joon-Hee
Chung Won-Hyong
Choi Jung-Woo
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Abstract
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Background: The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds.
Objective: The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski’s horse).
Results: Using the equine reference genome assembly (EquCab 2.0), more than ~?6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function.
Conclusion: We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.
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KEYWORD
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Jeju horse, Przewalski's horse, Re-sequencing, Single-nucleotide polymorphism
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