Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse.
Genes Genomics
; 41(6): 621-628, 2019 06.
Article
em En
| MEDLINE
| ID: mdl-30941726
ABSTRACT
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.Palavras-chave
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MEDLINE
Assunto principal:
Genoma
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Polimorfismo de Nucleotídeo Único
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Cavalos
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article