Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse.
Abstract: Hokkaido Native Horse (HKD) is a horse breed native to Hokkaido in Japan known for the traits such as coat color with no white spots and adaptability to the local cold climate. To examine whether those traits of HKD are conferred at the DNA level, we attempted to identify fixed DNA regions in HKD individuals, that is, the selection signatures of HKD. A comparison of genome-wide single nucleotide polymorphism genotypes in 58 HKD individuals by principal component analysis, and cluster analysis between breeds, including HKD, and within the HKD individuals indicated the genetic independence of HKD as a breed. Tajima's D analysis and runs of homozygosity analysis identified 23 selection signatures unique to HKD (P < 0.05), and following database search found 20 traits that were associated with those selection signatures; among these traits, coat color traits, face and body markings, showed the highest important value (0.50 and 0.46). Enrichment analysis of genes in the selection signatures identified six gene ontology terms (P < 0.05), and a term related to innate immunity (regulation of defense response; GO:0031347) showed the highest positive fold enrichment value (7.13). These results provide the first scientific evidence of a genetic basis for the traits of HKD.
© 2023 Japanese Society of Animal Science.
Publication Date: 2023-11-20 PubMed ID: 37983921DOI: 10.1111/asj.13884Google Scholar: Lookup
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Summary
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The article describes a study into the genetic basis of Hokkaido Native Horses’ unique traits such as their solid coat color and strong immunity. The researchers identified unique DNA regions associated with these traits, providing scientific evidence for the distinctive characteristics of this breed.
Objective and Methodology
- The purpose of this study was to investigate whether the unique HKD traits, like a solid-color coat and strong innate immunity, are determined at the DNA level.
- 58 HKD individuals were examined using genome-wide single nucleotide polymorphism genotypes. The research aimed to identify fixed DNA regions, known as selection signatures, unique to the HKD breed.
- The researchers used principal component analysis and cluster analysis to compare between different breeds, and even within the HKD breed. The resulting data indicated that the HKD breed is genetically independent.
Results and Findings
- Tajima’s D analysis and runs of homozygosity tests identified 23 selection signatures unique to the HKD breed.
- Database search connecting these selection signatures with various traits revealed that 20 traits were associated with these signatures. Among these, the traits related to coat color, face, and body markings were ranked as the most important.
- Further analysis of the genes within these selection signatures identified six gene ontology terms (collections of standardized gene attributes), and one term related to innate immunity showed the highest positive fold enrichment value (7.13).
Conclusion
- In summary, the research offers the first scientific evidence substantiating the genetic basis for the unique characteristics of the Hokkaido native horse breed, particularly its solid-colored coat and robust immune response.
Cite This Article
APA
Amano T, Yokawa H, Masuda Y, Tozaki T, Kawai M, Shirai K.
(2023).
Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse.
Anim Sci J, 94(1), e13884.
https://doi.org/10.1111/asj.13884 Publication
Researcher Affiliations
- Laboratory of Animal Genetics, Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Hokkaido, Japan.
- Laboratory of Animal Genetics, Graduate School of Dairy Science, Rakuno Gakuen University, Hokkaido, Japan.
- Laboratory of Animal Breeding, Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Hokkaido, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan.
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan.
- Hokkaido Native Horse Conservation Association, Hokkaido, Japan.
MeSH Terms
- Humans
- Horses / genetics
- Animals
- Genome
- Genotype
- Homozygote
- DNA
- Immunity, Innate / genetics
- Polymorphism, Single Nucleotide / genetics
- Selection, Genetic
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