Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.
Abstract: Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. Results: Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. Conclusions: Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses.
Publication Date: 2014-07-04 PubMed ID: 24996778PubMed Central: PMC4097168DOI: 10.1186/1471-2164-15-562Google Scholar: Lookup
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Summary
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The research article is an analysis of different types of horse breeds, precisely the breed and non-breed horses, using Next Generation Sequencing. The study discovers novel genetic markers and reveals unique characteristics in these two horses’ groups, suggesting an impactful role in their domestication process.
Research Objective and Methodology
- The aim of the study was to uncover the various genetic influences on selective forces that shape the characteristics of breed and non-breed horses.
- The study employed next-generation sequencing techniques to achieve this aim, focusing its attention on four distinct horse populations.
- Five horses underwent whole-genome sequencing, a procedure that helps outline an organism’s complete DNA sequence.
- The sequencing data generated was compared to existing horse variant databases and previous reports to spot novelty.
Research Findings
- The whole-genome sequencing revealed over 10 million single nucleotide polymorphisms (SNPs), or variations in a single DNA building block known as a nucleotide, and more than 1.3 million insertion/deletion polymorphisms (indels), which are additions or subtractions in a nucleotide at a specific place in a gene.
- By comparing these findings with existing information, the researchers identified over 3 million novel SNPs and over 800,000 novel indels.
- The individual variants’ distribution analysis resulted in a significant discovery of private mutations. The non-breed horses showed an enrichment of private mutations in the coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis, and cellular components.
- Conversely, the breed horses showed private mutations in genes affecting various other functions such as cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, and developmental processes of the nervous system and ectoderm.
Conclusion and Implications
- The next-generation sequencing data provided crucial insights into breed and non-breed horses’ character differences.
- The identification of a large number of novel variants and their function annotations hints at the potential for future analyses of these animals.
- These specific variants could play a defining role in characterizing breed and non-breed horses, thereby shedding light on the mechanics of their domestication process.
Cite This Article
APA
Metzger J, Tonda R, Beltran S, Agueda L, Gut M, Distl O.
(2014).
Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.
BMC Genomics, 15(1), 562.
https://doi.org/10.1186/1471-2164-15-562 Publication
Researcher Affiliations
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany. ottmar.distl@tiho-hannover.de.
MeSH Terms
- Animals
- Animals, Domestic / genetics
- Evolution, Molecular
- High-Throughput Nucleotide Sequencing
- Horses / genetics
- INDEL Mutation
- Male
- Molecular Sequence Annotation
- Polymorphism, Single Nucleotide
- Selection, Genetic
- Sequence Analysis, DNA
References
This article includes 58 references
Citations
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