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Home / Equine Research Bank / Genes (Basel) / Short Insertion and Deletion Discoveries via Whole-Genome Se...
Genes2023; 14(3); 638; doi: 10.3390/genes14030638

Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses.

Abstract: Thoroughbreds are some of the most famous racehorses worldwide and are currently animals of high economic value. To understand genomic variability in Thoroughbreds, we identified genome-wide insertions and deletions (INDELs) and obtained their allele frequencies in this study. INDELs were obtained from whole-genome sequencing data of 101 Thoroughbred racehorses by mapping sequence reads to the horse reference genome. By integrating individual data, 1,453,349 and 113,047 INDELs were identified in the autosomal (1-31) and X chromosomes, respectively, while 18 INDELs were identified on the mitochondrial genome, totaling 1,566,414 INDELs. Of those, 779,457 loci (49.8%) were novel INDELs, while 786,957 loci (50.2%) were already registered in Ensembl. The sizes of diallelic INDELs ranged from -286 to +476, and the majority, 717,736 (52.14%) and 220,672 (16.03%), were 1-bp and 2-bp variants, respectively. Numerous INDELs were found to have lower frequencies of alternative (Alt) alleles. Many rare variants with low Alt allele frequencies (<0.5%) were also detected. In addition, 5955 loci were genotyped as having a minor allele frequency of 0.5 and being heterogeneous genotypes in all the horses. While short-read sequencing and its mapping to reference genome is a simple way of detecting variants, fake variants may be detected. Therefore, our data help to identify true variants in Thoroughbred horses. The INDEL database we constructed will provide useful information for genetic studies and industrial applications in Thoroughbred horses, including a gene-editing test for gene-doping control and a parentage test using INDELs for horse registration and identification.
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Publication Date: 2023-03-03 PubMed ID: 36980910PubMed Central: PMC10048024DOI: 10.3390/genes14030638Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses a study which maps the entire genome of 101 Thoroughbred racehorses to identify genetic variations, specifically insertions and deletions (INDELs), in order to construct a database that can assist in genetic studies and commercial applications.

Methodology

  • The research team conducted whole-genome sequencing of 101 Thoroughbred racehorses. The aim was to understand the genetic diversity present within these horses by identifying genome-wide insertions and deletions (INDELs).
  • The sequence reads were then mapped to a reference horse genome, which allowed the scientists to identify sections of the genome where sequences were either inserted or deleted.

Findings

  • The researchers were able to identify approximately 1.5 million INDELs within the genomes. Some INDELs were identified on the mitochondrial genome, while the rest were identified in the autosomal and X chromosomes.
  • About half of these INDELs were novel or not previously documented, and the other half were already known and registered in the Ensembl database.
  • Many of the identified INDELs are of very small size i.e., 1- to 2-bp (base pair) variants. These represent substantial genetic variability among Thoroughbreds.
  • It was observed that many INDELs have lower frequencies of alternative alleles, indicating that these genetic variations are not common among the population of Thoroughbreds.
  • In addition to common variants, researchers also detected many rare variants with low alternate allele frequencies.

Implications

  • The data obtained from the research could be useful for identifying true genetic variants within Thoroughbred horses. This can be critical in studies which aim to understand the genetic makeup of these horses and differentiate between genuine and fake variants.
  • The INDELs identified form a database that could potentially be used for a range of applications – both scientific and corporate – involving Thoroughbred horses. For example, it could be useful in gene-editing tests for gene-doping control in horse racing. It could also assist with parentage tests using INDELs for horse registration and identification purposes.

Cite This Article

APA
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Takahashi Y, Nagata SI. (2023). Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses. Genes (Basel), 14(3), 638. https://doi.org/10.3390/genes14030638

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 14
Issue: 3
PII: 638

Researcher Affiliations

Tozaki, Teruaki
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya 320-0851, Tochigi, Japan.
Ohnuma, Aoi
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya 320-0851, Tochigi, Japan.
Kikuchi, Mio
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya 320-0851, Tochigi, Japan.
Ishige, Taichiro
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya 320-0851, Tochigi, Japan.
Kakoi, Hironaga
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya 320-0851, Tochigi, Japan.
Hirota, Kei-Ichi
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya 320-0851, Tochigi, Japan.
Takahashi, Yuji
  • Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke 329-0412, Tochigi, Japan.
Nagata, Shun-Ichi
  • Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya 320-0851, Tochigi, Japan.

MeSH Terms

  • Horses / genetics
  • Animals
  • Genotype
  • Sequence Analysis
  • Genomics
  • INDEL Mutation
  • Genome, Mitochondrial

Conflict of Interest Statement

There are no competing interests, including patents, products in development, or marketed products, to declare concerning this study.

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