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Genetics, selection, evolution : GSE2019; 51(1); 22; doi: 10.1186/s12711-019-0465-7

Genomic measures of inbreeding in the Norwegian-Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits.

Abstract: Since the 1950s, the Norwegian-Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequently, the aims of the current study were to estimate genomic-based inbreeding coefficients, i.e. the proportion of runs of homozygosity (ROH), for a sample of NSCT individuals using high-density genotyping array data, and subsequently to compare the resulting rate of genomic-based F (F) to that of pedigree-based F (F) coefficients within the breed. Results: A total of 566 raced NSCT were available for analyses. Average F ranged from 1.78 to 13.95%. Correlations between F and F were significant (P < 0.001) and ranged from 0.27 to 0.56, with F and F from 2000 to 2009 increasing by 1.48 and 3.15%, respectively. Comparisons of ROH between individuals yielded 1403 regions that were present in at least 95% of the sampled horses. The average percentage of a single chromosome covered in ROH ranged from 9.84 to 18.82% with chromosome 31 and 18 showing, respectively, the largest and smallest amount of homozygosity. Conclusions: Genomic inbreeding coefficients were higher than pedigree inbreeding coefficients with both methods showing a gradual increase in inbreeding level in the NSCT breed between 2000 and 2009. Opportunities exist for the NSCT industry to develop programs that provide breeders with easily interpretable feedback on regions of the genome that are suboptimal from the perspective of genetic merit or that are sensitive to inbreeding within the population. The use of molecular data to identify genomic regions that may contribute to inbreeding depression in the NSCT will likely prove to be a valuable tool for the preservation of its genetic diversity in the long term.
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Publication Date: 2019-05-27 PubMed ID: 31132983PubMed Central: PMC6537210DOI: 10.1186/s12711-019-0465-7Google Scholar: Lookup
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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.

This research studied the levels of inbreeding in the Norwegian-Swedish Coldblooded Trotter (NSCT) horse breed. The researchers used advanced genomics to estimate these levels and compared it with traditional pedigree-based methods, finding that inbreeding increased between 2000 and 2009 and highlighting the potential for identifying genetically weak areas in the breed’s gene pool for improvement.

Objective and Methodology

  • The study investigated the levels of inbreeding in the Norwegian-Swedish Coldblooded Trotter (NSCT), a breed of horse that has been selectively bred for harness racing since the 1950s.
  • The primary objectives were to estimate genomic-based inbreeding coefficients using a high-density genotyping array data, and to compare these with traditional pedigree-based inbreeding coefficients.
  • By comparing these two methods, the researchers hoped to provide valuable insights for maintaining the genetic diversity within this breed.

Results and Findings

  • A total of 566 raced NSCT were available for analyses. The average genomic inbreeding coefficient ranged from 1.78 to 13.95%.
  • The correlation between genomic-based (F) and pedigree-based (F) inbreeding coefficients were found to be statistically significant, with values ranging between 0.27 and 0.56.
  • The largest amount of homozygosity was found on chromosome 31, with the smallest on chromosome 18.
  • The study found that genomic inbreeding coefficients were higher than pedigree inbreeding coefficients, indicating that traditional methods may underestimate the extent of inbreeding.

Conclusions and Future Directions

  • Both methods showed a gradual increase in inbreeding level in the NSCT breed between 2000 and 2009. This presents an opportunity for the NSCT industry to develop schemes that provide breeders with feedback on regions of the genome that are suboptimal from the perspective of genetic merit.
  • Use of molecular data to localize genomic regions that may contribute to inbreeding depression in the NSCT will likely be a valuable tool for preserving the breed’s genetic diversity in the long term.
  • The findings of the study offer implications for the NSCT industry, potentially informing breeding practices to mitigate the effects of inbreeding and protect the breed’s genetic diversity.

Cite This Article

APA
Velie BD, Solé M, Fegraeus KJ, Rosengren MK, Røed KH, Ihler CF, Strand E, Lindgren G. (2019). Genomic measures of inbreeding in the Norwegian-Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits. Genet Sel Evol, 51(1), 22. https://doi.org/10.1186/s12711-019-0465-7

Publication

Genetics, selection, evolution : GSE
ISSN: 1297-9686
NlmUniqueID: 9114088
Country: France
Language: English
Volume: 51
Issue: 1
Pages: 22
PII: 22

Researcher Affiliations

Velie, Brandon D
  • School of Life and Environmental Sciences, University of Sydney, Sydney, Australia. brandon.velie@sydney.edu.au.
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. brandon.velie@sydney.edu.au.
Solé, Marina
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Fegraeus, Kim Jäderkvist
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Rosengren, Maria K
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Røed, Knut H
  • Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway.
Ihler, Carl-Fredrik
  • Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway.
Strand, Eric
  • Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway.
Lindgren, Gabriella
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
  • Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium.

MeSH Terms

  • Animals
  • Female
  • Genome-Wide Association Study / methods
  • Homozygote
  • Horses / genetics
  • Horses / physiology
  • Inbreeding
  • Male
  • Pedigree
  • Quantitative Trait Loci
  • Selective Breeding

Grant Funding

  • H-15-47-075 / Swedish-Norwegian Foundation for Equine Research

Conflict of Interest Statement

The authors have the following interests: GL is a co-inventor on a granted patent concerning commercial testing of the DMRT3 mutation: A method to predict the pattern of locomotion in horses. PCT EP 12,747,875.8. European patent registration date: 2011-05-05, US patent registration date: 2011-08-03. There are no further patents, products in development, or marketed products to declare.

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Citations

This article has been cited 8 times.
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